Speaker: Lic. JUAN ROSAS, (MSc.) Programa de Arroz INIA-Uruguay y estudiante de Doctorado en Ciencias Agrarias de la Universidad de la República de Uruguay
This document summarizes the presentation of Adithya P Balakrishnan on MAGIC (Multi-parent Advanced Generation Intercross) populations. It discusses how MAGIC populations are constructed using multiple parental lines that are intercrossed and selfed over multiple generations. This results in a population with increased genetic diversity and higher mapping resolution compared to biparental populations. The document provides examples of MAGIC populations developed in Arabidopsis thaliana and rice. It describes the phenotypic evaluation and genetic analysis, including QTL mapping, that has been carried out on these MAGIC populations.
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
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
The document discusses the AMMI model for analyzing genotype by environment interactions in plant breeding experiments. It begins by introducing the concept of genotype by environment interaction and different models used for stability analysis. It then describes the AMMI model in detail, including that it combines ANOVA and PCA to analyze main and interaction effects. Key features of AMMI mentioned are that it identifies patterns of interaction, provides reliable genotype performance estimates, and enables visualization of relationships through biplots. Examples are given of crops AMMI has been applied to successfully.
Introduction:
Proposed by Meuwissen et al. (2001)
GS is a specialized form of MAS, in which information from genotype data on marker alleles covering the entire genome forms the basis of selection.
The effects associated with all the marker loci, irrespective of whether the effects are significant or not, covering the entire genome are estimated.
The marker effect estimates are used to calculate the genomic estimated breeding values (GEBVs) of different individuals/lines, which form the basis of selection.
Why to go for genomic selection:
Marker-assisted selection (MAS) is well-suited for handling oligogenes and quantitative trait loci (QTLs) with large effects but not for minor QTLs.
MARS attempts to take into account small effect QTLs by combining trait phenotype data with marker genotype data into a combined selection index.
Based on markers showing significant association with the trait(s) and for this reason has been criticized as inefficient
The genomic selection (GS) scheme was to rectify the deficiency of MAS and MARS schemes. The GS scheme utilizes information from genome-wide marker data whether or not their associations with the concerned trait(s) are significant.
GEBV: GenomicEstimated Breeding Values-
The sum total of effects associated with all the marker alleles present in the individual and included in the GS model applied to the population under selection
Calculated on a single individual basis
Gene-assisted genomic selection:
A GS model that uses information about prior known QTLs, the targeted QTLs were accumulated in much higher frequencies than when the standard ridge regression was used
The sum total of effects associated with all the marker alleles present in the individual and included in the GS model applied to the population under selection
Calculated on a single individual basis
Population used:
Training population: used for training of the GS model and for obtaining estimates of the marker-associated effects needed for estimation of GEBVs of individuals/lines in the breeding population.
Breeding population: the population subjected to GS for achieving the desired improvement and isolation of superior lines for use as new varieties/parents of new improved hybrids.
Training population-
large enough: must be representative of the breeding population: max. trait variance with marker : by cluster analysis
should have either equal or comparable LD, LD decay rates with breeding populations
Updated by including individuals/lines from the breeding population
Training more than one generation
Low colinearity between markers is needed since high colinearity tends to reduce prediction accuracy of certain GS models. (colinearity disturbed by recombination)
1. Association mapping uses linkage disequilibrium in natural populations to identify markers closely linked to genes influencing traits, allowing for higher resolution than traditional linkage mapping.
2. Key factors for successful association mapping include choosing diverse germplasm with extensive recombination history, collecting high-quality phenotypic data across environments, genotyping candidate genes and markers, and using statistical methods to account for population structure.
3. Combining association mapping with traditional QTL mapping and the various available software tools allows for rapid dissection and evaluation of complex traits.
Multiple inbred founder lines are inter-mated for several generations prior to creating inbred lines, resulting in a diverse population whose genomes are fine scale mosaics of contributions from all founders.
This document discusses genomic selection in plants. It begins with an introduction to genomic selection and its history. Genomic selection uses dense genetic markers and phenotypic data from a reference population to develop prediction equations that can then be applied to other populations to estimate genomic breeding values without additional phenotyping. The document outlines the steps involved, including preparing phenotypic and genotypic data, constructing prediction models, fitting and evaluating models, and applying genomic selection in breeding programs. It provides examples of software used and factors that affect prediction accuracy. The document concludes with two case studies, one on genomic selection for hybrid rice and another on genomic selection to improve wheat grain quality.
This document summarizes the presentation of Adithya P Balakrishnan on MAGIC (Multi-parent Advanced Generation Intercross) populations. It discusses how MAGIC populations are constructed using multiple parental lines that are intercrossed and selfed over multiple generations. This results in a population with increased genetic diversity and higher mapping resolution compared to biparental populations. The document provides examples of MAGIC populations developed in Arabidopsis thaliana and rice. It describes the phenotypic evaluation and genetic analysis, including QTL mapping, that has been carried out on these MAGIC populations.
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
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
The document discusses the AMMI model for analyzing genotype by environment interactions in plant breeding experiments. It begins by introducing the concept of genotype by environment interaction and different models used for stability analysis. It then describes the AMMI model in detail, including that it combines ANOVA and PCA to analyze main and interaction effects. Key features of AMMI mentioned are that it identifies patterns of interaction, provides reliable genotype performance estimates, and enables visualization of relationships through biplots. Examples are given of crops AMMI has been applied to successfully.
Introduction:
Proposed by Meuwissen et al. (2001)
GS is a specialized form of MAS, in which information from genotype data on marker alleles covering the entire genome forms the basis of selection.
The effects associated with all the marker loci, irrespective of whether the effects are significant or not, covering the entire genome are estimated.
The marker effect estimates are used to calculate the genomic estimated breeding values (GEBVs) of different individuals/lines, which form the basis of selection.
Why to go for genomic selection:
Marker-assisted selection (MAS) is well-suited for handling oligogenes and quantitative trait loci (QTLs) with large effects but not for minor QTLs.
MARS attempts to take into account small effect QTLs by combining trait phenotype data with marker genotype data into a combined selection index.
Based on markers showing significant association with the trait(s) and for this reason has been criticized as inefficient
The genomic selection (GS) scheme was to rectify the deficiency of MAS and MARS schemes. The GS scheme utilizes information from genome-wide marker data whether or not their associations with the concerned trait(s) are significant.
GEBV: GenomicEstimated Breeding Values-
The sum total of effects associated with all the marker alleles present in the individual and included in the GS model applied to the population under selection
Calculated on a single individual basis
Gene-assisted genomic selection:
A GS model that uses information about prior known QTLs, the targeted QTLs were accumulated in much higher frequencies than when the standard ridge regression was used
The sum total of effects associated with all the marker alleles present in the individual and included in the GS model applied to the population under selection
Calculated on a single individual basis
Population used:
Training population: used for training of the GS model and for obtaining estimates of the marker-associated effects needed for estimation of GEBVs of individuals/lines in the breeding population.
Breeding population: the population subjected to GS for achieving the desired improvement and isolation of superior lines for use as new varieties/parents of new improved hybrids.
Training population-
large enough: must be representative of the breeding population: max. trait variance with marker : by cluster analysis
should have either equal or comparable LD, LD decay rates with breeding populations
Updated by including individuals/lines from the breeding population
Training more than one generation
Low colinearity between markers is needed since high colinearity tends to reduce prediction accuracy of certain GS models. (colinearity disturbed by recombination)
1. Association mapping uses linkage disequilibrium in natural populations to identify markers closely linked to genes influencing traits, allowing for higher resolution than traditional linkage mapping.
2. Key factors for successful association mapping include choosing diverse germplasm with extensive recombination history, collecting high-quality phenotypic data across environments, genotyping candidate genes and markers, and using statistical methods to account for population structure.
3. Combining association mapping with traditional QTL mapping and the various available software tools allows for rapid dissection and evaluation of complex traits.
Multiple inbred founder lines are inter-mated for several generations prior to creating inbred lines, resulting in a diverse population whose genomes are fine scale mosaics of contributions from all founders.
This document discusses genomic selection in plants. It begins with an introduction to genomic selection and its history. Genomic selection uses dense genetic markers and phenotypic data from a reference population to develop prediction equations that can then be applied to other populations to estimate genomic breeding values without additional phenotyping. The document outlines the steps involved, including preparing phenotypic and genotypic data, constructing prediction models, fitting and evaluating models, and applying genomic selection in breeding programs. It provides examples of software used and factors that affect prediction accuracy. The document concludes with two case studies, one on genomic selection for hybrid rice and another on genomic selection to improve wheat grain quality.
Development of chromosome substitution lines and their utilization in crop im...PranayReddy71
This document discusses the development and use of chromosome substitution lines for genetic improvement in crop plants. It describes the process of chromosome substitution where one or more chromosomes from one species or variety are replaced by chromosomes from another related species through crossing and backcrossing. Examples are provided of chromosome substitution lines developed in cotton, brassica, and rice to transfer useful traits such as disease resistance. The document outlines methods for developing chromosome substitution lines using marker-assisted selection and backcrossing over multiple generations. It highlights achievements in various crops where chromosome substitution lines were used to develop new varieties with improved resistance to diseases and pests.
The document discusses MAGIC (Multi-parent Advanced Generation Inter-Cross) populations, which are created by intercrossing multiple parent lines over several generations. This increases recombination and genetic diversity. Key points:
- MAGIC populations allow more precise mapping of QTLs controlling quantitative traits compared to biparental populations.
- Two case studies describe the development of MAGIC populations in rice with 8 founders each, and tomato with 8 founders. Traits like yield, disease resistance, and abiotic stress tolerance were evaluated.
- Advantages include exploiting more genetic variation, developing varieties with favorable trait combinations, and more accurate gene mapping. Limitations include requiring more time, resources for phenotyping and breeding.
This document is a seminar submission by Varsha Gayatonde on the topic of genome wide association studies. It includes an introduction to genetic mapping, key terminology used in GWAS such as linkage disequilibrium and minor allele frequency. It then discusses the history and concepts of GWAS, including a comparison to biparental mapping. Specific examples of GWAS in crops such as Arabidopsis, rice, and maize are also mentioned.
This document summarizes a seminar presentation on genomic selection for crop improvement. The key points are:
1. Genomic selection is a specialized form of marker-assisted selection that uses dense molecular markers covering the entire genome to predict the genetic value or breeding value of individuals based on their genotypes.
2. The process of genomic selection involves developing a training population with both genotypic and phenotypic data to train statistical models, estimating genomic estimated breeding values (GEBVs) for individuals in a breeding population based only on their genotypes using the trained models, and selecting best individuals for further breeding.
3. Common statistical models used in genomic selection include ridge regression best linear unbiased prediction, Bayesian regression, and machine learning
This document discusses allele mining as a technique for improving crops. It defines allele mining as identifying allelic variation within genetic resources collections to find superior alleles. There are two main approaches - TILLING based allele mining which uses mutagenized populations and enzymatic cleavage to find mutations, and sequencing-based allele mining which uses PCR and sequencing to identify natural variation. Both have benefits and limitations. Applications of allele mining include finding alleles for resistance, abiotic stress tolerance, and improved yield and quality. Overall, allele mining is a promising approach for utilizing genetic resources to discover variants that can aid crop breeding.
Advanced biometrical and quantitative genetics akshayAkshay Deshmukh
Additive and Multiplicative Model
Shifted Multiplicative Model
Analysis and Selection of Genotype
Methods and steps to select the best model
Bioplot and mapping genotype
Association mapping, also known as "linkage disequilibrium mapping", is a method of mapping quantitative trait loci (QTLs) that takes advantage of linkage disequilibrium to link phenotypes to genotypes.Varioius strategey involved in association mapping is discussed in this presentation
Power Point is deals with the different aspects of Quantitative genetics in plant breeding it converse Basic Principles of Biometrical Genetics, estimation of Variability, Correlation, Principal Component Analysis, Path analysis, Different Matting design and Stability so on
This document discusses the use of marker-assisted selection (MAS) in plant breeding. It begins by outlining some key challenges in plant breeding, then describes how MAS can accelerate the breeding cycle by allowing selection at early generations. It provides details on different types of MAS, including marker-assisted backcrossing, pyramiding of multiple genes, and early generation selection. Examples are given of MAS being used to introgress submergence tolerance and salinity tolerance genes into rice varieties. The document also discusses some reasons for the low impact of MAS to date, such as insufficient linkage between markers and traits.
Molecular markers and Functional molecular markersChandana B.R.
This document discusses functional markers and their development and use in plant breeding. It begins by defining markers and describing different types of markers used historically, from morphological to molecular markers. It then focuses on functional markers, which are derived from polymorphisms within genes that affect traits of interest. The document discusses different types of functional markers like SSR and SNP-based markers. It notes advantages of functional markers include not requiring validation and providing direct information about gene effects. Limitations include that many genes have not been functionally characterized. The document ends with a case study using EST-SSR markers to estimate genetic diversity in maize breeding populations.
Synthetic hexaploid wheat is an artificial hybrid of tetraploid wheat and Aegilops tauschii that contains 42 chromosomes. It was first created in 1946 and numerous synthetic hexaploid wheats have since been produced globally. Compared to natural hexaploid wheat, synthetic hexaploid wheat is estimated to have lost fewer genes following polyploidization and shows subgenome dominance of the D genome over the A and B genomes. Allopolyploidization leads to genomic changes in synthetic hexaploid wheat including DNA elimination, gene silencing, and duplication. Molecular characterization shows that synthetic hexaploid wheat retains parental expression level dominance and has nonadditively activated gene expression contributing to its hybrid vigor.
This document summarizes a seminar on the molecular basis of heterosis, or hybrid vigor, in crop plants. It discusses the history of research on heterosis dating back to Darwin. Modern research shows that heterozygous hybrids often outperform their homozygous parents in traits like yield, growth, and stress resistance. Several genetic models have been proposed to explain heterosis, including dominance, overdominance, and epistasis, but no single model is sufficient. Omics studies of hybrids and polyploids have found both additive and non-additive changes in gene expression, proteins, and metabolites involved in growth, development, stress response, and signaling pathways.
The document discusses various types of mapping populations that can be used for linkage mapping of genetic markers and quantitative trait loci (QTL) in plants. It describes biparental populations like F2, backcross, recombinant inbred lines (RILs), and doubled haploids. It also discusses multiparental populations like immortalized F2 and MAGIC (Multi-parent Advanced Generation Intercross) populations. The key properties, advantages, and disadvantages of different mapping populations are summarized. Mapping populations are crucial resources that enable the construction of dense genetic linkage maps and identification of genomic regions associated with traits.
Within the last twenty years, molecular biology has revolutionized conventional breeding techniques in all areas. Biochemical and Molecular techniques have shortened the duration of breeding programs from years to months, weeks, or eliminated the need for them all together. The use of molecular markers in conventional breeding techniques has also improved the accuracy of crosses and allowed breeders to produce strains with combined traits that were impossible before the advent of DNA technology
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.
QTL is a gene or the chromosomal region that affects a quantitative trait, which should be polymorphic (have allelic variation) to have an effect in a population, must be linked to a polymorphic marker allele to be detected. The QTL mapping consists of 4 steps, like the development of mapping population, generation of polymorphic marker data set among the parents, construction of linkage map, and finally the QTL analysis
All the above steps are described in these slides very briefly along with two case studies.
This document summarizes a seminar on breeding concepts and crop improvement in chickpea. It discusses the floral biology of chickpea, including emasculation and pollination techniques. Breeding objectives for chickpea include increasing yield, biotic and abiotic stress resistance, and quality traits. Key breeding techniques used are mass selection, pure line selection, and hybridization methods like bulk hybridization and pedigree breeding. Varieties developed through these techniques with important traits are mentioned. The document provides information on the present uses of chickpea and production constraints.
Bioetcnology applications in male sterility and hybrid production Anilkumar C
This document discusses various methods of inducing male sterility for plant breeding applications. It describes three main types of male sterility - cytoplasmic, nuclear, and chemically-induced. Cytoplasmic male sterility is maternally inherited and can be autoplastic or alloplastic in origin. Nuclear male sterility is governed by nuclear genes. The document also discusses use of cytoplasmic male sterility in hybrid seed production systems using A, B, and R lines. Additionally, it outlines methods for inducing male sterility through recombinant DNA technology, including use of dominant male sterility genes, inducible sterility systems, and two-component systems.
This document provides information on rice diseases found in Louisiana, including symptoms, causal organisms, and distribution for each disease. It was prepared by professors at the LSU AgCenter Rice Research Station and Department of Plant Pathology and Crop Physiology. Over 30 diseases that affect rice seeds/seedlings, roots/crowns, leaves, stems/sheaths, panicles/grains are described. Photos and additional details can be accessed by clicking on each disease name. Suggested sources for more information are also provided.
This document discusses several diseases that affect rice, including leaf blast, node blast, neck blast, sheath blight, sheath rot, false smut, brown spot, bacterial leaf blight, and tungro. Leaf blast causes eye shaped spots on leaves that spread from lower to upper leaves, killing the leaves. Node blast causes black patches on infected rice nodes. Neck blast causes greyish brown lesions on the neck that can cause grains to fall. Sheath blight causes irregular purple brown lesions on leaf sheaths. Sheath rot causes irregular chocolate brown spots on leaf sheaths. False smut causes yellowish soft balls to form on grains. Brown spot causes circular reddish brown lesions on leaves surrounded by a
Development of chromosome substitution lines and their utilization in crop im...PranayReddy71
This document discusses the development and use of chromosome substitution lines for genetic improvement in crop plants. It describes the process of chromosome substitution where one or more chromosomes from one species or variety are replaced by chromosomes from another related species through crossing and backcrossing. Examples are provided of chromosome substitution lines developed in cotton, brassica, and rice to transfer useful traits such as disease resistance. The document outlines methods for developing chromosome substitution lines using marker-assisted selection and backcrossing over multiple generations. It highlights achievements in various crops where chromosome substitution lines were used to develop new varieties with improved resistance to diseases and pests.
The document discusses MAGIC (Multi-parent Advanced Generation Inter-Cross) populations, which are created by intercrossing multiple parent lines over several generations. This increases recombination and genetic diversity. Key points:
- MAGIC populations allow more precise mapping of QTLs controlling quantitative traits compared to biparental populations.
- Two case studies describe the development of MAGIC populations in rice with 8 founders each, and tomato with 8 founders. Traits like yield, disease resistance, and abiotic stress tolerance were evaluated.
- Advantages include exploiting more genetic variation, developing varieties with favorable trait combinations, and more accurate gene mapping. Limitations include requiring more time, resources for phenotyping and breeding.
This document is a seminar submission by Varsha Gayatonde on the topic of genome wide association studies. It includes an introduction to genetic mapping, key terminology used in GWAS such as linkage disequilibrium and minor allele frequency. It then discusses the history and concepts of GWAS, including a comparison to biparental mapping. Specific examples of GWAS in crops such as Arabidopsis, rice, and maize are also mentioned.
This document summarizes a seminar presentation on genomic selection for crop improvement. The key points are:
1. Genomic selection is a specialized form of marker-assisted selection that uses dense molecular markers covering the entire genome to predict the genetic value or breeding value of individuals based on their genotypes.
2. The process of genomic selection involves developing a training population with both genotypic and phenotypic data to train statistical models, estimating genomic estimated breeding values (GEBVs) for individuals in a breeding population based only on their genotypes using the trained models, and selecting best individuals for further breeding.
3. Common statistical models used in genomic selection include ridge regression best linear unbiased prediction, Bayesian regression, and machine learning
This document discusses allele mining as a technique for improving crops. It defines allele mining as identifying allelic variation within genetic resources collections to find superior alleles. There are two main approaches - TILLING based allele mining which uses mutagenized populations and enzymatic cleavage to find mutations, and sequencing-based allele mining which uses PCR and sequencing to identify natural variation. Both have benefits and limitations. Applications of allele mining include finding alleles for resistance, abiotic stress tolerance, and improved yield and quality. Overall, allele mining is a promising approach for utilizing genetic resources to discover variants that can aid crop breeding.
Advanced biometrical and quantitative genetics akshayAkshay Deshmukh
Additive and Multiplicative Model
Shifted Multiplicative Model
Analysis and Selection of Genotype
Methods and steps to select the best model
Bioplot and mapping genotype
Association mapping, also known as "linkage disequilibrium mapping", is a method of mapping quantitative trait loci (QTLs) that takes advantage of linkage disequilibrium to link phenotypes to genotypes.Varioius strategey involved in association mapping is discussed in this presentation
Power Point is deals with the different aspects of Quantitative genetics in plant breeding it converse Basic Principles of Biometrical Genetics, estimation of Variability, Correlation, Principal Component Analysis, Path analysis, Different Matting design and Stability so on
This document discusses the use of marker-assisted selection (MAS) in plant breeding. It begins by outlining some key challenges in plant breeding, then describes how MAS can accelerate the breeding cycle by allowing selection at early generations. It provides details on different types of MAS, including marker-assisted backcrossing, pyramiding of multiple genes, and early generation selection. Examples are given of MAS being used to introgress submergence tolerance and salinity tolerance genes into rice varieties. The document also discusses some reasons for the low impact of MAS to date, such as insufficient linkage between markers and traits.
Molecular markers and Functional molecular markersChandana B.R.
This document discusses functional markers and their development and use in plant breeding. It begins by defining markers and describing different types of markers used historically, from morphological to molecular markers. It then focuses on functional markers, which are derived from polymorphisms within genes that affect traits of interest. The document discusses different types of functional markers like SSR and SNP-based markers. It notes advantages of functional markers include not requiring validation and providing direct information about gene effects. Limitations include that many genes have not been functionally characterized. The document ends with a case study using EST-SSR markers to estimate genetic diversity in maize breeding populations.
Synthetic hexaploid wheat is an artificial hybrid of tetraploid wheat and Aegilops tauschii that contains 42 chromosomes. It was first created in 1946 and numerous synthetic hexaploid wheats have since been produced globally. Compared to natural hexaploid wheat, synthetic hexaploid wheat is estimated to have lost fewer genes following polyploidization and shows subgenome dominance of the D genome over the A and B genomes. Allopolyploidization leads to genomic changes in synthetic hexaploid wheat including DNA elimination, gene silencing, and duplication. Molecular characterization shows that synthetic hexaploid wheat retains parental expression level dominance and has nonadditively activated gene expression contributing to its hybrid vigor.
This document summarizes a seminar on the molecular basis of heterosis, or hybrid vigor, in crop plants. It discusses the history of research on heterosis dating back to Darwin. Modern research shows that heterozygous hybrids often outperform their homozygous parents in traits like yield, growth, and stress resistance. Several genetic models have been proposed to explain heterosis, including dominance, overdominance, and epistasis, but no single model is sufficient. Omics studies of hybrids and polyploids have found both additive and non-additive changes in gene expression, proteins, and metabolites involved in growth, development, stress response, and signaling pathways.
The document discusses various types of mapping populations that can be used for linkage mapping of genetic markers and quantitative trait loci (QTL) in plants. It describes biparental populations like F2, backcross, recombinant inbred lines (RILs), and doubled haploids. It also discusses multiparental populations like immortalized F2 and MAGIC (Multi-parent Advanced Generation Intercross) populations. The key properties, advantages, and disadvantages of different mapping populations are summarized. Mapping populations are crucial resources that enable the construction of dense genetic linkage maps and identification of genomic regions associated with traits.
Within the last twenty years, molecular biology has revolutionized conventional breeding techniques in all areas. Biochemical and Molecular techniques have shortened the duration of breeding programs from years to months, weeks, or eliminated the need for them all together. The use of molecular markers in conventional breeding techniques has also improved the accuracy of crosses and allowed breeders to produce strains with combined traits that were impossible before the advent of DNA technology
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.
QTL is a gene or the chromosomal region that affects a quantitative trait, which should be polymorphic (have allelic variation) to have an effect in a population, must be linked to a polymorphic marker allele to be detected. The QTL mapping consists of 4 steps, like the development of mapping population, generation of polymorphic marker data set among the parents, construction of linkage map, and finally the QTL analysis
All the above steps are described in these slides very briefly along with two case studies.
This document summarizes a seminar on breeding concepts and crop improvement in chickpea. It discusses the floral biology of chickpea, including emasculation and pollination techniques. Breeding objectives for chickpea include increasing yield, biotic and abiotic stress resistance, and quality traits. Key breeding techniques used are mass selection, pure line selection, and hybridization methods like bulk hybridization and pedigree breeding. Varieties developed through these techniques with important traits are mentioned. The document provides information on the present uses of chickpea and production constraints.
Bioetcnology applications in male sterility and hybrid production Anilkumar C
This document discusses various methods of inducing male sterility for plant breeding applications. It describes three main types of male sterility - cytoplasmic, nuclear, and chemically-induced. Cytoplasmic male sterility is maternally inherited and can be autoplastic or alloplastic in origin. Nuclear male sterility is governed by nuclear genes. The document also discusses use of cytoplasmic male sterility in hybrid seed production systems using A, B, and R lines. Additionally, it outlines methods for inducing male sterility through recombinant DNA technology, including use of dominant male sterility genes, inducible sterility systems, and two-component systems.
This document provides information on rice diseases found in Louisiana, including symptoms, causal organisms, and distribution for each disease. It was prepared by professors at the LSU AgCenter Rice Research Station and Department of Plant Pathology and Crop Physiology. Over 30 diseases that affect rice seeds/seedlings, roots/crowns, leaves, stems/sheaths, panicles/grains are described. Photos and additional details can be accessed by clicking on each disease name. Suggested sources for more information are also provided.
This document discusses several diseases that affect rice, including leaf blast, node blast, neck blast, sheath blight, sheath rot, false smut, brown spot, bacterial leaf blight, and tungro. Leaf blast causes eye shaped spots on leaves that spread from lower to upper leaves, killing the leaves. Node blast causes black patches on infected rice nodes. Neck blast causes greyish brown lesions on the neck that can cause grains to fall. Sheath blight causes irregular purple brown lesions on leaf sheaths. Sheath rot causes irregular chocolate brown spots on leaf sheaths. False smut causes yellowish soft balls to form on grains. Brown spot causes circular reddish brown lesions on leaves surrounded by a
Single Nucleotide Polymorphism Analysis
Predictive Analytics and Data Science Conference May 27-28
Asst. Prof. Vitara Pungpapong, Ph.D.
Department of Statistics
Faculty of Commerce and Accountancy
Chulalongkorn University
This document provides an overview of genetic polymorphism and its relationship to periodontal disease. It begins with definitions of key genetic terms like allele, chromosome, DNA and discusses different types of genetic disorders. It then examines various human gene polymorphisms that have been associated with periodontal diseases, such as IL-1, IL-10, TNF-α, and FcγR gene polymorphisms. The document reviews studies that have investigated the relationship between these polymorphisms and chronic or aggressive periodontitis. It concludes by stating that identifying genetic risk factors could allow for more personalized prevention and treatment approaches for periodontal diseases in the future.
The document discusses several common rice diseases found in the Philippines, including their symptoms, causal organisms, and management options. Sheath blight, rice blast, sheath rot, bakanae, brown spot, narrow brown spot, bacterial leaf blight, bacterial leaf streak, and rice tungro are described. The diseases can be managed through host plant resistance, cultural practices like fertilization and water management, and fungicide or pesticide application when needed. Correct diagnosis of diseases is important for effective management.
A single-nucleotide polymorphism (SNP) is a variation in a single DNA building block (nucleotide) that differs between members of a species. SNPs are the most common type of genetic variation among humans, with around 0.1% of bases differing between individuals. They can occur in coding regions, where they may alter the resulting protein, or non-coding regions. SNPs are significant for mapping genes and studying an individual's predisposition to diseases like cancer or response to medications. They can be identified by comparing DNA sequences from many individuals or through laboratory techniques like SNP genotyping.
general information regarding single nucleotide polymorphism.
A Single Nucleotide Polymorphisms (SNP), pronounced “snip,” is a genetic variation when a single nucleotide (i.e., A, T, C, or G) is altered and kept through heredity.
Presentation 17 : Preliminary results on genetic resistance to AHPND andWSSV ...ExternalEvents
http://www.fao.org/documents/card/en/c/28b6bd62-5433-4fad-b5a1-8ac61eb671b1/
International Technical Seminar/Workshops on Acute hepatopancreatic necrosis disease (AHPND)
Dr. Andres Perez - PRRS Epidemiology: Best Principles of Control at a Regiona...John Blue
PRRS Epidemiology: Best Principles of Control at a Regional Level - Dr. Andres Perez, University of Minnesota, from the 2015 North American PRRS Symposium, December 4 - 5, 2015, Chicago, IL, USA.
More presentations at http://www.swinecast.com/2015-north-american-prrs-symposium
Bio 106
Lecture 11 Genes in Populations
A. Population Genetics
B. Gene Frequencies and Equilibrium
1. Gene Frequencies
2. Gene Pool
3. Model System for Population Stability (Hardy – Weinberg Law)
2
cces2015
C. Changes in Gene Frequencies
1. Mutation
2. Selection
2.1 Relative Fitness
2.2 Selections and Variability
2.3 Selection and Mating
3. Systems
4. Migration
5. Genetic Drift
3
cces2015
D. Race and Species Formation
1. The Concept of Races
2. The Concept of Species
2.1 Reproductive Isolating Mechanisms
2.2 Rapid Speciation
In light of the 'Soils and pulses: symbiosis for life – A contribution to the Agenda 2030' event that took place at the Food and Agriculture Organization of the UN (FAO), Bioversity International's researcher Paola De Santis highlighted the importance of pulse diversity in managing pests and diseases in farmers' fields. Planting diverse pulse varieties can reduce the farm’s vulnerability to pests and diseases, and is a risk management strategy for unpredictability in rainfall and temperatures.
Learn more about Bioversity International's research on managing pests and diseases: http://bit.ly/23ZWtBW
Using pulse diversity to manage pests and diseasesExternalEvents
Using pulse diversity to manage pests and diseases
Smallholder farmers grow many traditional varieties of pulses for their resistance to pests and diseases, and adaptation to climate extremes. Genetic uniformity in monocultures leads to vulnerability, so increasing on-farm diversity of pulses may reduce losses from pests and diseases if the diversity includes relevant resistant traits. Studies found that higher varietal diversity on farms was linked to reduced damage from diseases like anthracnose. Experiments also showed that mixtures of resistant and susceptible bean varieties reduced damage from bean fly, especially when arranged in alternate rows rather than randomly mixed. Maintaining diversity requires farmers have access to quality seeds of diverse varieties.
Identification of Ralstonia Solanacearum in Kyrgyzstan’s Potato Fields and th...Agriculture Journal IJOEAR
Abstract— In this study, we have used well-known, efficient methods and bioassay for systematic screening of R. solanacearum for identification of its phenotype and biochemical profile, as well as for pathogenicity and virulence. As a result, an aggressive race — Biovar 3 — was most isolated from the potato fields of the Issyk-Kul region, especially in fields where the Picasso variety was grown. The isolated indigenous strains of Streptomyces diastatochromogenesstrain sk-6 and Streptomyces bambergiensis strain k1-3 has the potential to be used as a biocontrol agent for the management of the bacterial wilt of potatoes, as indicated by the reduced percentage wilt incidence. Root zone and soil application of Streptomyces diastatochromogenesstrain sk-6 and Streptomyces bambergiensis strain k1-3 at a dose of 108 cell/ml significantly reduced disease incidence and increased the growth of potato plants. The disease’s progress was reduced by 60% and 56% in plants inoculated with Streptomyces diastatochromogenesstrain sk-6 and Streptomyces bambergiensis strain k1-3, respectively.
Bacterial panicle blight is a major rice disease caused mainly by Burkholderia glumae. Cultural practices and chemical controls have proven ineffective at managing the disease. Researchers are screening rice varieties for disease resistance and have identified 10 lines with moderate to high resistance, including popular varieties like LM-1, Nipponbare, and Jupiter. Breeding efforts aim to develop new resistant varieties through crosses and population evaluations.
Bacterial panicle blight is a major rice disease caused mainly by Burkholderia glumae. Cultural practices and chemical controls have proven ineffective at managing the disease. Researchers are screening rice varieties for disease resistance and have identified 10 lines with moderate to high resistance, including popular varieties like LM-1, Nipponbare, and Jupiter. Breeding efforts aim to develop new resistant varieties through crosses and evaluations of thousands of lines each year.
Bacterial panicle blight is a major rice disease caused mainly by Burkholderia glumae. Cultural practices and chemical controls have proven ineffective at managing the disease. Researchers are screening rice varieties for disease resistance and have identified 10 lines with moderate to high resistance, including popular varieties like LM-1, Nipponbare, and Jupiter. Breeding efforts aim to develop new resistant varieties through crosses and population evaluations.
Advances in the research to achieve resistance to wheat rustsCIMMYT
Advances in research to achieve resistance to wheat rusts were presented. The presentation discussed the background on resistance to wheat rusts, characterization of resistance including seedling and adult plant resistance, utilization of adult plant resistance, and mapping and QTL analysis of resistance genes. Key advances included the identification of adult plant resistance genes such as Lr34, Lr46, and Sr2, as well as efforts to clone resistance genes to better understand the genetic basis of resistance. International collaborations were also highlighted as important to breed durable rust resistance in wheat.
Arabadopsis Thaliana Quorum Sensing ProposalBeau Smith
This grant proposal aims to test the effects of expressing quorum sensing inhibitors (QSIs) in Arabidopsis thaliana on resistance to food crop pathogens. The researchers hypothesize that A. thaliana transformed to express farnesol and QsdH will show increased resistance to Pseudomonas syringae and Puccinia triticina compared to wild-type plants. They plan to use CRISPR/Cas9 to generate plants expressing QSIs from different promoters and expose them to pathogens. If successful, this research could help reduce crop losses from disease without pesticides and provide insights into clinical applications of quorum sensing inhibition.
This document provides an overview of Theme 1 of the RTB Annual Meeting, which focuses on unlocking the value and use potential of genetic resources. It discusses several research objectives, including population structure analysis, assessment of genetic diversity, gap analysis, variety identification, and genome sequencing efforts. Genome sequencing projects on potato, banana, and other crops are described. Studies on genetic diversity of yams, gap analysis of potato and sweet potato, and population structure analysis of Ghanaian yams are summarized. Genome sequencing and bioinformatics collaborations between centers are also mentioned.
Use of Agrobiodiversity for Pest and Disease Management Carlo Fadda, Bioversi...World Agroforestry (ICRAF)
The document summarizes research on using agrobiodiversity to manage pests and diseases. The research involved working with over 1500 smallholder farmers across multiple crops and locations. It found that higher crop diversity on farms reduced vulnerability to pests and diseases by disrupting pest and pathogen transmission. Analyzing over 2000 farmer interviews and field trials, the research also identified traditional crop varieties with different levels of resistance to different pests and diseases, providing options to reduce crop losses. Overall, the research found that agrobiodiversity benefits smallholder farmers by reducing crop failure risks from biotic stresses.
This document summarizes research on using agrobiodiversity to manage pests and diseases. The research involved working with over 1500 smallholder farmers across multiple crops and locations. It found that higher crop diversity on farms reduced vulnerability to pests and diseases by disrupting pest and pathogen transmission. Analyzing over 2000 farmer interviews and field trials, it also showed that traditional crop varieties maintained genetic resistance relevant to local conditions and pests. The research concluded that supporting on-farm agrobiodiversity benefits smallholder food security and livelihoods by reducing crop losses from biotic stresses.
This document summarizes research on using agrobiodiversity to manage pests and diseases. The research involved working with over 1500 smallholder farmers across multiple crops and locations. It found that higher crop diversity on farms reduced vulnerability to pests and diseases by disrupting pest and pathogen transmission. Analyzing over 2000 farmer interviews and field trials, the research also identified traditional crop varieties with different resistance profiles that could help smallholders reduce crop losses from biotic stresses with low-input options. Overall, the research concluded that agrobiodiversity benefits smallholder food security and livelihoods by decreasing crop failure risks from pests and diseases.
The document discusses new strategies for breeding wheat for durable resistance to yellow rust, including leveraging non-host resistance and pattern triggered immunity, identifying natural variation in landraces and synthetics, mapping quantitative trait loci in multi-parent populations, and combining favourable alleles from different sources into elite lines. Research is exploring receptor-like kinases that may encode components of non-host resistance and pyramiding resistance quantitative trait loci.
Biodiversity sustains a wide variety of genetic traits that are very valuable for the potato's adaption to changing environments and successful cultivation in the future. However, several factors are threatening biodiversity in the Andes. For this reason, it is necessary for monitoring to be done with a standardized system and common observation parameters. Here we explain how participatory mapping and survey methods are used for the systematic monitoring of potato landraces in the Andes.
Durante la Semana de la Agricultura y la Alimentación, el Programa de Investigación del CGIAR en Cambio Climático, Agricultura y Seguridad Alimentaria – CCAFS, la Organización de las Naciones Unidas para la Alimentación y la Agricultura, FAO, y el Centro Internacional de Agricultura Tropical – CIAT, apoyaron la II Reunión Internacional de Ministros y altas autoridades de agricultura sobre agricultura sostenible y cambio climático con un documento base y su presentación sobre los retos que representa el cambio climático para la agricultura en Latino América y el Caribe.
Taller sobre intervenciones en nutrición, género y agricultura: situación actual y oportunidades futuras’, organizado por el CIAT y HarvestPlus en Ciudad de Guatemala. Leer más: http://ow.ly/XNIv30mGYBv
Impacto de las intervenciones agricolas y de salud para reducir la deficienci...CIAT
Este documento resume un estudio realizado en Guatemala para evaluar el impacto de entregar semilla biofortificada de frijol en aspectos socioeconómicos y de salud nutricional. El estudio utilizó un diseño de ensayo clúster aleatorio en comunidades rurales asignadas a recibir semilla biofortificada o no. Los resultados preliminares mostraron pocos cambios socioeconómicos entre grupos. Los resultados de línea base encontraron altas tasas de anemia y deficiencia de hierro, con el frijol contribuyendo signific
Agricultura sensible a la nutrición en el Altiplano. Explorando las perspecti...CIAT
Taller sobre intervenciones en nutrición, género y agricultura: situación actual y oportunidades futuras’, organizado por el CIAT y HarvestPlus en Ciudad de Guatemala. Leer más: http://ow.ly/XNIv30mGYBv
El rol de los padres en la nutrición del hogarCIAT
Este documento presenta los resultados preliminares de un estudio sobre las dinámicas intra-hogar y su impacto en la nutrición de familias agrícolas en Guatemala. Los hallazgos incluyen que las mujeres tienden a estar más desempoderadas que los hombres, y los niños en hogares con mujeres desempoderadas tienen más probabilidades de sufrir retraso en el crecimiento. Además, las preferencias de alimentos y labores varían entre hombres y mujeres dependiendo del ingreso disponible. Considerar tanto a padres como madres es importante para proyectos de nut
Scaling up soil carbon enhancement contributing to mitigate climate changeCIAT
This document summarizes Session 3 of a symposium on scaling up soil carbon enhancement to contribute to climate change mitigation. It discusses: 1) The potential for climate change
Impacto del Cambio Climático en la Agricultura de República DominicanaCIAT
El Banco Interamericano de Desarrollo (BID) y el Centro Internacional de Agricultura Tropical (CIAT), con el apoyo de los Programas de Investigación de CGIAR sobre Políticas, Instituciones y Mercados (PIM) y sobre Cambio Climático, Agricultura y Seguridad Alimentaria (CCAFS), se han asociado para comprender, a través de la ciencia, el impacto del cambio climático en cultivos claves y el impacto económico en la productividad de la agricultura en países de ALC.
BioTerra: Nuevo sistema de monitoreo de la biodiversidad en desarrollo por el...CIAT
BioTerra es un sistema innovador de monitoreo de la biodiversidad y sus amenazas desarrollado por el Programa Riqueza Natural de la Agencia de los Estados Unidos para el Desarrollo Internacional (USAID), y sus socios locales – el Centro Internacional de Agricultura Tropical (CIAT) y el Instituto Alexander von Humboldt (IAvH) – para apoyar al gobierno colombiano en el cumplimiento de las metas y compromisos de conservación de la biodiversidad. Este sistema busca complementar y aunar esfuerzos existentes de monitoreo de la biodiversidad y sus amenazas, a nivel nacional y regional.
Cacao for Peace Activities for Tackling the Cadmium in Cacao Issue in Colo...CIAT
El taller ‘Cacao libre de cadmio’, organizado por el CIAT, CIRAD, y la AFD, se lleva a cabo del 12 al 14 de marzo en la sede del CIAT en Palmira,y tiene como objetivo integrar un consorcio de actores y disciplinas claves de la región, así como elaborar un proyecto de investigación aplicada que dé respuesta a este problema que afecta a los cacaoteros de Colombia, Perú y Ecuador. http://ow.ly/J43p30iU0UZ
Tackling cadmium in cacao and derived products – from farm to forkCIAT
El taller ‘Cacao libre de cadmio’, organizado por el CIAT, CIRAD, y la AFD, se lleva a cabo del 12 al 14 de marzo en la sede del CIAT en Palmira,y tiene como objetivo integrar un consorcio de actores y disciplinas claves de la región, así como elaborar un proyecto de investigación aplicada que dé respuesta a este problema que afecta a los cacaoteros de Colombia, Perú y Ecuador. http://ow.ly/J43p30iU0UZ
Cadmium bioaccumulation and gastric bioaccessibility in cacao: A field study ...CIAT
El taller ‘Cacao libre de cadmio’, organizado por el CIAT, CIRAD, y la AFD, se lleva a cabo del 12 al 14 de marzo en la sede del CIAT en Palmira,y tiene como objetivo integrar un consorcio de actores y disciplinas claves de la región, así como elaborar un proyecto de investigación aplicada que dé respuesta a este problema que afecta a los cacaoteros de Colombia, Perú y Ecuador. http://ow.ly/J43p30iU0UZ
Geographical Information System Mapping for Optimized Cacao Production in Col...CIAT
El taller ‘Cacao libre de cadmio’, organizado por el CIAT, CIRAD, y la AFD, se lleva a cabo del 12 al 14 de marzo en la sede del CIAT en Palmira,y tiene como objetivo integrar un consorcio de actores y disciplinas claves de la región, así como elaborar un proyecto de investigación aplicada que dé respuesta a este problema que afecta a los cacaoteros de Colombia, Perú y Ecuador. http://ow.ly/J43p30iU0UZ
El documento resume los resultados de una investigación sobre el contenido de cadmio en granos de cacao en Perú. La investigación analizó muestras de suelo, hojas y granos de cacao de varias regiones para determinar las relaciones entre los contenidos de cadmio. Los resultados mostraron que eliminar la testa de los granos tiende a disminuir el contenido de cadmio. Además, se proponen nuevos protocolos de poscosecha y prácticas agrícolas para reducir los contenidos de cadmio en el suelo, las plantas y los
Técnicas para disminuir la disponibilidad de cadmio en suelos de cacaoterasCIAT
El taller ‘Cacao libre de cadmio’, organizado por el CIAT, CIRAD, y la AFD, se lleva a cabo del 12 al 14 de marzo en la sede del CIAT en Palmira,y tiene como objetivo integrar un consorcio de actores y disciplinas claves de la región, así como elaborar un proyecto de investigación aplicada que dé respuesta a este problema que afecta a los cacaoteros de Colombia, Perú y Ecuador. http://ow.ly/J43p30iU0UZ
El taller ‘Cacao libre de cadmio’, organizado por el CIAT, CIRAD, y la AFD, se lleva a cabo del 12 al 14 de marzo en la sede del CIAT en Palmira,y tiene como objetivo integrar un consorcio de actores y disciplinas claves de la región, así como elaborar un proyecto de investigación aplicada que dé respuesta a este problema que afecta a los cacaoteros de Colombia, Perú y Ecuador. http://ow.ly/J43p30iU0UZ
El taller ‘Cacao libre de cadmio’, organizado por el CIAT, CIRAD, y la AFD, se lleva a cabo del 12 al 14 de marzo en la sede del CIAT en Palmira,y tiene como objetivo integrar un consorcio de actores y disciplinas claves de la región, así como elaborar un proyecto de investigación aplicada que dé respuesta a este problema que afecta a los cacaoteros de Colombia, Perú y Ecuador. http://ow.ly/J43p30iU0UZ
de la región, así como elaborar un proyecto de investigación aplicada que dé respuesta a este problema que afecta a los cacaoteros de Colombia, Perú y Ecuador. http://ow.ly/J43p30iU0UZ
El taller ‘Cacao libre de cadmio’, organizado por el CIAT, CIRAD, y la AFD, se lleva a cabo del 12 al 14 de marzo en la sede del CIAT en Palmira,y tiene como objetivo integrar un consorcio de actores y disciplinas claves de la región, así como elaborar un proyecto de investigación aplicada que dé respuesta a este problema que afecta a los cacaoteros de Colombia, Perú y Ecuador. http://ow.ly/J43p30iU0UZ
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.
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...Travis Hills MN
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
Authoring a personal GPT for your research and practice: How we created the Q...Leonel Morgado
Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...AbdullaAlAsif1
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
When I was asked to give a companion lecture in support of ‘The Philosophy of Science’ (https://shorturl.at/4pUXz) I decided not to walk through the detail of the many methodologies in order of use. Instead, I chose to employ a long standing, and ongoing, scientific development as an exemplar. And so, I chose the ever evolving story of Thermodynamics as a scientific investigation at its best.
Conducted over a period of >200 years, Thermodynamics R&D, and application, benefitted from the highest levels of professionalism, collaboration, and technical thoroughness. New layers of application, methodology, and practice were made possible by the progressive advance of technology. In turn, this has seen measurement and modelling accuracy continually improved at a micro and macro level.
Perhaps most importantly, Thermodynamics rapidly became a primary tool in the advance of applied science/engineering/technology, spanning micro-tech, to aerospace and cosmology. I can think of no better a story to illustrate the breadth of scientific methodologies and applications at their best.
ESR spectroscopy in liquid food and beverages.pptxPRIYANKA PATEL
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
ESPP presentation to EU Waste Water Network, 4th June 2024 “EU policies driving nutrient removal and recycling
and the revised UWWTD (Urban Waste Water Treatment Directive)”
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.
The binding of cosmological structures by massless topological defectsSérgio Sacani
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
The binding of cosmological structures by massless topological defects
GWAS of Resistance to Stem and Sheath Diseases of Uruguayan Advanced Rice Breeding Germplasm
1. Doctorate in Agricultural Sciences
Facultad de Agronomía - Universidad de la República
Collaborating Institutions: Cornell University – CIAT - FLAR
GWAS of Resistance to Stem and Sheath
Diseases of Uruguayan Advanced Rice
Breeding Germplasm
Juan Rosas
Advisors: Jean-Luc Jannink – Lucía Gutierrez
Special Comittee: Marcos Malosetti (Wageningen University)
Álvaro Roel (INIA)
Funding: MBBISP, INIA (Rice Program, Rice GWAS
3. Doctorate Program Timeline
2012 2013 2014 2015 2016
Cornell U.
1st. Anual
Committee
Meeting
CIAT CU/UW
Field pheno
typing
Greenhouse phenotyping (ROS & SCL)
GH ph.
(R.Solani)
MBBISP Scholarship
1 2 3 4 5 6 7 8 9 10 11 12 1 2 3 4 5 6 7 8 9 10 11 12 1 2 3 4 5 6 7 8 9 10 11 12 1 2 3 4 5 6 7 8 9 10 11 12 1 2 3 4 5 6 7 8 9 10 11 12
Official start
Oct 2012
Expected
completion
Thesis Project
Defense
Sep 2013
2nd Anual
Committee
Meeting
Paper I Paper II
Paper III
Paper IV
Year 1 Year 2 Year 3 Year 4 Year 5
Training in Statistics
4. Rice facts
Why rice matters to
Uruguay?
– Rice is the 3rd top
Uruguayan export.
– It accounts for 7% of
country’s total income
Source: www.uruguayxxi.gub.uy
0
200
400
600
800
1000
1200
1400
1600
2009 2010 2011 2012
USDx106
Soybeans
Meat
Rice
Wheat
5. Uruguay facts
Why Uruguay matters to rice?
Uruguay is the 7th major world rice exporter
Source: FAOSTAT
0
1000
2000
3000
4000
5000
6000
7000
8000
9000
10000
tx106
Top Ten World Rice Exporters
6. Uruguay facts
Why Uruguay matters to rice?
Uruguayan rice
yields are among
the highest of the
world
Source: http://ricestat.irri.org
(Alphabetic order)
CountryAverageYieldin2010(t/ha)
7. Rice’s biggest adversaries
What are the major constraints to rice production worldwide?
Abiotic:
Water scarcity, poor soil conditions
Extreme temperatures
Biotic (fungal diseases):
1. Blast (Pyricularia oryzae)
2. Sheath and stem diseases
Worldwide: Uruguay & other temperate areas:
Rhizoctonia solani Sclerotium oryzae
Rhizoctonia oryzae-sativae
9. Stem Rot
• The fungus forms sclerotia
• Sclerotia can survive 1-2
years in soil surface or water,
but prefers rice stubble.
10. Stem Rot
• Flooding help floating sclerotia reach the stems
Early flooding = early infection = more severity
• Stem surface promotes sclerotia germination
• During the first day of contact, mycelium start
developing
• Appresoria penetrates host tissue and hyphae
invades it
14. Stem Rot
• Stem rotting prevents
nutrient translocation
• Bad starch formation
• Chalky and brittle grains
• Bad milling quality
15. Stem Rot
• Advanced rotting weaken
stems and promotes lodging
• Not easy to harvest!
• The fungus forms new
sclerotia
• Sclerotia can survive 1-2
years in soil surface or water,
but prefers rice stubble.
16. Aggregated Sheath Spot
Causal agent
• Rhizoctonia oryzae-sativae (Mordue
1974).
• Geographical distribution:
Irrigated rice growing areas worldwide,
most relevant in sub-tropical and
temperate areas.
17. Aggregated Sheath Spot
• Very similar cycle to that of Stem rot
• First days of infection may be
asymptomatic
21. Aggregated Sheath Spot
• Rhizoctonia oryzae-sativae also
produces sclerotia
• Sclerotia can survive in soil surface or
water, but prefers rice stubble.
22. Rice’s adversaries strike again
Major constraints to rice production
Abiotic:
Water scarcity
Poor soil conditions
Extreme temperatures
Biotic (fungal diseases):
1. Blast (Pyricularia oryzae)
2. Sheath and stem diseases
Worldwide: Uruguay & other temperate areas:
Rhizoctonia solani Sclerotium oryzae
Rhizoctonia oryzae-sativae
23. The Uruguayan Rice Defensive Line
How do we face to these constraints to get those high yields?
Abiotic:
Water scarcity
Poor soil conditions
Extreme temperatures
Biotic (fungal diseases):
1. Blast (Pyricularia oryzae)
2. Sheath and stem diseases
Worldwide: Uruguay & other temperate areas:
Rhizoctonia solani Sclerotium oryzae
Rhizoctonia oryzae-sativae
New high-yield cold
tolerant varieties
New molecular markers
for cold tolerance
Resistance genes in high-
yielding advanced lines
Extended use of
optimum
management
practices
100% Irrigated
24. A Hole in the Defensive Line
Top Uruguayan varieties are susceptible to St & Sh diseases
Source: Avila 2000 & 2001.
Sterility, dead sheaths and
lodging caused by Aggregated
Sheath Spot in INIA Tacuarí
(grown in 15% of the area)
Severe lodging caused by
Stem Rot in El Paso 144
(grown in 50% of the area)
25. Patching the Hole with Fungicide
– Varietal susceptibility = Dependence on fungicide
– Dependence on fungicide = higher input costs
= trace levels in grain and environment
– Trace levels = less top markets, lower price, environmental impact
Dependence on fungicide = less economic and environmental sustainability
Genetic resistance to
St&Sh diseases is
environmentally and economically
the best option.
26. Genetics of the resistance to StR
• Quantitatively inherited (Ferreira & Webster 1975)
• RILs with O. rufipogon introgressions (Ni et al 2001):
– QTL in ch. 2, AFLP marker TAA/GTA167 45% phen. var.
– QTL in ch. 3, RM232 - RM251 40% phen. var.
27. Genetics of the resistance to AShS
•Unknown but most likely quantitatively inherited as for to other
Rhizoctonias.
•QTL reported for resistance to R. solani (Srinivasachary et al.
2011):
–16 consistent QTL (at least in 2 independent reports)
• 7 QTL for escape mechanism (morphology or cycle, often
undesirable traits)
• 9 QTL hypothetically physiologic resistance mechanisms
Importance of phenotyping to detect relevant QTL.
28. Quantitative Trait Loci Discovery
GWAS
•Uses pre-existent populations
•Simultaneously consider all allele diversity
•Exploits multiple recombination events
•“ready-to-use” SNP into the breeding
germplasm
Traditional bi-parental QTL studies
•Population generation is time and
resource consuming
•Limited # and significance of
detectable QTL (low allelic diversity)
•Low mapping precision (few
recombinations)
29. GWAS
SNP 1
Alelles: 0 or 1
Genotype Phenotype
0 6 9 1 7 5
Disease scores
Do not reject identity
between phenotypic means,
p-value >>0.001
-log10(p-value) << 3
Phenotype
Genotype0 1
No association (negative)
-log10(p-value)
SNP1
Loci or position
30. GWAS
SNP 2
Alelles: 0 or 1
Genotype Phenotype
0 6 9 1 7 5
Disease scores
Phenotype
Genotype0 1
Reject identity between
phenotypic means,
p-value <0.001
-log10(p-value) > 3
-log10(p-value)
SNP1
SNP2
Association (positive)
Loci or position
31. GWAS
The same for every SNP
Alelles: 0 or 1
Genotype Phenotype
0 6 9 1 7 5
Disease scores
-log10(p-value)
Manhattan plot
Loci or position
32. GWAS
What are the key issues for GWAS?
As GWAS relies on correlation between phenotype & allelic
states of marker’s loci
– Non-linkage correlations between loci leads to false positives
– i.e., False positives due to relationship among lines:
• CROASE: Population estructure (sub-species, origin)
• FINE: Kinship or co-ancestry (shared close ancestors)
33. Correcting for Population Structure
• Pritchard et al. 2000:
•Correlations between unlinked markers to estimate p
sub-populations
•Probabilistic assignation of each n individual to one or
more (admixtures) p.
•STRUCTURE software facilitates to build a Q matrix n x p
(estimates of each n belonging to a p)
34. Correcting for Population Structure
•Patterson et al.2006
Principal component analysis (PCA)
• Statistically determines the minimum number of
sub-groups (axes) which significantly explain genetic
variation (from genotypic data).
35. Correcting for Kinship
• Loiselle et al. 1995 and Hardy & Vekemans, 2002
SPAGeDi software
• Estimates the probability of identity-by-state (not by
common ancestry) of alleles of random molecular
markers = kinship coeficient.
36. GWAS: Unified Mixed Model
y: phenotypic data
S: incidence matrix that relates y with the SNP effects
α : vector of SNP effects
Q: relates y with the p fitting values
v: vector of estimates of fitting to a sub-population (estimated with
STRUCTURE)
K: relates y with the estimated kinship coefficients
u : vector of kinship coefficients
e: vector of residual effects
e KuQvSy
• Yu et al. 2006
37. Keys for a succesful GWAS
– Increase power optimizing phenotyping:
• Minimize Phenotypic variance
• Maximize Heritability
–Minimize false positive discovery by correcting causes of
marker correlation other than linkage:
• Population structure and kinship (subspecies, common
ancestry)
–In rice: consider ancient divergence between subspecies
(explore separate analyses)
38. Recap…
• Uruguay is a top rice exporter; Rice is a top Uruguayan
commodity
• Top Uruguayan varieties are susceptible to Sclerotium oryzae
(SCL) and Rhizoctonia oryzae-sativae (ROS), suffering losses
up to 20%.
• Genetic resistance is the best strategy
• Resistance to St & Sh diseases is quantitative
• GWAS is a good option for QTL discovery in breeding
population
• Good phenotyping is key for GWAS
39. Objectives
General Objective: Identify QTL for SCL and ROS that enable breeding new high-
yielding cultivars with improved resistance to these diseases.
Specific Objectives / Papers:
I. Greenhouse phenotyping methodology (Paper 1).
a. Choosing best inoculation method
b. Applying it in high-throughput phenotyping greenhouse experiments
II. QTL for resistance to SCL and ROS in greenhouse and field (Papers 2 and 3).
III. Explore correlations between resistance to the three diseases (SCL, ROS and R.
solani) Paper 4.
40. Materials & Methods 1: Inoculation Methods
• Inoculation Methods
Method Description
I 5-mm agar disc with growing micellium attached to stems
II Flooded trays spread with sclerotia
III Suspension of sclerotia in CMC
IV Suspension of sclerotia in CMC covered with foil
V Detached stems in test tube with water + sclerotia
41. Materials & Methods 1: Inoculation Methods
• Plant Materials
Cultivar Subsp. Origin ROS SCL R. Solani
El Paso 144 Indica Uy Int Int ?
INIA Olimar Indica Uy Int Int ?
Tetep Indica Vietnam ? Res Res
INIA Tacuari Trop. Jap. Uy Int Int ?
Parao Trop. Jap. Uy Int Int ?
Lemont Trop. Jap. US ? Sus Sus
42. Materials & Methods 1: Inoculation Methods
• Greenhouse conditions
• Temperature: 28/18 °C day/night
• RH: 80/90% relative humidity
• Light time: 12 h
• Fungal Isolates
• ROS: soil after INIA Tacuarí in UEPL 200
• SCL: plant Samba cv. In UEPL 2011
• Experimental Design: CRD, 6 rep. EU: pot with 4 plants
• Analysis:
Model with design factors
Method compared by
r
H
G
G
22
2
2
e
ijig e ijY
43. Results 1: Inoculation Methods
• Best IM: I (agarose disk with micellium), for both pathogens
Pathogen Method 2
G 2
R H2
ROS I (agar disk) 0.03 0.06 0.75
ROS II (flooded trays) 0.07 0.20 0.67
ROS III (CMC) 0.00 0.31 0.05
ROS IV (CMC+foil) 0.16 0.69 0.58
ROS V (tiller in tube) 1.25 5.24 0.59
SCL I (agar disk) 1.35 0.56 0.94
SCL II (flooded trays) 0.94 0.61 0.90
SCL III (CMC) 0.73 1.05 0.81
SCL IV (CMC+foil) 1.31 1.00 0.89
SCL V (tiller in tube) 0.92 2.04 0.73
2
G 2
e 2
H2
G 2
e 2
H
45. M & M 2: Greenhouse Phenotyping
• 3 exp. for ROS, 2 exp. for SCL
• Population: 641 advanced INIA’s inbred lines
• 316 indica
• 325 tropical japonica
• Inoculation I (Agar discs)
• Same greenhouse conditions and fungal isolates than IM
• Experimental Design:
• Federer’s unrep, augmented RCBD, 12 blocks
• Replicated checks: El Paso 144, INIA Olimar, Tetep, Parao, INIA Tacuarí and Lemont
• EU: pot with 4 plants
• Stem width measured as covariate.
46. M & M 2: Greenhouse Phenotyping
• Statistical Models:
BAS Compared based
SPA on
(Cullis et al. 2006)
Yij, Yijmn disease score
intercept
g Random block effect with and j={1,...,12}
Gj = gk + cl genotypic effect,
gk random effect of kth genoline with gk ~N(0,2
G), k={1,...,641}
cl fixed effect of lth check, l={1,…,6}
Rm random row effect, Rm ~N(0,2
r), m={1,...,35}
Cn random column effect , Cn ~N(0,2
c), n={1,...,26}
eij, eijmn residual, gk ~N(0,2
G)
ijjiij GY eg
ijmninimjiijmn CRGY eg )()(
),0(~ 2
Bi N g
2
2
2
1
G
BLUP
g
v
H
47. Results 2: Greenhouse Phenotyping
• Medium to high H2. GxE interaction. Adapted sources of partial resistance
48. M & M 3: Field Phenotyping
• Same population than Greenhouse exp.
• 2010, 2011, 2012: “Historical” data
RCBD, 3 rep, natural infection. Checks:
El Paso 144, INIA Olimar, Parao, INIA Tacuarí
• 2013:
Augmented alpha-lattice design, 6 rep, artificial inoculation
• Same fungal isolates than greenhouse experiments.
• Replicated checks: El Paso 144, INIA Olimar, Tetep, Parao, INIA Tacuarí and Lemont
• EU: hill plots with ~10 adult plants
• Length of life cycle measured as covariate.
49. Materials & Methods 3: Field Phenotyping
• Statistical Models:
BAS Compared based
COV on
SPA (Cullis et al. 2006)
CSP
Yij, Yijmn disease score
overall mean
g block effect, j={1,...,6}
Gj = gk + cl genotypic effect,
gk random effect of kth genoline, gk ~N(0,2
G), k={1,...,641}
cl fixed effect of lth check, l={1,…,6}
eij, eijmn residual, gk ~N(0,2
G)
Rm row effect, Rm ~N(0,2
r), m={1,...,90}
Cn column effect, Cn ~N(0,2
c), n={1,...,45}
xij length of life cycle of ith genotype in jth block
b regression slope of covariate
ijjiij GY eg
ijijjiij xGY ebg
ijmnnmjiijmn CRGY eg
ijmnnmijjiijmn CRxGY ebg
2
2
2
1
G
BLUP
g
v
H
50. Results 3: Field Phenotyping (ROS)
• Low to medium H2. GxE interaction. Adapted sources of partial resistance
H2=0.42
H2=0.15
H2=0.06
H2=0.43
51. Results 3: Field Phenotyping (SCL)
• Medium to high H2. Lesser GxE interaction. Adapted sources of partial R
H2=0.50
H2=0.24
H2=0.45
H2=0.72
52. M & M 4: Genotypic data
GBS raw
data
HapMaps
130K SNP
Bioinformatic processing
• Tag count (collapse identical reads)
• Alignment with reference genome (Nipponbare)
• Tassel Pipeline
• Hapmap filtering
• Lines with ≥5% SNP
• SNP called in ≥5% lines
• Allele frequency (intra line) ≥5%
Indica 316 lines
94K SNP
641 lines
57K SNP
FILLIN
Imputation Japonica 325 lin.
44K SNP
Indica 316 lines
18K SNP
Japonica 325 lin.
12K SNP
Conjoint
SNP
filtering
Separate
SNP
filtering
•SNP w/Allele frequency
(inter lines) ≥5%
•Lines w/ ≥5% SNP data
< 50% missing
53. Results 4: Genotypic data, whole, non imputed
641 lines
57K SNP
• Genotype data:
Most of the SNP are
between-subesp.
polymorphisms
54. Results 4: Genotypic data, partial results
Indica 316 lines
94K SNP
641 lines
57K SNP
FILLIN
Imputation Japonica 325 lin.
44K SNP
Indica 316 lines
18K SNP
Japonica 325 lin.
12K SNP
Conjoint
SNP
filtering
Separate
SNP
filtering
•SNP w/Allele frequency
(inter lines) ≥5%
•Lines w/ ≥5% SNP data
< 50% missing
55. Results 4: Genotypic data, whole population
641 lines
57K SNP
• Genetic Map:
dense SNP
evenly distributed
in all 12 chr.
56. Results 4: Genotypic data, whole population
641 lines
57K SNP
• PCA:
PC1: inter subspecies
variation
PC2: inter indica variation
indica
japonica
57. Results 4: Genotypic data, whole population
641 lines
57K SNP
• PCA:
PC1 ~50% gv
PC2 ~5% gv
58. Results 4: Genotypic data, Indica ssp
• Genotype data:
Some big blocks with
low LD decay.
Indica 316 lines
18K SNP
59. Results 4: Genotypic data, Indica ssp
• Genetic Map:
Many fixed
regions, including
all Chr. 11
Indica 316 lines
18K SNP
60. Results 4: Genotypic data, Indica ssp
• PCA:
Over-represented
“Olimar-like” lines from
FLAR and INIA
Indica 316 lines
18K SNP
El Paso 144
INIA Olimar FLAR
INIA
61. Results 4: Genotypic data, Indica ssp
• PCA:
PC1 to 8 explain
~50%gv
Indica 316 lines
18K SNP
62. Results 4: Genotypic data, Japonica, non imputed
• Genotype data:
Haplotype blocks
.
Japonica 325 lin.
12K SNP
63. Results 4: Genotypic data, Japonica ssp
• Genetic Map:
Many fixed
regions
Japonica 325 lin.
12K SNP
65. Results 4: Genotypic data, Japonica ssp
• PCA: More than 10
PC to explain 50% gv
Japonica 325 lin.
12K SNP
66. Materials & Methods 5: GWAS
y: phenotypic data
b : vector of SNP fixed effects
X: incidence matrix that relates y with the SNP effects
v: vector of fixed estimates of fitting to a sub-
population (estimated with STRUCTURE)
Q: incidence matrix for population effects
u : vector of kinship coefficients, Var(u)=K2 , K
kinship matrix
Z: relates y with the estimated kinship coefficients
e: vector of residual effects, Var(e)=I2
e
eb ZuQvXy
• Mixed model (Yu et al. 2006, Malosetti et al. 2007)
“Q+K”, as implemented in GWAS
function from rrBLUP package:
eb QvXy
“Eigenstrat”, as implemented in
GWAS.analysis function from
mmQTL package:
y: phenotypic data
b : vector of SNP fixed effects
X: incidence matrix that relates y with the SNP effects
v: vector of random PC scores (eigenvalues).
Q: relates y with the PC scores
e: vector of residual effects, Var(e)=I2
e
67. Results 5: GWAS
Indica 316 lines
94K SNP
641 lines
57K SNP
FILLIN
Imputation Japonica 325 lin.
44K SNP
Indica 316 lines
18K SNP
Japonica 325 lin.
12K SNP
Conjoint
SNP
filtering
Separate
SNP
filtering
•SNP w/Allele frequency
(inter lines) ≥5%
•Lines w/ ≥5% SNP data
< 50% missing
Field GH
Eigenstrat ROS SCL ROS SCL
Q+K ROS SCL ROS SCL
Eigenstrat ROS SCL ROS SCL
Q+K ROS SCL ROS SCL
Eigenstrat ROS SCL ROS SCL
Q+K ROS SCL ROS SCL
Eigenstrat ROS SCL ROS SCL
K ROS SCL ROS SCL
Eigenstrat ROS SCL ROS SCL
K ROS SCL ROS SCL
68. Results 5: GWAS – ROS in Japonica
• QTLxE interaction.
• Consistent QTL: chr. 3 ~1 Kb
Field 2010 Field 2011 Field 2012 Field 2013
GH ROS1 GH ROS2 GH ROS3
69. Results 5: GWAS – ROS in Indica
• QTLxE interaction
• Consistent QTL: chr. 3 ~1 Kb
•. QTL chr. 3Field 2010 Field 2011 Field 2012 Field 2013
GH ROS1 GH ROS2 GH ROS3
70. Results 5: GWAS – SCL in Japonica
• QTLxE interaction.
• Consistent QTL: chr. 3 ~1 Mb chr. 9 ~14 Mb
Field 2010 Field 2011 Field 2012 Field 2013
GH SCL1 GH SCL2
71. Results 4: GWAS – SCL in Indica
Field 2010 Field 2011 Field 2012 Field 2013
GH SCL1 GH SCL2
• QTLxE interaction.
• Consistent QTL: chr. 3 ~1 Mb chr. 9 ~14 Mb
72. Results 4: GWAS
Summary:
• QTL at ~1 Kb Chr. 1 for both pathogens, both
subspecies and all environments
• QTL at ~14 Kb Chr. 9 for SCL, both subspecies,
almost all environments
73. Future Work
• Greenhouse phenotyping for resistance to R. solani at CIAT
• Analysis of phenotypic means
• Association analysis:
• LD blocks and haplotypes
• GWAS for R. solani
74. Coordinación
Victoria Bonnecarrere
Mejoramiento
Pedro Blanco
Fernando Pérez de Vida
Fitopatología
Sebastián Martínez
Bioinformática
Silvia Garaycochea
Schubert Fernández
Marcadores moleculares
Victoria Bonnecarrere
Wanda Iriarte
Bioestadística
Lucía Gutierrez
Gastón Quero
Natalia Berberián
Juan Rosas
Cornell University
Eliana Monteverde
Susan McCouch
Jean-Luc Jannink
Proyecto Mapeo Asociativo en
Arroz Uruguayo