To predict the embryogenic performances of 5 upper amazon cocoa parents, the discriminant model of Wilks’ Lambda was used. Five parents, namely IMC67, P19A, Pa13, Pa121 and Pa150 were used. Staminodes and petals from these parents were extracted of flower buds then cultured in vitro onto 2 callogenesis media, namely PCG1 and PCG3. The Principal Component (PCA), Hierarchical Cluster HCA) and Factorial Discriminant Analyses (FDA) were performed. As for the PCA, a single, namely the number of callogenic explants, out of 5 measured variables, was dropped from the study. Two classes were identified from the PCA and HCA, then confirmed via the FDA. Clones P19A and Pa13 belonging to Class C2, displayed the highest embryogenic performances. Earlier study relying on multivariate analysis implying hybrids and these 5 cocoa parents revealed results approximately similar. The model predicting the embryogenic performances is spelt Z1 = -3.310 + 4.532*Ncalem. In oil palm, 2 models, the first one predicting the biomass production and the second one modeling the number of harvested shoots from somatic embryos were proposed. From model proposed here, the embryogenic performances of the best genotypes will vary from 1.3725 to 1.7402. Their discriminating score Z1 will oscillate from 2.910 to 4.576. This model will allow the predicting of membership class of a new observation from its values of the number of embryogenic explants.
Marker assisted breeding in Maize, genotypic selection with the help of markers increases selection efficiency and helps in quicker advancement of breeding programmes.
When breeding diploid potatoes, tetraploid progeny can result from the union of 2n eggs and 2n pollen in 2x-2x crosses. Thirty-three crosses were made to examine tetraploid progeny frequency in 2x-2x crosses. All crosses were between S. tuberosum dihaploids and diploid self-compatible donors, M6 and DRH S6-10-4P17. Using chloroplast counting for ploidy determination, the frequency of tetraploid progeny was as high as 45% in one of the 33 crosses. Based upon single nucleotide polymorphism (SNP) genotyping, the tetraploid progeny were attributed to bilateral sexual polyploidization (BSP), which is caused by the union of 2n egg and 2n pollen. Dihaploids were identified that produce lower frequencies of 2n eggs. The results of this study suggest that S. tuberosum dihaploids with a high frequency of 2n eggs should be avoided in 2x - 2x crosses for diploid breeding programs.
Haploid induction of allelic diversity populations in maizeNaveen Jakhar
This document summarizes a power point presentation on haploid induction of allelic diversity in maize populations. It discusses two hypotheses for how haploid embryos are formed, outlines the objectives and methods used, and summarizes the results. The methodology involved selecting maize races from different elevations and examining their haploid induction rates when crossed with a maternal haploid inducer. Races from low elevations had significantly higher haploid induction rates than mid or high elevation races. Certain races like TuxpeñoNorteño also had significantly higher rates than others like Conico. The document provides background on haploid induction and doubling techniques in maize breeding.
Waksman Student Scholars Program PosterWesley Kwong
The document describes an experiment to sequence the DNA of the duckweed plant Landoltia punctata and analyze the protein encoded. Researchers used PCR to amplify duckweed DNA inserted into bacteria. Restriction digest isolated the duckweed DNA, which was sequenced. Analysis identified the protein as Mitogen-Activated Protein Kinase (MAPK), which regulates cellular responses to stimuli and contains conserved domains. The 3D structure of this protein is similar to the human MAPK protein, indicating an evolutionary advantage across kingdoms.
This document discusses general combining ability (GCA) and specific combining ability (SCA) in plant breeding. GCA is due to additive genetic effects and refers to a genotype's average performance in crosses. SCA is due to non-additive genetic effects and refers to when certain crosses perform better or worse than expected. GCA is estimated using half-sib mating and helps identify best parents for hybridization. SCA is estimated using full-sib mating and helps identify best cross combinations. The document outlines procedures for estimating and utilizing GCA and SCA over multiple generations or seasons in plant breeding programs.
This document provides an introduction to genomic selection for crop improvement. It discusses how genomic selection works and the steps involved, including creating a training population, genotyping and phenotyping the training population, model training, genotyping the breeding population, calculating genomic estimated breeding values, and making selection decisions. Some advantages of genomic selection are greater genetic gains per unit of time compared to phenotypic selection and the ability to select for low heritability traits. Factors that can affect the accuracy of genomic predicted breeding values include the prediction model used, population size, marker density and type, trait heritability, and number of causal variants. Genomic selection is being applied to plant breeding programs for traits like disease resistance and yield to help meet future food
Marker assisted breeding in Maize, genotypic selection with the help of markers increases selection efficiency and helps in quicker advancement of breeding programmes.
When breeding diploid potatoes, tetraploid progeny can result from the union of 2n eggs and 2n pollen in 2x-2x crosses. Thirty-three crosses were made to examine tetraploid progeny frequency in 2x-2x crosses. All crosses were between S. tuberosum dihaploids and diploid self-compatible donors, M6 and DRH S6-10-4P17. Using chloroplast counting for ploidy determination, the frequency of tetraploid progeny was as high as 45% in one of the 33 crosses. Based upon single nucleotide polymorphism (SNP) genotyping, the tetraploid progeny were attributed to bilateral sexual polyploidization (BSP), which is caused by the union of 2n egg and 2n pollen. Dihaploids were identified that produce lower frequencies of 2n eggs. The results of this study suggest that S. tuberosum dihaploids with a high frequency of 2n eggs should be avoided in 2x - 2x crosses for diploid breeding programs.
Haploid induction of allelic diversity populations in maizeNaveen Jakhar
This document summarizes a power point presentation on haploid induction of allelic diversity in maize populations. It discusses two hypotheses for how haploid embryos are formed, outlines the objectives and methods used, and summarizes the results. The methodology involved selecting maize races from different elevations and examining their haploid induction rates when crossed with a maternal haploid inducer. Races from low elevations had significantly higher haploid induction rates than mid or high elevation races. Certain races like TuxpeñoNorteño also had significantly higher rates than others like Conico. The document provides background on haploid induction and doubling techniques in maize breeding.
Waksman Student Scholars Program PosterWesley Kwong
The document describes an experiment to sequence the DNA of the duckweed plant Landoltia punctata and analyze the protein encoded. Researchers used PCR to amplify duckweed DNA inserted into bacteria. Restriction digest isolated the duckweed DNA, which was sequenced. Analysis identified the protein as Mitogen-Activated Protein Kinase (MAPK), which regulates cellular responses to stimuli and contains conserved domains. The 3D structure of this protein is similar to the human MAPK protein, indicating an evolutionary advantage across kingdoms.
This document discusses general combining ability (GCA) and specific combining ability (SCA) in plant breeding. GCA is due to additive genetic effects and refers to a genotype's average performance in crosses. SCA is due to non-additive genetic effects and refers to when certain crosses perform better or worse than expected. GCA is estimated using half-sib mating and helps identify best parents for hybridization. SCA is estimated using full-sib mating and helps identify best cross combinations. The document outlines procedures for estimating and utilizing GCA and SCA over multiple generations or seasons in plant breeding programs.
This document provides an introduction to genomic selection for crop improvement. It discusses how genomic selection works and the steps involved, including creating a training population, genotyping and phenotyping the training population, model training, genotyping the breeding population, calculating genomic estimated breeding values, and making selection decisions. Some advantages of genomic selection are greater genetic gains per unit of time compared to phenotypic selection and the ability to select for low heritability traits. Factors that can affect the accuracy of genomic predicted breeding values include the prediction model used, population size, marker density and type, trait heritability, and number of causal variants. Genomic selection is being applied to plant breeding programs for traits like disease resistance and yield to help meet future food
Genomic selection (GS) is a method for predicting an individual's genetic merit based on its genome-wide marker data. It allows for selection to take place in the laboratory based on genomic estimated breeding values. Key factors for the success of GS include the size and type of the training population, marker density and type, availability of high-density genome-wide markers, and appropriate statistical prediction models. Ridge regression BLUP and Bayesian regression methods are commonly used prediction models. Future directions for improving GS include determining optimal training population design, modeling non-additive genetic effects, and managing long-term genetic gain.
This document summarizes three case studies on using marker-assisted breeding techniques:
1) Introgressing rice QTLs controlling root traits from donor Azucena into recipient Kalinga III. Five target QTLs were introgressed over three backcrosses using foreground, background, and recombinant selection with RFLPs and SSRs.
2) Introgressing the submergence tolerance Sub1 QTL from donor IR49830 into popular rice variety Swarna. The QTL was introgressed over three backcrosses and a BC3F2 line identified with minimal donor DNA.
3) Introgressing drought tolerance QTLs from donor CML247 into
This document summarizes a paper that presents a new tool called Simulated Annealing Single Cell (SASC) for inferring cancer progression from single-cell sequencing data. SASC allows for the loss of mutations, which violates the common assumption that mutations cannot occur in the same location. SASC uses simulated annealing, a heuristic technique, to search for maximum likelihood trees representing cancer evolution. It was shown to accurately infer ancestor-descendant mutation relationships and detect mutation losses on both simulated and real single-cell sequencing data, outperforming existing tools that do not allow for mutation loss. The paper concludes that SASC provides an improved model for analyzing intra-tumor heterogeneity from single-cell data.
The document discusses allele mining, which aims to identify allelic variations in genetic resources collections that are relevant for traits of interest. It describes how allele mining works to unlock hidden genetic variation by identifying single nucleotide polymorphisms and new haplotypes. The document then provides details on a case study of allele mining focused on three genes - calmodulin, LEA3, and SalT - important for abiotic stress tolerance in rice and related species. Primers were developed to amplify regions of these three genes from 64 accessions representing rice and other grasses.
This document discusses combining ability analysis in plant breeding. It defines combining ability as the ability of a genotype to transmit superior performance in crosses. There are two types of combining ability: general combining ability (GCA), which is the average performance of a genotype in crosses, and specific combining ability (SCA), which is the performance in a specific cross. The document outlines methods to estimate GCA and SCA, including diallel crosses, and how this analysis can be used to select parents for hybridization and identify superior cross combinations.
Enhancing Genetic Gains through Innovations in Breeding ApproachesICARDA
The document discusses methods for accelerating genetic gain in self-pollinating crops through innovations in breeding approaches. It proposes using a model similar to animal breeding called the "animal model" which involves crossing heterozygous S1 plants before selfing and selection, rather than crossing after selfing. This allows linkage of phenotypic and relationship data across generations for BLUP prediction. Analysis of two cycles of selection for ascochyta blight resistance in field peas showed high prediction accuracy and potential for accelerated genetic gain compared to traditional methods. However, further research is needed to optimize selection methods and address genotype by environment interaction. The document also discusses using accelerated generation cycling through rapid flowering and seed development to enable more generations per year for trait intro
Accelerating crop genetic gains with genomic selectionViolinaBharali
This document discusses genomic selection (GS), a plant and animal breeding technique that uses genome-wide molecular markers to predict and select for an individual's genetic merit or breeding value. GS can accelerate genetic gain compared to traditional breeding by increasing selection intensity and accuracy. Key points covered include: how GS works, factors affecting its accuracy, challenges like genotype-environment interaction, and examples of its successful application in maize and wheat breeding programs.
MARKER-ASSISTED BREEDING FOR RICE IMPROVEMENTFOODCROPS
This document discusses marker-assisted breeding for rice improvement. It begins with an outline of the topics to be covered, which include the theory and practice of marker-assisted selection, marker-assisted breeding schemes, and a case study of marker-assisted backcrossing done at IRRI. The first section defines marker-assisted selection and describes its advantages over phenotypic selection, such as earlier selection and greater reliability. Subsequent sections discuss specific marker-assisted breeding schemes like backcrossing, pyramiding traits, and early generation selection. The document concludes with details of IRRI's case study using markers to backcross a submergence tolerance gene into popular rice varieties.
Marker assisted selection for complex traits in agricultural cropsAparna Veluru
Marker-assisted selection (MAS) uses DNA markers linked to traits of interest to assist plant breeders in selecting desirable plants. MAS has advantages over phenotypic selection like enabling selection at early stages. MAS breeding schemes include marker-assisted backcrossing to introgress traits while minimizing linkage drag, and pyramiding to combine multiple genes/QTLs. Case studies demonstrate using MAS to develop rice varieties with submergence tolerance and improve yield traits. However, limitations include inconsistent QTL-marker associations across environments and difficulties evaluating complex trait genetics like epistasis. Future work aims to optimize MAS efficiency and integration with plant breeding.
Abstract— Taxus Chinensis var. mairei is a valuable plant species for timber and taxoids isolated from this species are very important compounds that are used for cancer treatment. Although chemical investigation on T. chinensis var. mairei are popular, functional identification of genes isolated from this species is rare. In this investigation, we have isolated TCAP3 gene and analyzed its expression pattern in different tissue and developmental stages through Real time-PCR; then we transformed this gene into Arabidopsis and analyzed its function. Our results demonstrated that its cDNA contains 846 bp bases (coding 197 amino acids) constituted by four typical domains, M, I, K, C with conserved motif, Phylogenetic analysis showed that TCAP3 is more ancient than angiosperm B class genes. Alignment of protein sequence demonstrated the conserved motifs, which illustrated that TCAP3 belongs to gymnosperm Gymno B class MADS-box genes with PI-derived, on C-teminal, which is similar structure to the Gymno B class MADS-box genes that they share the same B class gene specific conserved motif. Expression analysis of TCAP3 in different tissue showed that it only expression in male strobilus, not in leaf, bud and female strobilus at different developmental stages. We divided the stages according to paraffin sections of male strobilus. The results indicated that TCAP3 expresses dynamically along with the male strobilus. Heterologous expression of TCAP3 in Arabidopsis demonstrated that TCAP3 was involved in flower, especially the filaments morphological development.
This document provides an overview of quantitative trait locus (QTL) mapping. It discusses what a QTL is, the types of mapping populations used in QTL mapping like recombinant inbred lines (RILs) and near isogenic lines (NILs), and statistical methods for QTL mapping including single marker analysis, interval mapping, and composite interval mapping. The document also covers factors that affect the power of QTL mapping and limitations of QTL mapping like low resolution and small effects of individual QTLs.
Rice breeding is both challenged and benefited by the fact that a successful varietal improvement program must embrace both the integration single genes that segregate in a simple Mendelian fashion as well as complex traits that are inherited in more quantitative ways. For decades the rice genetics community has produced a wealth of knowledge about these single genes and has developed markers that allow a breeder to track them in a population. However, marker assisted selection (MAS) alone is insufficient to drive the rates of genetic gain for more complex traits that are equally necessary. This presentation will describe the attempts made in the Favorable Environments Breeding program at IRRI to integrate the selection for single genes appropriate for MAS into a more complex population improvement strategy designed to improve quantitatively inherited traits.
Assesment of genetic divergence in chickpea kabuli cultivarsNaveen Jakhar
This study aims to assess genetic divergence among 42 chickpea cultivars and investigate relationships between traits and seed yield. The study will be conducted in Allahabad, India in a randomized block design with 3 replications. Data on days to flowering, plant height, branches, pods, seeds/pod, maturity, seed index, biological yield, seed yield, and harvest index will be collected. Statistical analyses including ANOVA, coefficient of variation, heritability, and D2 analysis will determine genetic diversity and relationships between traits and yield to identify parents for hybridization and breeding to improve chickpea varieties.
This document discusses marker-assisted backcrossing (MAB) for introgressing traits from a donor parent into a recipient line. MAB uses DNA markers linked to target genes/QTLs to aid in selection. Markers can be used for foreground selection of target genes, background selection to recover the recipient genome, and recombinant selection to minimize linkage drag. A case study is described where MAB was used over multiple generations to introgress 5 drought resistance QTLs from a donor rice variety into a recipient variety. Through foreground, background, and recombinant selection using DNA markers, lines were developed with the target QTLs and most of the recipient genetic background.
MARKER ASSISTED SELECTION IN CROP IMPROVEMENTVinod Pawar
The document summarizes a presentation on marker assisted selection in crop improvement. It begins with an introduction to MAS and its advantages over conventional breeding. It then discusses key aspects of MAS including marker genotyping platforms, MAS breeding schemes such as foreground and background selection to minimize linkage drag, and case studies on MAS for trait pyramiding in rice and introgressing stay-green QTLs in sorghum. The conclusion emphasizes that MAS can be a useful supplement to conventional breeding programs for developing new crop varieties in a time-efficient manner.
Gene pyramiding in tomato involves combining desirable genes from multiple parents into a single genotype to improve specific traits. It can enhance disease resistance, drought tolerance, yield, and fruit quality. One study found that pyramiding two virus resistance genes (Ty-2 and Ty-3) in tomato improved resistance to three viruses and had higher yields than lines with single genes. Another study found that pyramiding introgressions from wild tomato species S. pennellii improved drought tolerance, yield, soluble solids content, and the ratio of soluble solids to fruit weight. A third study showed that pyramiding quality trait genes increased antioxidant levels, soluble solids, and yield compared to lines with single introgressions. Gene
This document describes the establishment of a fibroblast cell line from frozen embryos of Arbor Acre broiler chickens. Key findings include:
1) Fibroblast cells were successfully isolated from fresh and frozen embryos and exhibited typical fibroblast morphology.
2) Cell viability was over 80% after thawing frozen embryos and fibroblasts showed a population doubling time of around 42 hours.
3) Karyotyping showed the cells had a normal diploid chromosome number of 78 for chickens and a high percentage of cells were diploid.
4) Transfection of cells with a fluorescent protein vector showed protein expression and formation of fluorescent colonies over time, indicating the cells could be genetically modified.
Final CSPG4 Presentation Abhinav Bhaskar 4-22-15.pptxABHINAV BHASKAR
- Researchers used CRISPR-cas9 gene editing to partially knockout the CSPG4 gene in the 1205Lu metastatic melanoma cell line, creating a new cell line called 1205Lu 2.4F6.
- Analysis through PCR, western blot, and cell growth assays showed the 2.4F6 cell line had reduced but not absent CSPG4 expression and slower tumor cell growth compared to the parental 1205Lu line.
- The results suggest that partial knockout of the CSPG4 gene through CRISPR-cas9 leads to haploinsufficiency and slower melanoma tumor cell growth, demonstrating the role of CSPG4 in promoting tumor formation and progression.
This document describes research aimed at improving the efficiency of somatic embryogenesis in coconut palms. The researchers evaluated secondary somatic embryogenesis and embryogenic callus multiplication, starting with plumule explants. Through a stepwise process involving primary and secondary somatic embryogenesis and callus multiplication over multiple cycles, the yield of somatic embryos produced from one original plumule explant was calculated to be 98,000 embryos, representing as much as a 50,000-fold increase compared to primary somatic embryogenesis alone. Histological analysis provided insights into the cellular development at different stages. The improved protocol allows for significantly higher somatic embryo production efficiency in coconut regeneration.
Genomic selection (GS) is a method for predicting an individual's genetic merit based on its genome-wide marker data. It allows for selection to take place in the laboratory based on genomic estimated breeding values. Key factors for the success of GS include the size and type of the training population, marker density and type, availability of high-density genome-wide markers, and appropriate statistical prediction models. Ridge regression BLUP and Bayesian regression methods are commonly used prediction models. Future directions for improving GS include determining optimal training population design, modeling non-additive genetic effects, and managing long-term genetic gain.
This document summarizes three case studies on using marker-assisted breeding techniques:
1) Introgressing rice QTLs controlling root traits from donor Azucena into recipient Kalinga III. Five target QTLs were introgressed over three backcrosses using foreground, background, and recombinant selection with RFLPs and SSRs.
2) Introgressing the submergence tolerance Sub1 QTL from donor IR49830 into popular rice variety Swarna. The QTL was introgressed over three backcrosses and a BC3F2 line identified with minimal donor DNA.
3) Introgressing drought tolerance QTLs from donor CML247 into
This document summarizes a paper that presents a new tool called Simulated Annealing Single Cell (SASC) for inferring cancer progression from single-cell sequencing data. SASC allows for the loss of mutations, which violates the common assumption that mutations cannot occur in the same location. SASC uses simulated annealing, a heuristic technique, to search for maximum likelihood trees representing cancer evolution. It was shown to accurately infer ancestor-descendant mutation relationships and detect mutation losses on both simulated and real single-cell sequencing data, outperforming existing tools that do not allow for mutation loss. The paper concludes that SASC provides an improved model for analyzing intra-tumor heterogeneity from single-cell data.
The document discusses allele mining, which aims to identify allelic variations in genetic resources collections that are relevant for traits of interest. It describes how allele mining works to unlock hidden genetic variation by identifying single nucleotide polymorphisms and new haplotypes. The document then provides details on a case study of allele mining focused on three genes - calmodulin, LEA3, and SalT - important for abiotic stress tolerance in rice and related species. Primers were developed to amplify regions of these three genes from 64 accessions representing rice and other grasses.
This document discusses combining ability analysis in plant breeding. It defines combining ability as the ability of a genotype to transmit superior performance in crosses. There are two types of combining ability: general combining ability (GCA), which is the average performance of a genotype in crosses, and specific combining ability (SCA), which is the performance in a specific cross. The document outlines methods to estimate GCA and SCA, including diallel crosses, and how this analysis can be used to select parents for hybridization and identify superior cross combinations.
Enhancing Genetic Gains through Innovations in Breeding ApproachesICARDA
The document discusses methods for accelerating genetic gain in self-pollinating crops through innovations in breeding approaches. It proposes using a model similar to animal breeding called the "animal model" which involves crossing heterozygous S1 plants before selfing and selection, rather than crossing after selfing. This allows linkage of phenotypic and relationship data across generations for BLUP prediction. Analysis of two cycles of selection for ascochyta blight resistance in field peas showed high prediction accuracy and potential for accelerated genetic gain compared to traditional methods. However, further research is needed to optimize selection methods and address genotype by environment interaction. The document also discusses using accelerated generation cycling through rapid flowering and seed development to enable more generations per year for trait intro
Accelerating crop genetic gains with genomic selectionViolinaBharali
This document discusses genomic selection (GS), a plant and animal breeding technique that uses genome-wide molecular markers to predict and select for an individual's genetic merit or breeding value. GS can accelerate genetic gain compared to traditional breeding by increasing selection intensity and accuracy. Key points covered include: how GS works, factors affecting its accuracy, challenges like genotype-environment interaction, and examples of its successful application in maize and wheat breeding programs.
MARKER-ASSISTED BREEDING FOR RICE IMPROVEMENTFOODCROPS
This document discusses marker-assisted breeding for rice improvement. It begins with an outline of the topics to be covered, which include the theory and practice of marker-assisted selection, marker-assisted breeding schemes, and a case study of marker-assisted backcrossing done at IRRI. The first section defines marker-assisted selection and describes its advantages over phenotypic selection, such as earlier selection and greater reliability. Subsequent sections discuss specific marker-assisted breeding schemes like backcrossing, pyramiding traits, and early generation selection. The document concludes with details of IRRI's case study using markers to backcross a submergence tolerance gene into popular rice varieties.
Marker assisted selection for complex traits in agricultural cropsAparna Veluru
Marker-assisted selection (MAS) uses DNA markers linked to traits of interest to assist plant breeders in selecting desirable plants. MAS has advantages over phenotypic selection like enabling selection at early stages. MAS breeding schemes include marker-assisted backcrossing to introgress traits while minimizing linkage drag, and pyramiding to combine multiple genes/QTLs. Case studies demonstrate using MAS to develop rice varieties with submergence tolerance and improve yield traits. However, limitations include inconsistent QTL-marker associations across environments and difficulties evaluating complex trait genetics like epistasis. Future work aims to optimize MAS efficiency and integration with plant breeding.
Abstract— Taxus Chinensis var. mairei is a valuable plant species for timber and taxoids isolated from this species are very important compounds that are used for cancer treatment. Although chemical investigation on T. chinensis var. mairei are popular, functional identification of genes isolated from this species is rare. In this investigation, we have isolated TCAP3 gene and analyzed its expression pattern in different tissue and developmental stages through Real time-PCR; then we transformed this gene into Arabidopsis and analyzed its function. Our results demonstrated that its cDNA contains 846 bp bases (coding 197 amino acids) constituted by four typical domains, M, I, K, C with conserved motif, Phylogenetic analysis showed that TCAP3 is more ancient than angiosperm B class genes. Alignment of protein sequence demonstrated the conserved motifs, which illustrated that TCAP3 belongs to gymnosperm Gymno B class MADS-box genes with PI-derived, on C-teminal, which is similar structure to the Gymno B class MADS-box genes that they share the same B class gene specific conserved motif. Expression analysis of TCAP3 in different tissue showed that it only expression in male strobilus, not in leaf, bud and female strobilus at different developmental stages. We divided the stages according to paraffin sections of male strobilus. The results indicated that TCAP3 expresses dynamically along with the male strobilus. Heterologous expression of TCAP3 in Arabidopsis demonstrated that TCAP3 was involved in flower, especially the filaments morphological development.
This document provides an overview of quantitative trait locus (QTL) mapping. It discusses what a QTL is, the types of mapping populations used in QTL mapping like recombinant inbred lines (RILs) and near isogenic lines (NILs), and statistical methods for QTL mapping including single marker analysis, interval mapping, and composite interval mapping. The document also covers factors that affect the power of QTL mapping and limitations of QTL mapping like low resolution and small effects of individual QTLs.
Rice breeding is both challenged and benefited by the fact that a successful varietal improvement program must embrace both the integration single genes that segregate in a simple Mendelian fashion as well as complex traits that are inherited in more quantitative ways. For decades the rice genetics community has produced a wealth of knowledge about these single genes and has developed markers that allow a breeder to track them in a population. However, marker assisted selection (MAS) alone is insufficient to drive the rates of genetic gain for more complex traits that are equally necessary. This presentation will describe the attempts made in the Favorable Environments Breeding program at IRRI to integrate the selection for single genes appropriate for MAS into a more complex population improvement strategy designed to improve quantitatively inherited traits.
Assesment of genetic divergence in chickpea kabuli cultivarsNaveen Jakhar
This study aims to assess genetic divergence among 42 chickpea cultivars and investigate relationships between traits and seed yield. The study will be conducted in Allahabad, India in a randomized block design with 3 replications. Data on days to flowering, plant height, branches, pods, seeds/pod, maturity, seed index, biological yield, seed yield, and harvest index will be collected. Statistical analyses including ANOVA, coefficient of variation, heritability, and D2 analysis will determine genetic diversity and relationships between traits and yield to identify parents for hybridization and breeding to improve chickpea varieties.
This document discusses marker-assisted backcrossing (MAB) for introgressing traits from a donor parent into a recipient line. MAB uses DNA markers linked to target genes/QTLs to aid in selection. Markers can be used for foreground selection of target genes, background selection to recover the recipient genome, and recombinant selection to minimize linkage drag. A case study is described where MAB was used over multiple generations to introgress 5 drought resistance QTLs from a donor rice variety into a recipient variety. Through foreground, background, and recombinant selection using DNA markers, lines were developed with the target QTLs and most of the recipient genetic background.
MARKER ASSISTED SELECTION IN CROP IMPROVEMENTVinod Pawar
The document summarizes a presentation on marker assisted selection in crop improvement. It begins with an introduction to MAS and its advantages over conventional breeding. It then discusses key aspects of MAS including marker genotyping platforms, MAS breeding schemes such as foreground and background selection to minimize linkage drag, and case studies on MAS for trait pyramiding in rice and introgressing stay-green QTLs in sorghum. The conclusion emphasizes that MAS can be a useful supplement to conventional breeding programs for developing new crop varieties in a time-efficient manner.
Gene pyramiding in tomato involves combining desirable genes from multiple parents into a single genotype to improve specific traits. It can enhance disease resistance, drought tolerance, yield, and fruit quality. One study found that pyramiding two virus resistance genes (Ty-2 and Ty-3) in tomato improved resistance to three viruses and had higher yields than lines with single genes. Another study found that pyramiding introgressions from wild tomato species S. pennellii improved drought tolerance, yield, soluble solids content, and the ratio of soluble solids to fruit weight. A third study showed that pyramiding quality trait genes increased antioxidant levels, soluble solids, and yield compared to lines with single introgressions. Gene
This document describes the establishment of a fibroblast cell line from frozen embryos of Arbor Acre broiler chickens. Key findings include:
1) Fibroblast cells were successfully isolated from fresh and frozen embryos and exhibited typical fibroblast morphology.
2) Cell viability was over 80% after thawing frozen embryos and fibroblasts showed a population doubling time of around 42 hours.
3) Karyotyping showed the cells had a normal diploid chromosome number of 78 for chickens and a high percentage of cells were diploid.
4) Transfection of cells with a fluorescent protein vector showed protein expression and formation of fluorescent colonies over time, indicating the cells could be genetically modified.
Final CSPG4 Presentation Abhinav Bhaskar 4-22-15.pptxABHINAV BHASKAR
- Researchers used CRISPR-cas9 gene editing to partially knockout the CSPG4 gene in the 1205Lu metastatic melanoma cell line, creating a new cell line called 1205Lu 2.4F6.
- Analysis through PCR, western blot, and cell growth assays showed the 2.4F6 cell line had reduced but not absent CSPG4 expression and slower tumor cell growth compared to the parental 1205Lu line.
- The results suggest that partial knockout of the CSPG4 gene through CRISPR-cas9 leads to haploinsufficiency and slower melanoma tumor cell growth, demonstrating the role of CSPG4 in promoting tumor formation and progression.
This document describes research aimed at improving the efficiency of somatic embryogenesis in coconut palms. The researchers evaluated secondary somatic embryogenesis and embryogenic callus multiplication, starting with plumule explants. Through a stepwise process involving primary and secondary somatic embryogenesis and callus multiplication over multiple cycles, the yield of somatic embryos produced from one original plumule explant was calculated to be 98,000 embryos, representing as much as a 50,000-fold increase compared to primary somatic embryogenesis alone. Histological analysis provided insights into the cellular development at different stages. The improved protocol allows for significantly higher somatic embryo production efficiency in coconut regeneration.
Genome-scale in silico atpE gene knockout in Escherichia coli could drive nov...Khadem2016
One of the applications of E. coli genome-scale model is in the biological discovery of underground metabolic functions of partially characterized genes and/or enzymes. Here we report for the first time, a failed prediction of atpE gene knockout of no growth in the most recent E. coli reconstruction iJ01366 model, and a positive experimental growth on glucose, enabling a model-driven biological discovery of the underground metabolic function of this gene in E. coli metabolism. These findings unfolded what could be described as either scope gaps in the reconstruction or true biological gaps (knowledge gaps) on the missing atpE gene function in E. coli metabolism. This study informs other studies that the gaps could be pursued into the E. coli metabolism, leading to a model-driven discovery in the future.
One of the applications of E. coli genome-scale model is in the biological discovery of underground metabolic functions of partially characterized genes and/or enzymes. Here we report for the first time, a failed prediction of atpE gene knockout of no growth in the most recent E. coli reconstruction iJ01366 model, and a positive experimental growth on glucose, enabling a model-driven biological discovery of the underground metabolic function of this gene in E. coli metabolism. These findings unfolded what could be described as either scope gaps in the reconstruction or true biological gaps (knowledge gaps) on the missing atpE gene function in E. coli metabolism. This study informs other studies that the gaps could be pursued into the E. coli metabolism, leading to a model-driven discovery in the future. This can be achieved by using gap filling algorithms (such as GrowMatch, SMILEY
Genome-scale in silico atpE gene knockout in Escherichia coli could drive nov...Khadem2016
One of the applications of E. coli genome-scale model is in the biological discovery of underground metabolic functions of partially characterized genes and/or enzymes. Here we report for the first time, a failed prediction of atpE gene knockout of no growth in the most recent E. coli reconstruction iJ01366 model, and a positive experimental growth on glucose, enabling a model-driven biological discovery of the underground metabolic function of this gene in E. coli metabolism. These findings unfolded what could be described as either scope gaps in the reconstruction or true biological gaps (knowledge gaps) on the missing atpE gene function in E. coli metabolism. This study informs other studies that the gaps could be pursued into the E. coli metabolism, leading to a model-driven discovery in the future. This can be achieved by using gap filling algorithms (such as GrowMatch, SMILEY
This document summarizes a study that developed a new microarray platform capable of simultaneously assessing aneuploidy, mitochondrial DNA content, and single-nucleotide polymorphisms in human polar bodies and embryos. The microarray was optimized and validated using cell lines and clinical samples. Results found the microarray detected aneuploidies with 97% accuracy and could accurately determine relative mitochondrial DNA quantities and genotypes, allowing confirmation of parental origin. The microarray provides information beyond chromosomal analysis alone that could improve embryo assessment and selection.
Identification and Evaluation of Heterotic Groups 4 JULY.pptxAlkaMScPBG
The document describes methods for identifying and evaluating heterotic groups in plant breeding, including hybridization, pedigree analysis, quantitative genetic analysis using diallel crosses, and molecular marker analysis. A study is described that classified 14 maize inbred lines into heterotic groups using diallel analysis. The lines were crossed in a diallel design and evaluated for traits like grain yield. Estimates of general and specific combining ability were used to classify the lines into heterotic groups, which was validated using biplot analysis and molecular markers. The results provided insights into the combining ability of different inbred lines with different testers under varying environments.
A novel phylum-level archaea characterized by combining single-cell and metag...Guillaume Reboul
This document summarizes the characterization of a novel archaeal phylum through a combined approach of single-cell genomics and metagenomics. The archaeon, referred to as N21, was found in a hot spring environmental sample through single-cell sorting and amplification. Its genome was then partially assembled from single-cell data. Metagenomic sequencing of the same sample provided additional genomic data, which was binned using the single-cell data, allowing reconstruction of a 1.55 Mbp high-quality draft genome. Phylogenetic analysis showed N21 represents a novel phylum-level lineage within the Euryarchaeota.
This document discusses a study on the biological attributes and feeding efficiency of the green lacewing (Chrysoperla carnea) against the sugarcane mealybug (Saccharicoccus sacchari). The objectives were to identify the biological attributes of C. carnea reared on S. sacchari, evaluate population density of S. sacchari on sugarcane varieties, and evaluate the feeding efficacy of C. carnea against S. sacchari. The methodology involved rearing C. carnea and S. sacchari under laboratory conditions and evaluating various biological parameters. Results showed developmental periods for different life stages of C. carnea and number of S. sacchari consumed at each lar
This document summarizes several adjunct techniques used in IVF laboratories including sperm DNA fragmentation testing, advanced sperm selection methods like IMSI and pICSI, embryo selection techniques like time-lapse imaging and PGS, and mitochondrial DNA load measurement. It reviews the current evidence for each technique, noting that while some like TL imaging show promise, the evidence is still limited and inconclusive for many techniques to recommend their routine use to improve IVF outcomes. Larger randomized controlled trials are still needed to prove effectiveness.
Comparison of Growth and Development of Pleurotus florida against Wastes from...Dr. siddhant
Two wastes from animal origin, viz., human hairs and egg shells were evaluated for different manifestations of white oyster mushroom, Pleurotus florida. The mushroom utilized both the
substrates for their growth and sporophore formation. The mycelial growth was significantly (P=0.05) faster on egg shell (18 days) as compared to human hair (23 days). The crop of mushroom was harvested in four flushes where human hairs showed higher yield and biological efficiency of mushroom (165 gm, 33%) than egg shells (155 gm, 31%), respectively. In respect of yield parameters such as yield, biological efficiency, number of mushroom fruit bodies and average weight of
sporophores, both the substrates were statistically at par to each other. Utilization of human hairs egg shells by P. florida reveals a new strategy for mycoremediation of these wastes.
This study evaluated and optimized somatic embryogenesis procedures for commercial cacao clones. In the first part, eight clones and a control clone were assessed using a modified standard protocol to produce primary and secondary somatic embryos. The second part aimed to improve primary somatic embryogenesis efficiency for two important clones, CCN 51 and CCN 10, by testing different explant types and culture conditions. The results showed that it is possible to produce plants through somatic embryogenesis, though efficiency varies greatly between genotypes requiring protocol optimization. Secondary somatic embryogenesis can increase embryo production ten-fold. The importance of adapting protocols to each genotype is discussed.
This study investigated whether bovine oocytes could support development of monkey embryos created through interspecies somatic cell nuclear transfer (iSCNT). Monkey and bovine skin fibroblasts were used to reconstruct embryos with enucleated bovine oocytes. The reconstructed monkey iSCNT embryos were cultured under different conditions and their Oct-4 expression and development were examined. While monkey iSCNT embryos showed similar early cleavage to bovine embryos, they did not develop past the 16-cell stage. Oct-4 expression was detected in monkey and bovine iSCNT embryos but bovine parthenotes only expressed Oct-4 at later stages. This suggests bovine cytoplasm can support monkey nucleus reprogramming but not full embryo development.
This document summarizes research using a 3×P3-EGFP marker to facilitate screening for transgenic silkworm Bombyx mori. Key findings:
- The 3×P3-EGFP marker was expressed in B. mori embryonic stemmata, nervous system, and other tissues from day 5 of development, allowing transgenic screening starting at the embryonic stage.
- Injecting the piggyBac vector carrying the 3×P3-EGFP marker into the anterior egg pole led to higher expression frequency in stemmata compared to posterior injections.
- Co-injecting the helper plasmid with the marker vector increased expression frequency compared to the vector alone, indicating transposon-
Crop genetic improvement and utilization in china. xinhai liExternalEvents
This document summarizes a case study on crop genetic resources in China. It discusses 1) the collection and conservation of crop germplasm resources in China through various national actions, 2) genomic characterization of crops like rice, wheat, millet, cotton through genome sequencing efforts that have identified genes for traits like yield, quality and stress resistance, and 3) advances in crop molecular breeding in China using techniques like marker-assisted selection, double haploid breeding, and transgenic breeding to develop new crop varieties with desired traits. The document concludes with perspectives on further improving germplasm through basic research and using novel techniques.
Development of First Multiparent Advanced Generation Inter-cross (MAGIC) Popu...ICRISAT
Pigeonpea is an important legume crop and molecular breeding can help improve it faster than conventional methods. Researchers are developing a multiparent advanced generation inter-cross (MAGIC) population for pigeonpea using 8 parental lines. As a first step, 28 two-way crosses were made between parental lines. Whole genome resequencing of parental lines is underway to identify SNPs for mapping traits in the MAGIC population, which will be generated through eight-way crosses and advanced by selfing.
Development and validation of an accurate quantitative real time polymerase c...t7260678
This document describes the development and validation of a quantitative real-time polymerase chain reaction (qPCR) method for comprehensive chromosomal aneuploidy screening of human blastocysts. The method was found to be highly accurate, correctly diagnosing aneuploidies in 97.6% of cell line samples and 98.6% of human blastocyst samples compared to conventional methods. The qPCR method can provide a diagnosis for all 24 chromosomes in only 4 hours, making it suitable for screening of blastocyst biopsies without the need for cryopreservation. This rapid method could allow for fresh euploid embryo transfers and improve outcomes for couples undergoing in vitro fertilization.
Development and validation of an accurate quantitative real time polymerase c...t7260678
This document describes the development and validation of a quantitative real-time polymerase chain reaction (qPCR) method for comprehensive chromosome screening of human blastocysts. The method was tested on cell lines and human blastocysts, showing high consistency with conventional karyotyping and microarray analyses, respectively. The qPCR method was able to accurately diagnose aneuploidy of all 24 chromosomes within 4 hours, demonstrating its potential for rapid comprehensive chromosome screening without the need for blastocyst cryopreservation.
This case report describes the first live birth resulting from pre-implantation genetic diagnosis (PGD) for Oculocutaneous Albinism type 1 (OCA1). A couple who were both carriers for OCA1 underwent two cycles of intracytoplasmic sperm injection with trophectoderm biopsy and next generation sequencing of the embryos. Two embryos were found to be normal and one was transferred, resulting in the live birth of a healthy baby boy without OCA1. This demonstrates the potential for PGD using trophectoderm biopsy and next generation sequencing to achieve successful pregnancies for couples at risk of passing on genetic diseases.
Similar to Predicting of the Embryogenic Performances of 5 Upper Amazon Cocoa Parents Using the Discriminant Model of Wilks? Lambda (20)
This study developed a low cost and affordable to small-scale farmers’ indirect air-cooling combined with evaporative cooling (IAC+EC) system for storage of fruit and vegetables under both arid and hot; and humid and hot climatic conditions. Field heat from freshly harvested produce should be immediately removed through cooling to the desired storage temperature. The aim of this study was to determine the effectiveness of IAC+EC system in terms of the cooling time requirement of the fresh tomato fruit. A fresh tomato cooling experiment to remove field heat during the summer month of September in Pietermaritzburg was conducted for 36 hours where the IAC+EC system was compared to storage under ambient conditions. The results showed that 16 hours was required to reduce the flesh temperature of tomatoes to 16.5°C while the flesh temperature for tomatoes under ambient conditions followed the ambient temperature profile with time of storage. The IAC+EC system reduced and maintained the microenvironment air temperature inside the coolers to 16.5°C - 19°C. The ambient temperature varied between 21 and 32°C. The results in this study are evidence that IAC+ EC system can be a choice for farmers, for cooling the fresh by reducing the field temperature after harvest.
Dioscorea rotundata is a staple food crop for millions of people in the tropical and subtropical regions. In vitro germplasm conservation is a very useful tool in yam improvement strategies but very little is known about the genetic integrity and stability of in-vitro conserved yam plants. In this study, 42 accessions from in vitro and field populations were genotyped using 11 microsatellite markers and 23 morphological descriptors to assess variability within and between accessions. Out of the 23 morphological variables used, 13 were identified as most discriminate and were used to cluster the accessions into 4 clusters using the unweighted pair group arithmetic mean average (UPGMA). Accession maintained in field as well as in in-vitro showed high genetic similarity (R2 = 0.91, p-value: 1e-04). Out of the 42 accessions analyzed, nine accessions maintained in the field and in-vitro displayed different genetic profiles. This study provided basic information on the possible somaclonal variation of yam accessions maintained through in-vitro. Further study with advanced tools such as next-generation sequencing is required to elucidate the nature of the observed variation within clones.
A study was carried out on plant density at the experimental field of the Institute of Agricultural Research for Development (IRAD) Nkolbisson, Yaoundé to determine the appropriate spacing to improve rainfed rice production in the bimodal rainfall forest zone of Cameroon. The experiment was conducted during the main cropping seasons of 2017 and 2018. The planting spacing used were 15cm x 15cm, 20cm x 20cm, 25cm x 25cm and 30cm x 30cm giving the plant populations of 444444, 250000, 160,000 and 111,111 plants / ha respectively using two varieties (Nerica 3 and Nerica 8). The experiment was laid out in a randomized complete block design with three replications. Significant differences were observed in the growth and yield across the years. Treatments were highly significant concerning the number of days to the appearance of the first flower, the number of days to 50% flowering, and the number of days to 50 % maturity. Plants were taller with more tillers and gave higher yields in 2017 than those of 2018. The spacing significantly affected the plant height, number of tillers, and panicle length for both varieties. The interaction of spacing and variety was significant for the number of tillers per m2 and the number of seeds per panicle, however, it was not for the weight of 1000 grains and the percentage of full bales. The yield components determining yield increase were the number of panicles / m2 and the number of seeds/panicles. Nerica 3 variety gave higher yields compared to the Nerica 8, the closer the spacing, the higher the yield. There were a strong significance and positive correlation between yield, number of panicles, and the number of grain per panicle. The spacing that gives the highest number of panicle per m2 was 15 cm X 15 cm and this spacing gave good yield in the region where the study was carried out.
Intermolecular interaction is the material basis for cells to achieve their functions, and protein-protein interaction is an important approach to illuminate the regulation network of biological molecules and has important theoretical significance and potential application value for revealing the activity law of life in nature. This paper mainly summarizes and analyzes the new advances and applications of modern biotechnologies in the study of protein-protein interactions, including local surface plasmon resonance (LSPR), yeast two-hybrid, GST-Pull-down, bimolecular fluorescence complementation, and coimmunoprecipitation. At the same time, the principles of different research methods for protein-protein interaction and their other applications in the field of life sciences are also discussed, all of these will provide a reference value for the analysis of protein-protein interaction and the molecular regulation mechanism of biomacromolecules.
Field experiment involving five improved onion (Allium cepa L.) varieties and carried out at Kulumsa Agricultural Research Center during the 2018 to 2019 cropping seasons under irrigated condition to identify the best performing variety for seed production to the target areas of Arsi Zone. The onion varieties included in the field experiment were (Nafis, Robaf, Nasic Red, Bombe Red, and Adama Red). The experimental design was a randomized complete block design (RCBD) with three replications. Phenological and growth parameters, seed yield, and yield components were studied. The result showed that Variety had a significant effect on most phonological and growth attributes as well as on yield attributes. The number of days to flowering and vigorously were significantly affected by variety; while plant height, days to boolting and branch number was not significantly influenced by variety. Flower stalks height and diameter, number of umbel per plant, and umbel diameter also significantly affected by variety. Seed yield per umbel and mean seed yield per hectare also showed a significance difference among varieties. The highest seed yield per hectare (1415.89 kg/ha) was recorded from Adama Red and followed by Nafis variety, whereas Nasic rerd, Bombe red and Robaf show no significance difference among each other, Therefore, it can be concluded that use of the improved onion varieties such as Adama red and Nafis is advisable and could be appropriate for onion seed production in the test area even though further testing is required to put the recommendation on a strong basis.
Rubber trees are among the important cultivated crops in Malaysia, and have contributed to the country’s overall economic growth since the 1950s. However, the existing anatomical and morphological studies are relatively insufficient. Currently, Hevea brasiliensis has been cultivated and planted commonly as a commercial planting clone, while Hevea camargoana remains to be a non-cultivated and underutilized rubber species. For many years, there only exists little information both in private plantations and government agencies that have carried out anatomical and morphological assessments on these underutilized species. There is little information about the characteristics of H.camargoana, thus raising the issue among plant breeders on how to best use this underutilized rubber species. This study attempts to investigate the taxonomic values and characteristics of Hevea brasiliensis and Hevea camargoana through anatomical and morphological studies.
Use of distributed electricity generation systems is currently increasing due to their economic and environmental benefits. Agricultural greenhouses require heat and electricity for covering their energy needs while their annual energy requirements vary significantly. Aim of the current work is the investigation of applying various distributed electricity generation systems in greenhouses. A review of different distributed generation systems currently used in various sectors as well as in greenhouses has been implemented. Various technologies are examined utilizing either renewable energies or fossil fuels in very efficient energy systems. Most of them are mature and cost-effective having lower environmental impacts compared with traditional centralized electricity generation technologies. Their use in greenhouses results in many benefits including the creation of an additional income for the farmer, reduction of carbon emissions into the atmosphere and increasing stability of the electric grid. It is suggested that distributed electricity generation systems should be used more in greenhouses when the necessary conditions are favorable.
Grain mold, considered the most important disease of sorghum, is associated with several fungal genera. The disease reduces both yield and quality. In this study, over 300 sorghum seed samples collected from Texas, Florida, and Georgia were evaluated for grain mold severity, seed weight, germination rate, and seed fungal community. Grain mold severity of the seed samples, except for those collected from Cameron, Texas, were rated 3 or higher, indicating that these sorghum lines were moderately susceptible under naturally-infected field conditions during the 2016 and 2017 growing seasons. Seed weight across surveyed locations ranged from 1.1 g to 4.0g for samples collected in Texas during the same period. Percent germination rates for samples collected in Texas ranged from 59.6% to 86.7%. Sorghum samples collected from Florida and Georgia exhibited moderately susceptible response to grain mold infection. Mean seed weight was 1.9 g for samples collected from Florida, while in Georgia, mean seed weight was 2.3 g. Germination rate was low for samples collected from Florida and Georgia. Mycological analysis of sorghum seed samples collected from farmers’ fields in Central and South Texas during the 2016 and 2017 growing seasons showed Alternaria species as the most frequently isolated fungal genus, accounting for 40% and 42 % in 2016 and 2017, followed by Fusarium incarnatum, F. acuminatum, F. equiseti, & F. semitectum Complex. In Florida and Georgia, Fusarium incarnatum, F. acuminatum, F. equiseti, & F. semitectum Complex was the most frequently recovered fungal species, accounting for 77% and 72% of the total. genera/species isolated from seed samples. Other fungal species, including Curvularia lunata, Bipolaris sp., Colletotrichum sublineola, F. verticillioides, Penicillium sp., Aspergillus flavus, F. thapsinum, F. oxysporum, F. sporotrichioides, F. graminearum, F. proliferatum, and Aspergillus niger were also isolated from sorghum seeds in various frequencies. In conclusion, the presence of large number of fungal genera associated with grain deterioration and their effect on other traits, makes management of this disease complex challenging. To identify grain mold resistant sources in a region, using the most dominant species in that region to screen the sorghum germplasm is recommended.
- The document describes national performance trials of potato varieties conducted in mid-altitude regions of Kenya between 2016 and 2017.
- Twenty-six potato genotypes, including four check varieties, were evaluated across six mid-altitude sites over two seasons. Yield and other agronomic data was collected.
- In the first season, genotypes, environments, and their interaction all significantly affected yield. Trans-Nzoia was the highest yielding site, with all genotypes yielding between 10-25 tons/ha. In the second season, only environments significantly impacted yield, with Trans-Nzoia again the highest.
The tests for the evaluation of seedling establishment, palatability and acceptability were carried out at the Teaching and Research Farm of the Department of Agricultural Technology and the Food Laboratory of the Department of Home and Rural Economics, Adamawa State College of Agriculture, Ganye, Adamawa State. The experimental designs used were Randomized Complete Block Design and the Completely Randomized Design. Some of the parameters measured were percentage seedling establishment, palatability, and acceptability tests. The highest mean percentage seedling establishment was observed in 12.00g levels of H. suaveolens whole powder treated shelled groundnut seeds (97.67, 97.00, and 94.00) at the three periods of storage. Percentage seedling establishment decreased with a decrease in levels of H. suaveolens whole powder. One of the major constraints to the use of plant materials as an alternative to synthetic insecticides is the issue of standardization in dosage of application. This work has suggested that, if groundnut seeds are to be used for sowing, they should be stored with a 12.00g level of H. suaveolens whole powder for every 300.00g for three months. However, if they are to be used for consumption, they could be stored with a 6.00g level of H. suaveolens whole powder for every 300.00g for at most three months. There was no significant difference between treated and untreated shelled groundnut seeds at the three periods of storage on the acceptability and palatability score of cooked groundnut at all dosages of application. All treatments were within the acceptable score rates even though the two rates of the synthetic insecticides, actellic dust were at the lowest acceptable score rate. The finding also showed that acceptability and palatability decreased with an increase in dosage of application. The periods of storage also had a significant impact on the mean percentage seedling establishment. It was observed that there was a higher percentage of seedling establishment when shelled groundnut seeds were stored from November- January. At this period of the year, the temperature and humidity are usually low and this might have necessitated the high state of inactivity and low performance of the bruchids compared to other periods of storage within the year.
1. The study examined the effects of mulching and irrigation on cocoa seedling survival and establishment during the dry season in Ghana.
2. Results showed that irrigation and mulching significantly increased soil moisture content. Cocoa seedlings raised in topsoil, mulched and irrigated had the highest survival rate of 94.5%, while seedlings without irrigation or mulching had the lowest survival rate of 47.1%.
3. Irrigation had a significant positive effect on cocoa seedling survival, plant height, and leaf number. Seedling survival was 89.6% under irrigation versus 65.6% without irrigation. Mulching alone did not significantly affect seedling survival.
Few years ago National Centre for Agricultural Mechanization (NCAM) launched melon sheller to reduce burden of obtaining melon oil and cake, and to enhance rural women’s productivity. This study looked at the productivity of promoted melon shelling technology and preference by rural women in Nigeria. Data were gathered from the NCAM workshop and survey of melon processors in Niger State. In the workshop, it was found that time allowed for soaking melon and covering with piece of clothes contributed to the productivity of the sheller. Results from survey revealed that 95.1% of the respondents’ preferred Internal Combustion technology and 90.2% liked electric-driven melon shellers over the manual one. Also, 69.5% obtained the shellers from local fabricators rather than NCAM. The technology led to increased turnout of melon (378kg/hr) and reduced wastages to 1.26kg out of 75.6kg. The study concluded that the promoted melon sheller is efficient and have positive implication on the rural women’s productivity and revenue. The study recommends that the rural women should put the melon sheller into its maximum capacity use. The NCAM should extend training to the local fabricators so that they can improve on the technology most especially in the areas of winnowing and washing of melon kernels.
Keeping in view of lack of recommended rates of N and NPS fertilizers, a field experiment was conducted to evaluate the effect of the newly introduced NPS fertilizer and nitrogen on growth, physiology and above ground biomass of garlic. Four NPS (0-0-0, 78.75-69-12.75, 105-92-17 and 131.25-115-21.25 kg N-P-S ha-1) and three nitrogen fertilizer rates (114.13, 228.26 and 278.33 kg N ha-1) were laid out in Randomized Complete Block Design with three replications. Significantly highest plant height (28.02 cm), leaf diameter (1.27 cm), dry and fresh weight (4.71 g and 6.11 g) and leaf length were recorded on garlic plants supplied with 105-92-17 kg N-P-S ha-1 and also the highest plant height (27.75 cm), leaf length (24.02 cm), fresh and dry weight (6.23 g and 5.04 g) were recorded on garlic plants supplied with 278.33 kg N ha-1. The interaction effect also show a significant effect in almost all the growth parameters; the early day to 50% emergence was recorded from a plot which received 228.26 kg N ha-1 and 105-92-17 kg NPS ha-1 and the highest plant height, leaf length, fresh and dry above ground biomass and leaf diameter were 29.62 cm, 25.60 cm, 6.93 g, 5.59 g and 1.4 cm, respectively were observed by the interaction of 278.33 kg N ha-1 and 105-92-17 kg N-P-S ha-1 with no significant difference with 228.26 N and 78.75-69-12.75 kg N-P-S ha−1. From this one season experiment, fertilizer rates 307.01-69-12.75 kg N-P-S ha−1 could be recommended for garlic production.
In the past, conservation effort has primarily focused on establishment of forest reserves for timber production, with minimal or no consideration to how these natural resources will help sustain or improve livelihoods of adjoining communities. This study examined the contribution of Aramoko forest reserve to the livelihoods of the adjoining communities in Ekiti State. One hundred and twenty pre-tested questionnaires were administered among the products collectors in the study area. Data collected were analysed and the result showed that 78.3 % of the respondents are married with 52.3 % of them male, while 50.8 % of the respondents aged between 51-70 years with 64.1 % having at least secondary education. Twenty-five (25) different products were collected by the respondents in the study area. These products include among others; timber with highest frequency of (120) followed by herbal plants (115), Archantina marginata (105), Thaumatococcus danielli (89), Bridelia ferruginea (70) and Irvingia garbonensis (65). The use of motor cycle accounted for 41.4 % of the respondents means of transportation, while 31.3 % of the respondents sell their product in bit at the village market. Picking, digging, plucking, cutting and uprooting were methods used for harvesting by the respondents while illegal felling (24 %) and indiscriminate bush burning (22.4 %) were the major conservation problem in the study area. Specifically, some of the products harvested are used for food, medicine, fuelwood, herbs and cultural purposes. The study recommends that research should be conducted into how these products can be artificially raised in the nursery for plantation establishment.
Cocoa farmer faces increasing challenging environment through exposure to risks factors which have impacted negatively on their production or output. Since farmers are primary producers and often times lack capacity to control risks factor, it is important to manage this factors. This study examines the cocoa farmers’ risk preferences and crop insurance perception and isolates the drivers of decision to uptake crop insurance among cocoa farmers in Ekiti state. The sample for the study consist of 200 cocoa farmers who were household heads selected through multi-stage sampling across four Local government areas of Ekiti State who are predominantly cocoa producers. Data collected on socio-demographic characteristics, perception of crop insurance and risk preferences, were analyzed using descriptive statistics and binary logistic model. Results showed that majority of the cocoa farmers were without crop insurance, with higher enrolment in Membership of cooperative society, owned their land, larger household size and lower educational level but higher level of farm experience when compared to cocoa farmers who are holding crop insurance. Farmers risk preferences showed no significant difference between farmers with or without insurance. Education (β=0.59), Household size (β=0.0029) and Debt use (β=0.02), Membership of cooperative (β=-4.53), Farming Experience (β=-2.51), Owned Land (β=-2.19) and Non-Farm Income (β=-0.65) were among the significant determinants of insurance uptake. Risk mitigating measures such as provision of necessary incentives such as improved varieties of cocoa seedling, as well as provision of fertiliser and approved pesticides, financial assistance, and simple processing technologies that produce standard cocoa bean plus a re-jigged Nigeria Agricultural Insurance Corporation (NAIC) for an improved discharge of its function are recommended.
Mitigation of climate change requires the decrease of greenhouse gas emissions into the atmosphere and the increasing use of renewable energies replacing fossil fuels. Agricultural greenhouses are energy-intensive agricultural systems using mainly fossil fuels. The use of renewable energies during their operation is limited so far. The possibility of using renewable energies for covering their energy needs has been investigated, focused on the Mediterranean region. Various sustainable energy technologies which are reliable, mature, cost-effective and broadly used in various applications are examined. These include solar-PV systems, low enthalpy geothermal energy, solid biomass burning, co-generation systems, high efficiency heat pumps and reuse of rejected industrial heat. Combined use of these systems in greenhouses can cover all their energy requirements in heat, cooling and electricity, reducing or zeroing their net CO2 emissions into the atmosphere due to operational energy use. It is concluded that depending on their local availability in Mediterranean countries, these benign energy technologies can assist greenhouse crop growers in the reduction of their carbon emissions, contributing in the achievement of the universal goal for climate change mitigation.
Field experiment was carried out under rain-fed conditions during the 2013 and 2014 cropping seasons at the Teaching and Research Farm of the Department of Agricultural Technology, Adamawa State College of Agriculture, Ganye, solely to develop an integrated pest management for the control of groundnut Aphid (Aphis craccivora Koch) [Homoptera: Aphididae]. The experimental Design used was the Randomized Complete Block Design (RCBD). Parameters measured were, average number of leaves per plot at 6 weeks after sowing, number of branches at 3 weeks after sowing, number of branches at 6 weeks after sowing, number of pods per plot, weight of harvested seeds per plot. The result obtained shows that, there was significant difference among the treatments in all the parameters measured at 0.05 level of probability using the Least Significant Difference (LSD). According to the results recorded, the highest mean yield of groundnut was obtained on plots treated with the combination of chemical and physical control methods (1444g) followed by plots treated with physical, chemical and cultural control methods combined (1296g). The highest mean number of pods per plant was recorded in the combination of physical, chemical and cultural control methods (18.00) followed by chemical and physical control methods as combined (15.00). The work shows that, the cultivation of groundnut with the control of groundnut Aphid (Aphis craccivora Koch) using integrated pest control applied as recommended facilitates better growth and guarantees good crop yield. The use of physical, chemical and cultural control method is profitable in Ganye Area of Adamawa State and is therefore suggested for use to local farmers.
Rice (Oryza sativa L.) is one of the most important food crops in the world. Purple rice, as a special rice with important nutritional and health functions, has important scientific significance and application value for genetic improvement of purple rice and breeding of new varieties through in-depth study on its agronomic and related quality traits and products processed, and analysis of its genetic basis. In this paper, the new progress of purple rice in agronomic traits, quality traits, environmental impacts on purple rice and genetic basis of purple rice seed coat in recent years were reviewed and analyzed, and the application prospects of purple rice processing products and purple gene in rice genetic improvement were also prospected. Thus, our results will provide important information and reference for breeding new purple rice varieties with good quality and high yield.
Groundnut is an important oil seed crop, grown throughout the tropics and sub tropics worldwide. It is one of the three economically important oilseed crops grown in Ethiopia. Groundnut is commonly produced by small scale farmers as food and cash crops in the study area. The area has potential to the production of Ground nut for food and nutrition security as well as export commodity. However, scarcity of varieties that fit to the environment is one of the major constraints of production. Therefore, this experiment was conducted to evaluate five Ground nut varieties and select early maturing varieties with considerable yield and agronomic traits. The field experiment was conducted in 2017 and 2018 at Abaya and varieties were planted in Randomized complete block design (RCBD). Data were collected on yield and important agronomic traits. The computed analysis of variance revealed significant variations among varieties for days to maturity, number of primary branches, number of pegs per plants, Grain yield and shelling percentage. The pooled over year mean of varieties indicated , Tole- 1 variety ( Check) is high yielding with mean grain yield of 4174.7kg followed by variety Sedi (3552.5kg/ha) and Babile local (3550.4kg/ha).Variety Sedi has special merit in terms of earliness and therefore recommended for moisture stress areas of Abaya and location with similar agro ecologies while Tole -1 (Standard check) is high yielding varieties and should be used in production until new varieties will be developed through selection/breeding program.
The document summarizes a field trial that examined the effects of applying locally available materials like liquid silicate rock fertilizer (LSRF), neem leaf botanical pesticide (BP), and black ants (BA) on cocoa production over 14 months in Indonesia. The key findings were:
1) Treatments with LSRF, LSRF+BP, LSRF+BA, and BA reduced pest and disease attacks on cocoa pods by 6-18% and increased bean production by 18-119% compared to the control, with LSRF providing the highest production increase of 119%.
2) The treatments increased polyphenol and lignin contents in cocoa pod shells, improving pod resistance to pests and
Evidence of Jet Activity from the Secondary Black Hole in the OJ 287 Binary S...Sérgio Sacani
Wereport the study of a huge optical intraday flare on 2021 November 12 at 2 a.m. UT in the blazar OJ287. In the binary black hole model, it is associated with an impact of the secondary black hole on the accretion disk of the primary. Our multifrequency observing campaign was set up to search for such a signature of the impact based on a prediction made 8 yr earlier. The first I-band results of the flare have already been reported by Kishore et al. (2024). Here we combine these data with our monitoring in the R-band. There is a big change in the R–I spectral index by 1.0 ±0.1 between the normal background and the flare, suggesting a new component of radiation. The polarization variation during the rise of the flare suggests the same. The limits on the source size place it most reasonably in the jet of the secondary BH. We then ask why we have not seen this phenomenon before. We show that OJ287 was never before observed with sufficient sensitivity on the night when the flare should have happened according to the binary model. We also study the probability that this flare is just an oversized example of intraday variability using the Krakow data set of intense monitoring between 2015 and 2023. We find that the occurrence of a flare of this size and rapidity is unlikely. In machine-readable Tables 1 and 2, we give the full orbit-linked historical light curve of OJ287 as well as the dense monitoring sample of Krakow.
Mechanisms and Applications of Antiviral Neutralizing Antibodies - Creative B...Creative-Biolabs
Neutralizing antibodies, pivotal in immune defense, specifically bind and inhibit viral pathogens, thereby playing a crucial role in protecting against and mitigating infectious diseases. In this slide, we will introduce what antibodies and neutralizing antibodies are, the production and regulation of neutralizing antibodies, their mechanisms of action, classification and applications, as well as the challenges they face.
TOPIC OF DISCUSSION: CENTRIFUGATION SLIDESHARE.pptxshubhijain836
Centrifugation is a powerful technique used in laboratories to separate components of a heterogeneous mixture based on their density. This process utilizes centrifugal force to rapidly spin samples, causing denser particles to migrate outward more quickly than lighter ones. As a result, distinct layers form within the sample tube, allowing for easy isolation and purification of target substances.
Discovery of An Apparent Red, High-Velocity Type Ia Supernova at 𝐳 = 2.9 wi...Sérgio Sacani
We present the JWST discovery of SN 2023adsy, a transient object located in a host galaxy JADES-GS
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. The transient was identified in deep James Webb Space Telescope (JWST)/NIRCam imaging from the JWST Advanced Deep Extragalactic Survey (JADES) program. Photometric and spectroscopic followup with NIRCam and NIRSpec, respectively, confirm the redshift and yield UV-NIR light-curve, NIR color, and spectroscopic information all consistent with a Type Ia classification. Despite its classification as a likely SN Ia, SN 2023adsy is both fairly red (
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BIRDS DIVERSITY OF SOOTEA BISWANATH ASSAM.ppt.pptxgoluk9330
Ahota Beel, nestled in Sootea Biswanath Assam , is celebrated for its extraordinary diversity of bird species. This wetland sanctuary supports a myriad of avian residents and migrants alike. Visitors can admire the elegant flights of migratory species such as the Northern Pintail and Eurasian Wigeon, alongside resident birds including the Asian Openbill and Pheasant-tailed Jacana. With its tranquil scenery and varied habitats, Ahota Beel offers a perfect haven for birdwatchers to appreciate and study the vibrant birdlife that thrives in this natural refuge.
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...Leonel Morgado
Current descriptions of immersive learning cases are often difficult or impossible to compare. This is due to a myriad of different options on what details to include, which aspects are relevant, and on the descriptive approaches employed. Also, these aspects often combine very specific details with more general guidelines or indicate intents and rationales without clarifying their implementation. In this paper we provide a method to describe immersive learning cases that is structured to enable comparisons, yet flexible enough to allow researchers and practitioners to decide which aspects to include. This method leverages a taxonomy that classifies educational aspects at three levels (uses, practices, and strategies) and then utilizes two frameworks, the Immersive Learning Brain and the Immersion Cube, to enable a structured description and interpretation of immersive learning cases. The method is then demonstrated on a published immersive learning case on training for wind turbine maintenance using virtual reality. Applying the method results in a structured artifact, the Immersive Learning Case Sheet, that tags the case with its proximal uses, practices, and strategies, and refines the free text case description to ensure that matching details are included. This contribution is thus a case description method in support of future comparative research of immersive learning cases. We then discuss how the resulting description and interpretation can be leveraged to change immersion learning cases, by enriching them (considering low-effort changes or additions) or innovating (exploring more challenging avenues of transformation). The method holds significant promise to support better-grounded research in immersive learning.
Immersive Learning That Works: Research Grounding and Paths ForwardLeonel Morgado
We will metaverse into the essence of immersive learning, into its three dimensions and conceptual models. This approach encompasses elements from teaching methodologies to social involvement, through organizational concerns and technologies. Challenging the perception of learning as knowledge transfer, we introduce a 'Uses, Practices & Strategies' model operationalized by the 'Immersive Learning Brain' and ‘Immersion Cube’ frameworks. This approach offers a comprehensive guide through the intricacies of immersive educational experiences and spotlighting research frontiers, along the immersion dimensions of system, narrative, and agency. Our discourse extends to stakeholders beyond the academic sphere, addressing the interests of technologists, instructional designers, and policymakers. We span various contexts, from formal education to organizational transformation to the new horizon of an AI-pervasive society. This keynote aims to unite the iLRN community in a collaborative journey towards a future where immersive learning research and practice coalesce, paving the way for innovative educational research and practice landscapes.
Predicting of the Embryogenic Performances of 5 Upper Amazon Cocoa Parents Using the Discriminant Model of Wilks? Lambda
1. Journal of Agriculture and Crops
ISSN: 2412-6381
Vol. 1, No. 2, pp: 26-32, 2015
URL: http://arpgweb.com/?ic=journal&journal=14&info=aims
*Corresponding Author
26
Academic Research Publishing Group
Predicting of the Embryogenic Performances of 5 Upper Amazon
Cocoa Parents Using the Discriminant Model of Wilks’ Lambda
Auguste Emmanuel Issali* Station Cocotier Port Bouët Marc Delorme, CNRA, 07 BP 13 Abidjan 07, Côte d’Ivoire
Deless Fulgence Thiemele Station de Recherche sur le Plantain, la Banane et l’Ananas à Bimbresso. CNRA, 01BP1536 Abidjan
01, Côte d’Ivoire
Franceline Doh Laboratoire d’entomologie, Université Nangui Abrogoua, 02 BP 801 Abidjan 02, Côte d'Ivoire
Eugène Pacôme Kouakou
Konan
Coordonnateur Scientifique du CNRA-Abidjan. 19, 21 Rue Jean Mermoz. 08 BP 33 Abidjan 08,
Côte d’Ivoire
1. Introduction
Cocoa tree is a cross-pollinated forest species originated from the rainforest of the South and Central America
[1]. It belongs to the Malvaceae [2]. Theobroma cacao L., is the only cultivated species from genus Theobroma used
for manufacturing of chocolate. Côte d’Ivoire is the largest producer of beans from cocoa tree. Its yielding accounts
for about 44.25% of the global one [3]. More than six millions people depend directly or indirectly on cocoa
cultivation. It accounts for 30% of working population [4].
Predictive model of the in vitro embryogenic performances of upper amazon cocoa parents has stayed little
known. Indeed, the sustainability of cocoa crop in producer countries depends largely on the cloning technique
control. In oil palm, Konan, et al. [5] suggested the modeling of interactions occurring during rooting of the somatic-
embryos derived plantlets. Likewise, in Konan, et al. [6], the modeling of the prediction of the amount of culture
biomass to be transferred and that of the number of harvested shoots at the end of each culture cycle were carried
out. Nonetheless, somatic embryogenesis technique is one of the means used for cocoa cloning [7-9]. The reliability
of this technique was tested successfully [10, 11]. With respect to prediction, the 5 upper amazon cocoa parents were
already structured, nonetheless in combination with their 6 hybrids [12]. Thus, no study has reported only the in vitro
embryogenic performances prediction of 5 upper amazon cocoa parents analysed here. The knowledge of this
prediction model would allow the rapid vegetative propagation of the best cocoa parents for the setting up of two-
clone seed orchard field. Likewise, this knowledge would allow the prediction of membership cluster of a new
observation from its somatic embryogenesis values. Moreover, it seems that one variable describing the somatic
embryogenesis might predict accurately the embryogenic performances among the 4 used in the study in cocoa
parents.
Abstract: To predict the embryogenic performances of 5 upper amazon cocoa parents, the discriminant model
of Wilks’ Lambda was used. Five parents, namely IMC67, P19A, Pa13, Pa121 and Pa150 were used.
Staminodes and petals from these parents were extracted of flower buds then cultured in vitro onto 2
callogenesis media, namely PCG1 and PCG3. The Principal Component (PCA), Hierarchical Cluster HCA) and
Factorial Discriminant Analyses (FDA) were performed. As for the PCA, a single, namely the number of
callogenic explants, out of 5 measured variables, was dropped from the study. Two classes were identified from
the PCA and HCA, then confirmed via the FDA. Clones P19A and Pa13 belonging to Class C2, displayed the
highest embryogenic performances. Earlier study relying on multivariate analysis implying hybrids and these 5
cocoa parents revealed results approximately similar. The model predicting the embryogenic performances is
spelt Z1 = -3.310 + 4.532*Ncalem. In oil palm, 2 models, the first one predicting the biomass production and the
second one modeling the number of harvested shoots from somatic embryos were proposed. From model
proposed here, the embryogenic performances of the best genotypes will vary from 1.3725 to 1.7402. Their
discriminating score Z1 will oscillate from 2.910 to 4.576. This model will allow the predicting of membership
class of a new observation from its values of the number of embryogenic explants.
Keywords: Membership class; PCG media; SCG medium; ED medium; Predicting equation; Communality.
2. Journal of Agriculture and Crops, 2015, 1(2): 26-32
27
The objective of work was to search for and identify a prediction model of the in vitro embryogenic
performances of 5 upper amazon cocoa parents.
2. Materials and Methods
2.1. Plant Material, Experimental Conditions and Design
Plant material was obtained from ancient research station of CNRA (Centre National de Recherche
Agronomique) based on Bingerville. The latter is located at 3° 52’ 59" West longitude and 5° 21’ 42" North latitude
and 59 m above sea. From 2002 to 2004, at the meteorological Bingerville Station of CNRA, the weekly
pluviometric total, weekly average maximum temperature, weekly average minimum temperature, average relative
humidity were 4186.80 mm, 30.63°C, 20.16°C, 77651.42 hours, 82.13%, respectively. Experiment was conducted
from January to February 2005. Flower buds were harvested at Bingerville then carried at the Central Biotechnology
Laboratory. They were prepared for culture purposes according to Li, et al. [7] and Young, et al. [13] protocols.
The 5 cocoa parents, namely IMC67, P19A, Pa13, Pa121 and Pa150, were planted in row in the fields B1A,
B1B and B10 of the Bingerville site according to a design without randomisation. These rows consisted of clones of
each of accessions represented in genebank. Only one cocoa tree for each parental clone was used during the
experiment.
With respect to culture initiation, a 5 x 2 x 2 factorial scheme in a modified completely randomised design was
used. Modifications concerned the culture of staminodes and petals in the same Petri dish. Treatments were prepared
in triplicate. In all, 6 treatments were obtained per genotype. Therefore, the 5 cocoa parents providing each 2
explants (staminodes and petals) were cultured onto 2 culture media. The latter consisted of Li, et al. [7]’s media.
These are PCG1 and PCG3 for culture initiation, SCG1 for secondary callus growth and ED with respect to embryos
development.
2.2. Explants Preparation, Culture Conditions and Media
Flower buds measuring 4-5 mm long were collected on the 5 cocoa parents twice a week, early in the morning.
They were used as a source of explants. Primary somatic embryos were obtained as described in Li, et al. [7] by
culturing staminode and petal explants onto 2 primary callogenesis media namely PCG1 and PCG3. Fourteen days
after the culture onto Primary Callus Growth (PCG) media, the callogenic explants were subcultured onto Secondary
Callus Growth (SCG). Fourteen days later, callogenic explants were again subcultured onto hormone free Embryos
Development medium (ED). Onto this one, they were subcultured threefold every 21 days.
2.3. Variables Measurement
At the end of 3 months of culture, the number of callogenic explants (Ncal), the number of embryogenic
explants (Ncalem), the embryos number yielded per embryogenic explant (Nemb) were scored. From these, the
average embryos number provided per embryogenic explant (Mece) as well as embryogenesis percentage (Pe) were
calculated.
2.4. Statistical Analysis
Collected data were subjected to the Principal Component (PCA), Hierarchical Cluster (HCA) and Factorial
Discriminant Analyses (FDA) by means of the softwares SPSS and Xlstat, versions 22.0 and 2007, respectively.
3. Results
3.1. Data Reduction by Means of the PCA
This reduction of collected data was achieved through : i) the analysis of the data factorizability, ii) choice of
principal components, iii) the choice of variables and iv) interpretation of the variability observed. Regarding the
factorizability, Kaiser-Meyer-Olkin (KMO) coefficient was 0.546, thus greater than 0.5. The Bartlett’s test of
sphericity was very highly significant (p-value = 0.002). Such a value for p-value is greater than the 0.10 level. The
meeting of these 2 conditions allowed the statement that data were factorizable.
As for the choice of used variables, only the number of callogenic explants was dropped. The 4 others were selected
for the rest of the study.
Concerning the choice of principal components, the first 2 were selected. They explained 99.86% total
variability. As far as the interpretation of variability is concerned, the first component explained 53.23% total
variability, as against 46.53% for the second one. It described parents expressing correct value of the mean of the
somatic embryos yielding. The second principal component represented parents displaying correct somatic
embryogenesis percentage.
3.1.1. Footnote related to the PCA
The analysis of the output from the PCA was carried out through the data factorizability, the choice of variables
and that of principal components as well as the interpreting of the variability expressed. Data factorizability was
appreciated using the Kaiser-Meyer-Olkin (KMO) coefficient and Bartlett’s test of sphericity. Regarding the first
one, the KMO was 0.546. Such a value was between 0.5 and 0.6 according to Kaiser’s scale. Thus, it was considered
to be poor. Nonetheless, it conferred correct factorial structure to data. For Bartlett’s test of sphericity, the statistics
3. Journal of Agriculture and Crops, 2015, 1(2): 26-32
28
Ncalem
NembMece
Pe
-1
-0.75
-0.5
-0.25
0
0.25
0.5
0.75
1
-1 -0.75 -0.5 -0.25 0 0.25 0.5 0.75 1
F2(46.63%)
F1 (53.23 %)
Variability of components F1 and F2 : 99.86 %
aftervarimax rotation
IMC67
P19A
Pa121
Pa13
Pa150
-1
-0.5
0
0.5
1
1.5
2
-2.5 -2 -1.5 -1 -0.5 0 0.5 1 1.5 2
D2(46.63%)
D1 (53.23 %)
Observations on plane 1-2 : 99.86%
aftervarimax rotation
C1
C2
of approximate Chi-square, which is associated with it, was 20.946 (p-value = 0.002). This statistics was high. The
probability which is associated with it was very smaller than 0.10 postulating that at least one of correlations
between variables is significantly other than zero. The meeting of these 2 conditions allowed the continuation of the
analysis.
For the choice of variables to use to interpret the variability, the number of explants callogenic was dropped.
Indeed, it discarded value of the correlation matrix, and thus made impossible not only the calculation of KMO
coefficient, but also the performing of Bartlett’s test of sphericity. Likewise, all of 4 selected variables showed
correct communalities revealed by their positioning on circle of correlations (Figure 1).
From 4 variables selected like relevant, 4 principal components were extracted using the Kaiser’s normalization
method.
As far as the choice of principal components is concerned, 2 were selected, because they accounted for more
than 70% total variability. The first one, namely component 1, described 53.23% total variability. It is defined by the
embryos number per embryogenic explant and the average number of embryos per embryogenic explant. It displayed
upper amazon cocoa parents expressing high yielding of embryos (Table 1). The second one, known as component 2,
explained 46.63% unexplained variability by component 1. It characterised the proportion of upper amazon cocoa
parents yielding the embryogenic explants (Table 1).
The projection of observations on the plane 1-2 of the PCA seemed to reveal the existence of 2 classes. First,
would consist of parents IMC67, Pa150 and Pa121, would differ from 2 others by a low mean of embryos yielding.
Second, composed of PA13 and P19A, would be distinguishable from the first by a high potential of yielding of
embryogenic explants (Figure 1; Table 1).
Figure-1. Communality of 3 measured variables and scatter plot structuring the 5 parents on the plane 1-2 of the correlation circle and that of the
factorial map, respectively, from the PCA.
Table 1 : Expressed variability and cosine squared of each of the variables measured on each of principal components 1 and 2.
F1 F2
Variability expressed (%) 53.23 46.63
Cumulative % 53.23 99.86
Cos² Ncalem 0.253 0.744
Nemb 0.913 0.085
Mece 0.933 0.066
Pe 0.030 0.970
Legend
Cos²: cosine squared.
3.2. Variability of 5 Upper Amazon Cocoa Parents On Basis of Their Callogenic and
Embryogenic Potential from the HCA
As far as the multivariate classification is concerned, the number of observations was smaller than the 100 level.
This allowed the choice the HCA instead the k-means multivariate method (http://www.lemoal.org/spss/). The
observations were clustered into 2 classes, confirming the reports done in the course of the analysis of the PCA.
Each accounted for 60% and 40% of the total number, respectively. Such percentages, very higher than 10% level,
allowed the validation of the analysis performed. Furthermore, at level 15 of the scale of dendrogramme the
truncation was done. This revealed the existence of differences. The analysis of data displayed that these differences
derived from only one variable out of 5 used. Thus, 4 did not discriminate classes, whereas 1 discriminated them
(Figure 2; Table 2).
4. Journal of Agriculture and Crops, 2015, 1(2): 26-32
29
Class C1 consisted of 3 observations, that is to say IMC67, Pa121 and Pa150. It differed from C2 by low
number of embryogenic explants (Ncalem), low embryos number per embryogenic explant (Nemb), low average
embryos number per embryogenic explant (Mece) and low embryogenesis percentage (Pe). On the contrary, it
recorded high number of callogenic explants (Ncal; Figure 2; Table 2).
Class C2 comprised 2 observations, namely P19A and Pa13. It stood out from C1 by high number of
embryogenic explants (Ncalem), high embryos number per embryogenic explant (Nemb), high average embryos
number per embryogenic explant (Mece) and high embryogenesis percentage (Pe). However, it showed low number
of callogenic explants (Ncal; Figure 2; Table 2).
Figure-2. Clustering of the 5 upper amazon cocoa parents from their callogenic and embryogenic values.
Table-2. Separation of the class means from the HCA based on Student t test.
Class Ncal Ncalem* Nemb Mece Pe
C1 15.070a 0.180a 0.474a 0.441a 1.039a
C2 13.686a 1.556b 6.140a 3.629a 8.068a
Mean 14.378 0.868 3.307 2.035 4.553
p-value 0.648 0.006 0.075 0.094 0.069
Legend : Ncalem*: variable expressing the number of embryogenic explants. Different letters accompanying average values
in column express significant difference between the 2 means according to Student t test at 5% threshold.
3.3. Predicting of the Somatic Embryos Yielding Based On the Analysis of the Classes
Conformity Provided By the HCA
Regarding the FDA, the conformity between the 2 classes was checked using the: i) looking for differences
between classes, ii) validation of the Wilks’ Lambda method, iii) estimate of the coefficients of the discriminant
function and iv) analysis of the communality. Before the assessing of 4 previous points, the relevance of measured
variables was analysed. Thus, the number of callogenic explants and the number of embryogenic explants were
identified to be relevant. Indeed, they recorded Variance Inflation Factor (VIF) lower than 10 level (VIF / Ncal =
1.513 ; VIF / Ncalem= 3.655). In contrast, the embryos number per embryogenic explant (Nemb), the average
embryos number per embryogenic explant (Mece) as well as the embryogenesis percentage (Pe) expressed VIF
higher than 10 level (VIF / Nemb = 487.504; VIF / Mece = 455.402; VIF / Pe = ∞). Therefore, the first 2 variables
were selected for the rest of the study, while the last 3 were dropped from the same study (Table 3).
The looking for the differences between the 2 classes identified was performed through the examination of
variance of measured variables on the one hand, as well as the analysis of Fisher-Snedecor F statistics and Wilks’
Lambda on the other hand. For the variance, those from the 2 selected variables appeared to be discriminant (Ncal =
13.419; Ncalem = 0.039). As for the Fisher-Snedecor’s F statistics, it was high (Ncal = 0.256; Ncalem = 46.704).
Concerning the Wilks’ Lambda, that of the 2 variables revealed relevant was lower or equal to 0.90 (Ncal = 0.900;
Ncalem = 0.060). Consequently, the analysis of the 3 abovementioned criteria showed the existence of differences
between 2 classes identified.
The validation of the Wilks’ Lambda method was assessed per step examining : i) the Box’s M statistics, ii) the
global correlation and iii) the Wilks’ Lambda which is associated them. Roughly, stepwise statistics showed that it
was possible to extract from 2 initially variables found relevant, only one containing the sufficient information
allowing the complete discriminating of the 2 previously identified classes. It concerned the number of embryogenic
explants. Indeed, in step 1, the entry of the number of callogenic explants trigerred discrimination of the clusters (λ =
Dendrogramme using Ward Method
Rescaled Distance Cluster Combine
C2
C1
5. Journal of Agriculture and Crops, 2015, 1(2): 26-32
30
-4.8
-3.2
-1.6
0
1.6
3.2
4.8
-6.4 -4.8 -3.2 -1.6 -1E-14 1.6 3.2 4.8 6.4
F2(00%)
F1 (100%)
Observations on plane 1-2 of the FDA: 100%
C1
C2
0.060; p-value = 0.006). More specifically, for the Box’s M statistics, the variance-covariance matrixes were
statistically equal (Box’s M = 0.103; p-value = 0.789) postulating that the linear FDA was preferable to the quadratic
one. The global correlations tended towards 1, namely 0.969 for the only discriminant function 1. This only
discriminant function 1 discriminated the 2 classes in the proportion of 100%. Regarding the Wilks’ Lambda linked
with the significance of test of the function 1, it was equal to 0.060 with p-value corresponding to 0.080. In short, the
Wilks’ statistics only allowed the validation of the function 1.
Classes C1 and C2 were placed on the function 1 (Figure 3). C1 was associated with the count of the
embryogenic parents, whereas C2 was related to their proportion (Table 2).
From these 2 classes, only one predicting equation was extracted. It is about : Z1 = -3.310 + 4.532*Ncalem.
The communality was assessed using the confusion matrix. It showed that in class C1, 100% observations
represented by parents IMC67, Pa121 and Pa150 were well-classified thanks to the predicting equation 1. Likewise,
in class C2, 100% observations represented by P19A and Pa13 were correctly classified (Table 4).
With respect to the pairwise distance, the one calculated between C1 and C2 was 42.957. The Hotelling T² test
associated with this distance was very highly significant (Hotelling T² = 107.599; p-value = 0.000; Tables 5 and 6).
Table-3. Searching for relevant variables through the Variance Inflation Factor (VIF).
Statistics Ncal Ncalem Nemb Mece Pe
Tolerance 0.661 0.274 0.002 0.002 0.000
VIF 1.513 3.655 487.504 455.402 ∞
Legend : VIF* : Variance Inflation Factor calculated from formula 1 / Tolerance. The latter itself is
calculated from formula 1 – R², where R² represents the coefficient of determination expressing the fit degree
of the data to model. It is calculated as follows : R² = 1 – sum of squares (factorial) / sum of squares (residual).
Table-4. Examination of the communality based on the confusion matrix
Membership class predicted
Ward method C1 C2 Total
Original Count C1 3 0 3
C2 0 2 2
% C1 100 0 100
C2 0 100 100
Table 5. Gap between the 2 identified classes measured from the Mahalanobis’ distances.
C1 C2
C1 0 42.957
C2 42.957 0
Table-6. Significance of the Mahalanobis’ distance between the classes C1 and C2 according to Hotelling T2
test.
Hotelling's T-Squared F df1 df2 p-value
107.599 107.599 1 4 0.000
Figure-3. Scatter plot showing the 2 classes constituted from the 5 upper amazon cocoa parents from the FDA.
6. Journal of Agriculture and Crops, 2015, 1(2): 26-32
31
4. Discussion
The predicting of the embryogenic performances of 5 upper amazon cocoa parents was analysed using the
discriminant model of Wilks’ Lambda. These 5 parents were already structured using multivariate approach [12];
nevertheless in combination with their 6 hybrids. Robinson, et al. [14], proposed one equation including 47
metabolites as predictors of the mature somatic embryos production in Pinus taeda. In oil palm, Konan, et al. [6]
stated the modeling of the prediction of the quantity of culture biomass to be transferred and that of the number of
harvested shoots at the end of each culture cycle. In Issali, et al. [12], 2 predicting equations predicted the
membership classes of analysed observations and even those from new observations to classify. Here, only one
equation namely Z1 = - 3.310 + 4.532*Ncalem allowed not only the complete discriminating of classes, but also the
predicting of membership class of new observations.
As far as the PCA is concerned, for the relevance of used variables, the number of embryogenic explants
(Ncalem), the embryos number per embryogenic explant (Nemb), the average embryos number per embryogenic
explant (Mece) and the embryogenic percentage (Pe) were revealed to be relevant (Figure 2; Table 1). They
expressed correct communality on the principal plane represented by principal components 1 and 2 (Figure 1; Table
1). They are less correlated among them. The number of callogenic explants was the only variable dropped from the
study. It hindered the calculation of the determinant of the correlation matrix, and thus the outputting of tables both
bearing the KMO and the result of Bartlett’s test of sphericity. In contrast, in Issali, et al. [12], the 5 introduced
variables in the analysis were all used in its rest. It may be believed that the difference of variables behaviour would
be due to modification of their distributions. Indeed, the dropping here of the modalities associated with 6 hybrids,
may have induced fundamental modifications of the structure of their distributions.
However, with respect to the FDA, only the number of embryogenic explants was revealed to be the most
discriminant, thus relevant. Consequently, the relevantness depends on the analysis method. On the contrary, in
Issali, et al. [12], the number of callogenic explants and the average embryos number per embryogenic explant were
revealed to be relevant. Therefore, in upper amazon cocoa parents, the number of embryogenic explants will be used
as a statistical predictor for the yielding of somatic embryos.
Class C1 consisting of upper amazon cocoa parents IMC67, Pa121 and Pa150 expressed the greatest callogenic
potential (Figures 1, 2 and 3). Using the univariate approach, only IMC67 and Pa121 belonged to the same cluster of
callogenesis [9]. Therefore, the 3 aforesaid clones could be used to make chocolate aroma, cocoa butter and
theobromin from the cell callus suspensions in bioreactors.
Class C2 represented by upper amazon cocoa parents P19A and Pa13 recorded, among others, the highest
number of embryogenic explants. In Issali, et al. [9], these 2 genotypes were characterised like highly embryogenic.
Minyaka, et al. [15] showed that IMC67 was more embryogenic than genotypes P7, SCA6, UPA409 and IFCS. Here
parent IMC67 is part of the least embryogenic class. The most likely explanation is to accept that the tissue culture
was not made at the same season. Indeed, the season, the climatic period and the phenological phases influence the
somatic embryogenesis expression in cocoa tree [8, 16, 17]. Therefore, parents P19A and Pa13 will be used to yield
somatic embryos with a view to increase the production of beans in the fields after on-station and on-farm
experiments.
The equation predicting the yielding of som atic embryos is linear function which is spelt Z1 = - 3.310 +
4.532*Ncalem. It showed that the number of embryogenic explants is the only statistical predictor reliable for the
somatic embryos yielding. Likewise, Konan, et al. [6], in oil palm, were also evidenced linear functions predicting
the quantity of culture biomass to be transferred and that of the number of harvested shoots at the end of each culture
cycle. In contrast, the model proposed in Robinson, et al. [14] took into account 47 predictors using a Bayesian
approach. Here, our predictive model incorporated only one predictor. Esse, et al. [18] proposed mathematical model
of enzymes involved in somatic embryogenesis process. This model predicts root growth of seedlings and that of
their hypocotyls. Our model only predicts embryogenic explants production, and thus somatic embryos. In Issali, et
al. [12], the average embryos number per embryogenic explant and the number of callogenic explants were the
statistical predictors more reliable. Consequently, the reliableness varied from study to study. For the prediction
purposes, the observations belonging to class C1, having expressed low potential of the somatic embryos yielding,
will range from 0.000 to 0.392. Their discriminating score Z1 will vary from -3.31 to -1.534 (Figure 3). Regarding
the class C2, its value from the number of embryogenic explants varied from 1.3725 to 1.7402. Its discriminating
score Z1 oscillated from 2.910 to 4.576 (Figure 3). Thus, all of observations equal or between these 2 scores will
express high embryogenic potential. This will allow the predicting of membership class from its values of the
embryogenic explants.
5. Conclusion
We postulated the hypothesis that one variable describing the somatic embryogenesis might predict accurately
the embryogenic performances among the 4 embryogenesis variables out of 5 used in cocoa parents analysed here.
Actually, the number of embryogenic explants was identified to be the best predictor for somatic-embryos yielding.
The 2 identified classes C1 and C2 represented 2 distinct entities of morphological differentiation. The pertinentness
of variables using the PCA differed from the one revealed via the FDA. Thus, it varied from analysis method to
another analysis method. Cocoa parents IMC67, Pa121 and Pa150 could be used to make chocolate aroma, cocoa
butter and theobromin from the cell callus suspensions in bioreactors. On the whole of 5 used variables, only the
number of embryogenic explants allowed the complete discriminating of classes. Cocoa parents P19A and Pa13