This study aimed to demonstrate that monomorphic molecular markers can contain useful genetic information. The researchers analyzed 20 rice genotypes with varying zinc content in grains, culms, and roots. They designed markers for genes related to zinc transport and found two were polymorphic by agarose gel electrophoresis. However, sequencing revealed nucleotide variations in four purportedly monomorphic markers as well. Single-marker analysis showed some of these nucleotide variations were significantly associated with zinc content traits. Specifically, variations in the monomorphic marker OsZIP5b correlated with grain zinc. This suggests monomorphic markers should not be excluded from studies as they may still provide informative genetic data.
Molecular characterization of rice (Oryza sativa L.) genotypes using target r...Innspub Net
In the present investigation, based on the seven rice putative candidate iron transporter genes, novel TRAP markers were developed. These markers were successfully employed in the molecular diversity study among 30 rice genotypes representing improved rice cultivars and land races with varied grain iron content (7.38 - 30.58 ppm). Totally, thirty TRAP primer combinations were screened, which generated 703 bands out of which 654 were polymorphic (93%) with an average of 21.8 bands per primer combination. The average polymorphic information content (PIC) values ranged from 0.09 (Osysl4b+ME05) to 0.25 (Osnramp5c+ME05, Osnramp1b+ME02 and Osysl4a +ME02). Gene diversity (H ˆ
) ranged from 0.10 (Osysl4b+ME05) to 0.31 (Osnramp1b + ME02 and Osysl4a +ME02). The Jaccard dissimilarity ranged from 0.15 to 0.52, explaining 37% of genetic variation (Table 4). Grouping of genotypes based on UPGMA and principal coordinate analysis (PCoA) were found comparable and grouping of genotypes into a different cluster was found mainly on the basis of pedigree relationships. TRAP markers revealed well resolved relationships among rice genotypes. The information generated from this study will helps to select parental combinations for breeding high iron content
rice varieties.
Analysis of Seed Proteins in Groundnut Cultivars (Arachis hypogaea L.)IJERA Editor
The seed protein contents and protein banding pattern were studied in commonly cultivated groundnut cultivars.
The groundnut cultivars such as ICGV00351, TMV-7, CO-4,CO-6 and TG-374 were used for quantitative and
qualitative analysis of seed proteins. The protein contents varied among the different varieties of groundnut. The
maximum protein content was observed in CO-6 followed by CO-4, TMV-7, ICGV00351 and TG-374. There
was a slight differences in protein content among the different cultivars. All the five cultivars of groundnut were
subjected to SDS-PAGE analysis. The results revealed that the variation in total number of bands and MW-Rf
values. The maximum number of MW-Rf value was noticed in TG-374 and ICGV00351, and the minimum
MW-Rf value was 11 recorded in CO-6 and TMV-7.
Genetic Variability for Antioxidant Activity and Total Phenolic Content in Fo...CrimsonpublishersNTNF
Total phenolic content and antioxidant activity were evaluated in 139 diverse genotypes of four pulse crops including 54 genotypes of chickpea (Cicer arietinum), 37 lentil (Lens culinaris), 21 pigeonpea (Cajanus cajan), and 26 blackgram (Vigna mungo). Results indicate significant genotypic variation (p < 0.01) for total phenolic content (TPC) as well as antioxidant activity (AOA). Amongst the four major pulse crops tested, maximum mean phenolic content was recorded in blackgram genotypes (7.01mg GAE/g), followed by lentil (3.46mg GAE/g), pigeonpea (3.32mg GAE/g) and chickpea (2.30mg GAE/g). In general, the Mediterranean landraces of lentil had higher phenolic content as compared to the other lentil varieties and breeding lines. Amongst the chickpea genotypes the phenolic content ranged from 0.40 to 5.63mg GAE/g and comparatively higher value for phenolic content was recorded in desi types (2.67mg GAE/g) as compared to the Kabuli types (1.05mg GAE/g). The antioxidant activity (AOA) was assayed in mature dry seeds utilizing DPPH (2,2-Diphenyl-1-picryl hydrazyl) radical scavenging assay which ranged from 1.73 to 19.14μmole Trolox/g tissue. As observed for TPC, highest AOA was also recorded in blackgram genotypes (19.14μmole Trolox/g tissue), followed by pigeonpea (2.72μmole Trolox/g tissue), chickpea (2.05μmole Trolox/g tissue) and lentil (1.73μmole Trolox/g tissue). Highly significant genotypic as well as phenotypic correlation (p<0.01) was recorded between phenolic content and antioxidant activity in chickpea, lentil as well as blackgram (rG values ranging from 0.268 to 0.850 and rP from 0.253 to 0.817), however, surprisingly the values were non-significant in case of pigeonpea. Strongest genotypic correlation was recorded in chickpea (rG=0.850), followed by lentil (rG =0.744), and blackgram (rG =0.268). High broad-sense heritability (h2bs) (0.89 to 0.97) for phenol content was recorded which indicates that substantial portion of total variation for phenolic content is due to genetic effects.
IJRET : International Journal of Research in Engineering and Technology is an international peer reviewed, online journal published by eSAT Publishing House for the enhancement of research in various disciplines of Engineering and Technology. The aim and scope of the journal is to provide an academic medium and an important reference for the advancement and dissemination of research results that support high-level learning, teaching and research in the fields of Engineering and Technology. We bring together Scientists, Academician, Field Engineers, Scholars and Students of related fields of Engineering and Technology
Proximate composition of seeds of hybrid varieties of minor milletseSAT Journals
Abstract Objective: The aim of present investigation was carried out to study the proximate composition of seeds of hybrid variety of minor millets. Materials and methods: The nine hybrid varieties of minor millets viz., Paspalum scrobiculatum (variety JK-41, JK-48 & JK-439), Eleusine coracana (variety DFM-1 & HR-374), Panicum sumatrense (variety JK- 8 & LMCO-2), Echinochloa frumentacea (variety BMVL-29 & BMVL-172) were analyzed for their proximate composition by AOAC method. Results and Conclusion: The proximate parameter such as moisture, total lipid, crude fibre, crude protein, carbohydrate, total ash, calcium, phosphorus and energy ranged from 10.44-13.97, 1.28-4.87, 3.27-13.59, 9.65-12.25, 72.97-84.88, 2.713-5.425, 0.016-0.34, 0.027-0.95 and 364.6-415.39 g/100g respectively. Nutritionally, minor millets are rich in macro nutrient and micro nutrient (protein, iron, calcium, phosphorus, fibre and vitamin content) which are normally deficient in Indian diets. Keywords: Minor millets, proximate composition, varieties of Paspalum scrobiculatum, Panicum sumatrense, Echinochloa frumentacea, Eleusine coracana.
ABSTRACT- Twenty two selection indices involving seed yield and six yield components were constructed using the
discriminatnt function technique. The efficiency of selection increased with the inclusion of more number of the characters
in the index. Selection indices were constructed adapting discriminant function which indicated that the maximum
genetic advance and relative efficiency can be obtained when seed yield was included as one of the characters in combination
with all other characters viz., plant height, days to 50% flowering, number of primary branches per plant, number of
secondary branches per plant, number of pods per plant and test weight. However higher relative efficiency was obtained
when a function yield was included as one of the component character in combination with number of pods per plant,
number of secondary branches per plant and test weight than to a function with all the character in combination with yield.
Key words- Pigeonpea, Genetic advance, Relative efficiency, Genotype
Molecular characterization of rice (Oryza sativa L.) genotypes using target r...Innspub Net
In the present investigation, based on the seven rice putative candidate iron transporter genes, novel TRAP markers were developed. These markers were successfully employed in the molecular diversity study among 30 rice genotypes representing improved rice cultivars and land races with varied grain iron content (7.38 - 30.58 ppm). Totally, thirty TRAP primer combinations were screened, which generated 703 bands out of which 654 were polymorphic (93%) with an average of 21.8 bands per primer combination. The average polymorphic information content (PIC) values ranged from 0.09 (Osysl4b+ME05) to 0.25 (Osnramp5c+ME05, Osnramp1b+ME02 and Osysl4a +ME02). Gene diversity (H ˆ
) ranged from 0.10 (Osysl4b+ME05) to 0.31 (Osnramp1b + ME02 and Osysl4a +ME02). The Jaccard dissimilarity ranged from 0.15 to 0.52, explaining 37% of genetic variation (Table 4). Grouping of genotypes based on UPGMA and principal coordinate analysis (PCoA) were found comparable and grouping of genotypes into a different cluster was found mainly on the basis of pedigree relationships. TRAP markers revealed well resolved relationships among rice genotypes. The information generated from this study will helps to select parental combinations for breeding high iron content
rice varieties.
Analysis of Seed Proteins in Groundnut Cultivars (Arachis hypogaea L.)IJERA Editor
The seed protein contents and protein banding pattern were studied in commonly cultivated groundnut cultivars.
The groundnut cultivars such as ICGV00351, TMV-7, CO-4,CO-6 and TG-374 were used for quantitative and
qualitative analysis of seed proteins. The protein contents varied among the different varieties of groundnut. The
maximum protein content was observed in CO-6 followed by CO-4, TMV-7, ICGV00351 and TG-374. There
was a slight differences in protein content among the different cultivars. All the five cultivars of groundnut were
subjected to SDS-PAGE analysis. The results revealed that the variation in total number of bands and MW-Rf
values. The maximum number of MW-Rf value was noticed in TG-374 and ICGV00351, and the minimum
MW-Rf value was 11 recorded in CO-6 and TMV-7.
Genetic Variability for Antioxidant Activity and Total Phenolic Content in Fo...CrimsonpublishersNTNF
Total phenolic content and antioxidant activity were evaluated in 139 diverse genotypes of four pulse crops including 54 genotypes of chickpea (Cicer arietinum), 37 lentil (Lens culinaris), 21 pigeonpea (Cajanus cajan), and 26 blackgram (Vigna mungo). Results indicate significant genotypic variation (p < 0.01) for total phenolic content (TPC) as well as antioxidant activity (AOA). Amongst the four major pulse crops tested, maximum mean phenolic content was recorded in blackgram genotypes (7.01mg GAE/g), followed by lentil (3.46mg GAE/g), pigeonpea (3.32mg GAE/g) and chickpea (2.30mg GAE/g). In general, the Mediterranean landraces of lentil had higher phenolic content as compared to the other lentil varieties and breeding lines. Amongst the chickpea genotypes the phenolic content ranged from 0.40 to 5.63mg GAE/g and comparatively higher value for phenolic content was recorded in desi types (2.67mg GAE/g) as compared to the Kabuli types (1.05mg GAE/g). The antioxidant activity (AOA) was assayed in mature dry seeds utilizing DPPH (2,2-Diphenyl-1-picryl hydrazyl) radical scavenging assay which ranged from 1.73 to 19.14μmole Trolox/g tissue. As observed for TPC, highest AOA was also recorded in blackgram genotypes (19.14μmole Trolox/g tissue), followed by pigeonpea (2.72μmole Trolox/g tissue), chickpea (2.05μmole Trolox/g tissue) and lentil (1.73μmole Trolox/g tissue). Highly significant genotypic as well as phenotypic correlation (p<0.01) was recorded between phenolic content and antioxidant activity in chickpea, lentil as well as blackgram (rG values ranging from 0.268 to 0.850 and rP from 0.253 to 0.817), however, surprisingly the values were non-significant in case of pigeonpea. Strongest genotypic correlation was recorded in chickpea (rG=0.850), followed by lentil (rG =0.744), and blackgram (rG =0.268). High broad-sense heritability (h2bs) (0.89 to 0.97) for phenol content was recorded which indicates that substantial portion of total variation for phenolic content is due to genetic effects.
IJRET : International Journal of Research in Engineering and Technology is an international peer reviewed, online journal published by eSAT Publishing House for the enhancement of research in various disciplines of Engineering and Technology. The aim and scope of the journal is to provide an academic medium and an important reference for the advancement and dissemination of research results that support high-level learning, teaching and research in the fields of Engineering and Technology. We bring together Scientists, Academician, Field Engineers, Scholars and Students of related fields of Engineering and Technology
Proximate composition of seeds of hybrid varieties of minor milletseSAT Journals
Abstract Objective: The aim of present investigation was carried out to study the proximate composition of seeds of hybrid variety of minor millets. Materials and methods: The nine hybrid varieties of minor millets viz., Paspalum scrobiculatum (variety JK-41, JK-48 & JK-439), Eleusine coracana (variety DFM-1 & HR-374), Panicum sumatrense (variety JK- 8 & LMCO-2), Echinochloa frumentacea (variety BMVL-29 & BMVL-172) were analyzed for their proximate composition by AOAC method. Results and Conclusion: The proximate parameter such as moisture, total lipid, crude fibre, crude protein, carbohydrate, total ash, calcium, phosphorus and energy ranged from 10.44-13.97, 1.28-4.87, 3.27-13.59, 9.65-12.25, 72.97-84.88, 2.713-5.425, 0.016-0.34, 0.027-0.95 and 364.6-415.39 g/100g respectively. Nutritionally, minor millets are rich in macro nutrient and micro nutrient (protein, iron, calcium, phosphorus, fibre and vitamin content) which are normally deficient in Indian diets. Keywords: Minor millets, proximate composition, varieties of Paspalum scrobiculatum, Panicum sumatrense, Echinochloa frumentacea, Eleusine coracana.
ABSTRACT- Twenty two selection indices involving seed yield and six yield components were constructed using the
discriminatnt function technique. The efficiency of selection increased with the inclusion of more number of the characters
in the index. Selection indices were constructed adapting discriminant function which indicated that the maximum
genetic advance and relative efficiency can be obtained when seed yield was included as one of the characters in combination
with all other characters viz., plant height, days to 50% flowering, number of primary branches per plant, number of
secondary branches per plant, number of pods per plant and test weight. However higher relative efficiency was obtained
when a function yield was included as one of the component character in combination with number of pods per plant,
number of secondary branches per plant and test weight than to a function with all the character in combination with yield.
Key words- Pigeonpea, Genetic advance, Relative efficiency, Genotype
Evaluation of seed storage proteins in common bean by some biplot analysisINNS PUBNET
In order to study of seed storage proteins, proteins samples of common bean genotypes were prepared by 0.2 M
NaCl of extracting soluble. Genotypes were located in two groups by cluster analysis using Wilks’ lambda
statistic. Two groups were different for yield components (number of pods per plant, number of seeds per plant
and seed weight). Factor analysis showed that two factors described 61% of total proteins variation. Correlated
bands with yield components characters had the highest coefficients for the first factor. This factor was named
“yield components proteins”. Protein bands via RM 58 and 64 had relationship with days to flowering.
Therefore, the second factor was named “phenologic proteins”. Genotypes were located in four groups by these
factors. Length, angle and presence of protein bands were important characteristics to explain graphical
information in GGE biplot compared to factor analysis. Get the full articles at: http://www.innspub.net/volume-3-number-5-may-2013/
Principal Component Analysis for Evaluation of Guinea grass (Panicum maximum...Agriculture Journal IJOEAR
Abstract— The present study was conducted to study the variability among the genotypes by Principal Component Analysis (PCA) in order to select those that are most suitable for breeding programme. This study included ten quantitative traits. The result of principal component analysis showed that the first four principal components with Eigen value greater than 0.88 contributed about 76.10 per cent of total variation in the population. The variability of the genotypes was interpreted based on four principal components, the first principal component described the yield level, the second principal component described the productivity and quality and the last two principal components described the quality of the fodder which indicating that the identified traits within the axes exhibited great influence on the phenotype and this could be effectively used for selection among the tested entries for further development of Guinea grass varieties with improved fodder yield and quality.
Analysis of some Capparis L. accessions from Turkey based on IRAP and seed pr...Agriculture Journal IJOEAR
Abstract— 15 accessions from 10 different grid square of Turkey were analysed based on IRAP and seed protein patterns in order to observe the genetic diversity in the gene pool of Capparis. High levels of polymorphisms were detected with IRAP primers (93%) and seed protein electrophoresis (55.5%). Specific delineation between C. spinosa and C. ovata, and segregations of the accessions related to infraspecific status and eco-geographical distributions were presented in the dendrograms and PCA analysis. Significantly correlation between IRAP markers and seed protein profiles of the specimens was detected (p< 0.0001). Combination of genomic/proteomic marker systems may be useful approach for determining the broad genetic diversity in gene pool of Capparis, identification of the germplasms and ecologically tolerant genotypes in breeding programs.
Screening Fenugreek genotypes for high callus induction and growth | IJAARInnspub Net
Fenugreek (Trigonella foenume-graecum) is a medicinal herb that has anti-diabetic properties. 4-hydroxyisoleucine, an important metabolite of this plant, is a good candidate for improving hepatic insulin resistance in type 2 diabetic patients. In vitro production of metabolites mainly relies on the ability of the tissue culture system to produce more and viable cells with maximum production rate. Callus induction is the first step of establishing plant cell based bioreactors which needs potential genotypes with higher and faster callus production. To find such genotypes, screening them is indispensable. In this research, we screened 21 Iranian landraces of fenugreek for callus induction and growth on MS medium supplemented with some plant growth regulators. The results showed different capacity of the screened genotypes in callus induction (P<0.05). Also, the type of explant had a significant effect on callus induction (P<0.05). Calli were able to produce 4-Hydroxyisulosine 67% of the amount in vivo samples.
Grain Yield and Some Quality Traits of Different Oat (Avena sativa L.) Genot...Agriculture Journal IJOEAR
Abstract— Oat cultivars should have both high yield potential and some quality criteria in accordance with using targets. Hence, grain yield and some quality traits of 25 oat genotypes grown in two consecutive years were studied. This study was carried out during the 2012–2013 and 2013–2014 growing seasons in Yozgat, Turkey. Grain yield, plant height, hectolitre weight, thousand grain weight, great percentage and grain composition (protein, fat, ash, acid detergent fiber (ADF), neutral detergent fiber (NDF), β-glucan and starch) were evaluated. Analysis of the combined data for two years showed significant genotypic differences for all traits. According to the average of two years, among the genotypes, grain yield varied from 2432.3 (2 numbered genotype) to 5650.2 (19 numbered genotype) kg ha-1, plant height from 76.3 to 128.3 cm, hectoliter weight from 41.5 to 52.3 kg, thousand grain weight from 24.5 to 41.3 g, groat percentage from 70.4 to 76.6 %, protein content from 11.1to 14.3 %, fat content from 5.86 to 8.47 %, ash ratio from 2.52 to 3.43 %, ADF content from 11.0 to 16.4 %, NDF content from 29.5 to 37.3 %, β-glucan content from 1.33 to 2.58 % and starch content ranged from 34.9 to 47.7 %. Grain yield was significantly and positively correlated with thousand grain weight (r = 0.253**) and neutral detergent fibre (r = 0.160**). However, correlations between grain yield with crude protein (r = -0.216**) and hectolitre weight (r = 0.246) were significantly and negative.
Dr. Ravi S Pandey-Resume for Assistant Professor/ Research Scientist in Bioch...Dr. Swami Gyan Prakash
Dear Member of Recruiter Committee,
I am writing this letter for a position of Assistant Professor/ Research Scientist in Biochemistry, Clinical-Biochemistry, Biotechnology and Molecular Biology. In brief, I am PhD in Medicinal Biochemistry and completed several successful projects as a Postdoctoral Scientist in different discipline of Biochemistry like Molecular Biology of Aging, Alternative splicing in human diseases, Epigenetic regulation in liver and breast cancer from India and USA. I came back to India in April 2010 and worked as a CSIR-Pool Scientist in the area of chromatin remodeling in breast cancer. My tenure has been completed recently. Thus, I am looking for a faculty position of Assistant Professor/ Research Scientist in Biochemistry, Clinical-Biochemistry, Biotechnology and Molecular Biology.
I am highly interested to trend the graduate students in Biochemistry, Biotechnology and Molecular Biology. Besides, I am very much motivated to lead projects in the area of Cancer Biology. Thus, I respectfully submit this letter of application, for I believe my experiences and commitment for teaching and research make me well qualified to meet the needs of Assistant Professor/ Research Scientist in Biochemistry, Clinical-Biochemistry, Biotechnology and Molecular Biology.
I am well acquainted with the molecular techniques associated with DNA, RNA and proteins research. Besides, I am expertise in planning and execution of experiments, mentoring PhD students, interpreting data, as well as writing and data preparation for manuscript publication. During my doctorate and post doctorate time, I taught graduate and postgraduate students on behalf of my mentors. I am well organized, goal oriented; self motivated research scientist and committed to train the student in area of Clinical Biochemistry and Molecular Biology along with lead research work in the area of Cancer Biology. I would appreciate for an interview opportunity to discuss about my background, qualification and expertise that may fit for the position.
Influence of carbon sources on α amylase production by brevibacillus sp. unde...eSAT Journals
Abstract Numerous marine microorganisms secrete enzymes which can provide new insights and understanding of enzymes. Marine microorganisms have been attracting more attention as source for novel enzymes. Secondary screening is strictly essential in any systematic screening programme which helps in detection of useful bacteria in fermentation processes. Secondary screening also provides information pertaining to the effect of different components of the medium. This is valuable in designing the medium that may be attractive as far as economic consideration is concerned. Natural carbon source, Saccharum officinarum (5%) produced maximum α-amylase while Triticum vulgare (4%) produced very low α-amylase. Synthetic carbon source when supplemented with maltose (1%) and sucrose (4%) regulated higher production of amylase. Starch (2%), dextrose (3%) and galactose (4%) exhibited average effect on production whereas lactose (3%) and mannitol (3%) decreased production. The α-amylase was found to have many applications in the field of starch processing, textile industry, improving shelf life of bread, ethanol production, sewage treatment and effluent treatment. Keywords: Brevibacillus borostelensis R1, Saccharum officinarum, Triticum vulgare, maltose, sucrose
Influence of carbon sources on α amylase production by brevibacillus sp. unde...eSAT Publishing House
IJRET : International Journal of Research in Engineering and Technology is an international peer reviewed, online journal published by eSAT Publishing House for the enhancement of research in various disciplines of Engineering and Technology. The aim and scope of the journal is to provide an academic medium and an important reference for the advancement and dissemination of research results that support high-level learning, teaching and research in the fields of Engineering and Technology. We bring together Scientists, Academician, Field Engineers, Scholars and Students of related fields of Engineering and Technology
Abstract— MicroRNAs (miRNAs) function on post-transcriptional gene silencing and regulate the gene expression by degrading the transcripts of their targets, leading to down-regulation of the target genes. Plant miRNAs have been reported to play important roles in developmental control, hormone secretion, cell proliferation, and response to environmental stresses. In this review, we have reviewed miRNA expression and its potential role in regulating cell differentiation in Arabidopsis and summarized the miRNAs regulated cell differentiation during root, shoot, leave, and embryo development. We have further described practical application of expression of miRNAs in plant molecular breeding.
Evaluation of seed storage proteins in common bean by some biplot analysisINNS PUBNET
In order to study of seed storage proteins, proteins samples of common bean genotypes were prepared by 0.2 M
NaCl of extracting soluble. Genotypes were located in two groups by cluster analysis using Wilks’ lambda
statistic. Two groups were different for yield components (number of pods per plant, number of seeds per plant
and seed weight). Factor analysis showed that two factors described 61% of total proteins variation. Correlated
bands with yield components characters had the highest coefficients for the first factor. This factor was named
“yield components proteins”. Protein bands via RM 58 and 64 had relationship with days to flowering.
Therefore, the second factor was named “phenologic proteins”. Genotypes were located in four groups by these
factors. Length, angle and presence of protein bands were important characteristics to explain graphical
information in GGE biplot compared to factor analysis. Get the full articles at: http://www.innspub.net/volume-3-number-5-may-2013/
Principal Component Analysis for Evaluation of Guinea grass (Panicum maximum...Agriculture Journal IJOEAR
Abstract— The present study was conducted to study the variability among the genotypes by Principal Component Analysis (PCA) in order to select those that are most suitable for breeding programme. This study included ten quantitative traits. The result of principal component analysis showed that the first four principal components with Eigen value greater than 0.88 contributed about 76.10 per cent of total variation in the population. The variability of the genotypes was interpreted based on four principal components, the first principal component described the yield level, the second principal component described the productivity and quality and the last two principal components described the quality of the fodder which indicating that the identified traits within the axes exhibited great influence on the phenotype and this could be effectively used for selection among the tested entries for further development of Guinea grass varieties with improved fodder yield and quality.
Analysis of some Capparis L. accessions from Turkey based on IRAP and seed pr...Agriculture Journal IJOEAR
Abstract— 15 accessions from 10 different grid square of Turkey were analysed based on IRAP and seed protein patterns in order to observe the genetic diversity in the gene pool of Capparis. High levels of polymorphisms were detected with IRAP primers (93%) and seed protein electrophoresis (55.5%). Specific delineation between C. spinosa and C. ovata, and segregations of the accessions related to infraspecific status and eco-geographical distributions were presented in the dendrograms and PCA analysis. Significantly correlation between IRAP markers and seed protein profiles of the specimens was detected (p< 0.0001). Combination of genomic/proteomic marker systems may be useful approach for determining the broad genetic diversity in gene pool of Capparis, identification of the germplasms and ecologically tolerant genotypes in breeding programs.
Screening Fenugreek genotypes for high callus induction and growth | IJAARInnspub Net
Fenugreek (Trigonella foenume-graecum) is a medicinal herb that has anti-diabetic properties. 4-hydroxyisoleucine, an important metabolite of this plant, is a good candidate for improving hepatic insulin resistance in type 2 diabetic patients. In vitro production of metabolites mainly relies on the ability of the tissue culture system to produce more and viable cells with maximum production rate. Callus induction is the first step of establishing plant cell based bioreactors which needs potential genotypes with higher and faster callus production. To find such genotypes, screening them is indispensable. In this research, we screened 21 Iranian landraces of fenugreek for callus induction and growth on MS medium supplemented with some plant growth regulators. The results showed different capacity of the screened genotypes in callus induction (P<0.05). Also, the type of explant had a significant effect on callus induction (P<0.05). Calli were able to produce 4-Hydroxyisulosine 67% of the amount in vivo samples.
Grain Yield and Some Quality Traits of Different Oat (Avena sativa L.) Genot...Agriculture Journal IJOEAR
Abstract— Oat cultivars should have both high yield potential and some quality criteria in accordance with using targets. Hence, grain yield and some quality traits of 25 oat genotypes grown in two consecutive years were studied. This study was carried out during the 2012–2013 and 2013–2014 growing seasons in Yozgat, Turkey. Grain yield, plant height, hectolitre weight, thousand grain weight, great percentage and grain composition (protein, fat, ash, acid detergent fiber (ADF), neutral detergent fiber (NDF), β-glucan and starch) were evaluated. Analysis of the combined data for two years showed significant genotypic differences for all traits. According to the average of two years, among the genotypes, grain yield varied from 2432.3 (2 numbered genotype) to 5650.2 (19 numbered genotype) kg ha-1, plant height from 76.3 to 128.3 cm, hectoliter weight from 41.5 to 52.3 kg, thousand grain weight from 24.5 to 41.3 g, groat percentage from 70.4 to 76.6 %, protein content from 11.1to 14.3 %, fat content from 5.86 to 8.47 %, ash ratio from 2.52 to 3.43 %, ADF content from 11.0 to 16.4 %, NDF content from 29.5 to 37.3 %, β-glucan content from 1.33 to 2.58 % and starch content ranged from 34.9 to 47.7 %. Grain yield was significantly and positively correlated with thousand grain weight (r = 0.253**) and neutral detergent fibre (r = 0.160**). However, correlations between grain yield with crude protein (r = -0.216**) and hectolitre weight (r = 0.246) were significantly and negative.
Dr. Ravi S Pandey-Resume for Assistant Professor/ Research Scientist in Bioch...Dr. Swami Gyan Prakash
Dear Member of Recruiter Committee,
I am writing this letter for a position of Assistant Professor/ Research Scientist in Biochemistry, Clinical-Biochemistry, Biotechnology and Molecular Biology. In brief, I am PhD in Medicinal Biochemistry and completed several successful projects as a Postdoctoral Scientist in different discipline of Biochemistry like Molecular Biology of Aging, Alternative splicing in human diseases, Epigenetic regulation in liver and breast cancer from India and USA. I came back to India in April 2010 and worked as a CSIR-Pool Scientist in the area of chromatin remodeling in breast cancer. My tenure has been completed recently. Thus, I am looking for a faculty position of Assistant Professor/ Research Scientist in Biochemistry, Clinical-Biochemistry, Biotechnology and Molecular Biology.
I am highly interested to trend the graduate students in Biochemistry, Biotechnology and Molecular Biology. Besides, I am very much motivated to lead projects in the area of Cancer Biology. Thus, I respectfully submit this letter of application, for I believe my experiences and commitment for teaching and research make me well qualified to meet the needs of Assistant Professor/ Research Scientist in Biochemistry, Clinical-Biochemistry, Biotechnology and Molecular Biology.
I am well acquainted with the molecular techniques associated with DNA, RNA and proteins research. Besides, I am expertise in planning and execution of experiments, mentoring PhD students, interpreting data, as well as writing and data preparation for manuscript publication. During my doctorate and post doctorate time, I taught graduate and postgraduate students on behalf of my mentors. I am well organized, goal oriented; self motivated research scientist and committed to train the student in area of Clinical Biochemistry and Molecular Biology along with lead research work in the area of Cancer Biology. I would appreciate for an interview opportunity to discuss about my background, qualification and expertise that may fit for the position.
Influence of carbon sources on α amylase production by brevibacillus sp. unde...eSAT Journals
Abstract Numerous marine microorganisms secrete enzymes which can provide new insights and understanding of enzymes. Marine microorganisms have been attracting more attention as source for novel enzymes. Secondary screening is strictly essential in any systematic screening programme which helps in detection of useful bacteria in fermentation processes. Secondary screening also provides information pertaining to the effect of different components of the medium. This is valuable in designing the medium that may be attractive as far as economic consideration is concerned. Natural carbon source, Saccharum officinarum (5%) produced maximum α-amylase while Triticum vulgare (4%) produced very low α-amylase. Synthetic carbon source when supplemented with maltose (1%) and sucrose (4%) regulated higher production of amylase. Starch (2%), dextrose (3%) and galactose (4%) exhibited average effect on production whereas lactose (3%) and mannitol (3%) decreased production. The α-amylase was found to have many applications in the field of starch processing, textile industry, improving shelf life of bread, ethanol production, sewage treatment and effluent treatment. Keywords: Brevibacillus borostelensis R1, Saccharum officinarum, Triticum vulgare, maltose, sucrose
Influence of carbon sources on α amylase production by brevibacillus sp. unde...eSAT Publishing House
IJRET : International Journal of Research in Engineering and Technology is an international peer reviewed, online journal published by eSAT Publishing House for the enhancement of research in various disciplines of Engineering and Technology. The aim and scope of the journal is to provide an academic medium and an important reference for the advancement and dissemination of research results that support high-level learning, teaching and research in the fields of Engineering and Technology. We bring together Scientists, Academician, Field Engineers, Scholars and Students of related fields of Engineering and Technology
Abstract— MicroRNAs (miRNAs) function on post-transcriptional gene silencing and regulate the gene expression by degrading the transcripts of their targets, leading to down-regulation of the target genes. Plant miRNAs have been reported to play important roles in developmental control, hormone secretion, cell proliferation, and response to environmental stresses. In this review, we have reviewed miRNA expression and its potential role in regulating cell differentiation in Arabidopsis and summarized the miRNAs regulated cell differentiation during root, shoot, leave, and embryo development. We have further described practical application of expression of miRNAs in plant molecular breeding.
S M Masiul Azam, Md Shahidul Islam, Parvin Shahanaz, Md Shafiqur Rahman and Sarder Md Shahriar Alam. “Molecular Characterization of Brassica Cultivars through RAPD Markers” United International Journal for Research & Technology (UIJRT) 1.3 (2019): 41-45.
Assessment of Genetic Diversity in 13 Local Banana (Musa Spp.) Cultivars Usin...paperpublications3
Abstract: A Study was conducted to investigate the genetic variability among 13 local banana cultivars using 3 SSR primers of Mb1-69, Mb1-113 and Mb1-134. All the primer pairs amplified a total of 29 different marker bands with an average of 9.6 bands per primer. Among the 29 bands only 4 bands were monomorphic and the rest 25 bands were polymorphic. The sizes of the amplified DNA bands in 13 local banana cultivars varied from 200 bp to 600 bp. The primer Mb1-113 amplified the highest (14) number of DNA bands and the primer Mb1-69 amplified the lowest (7) number of DNA bands whilst primer Mb1-134 amplified 8 DNA bands. The values of pair-wise genetic distances ranged from 1.00 to 9.00 indicating the presence of wide genetic diversity. The dendogram constructed based on phylogenetic relationship analysis revealed that the highest genetic diversity (9.00) found between the cultivars champa and jawayta and also the cultivars champa and jahazy whilst the lowest (1.00) between the cultivars doubled haploid and kathaly, doubled haploid and sorishafruity, doubled haploid and amritsagor and doubled haploid and ganasundory. The UPGMA dendogram has segregated the 13 local banana cultivars into two major clusters. Agnishwar and champa formed in cluster 1 and the rest of the cultivars like sobri jesore, sobri, anazy, kathaly, jawayta, sorishafruity, amritsagor, jahazy, bangle, ganasundory and doubled haploid have constituted the cluster 2.
Genetic diversity in pea germplasm using RAPD MarkersShujaul Mulk Khan
Selection of the genotypes using plasmid assisted technology provides an efficient and useful tool for elaborating genetic relationships among genotypes. In present study, 48 Pea (Pisum sativum var sativum L.) genotypes obtained from different sources were analyzed through 20 RAPD, DNA markers for assessment of intraspecific DNA variations. Results revealed that significant variations were present in minor bands. Major bands also showed significant diversity. Considerable variations were also recorded in density of some common bands. Maximum and minimum genetic diversity i.e., 80% and 20% was found among 08 and 23 comparisons, respectively from banding profile. These variations can be
used further for enhancing variability, a prerequisite for crop breeding. Phylogenetic clustering (through dendrogram analysis) of genotypes revealed that genetic diversity is independent of origin of genotypes. Forty eight genotypes of pea clustered in three main groups A, B and C comprising 23, 5 and 20 genotypes, respectively. Group A1 and C1 included the most distantly related genotypes and hence can be recommended for breeding to obtain genetically diverse segregating populations.
The International Journal of Engineering and Science (IJES)theijes
The International Journal of Engineering & Science is aimed at providing a platform for researchers, engineers, scientists, or educators to publish their original research results, to exchange new ideas, to disseminate information in innovative designs, engineering experiences and technological skills. It is also the Journal's objective to promote engineering and technology education. All papers submitted to the Journal will be blind peer-reviewed. Only original articles will be published.
Factor and Principal Component Analyses of Component of Yield and Morphologic...Premier Publishers
The research was conducted to evaluate the yield performance, genetic variation and diversity of the rice genotypes for breeding purposes. Genetic variability and diversity assessment for component of yield and morphological traits among sixteen lowland rice genotypes were carried out at three locations namely Akungba, Akure and Okitipupa during the rainy seasons of 2013, 2014 and 2015. The experiment was conducted in a randomized complete block design (RCBD) replicated three times, a plot size of 3m x 3m and spacing of 20cm x 20cm was adopted to make a total plant density of 250,000 stands/ha. Cultural operations such as weeding, fertilizer and pesticide applications were carried out as appropriate. Data were collected on plant height, number of tillers per hill, effective tillers, tiller without panicle, flag leaf length, panicle length, panicle weight, number of grains per panicle, number of spikelets per panicle, one thousand grains weight, grain length, grain width, number of days to panicle initiation, number of days to maturity and grain yield per hill. Factor analysis indicated that the first five factors accounted for 79.3 % phenotypic variability, number of tillers, effective tillers with panicle, number of days to flowering and number of days to maturity exhibited 1.00 communality. The first eight principal components had cumulative variance of 93.1 %, whereas, PC(s) 1 and 2 had eigen value greater than 2.0. Therefore, factor and principal component analyses identified some similar characters as the most important for classifying the variation among rice genotypes and these include grain yield, panicle weight, panicle length, one thousand grain weight and number of effective tillers per hill.
Molecular Diversity Analysis of Some Local Ginger (Zingiber officinale) Genot...AI Publications
Ginger (Zingiber officinale) rhizomes have been widely used as a spice and flavoring agent in foods and beverages in Bangladesh as well as in all over the world for its economical and medicinal values. The present investigation was undertaken for the assessment of 13 local ginger genotypes collected from different region of Bangladesh through 7 RAPD primers. Genomic DNA was extracted from ginger genotypes using CTAB method. A total of 34 distinct and differential amplification bands ranging from 150-1200 bp were observed with an average of 1.14 polymorphic bands per primer. The overall gene diversity was detected 0.8052 and the value of PIC was detected 0.7532. The RAPD marker generate enough polymorphism for possible use in diversity studies through cluster analysis and principal component analysis (PCA). PCA classified 13 ginger genotypes into four groups and showed in two dimensional scatter plot. The genetic similarity coefficients among genotypes ranged from 0.103 to 0.654. Cluster analysis based on Jaccard’s similarity-coefficient using UPGMA grouped the genotypes into two clusters: Cluster A and Cluster B. The cluster ‘A’ had only one genotype Kaptai local and the second cluster ‘B’ had rest of twelve genotypes. The prevalence level of polymorphism in the local genotypes of ginger will help to breeders for ginger improvement program.
Detection of Genetic variation in tissue culture clones of date palm using IS...IJSRD
Date palm is a plant having high nutritional value and long life (yielding up to 100 years). Phoenix dactylifera requires 2-5 males for pollination of 100 females’ plant depending up on genetic and environment factors. Therefore paternity variation expected to very low according to PCR based techniques, Even though we have tried to find out genetic variation among tissue culture cloned plant. Tissue culture technique can be used for genetic improvement of date palm. The main purpose of this study was to evaluate the genetic variation in the tissue culture clones of date palm by using ISSR primers among mother and it’s two clones. The plant DNA was extracted and subjected to detection of genetic variation in two groups of date palm using ISSR primers. In this study ISSR primers produced monomorphic bands within group-1 and group-2. Genetic variation in tissue culture clones of date palm was not detecte by UBC primer series.
Aim of the present study was production biomass by induction of multiple shoots from Bambusa bambos. In general, the efficient and reproducible procedure for the propagation of bamboo can be achieved by seed propagation, clump division, and rhizome for small scale. In case of mass scale propagation, this technique would be highly insufficient and inefficient. For efficient production of bamboo, Micropropagation technique is used in large scale production. Nodal segment from fields grown clumps were used as the explants to develop a method of in vitro Micropropagation in bamboo. Plant growth hormone BAP (benzyl amino purine), KIN (kinetin), NAA (1- naphthalene acetic acid), IBA (indole-3 butyric acid), IAA (indole-3 acetic acid) was studied on in-vitro Micropropagation of the effective shoot and roots of bamboo. Effective axillary bud breaking was achieved in Murashige and Skoog (MS) media. Nodal explants culture was inoculated in both solid (0.8%) and liquid MS media and observed the maximum proliferation of shoot in solid MS medium (4/ nodal explants). The concentration of sucrose was varied and their growth was examined. The sucrose was optimized (3%). Under the optimized sucrose condition, the hormone was varied and growth was examined. Under this condition, BAP response was high. Thus the concentration of BAP was varied for further studies. The response was high in 3 mg/l of BAP concentration. This review briefly provides the state-of-the-art information on tissue culture mediated biotechnologically interventions made in bamboo for large scale Micropropagation. The established protocol will be of help to stakeholders in edible bamboo trade to conserve gene-pool and increase productivity. Key-words- Bamboo, Micropropagation, Tissue culture, Multiple shoots, Benzyl amino purine
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Indian J. Genet., 74(4) Suppl., 596-601 (2014)
DOI: 10.5958/0975-6906.2014.00896.7
Abstract
Molecular markers have been assisting breeders in crop
improvement. Judicious integration of molecular markers
with conventional breeding practices has contributed
numerous improved varieties. In the process of MAS,
monomorphic markers are most often eliminated from
further investigations assuming that they are non-
informative. In this study, efforts were made to elucidate
information from monomorphic markers. Twenty rice
genotypes contrasting for grain zinc content were
selected. Specific markers were designed to the already
reported genes associated with micronutrient transport
from soil to grain. Among designed markers, only OsZIP6c
and OsZIP3b were polymorphic and Single-Marker
Analysis revealed that OsZIP6c was associated with culm
zinc content. Sequencing of amplicons of six markers
including four monomorphic markers revealed that
nucleotide variations were present in monomorphic
markers as well. SMA for nucleotide variations revealed
that OsZIP5b, a monomorphic marker on agarose,
contained nucleotide changes significantly associated
with grain zinc content. This clearly demonstrates that
monomorphic markers are as informative as polymorphic
markers and should not be eliminated from the study.
Key words: Bioinformatics, MAS, molecular markers,
monomorphism, polymorphism, rice,
sequencing, SMA, zinc
Introduction
Use of Molecular markers in the field of crop
improvement has been a huge success in the recent
past. Discovery of tools like PCR, sequencing,
improvements in the fields of genomics, transcriptomics
and proteomics have given further impetus [1]. As every
molecular marker follow mendelian pattern of
inheritance, it was very easy for plant scientists to
employ them in selecting plants. Hence, the molecular
markers tagged with a particular trait are used in
selection of elite genotypes eliminating any influence
of environment. To ease the selection process,
molecular maps are constructed [2]. The first step in
molecular map construction, QTL mapping and/or
marker-assisted breeding programs is to screen a large
number (different kinds) of molecular markers using set
of parental lines. Monomorphic markers are usually
eliminated from the further study. Most often, using
biparental populations, maps are constructed, QTL
tagging done and MAS practiced using polymorphic
markers [3]. The monomorphic markers, which are
eliminated from the study, could be the ones that are
associated with the trait of interest. Some of the
consequence related to this strategy is discussed in this
paper with a practical suggestion to make better use of
monomorphic markers and improve the chances of
success.
Materials and methods
Research material comprised of ten genotypes with high
and ten with low grain Zn content selectedbased on
earlier studies [4, 5]using AAS (Atomic Absorption
Spectrophotometer) and XRF (X Ray Fluorescence).
The selected genotypes were grown during Summer-
2013 in homogenously mixed soil. The fertilizers applied,
irrigation and other management practices were similar
for all the genotypes. Estimation of Zn content in the
mature grains, culm and roots were done in XRF facility
(Oxford Instruments, X-Supreme8000) available at
MSSRF (M S Swaminathan Research Foundation,
Chennai). For molecular marker analyses, DNA from
all the 20 genotypes was isolated by using CTAB
method [6].
*Corresponding author’s e-mail: heshashidhar@uasbangalore.edu.in
Published by the Indian Society of Genetics & Plant Breeding, F2, First Floor, NASC Complex, PB#11312, IARI, New Delhi 110012
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Monomorphic molecular markers are as informative as polymorphic
molecular markers
K. M. Sumantha Holla, Jameel Ahmad Khan, M. S. Sowjanya and H. E. Shashidhar*
Department of Plant Biotechnology, University of Agricultural Sciences, Bangalore 560065
(Received : September 2014 ; Revised : November 2014; Accepted: November 2014)
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The nucleotide sequences of known Zn genes
explored were downloaded by Nucleotide database of
NCBI. Pick primer tool in NCBI (in collaboration with
Primer3) was used to design primers specific to the
genes targeted [7]. PCR (Eppendorf, Mastercycler
Nexus Gradient) for candidate markers was performed.
Single-Marker Analysis (SMA) was done for results at
3% agarose gel, by using SPSS package (Version 16.0).
Sequencing of the amplified products was done
at “Chromus Biotech Private Ltd, India”. Sequences
obtained were aligned using Clustalw(http://
www.ebi.ac.uk/Tools/msa/clustalw2)[8]. Jalview tool [9]
of the clustalw website was used for the identification
of the variations present in these sequences. Sequence
of all 22 genotypes (including two checks: Azucena and
Moromutant) for six candidate gene chosen was aligned
and variations were recorded at each base. Starting loci
of the amplicon is considered as position 1 and end
point varied with each primer. Any changes in any
position of these sequences with any base pair or ‘in-
dels’ were recorded, statistical analysis was done to
establish association. Each possible change at any
position of the sequence was scored. For sequences
having same nucleotide as the consensus sequences
was scored as “1”, any change was scored as 2, 3 or 4
depending upon the nucleotide substituted. In case of
deletion at that locus, it was scored as 9. These scores
were then used for the analysis using SPSS (v16.0) for
associating these variations in the nucleotide level with
the phenotypic variation for Zn content in the root, culm
and grain.
Results and discussion
Availability of genetic variability is very important in any
crop to understand the genetics of any traits [10]. To
understand any gene affecting the trait, it has to be
studied in diverse genotypes with a good amount of
phenotypic and genotypic variation. The selected
genotypes were having variations indeed (Table 1).
Highest grain Zn in brown rice was observed in AM-65
(43.95 ppm), lowest in Sarabasti (22.85ppm). Highest
culm Zn content was observed in Sarabasti (12.80ppm),
lowest in AM-1 (0.40ppm). Highest root Zn content was
observed in Satabdhi (6.95ppm), lowest in Nuadhusara
(0.20ppm). Although genotypes have been selected
based on the grain Zn content, these genotypes also
exhibited variations to Zn content in culm and roots.
Molecular marker analysis of selected genotypes
The list of all the Zn transporters obtained by literature
survey is shown in Table 2. There are many genes
Table 1. Mean zinc content (mg kg
–1
) in the selected
genotypes of rice
Genotype Brown Culm Root
rice Zn Zn Zn
AM-1 42.22 0.40 1.81
AM-143 43.53 1.23 4.18
AM-65 43.92 4.05 3.00
AM-72 42.37 3.60 3.31
AM-81 41.23 4.31 2.92
AM-94B 42.35 2.17 1.90
BJ-18 25.88 10.70 4.22
BJ-24(K) 41.50 4.52 0.20
BPT 5204 /ChittiMutyalu-MS 42.10 4.80 0.60
EdavankudiPokkali 41.93 0.61 0.90
Improved ChittiMutyalu 27.67 1.03 4.59
Kalanamak-Birdapur 27.85 10.30 2.10
KalluRandaikar 24.67 6.89 5.24
KarnaMahsuri 27.67 0.81 1.60
Nuadhusara 28.53 6.90 0.20
R 133-968-2-1 27.78 4.55 3.67
Sarabasti 23.12 12.27 2.30
Satabdhi 28.4 5.30 6.68
Tara 28.87 2.40 5.76
Vandana 42.00 10.63 0.62
Table 2. List of Zn transporters in rice used in the study
S.No. Transporter Plant part
1 OsZIP1 Root
2 OsZIP2 Culm
3 OsZIP3 Root
4 OsZIP4 Culm/grain
5 OsZIP5 Culm/grain
6 OsZIP6 Root/culm/flower
7 OsZIP7 Grain/culm
8 OsZIP8 Root/culm/grain
9 OsYSL2 Grain/culm
10 OsNramp Grain/culm
11 OsIRT1 Culm/root
12 OsNAC Leaf/root
13 OsNAAT1 Culm/leaf
14 OsNAS3 Culm/leaf
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598 K. M. Sumantha Holla et al. [Vol. 74, No. 4, Suppl.
belonging to family of OsZIP, OsYSL, OsIRT,
OsNRAMP, OsNAC and OsNAAS. All the genes in
these family’s needs to be explored in depth to obtain a
clear idea about how these transporters are working
and how the available knowledge can be employed to
enhance the Zn content in rice grains. Improvements in
the field of bioinformatics have become a boon for plant
breeders, especially for those who are practicing marker-
assisted selection [11]. Current study is also one of such
examples where bioinformatics tools were applied with
marker-assisted selection. Application of bioinformatics
will not only make study more focused but it also reduced
the cost involved in conducting research.
Primers designed in the NCBI database have
worked with a size variation for about 50-100bp but,
OsZIP7a and OsZIP7b primers did not amplify anything
in all the 20 selected genotypes, even after many cycles
of repetition and hence, they were eliminated for further
analysis. This could be because japonica rice
sequences were used for primer design and
amplification was done in indica rice. The genomic
variation between the two is well documented. Only
OsZIP3b and OsZIP6c were able to detect the
polymorphism in the selected genotypes (Fig. 1) and
OsZIP6c was associated with culm Zn content (Table
3). Many of the scientific studies conducted till today
would have either stopped the experiment right here as
the there was a marker discovered to be associated
with the trait of interest or even if they have proceeded
for sequencing, would have left all those markers which
were monomorphic.
Monomorphism vs polymorphism
Main objective of the experiment was to dissect the
information which is probably hidden in the
monomorphic markers as well. Hence, along with two
polymorphic markers namely OsZIP3b and OsZIP6c
four monomorphic markers namely OsZIP4a, OsZIP5b,
OsYSL2b and OsNramp were also selected for
sequencing. These markers are those markers which
would have dropped from the further investigation.
Many nucleotide changes were recorded in five
out of six amplicons studied. In case of OsYSL2b, there
was no variation present but other 5 primers had
nucleotide changes in their amplicons. In case of
OsZIP6c, as it is polymorphic, there was huge difference
in expected (431bp) and observed product size (780bp)
in some genotypes. This was due to huge insertion of
sequences at two locations. Along with these huge
insertions G to A; T to C transitions were also observed.
For OsZIP3b major changes were deletions, A to C; G
to T or C transversions and T to C transitions. These
two were polymorphic markers.
In case of other three makers which were
monomorphic in the agarose gel, nucleotide changes
were present which was quite interesting and worth
observing. In case of OsNramp, major changes include
deletions, G to C transversion; G to A transition changes.
For OsZIP4a, most of the cases, it was G to A transitions.
There was a deletion, A or G to C; T to A or G
transversions also recorded. For OsZIP5b, changes
were diverse (Fig. 2). G to C; G to T; A to T transversions
and A to G; G to A transitions were major along with
three insertions. The results of SMA revealed that there
is an association between five nucleotide changes in
OsZIP5b and grain Zn content; and between eight
nucleotide changes in OsZIP6c and culm Zn content
(Table 4). Nucleotide changes inthree other primers for
OsZIP3b, OsNramp, OsZIP4a manifested no
association with trait in this set of genotypes used. The
nucleotide changes present in OsZIP5b and OsZIP6c
L: 100bp ladder; 1: AM-65; 2: AM-143; 3: AM-72; 4: AM-94B; 5: AM-1; 6: BPT5204/Chittimutyalu MS; 7: Vandana; 8:
Edavankudi Pokkali; 9: BJ-24(K); 10: AM-81; A: Sarabasti; B: Kallu Randaikar; C: BJ-18; D: Improved Chitti Mutyalu;
E: Karna Mahsuri; F:R 133-968-2-1; G: Kalanamak-Birdapur; H: Satabdhi; I: Nuadhusara; J: Tara; a: Azucena; b:
Moromutant
Fig. 1. Agarose gel profile of OsZIP6c and OsZIP3b
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has to be validated in other set of genotypes and can
be used as SNPs for improvement of Zn content.
Analysis of sequences of OsZIP6c revealed that
there were eight nucleotide changes associated with
Fig. 2. Multiple sequence alignment of amplicons of OsZIP5b
Table 3. Single-marker analysis of OsZIP3b and
OsZIP6c
Primer Zn content in P value R2
value
OsZIP3b Grain 0.909 0.001
Culm 0.446 0.033
Root 0.874 0.001
OsZIP6c Grain 0.323 0.054
Culm 0.001** 0.438
Root 0.247 0.074
*Significant at 5%; **Significant at 1%
Table 4. Single-marker analysis for nucleotide changes
in OsZIP3b and OsZIP6c
Primer_position Zn content in P value R2
value
OsZIP5b_144 Grain 0.020* 0.265
OsZIP5b_177 Grain 0.004** 0.381
OsZIP5b_330 Grain 0.020* 0.265
OsZIP5b_345 Grain 0.009** 0.324
OsZIP6c_217 Culm 0.006** 0.352
OsZIP6c_365 Culm 0.001** 0.438
OsZIP6c_367 Culm 0.015* 0.288
OsZIP6c_369 Culm 0.001** 0.438
OsZIP6c_380 Culm 0.007** 0.444
OsZIP6c_381 Culm 0.001** 0.438
OsZIP6c_441 Culm 0.007** 0.440
OsZIP6c_442 Culm 0.001** 0.438
*Significant at 5%; **Significant at 1%
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600 K. M. Sumantha Holla et al. [Vol. 74, No. 4, Suppl.
culm Zn content. It was polymorphic on agarose gel
and was significantly associated with culm Zn content.
There were two huge insertions between 211-364
th
position and 369-633
rd
position. These two inserts were
significantly associated with culm Zn content. The
phenotypic variance for these inserts was also high in
the range of 43.8 to 44.4%. Agarose gel polymorphism
among the four genotypes which have high culm Zn
content matched with the sequence insertion in these
four genotypes with high culm Zn content. Further,
variations at two other positions of for OsZIP6c namely,
365th
and 367th
positions, which were significantly
associated with culm Zn content, were outside the
insertions. Interestingly, these two positions were
exactly in between those two huge insertions,
suggesting that these two positions represented two new
variations identified by sequencing in addition to those
variations identified on agarose gel. Thus, sequencing
has been shown to identify more variations in the marker
which are polymorphic.
OsZIP5b manifested significant association with
grain Zn content at four different positions namely, 144th
,
177
th
, 330
th
and 345
th
. This OsZIP5b was completely
monomorphic at agarose gel. In usual case, this marker
would have dropped from the analysis thinking that there
is no scope for further improvement, as variations are
not visualized. The phenotypic variance exhibited by
nucleotide changes in OsZIP5b for grain Zn content was
also high ranging from 26.5% to 38.1%. Two positions
were highly associated with a significance of 1%, two
others were association with a significance of 5%. If at
all this marker was dropped from the experiment, there
would have been no explanation for about 26-38% of
the variation exhibited by the trait. These results also
illustrate that a single nucleotide change in the gene
can lead to significant changes in the phenotype, which
is very valuable for a breeder to improve the trait.
This clearly demonstrates that monomorphic
markers are as meaningful as polymorphic markers.
They have a lot of information hidden in them waiting to
be dissected and still arelargely being rejected by most
of the researchers across the globe. There is a need of
understanding such so called “monomorphic markers”
so as to understand some of the complex traits like Zn
accumulation as we do not have efficient markers
discovered tightly associated with the trait. With rapid
advances in technology, cost of sequencing is coming
down [12, 13]. One more strategy to reduce cost and to
get more successful results is, using bioinformatics [14].
There is also availability of large number of
bioinformatics resources which can help us in targeting
the desired genomic sequences instead of searching
all over the genome.
This study also clearly demonstrates usage of
bioinformatics resources for targeted dissecting of
complex traits and also combined use of bioinformatics
and sequencing todissect the hidden meaning in the
monomorphic markers. Days are to come where
sequencing cost is going to decrease further enabling
us to exploit this particular tool to the maximum extent
possible. “Focussed search and intelligent sequencing”
would dissect the code hidden in the markers which
would efficiently assist a breeder in combating some of
the global threats like micronutrient deficiency, drought
etc., which are lot more complicated to be solved.
Acknowledgement
Authors thankfully acknowledge the funding provided
by Department of Biotechnology, Govt. of India for Rice
Micronutrient Biofortification Phase-II to Dr H E
Shashidhar and MSSRF for providing XRF facility.
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