The cost of potato cultivation has been found 17 to 24 per cent higher under contract farming ove... more The cost of potato cultivation has been found 17 to 24 per cent higher under contract farming over various costs than under non-contract system, mainly due to high investments on seeds, fertilizers and machine power. Yield has been found 255.78 quintals per ha in the contract farms, which is 8.84 per cent higher over the potato yield obtained from the non-contract farms. Gross income has been Rs 99753 per ha in the contract farms as against Rs 41572 per ha in non-contract system. The sale price of potato has been found much higher (Rs 390/q) for contract than non-contract farms (Rs 177 /q). The net return over operational cost (cost 'A1') has been found as Rs 11882 per ha in non-contract farms, which increased more than five-times under contract farming system, it being Rs 62982 per ha. Similarly, the net return has been found five-and-a-half times more in contract than non-contract system over cost C1 (without rental value of the land). The net return over cost C2 has been ...
A field experiment was conducted during the year 2007–08 and 2008–09 to find out the most remuner... more A field experiment was conducted during the year 2007–08 and 2008–09 to find out the most remunerative winter vegetables grown as intercrops with autumn planted sugarcane. Six treatments formulated with intercropping i.e. sugarcane sole, sugarcane+ radish, sugarcane+ onion, sugarcane+ fenugreek, sugarcane+ Frenchbean and sugarcane+ potato in randomized block design. Based on the two years study, onion intercropping was selected as most remunerative in autumn cane with the highest cane equivalent yield (147.9 t/ha) and net return (Rs. 192340) among all the intercropping systems. Sugarcane + potato intercropping was also found comparable with sugarcane+onion produced cane equivalent yield of 147.0 t/ha and net return (Rs. 188680/ha). Whereas, lowest cane equivalent yield and net return recorded under sugarcane+ fenugreek intercropping system among the vegetables.
The study identified 9045 high-quality SNPs employing both genome-wide GBS-and candidate gene-bas... more The study identified 9045 high-quality SNPs employing both genome-wide GBS-and candidate gene-based SNP genotyping assays in 172, including 93 cultivated (desi and kabuli) and 79 wild chickpea accessions. The GWAS in a structured population of 93 sequenced accessions detected 15 major genomic loci exhibiting significant association with seed coat color. Five seed color-associated major genomic loci underlying robust QTLs mapped on a high-density intra-specific genetic linkage map were validated by QTL mapping. The integration of association and QTL mapping with gene haplotype-specific LD mapping and transcript profiling identified novel allelic variants (non-synonymous SNPs) and haplotypes in a MATE secondary transporter gene regulating light/yellow brown and beige seed coat color differentiation in chickpea. The down-regulation and decreased transcript expression of beige seed coat color-associated MATE gene haplotype was correlated with reduced proanthocyanidins accumulation in the mature seed coats of beige than light/yellow brown seed colored desi and kabuli accessions for their coloration/pigmentation. This seed color-regulating MATE gene revealed strong purifying selection pressure primarily in LB/YB seed colored desi and wild Cicer reticulatum accessions compared with the BE seed colored kabuli accessions. The functionally relevant molecular tags identified have potential to decipher the complex transcriptional regulatory gene function of seed coat coloration and for understanding the selective sweep-based seed color trait evolutionary pattern in cultivated and wild accessions during chickpea domestication. The genome-wide integrated approach employed will expedite marker-assisted genetic enhancement for developing cultivars with desirable seed coat color types in chickpea.
DNA research : an international journal for rapid publication of reports on genes and genomes, Jan 17, 2015
We developed 21,499 genome-wide insertion-deletion (InDel) markers (2- to 54-bp in silico fragmen... more We developed 21,499 genome-wide insertion-deletion (InDel) markers (2- to 54-bp in silico fragment length polymorphism) by comparing the genomic sequences of four (desi, kabuli and wild C. reticulatum) chickpea [Cicer arietinum (L.)] accessions. InDel markers showing 2- to 6-bp fragment length polymorphism among accessions were abundant (76.8%) in the chickpea genome. The physically mapped 7,643 and 13,856 markers on eight chromosomes and unanchored scaffolds, respectively, were structurally and functionally annotated. The 4,506 coding (23% large-effect frameshift mutations) and regulatory InDel markers were identified from 3,228 genes (representing 11.7% of total 27,571 desi genes), suggesting their functional relevance for trait association/genetic mapping. High amplification (97%) and intra-specific polymorphic (60-83%) potential and wider genetic diversity (15-89%) were detected by genome-wide 6,254 InDel markers among desi, kabuli and wild accessions using even a simpler cost-e...
Grain legumes are the primary sources of oil, fiber, and protein-rich food and feed. Crops adapta... more Grain legumes are the primary sources of oil, fiber, and protein-rich food and feed. Crops adaptation to climate change is one of the major challenges to scientific community in the 21st century. Grain legumes have narrow genetic base due to bottlenecks associated with domestication. Genes for desirable traits are embedded in biodiversity. ICRISAT genebank holds 49,819 accessions of its mandate grain legumes. Core/mini core collections have been suggested as resource to discover new sources of variations for enhanced use of germplasm in crop breeding. Using mini core approach trait-specific genetically diverse germplasm for resistance to drought, salinity, water logging, heat stress, pest, diseases, herbicide, and for agronomic and nutritional traits have been identified. The evidence to date suggests increased use of germplasm in legumes breeding at ICRISAT since formation of mini core collections. The crops have moved from orphan to genomic resources rich crops. The chickpea and p...
We identified 44844 high-quality SNPs by sequencing 92 diverse chickpea accessions belonging to a... more We identified 44844 high-quality SNPs by sequencing 92 diverse chickpea accessions belonging to a seed and pod trait-specific association panel using reference genome-and de novo-based GBS (genotyping-by-sequencing) assays. A GWAS (genome-wide association study) in an association panel of 211, including the 92 sequenced accessions, identified 22 major genomic loci showing significant association (explaining 23-47% phenotypic variation) with pod and seed number/plant and 100-seed weight. Eighteen trait-regulatory major genomic loci underlying 13 robust QTLs were validated and mapped on an intra-specific genetic linkage map by QTL mapping. A combinatorial approach of GWAS, QTL mapping and gene haplotype-specific LD mapping and transcript profiling uncovered one superior haplotype and favourable natural allelic variants in the upstream regulatory region of a CesA-type cellulose synthase (Ca_Kabuli_CesA3) gene regulating high pod and seed number/ plant (explaining 47% phenotypic variation) in chickpea. The up-regulation of this superior gene haplotype correlated with increased transcript expression of Ca_Kabuli_CesA3 gene in the pollen and pod of high pod/seed number accession, resulting in higher cellulose accumulation for normal pollen and pollen tube growth. A rapid combinatorial genome-wide SNP genotyping-based approach has potential to dissect complex quantitative agronomic traits and delineate trait-regulatory genomic loci (candidate genes) for genetic enhancement in crop plants, including chickpea. Chickpea (Cicer arietinum L.), a member of family Fabaceae is an annual, diploid, self-pollinated crop species with a very small genome size of ~740 Mbp. It is the most cultivated food legume/pulse crop worldwide that serves as an important dietary source of protein with essential amino acids for human. The seed and pod characters are major yield contributing traits of chickpea and vary widely across global germplasm collections, landraces and cultivated desi and kabuli accessions. Considering the agronomic importance of seed and pod traits, multiple efforts have been made for molecular mapping of quantitative trait loci (QTLs) governing major seed and pod yield contributing traits, including seed and pod number, double podding and seed weight in chickpea 1-31. Unfortunately, due to lack of requisite intra-specific polymorphism in chickpea, no such robust genes/QTLs associated with seed and pod traits have been identified/fine mapped hitherto, which can be utilized for marker-assisted genetic
Foxtail millet (Setaria italica (L.) P. Beauv.) is an ideal crop for changing climates and stress... more Foxtail millet (Setaria italica (L.) P. Beauv.) is an ideal crop for changing climates and stressed environments due to its short duration, high photosynthetic efficiency and good level of resistance to pest and diseases. Soil salinisation is an increasing problem, with 23% of the global cultivated land already affected. Foxtail millet has potential as a crop for salt-affected soils, with its high tolerance to salinity. The foxtail millet core collection (n = 155) was screened in a soil saturated once with 100 mm NaCl and in a non-saline control in 2008 and a subset (n = 84) in 2009 in a partly controlled environment using Alfisol to identify the best salt-tolerant germplasm. Plants were grown in pots and protected from rain. The salinity response was measured as grain yield per pot. Genotype and salinity × genotype interaction effects were significant for most traits, and there was a large range of yield and biomass variation across accessions. Salinity delayed panicle emergence an...
We discovered 26785 and 16573 high-quality SNPs differentiating two parental genotypes of a RIL m... more We discovered 26785 and 16573 high-quality SNPs differentiating two parental genotypes of a RIL mapping population using reference desi and kabuli genome-based GBS assay. Of these, 3625 and 2177 SNPs have been integrated into eight desi and kabuli chromosomes, respectively in order to construct ultra-high density (0.20-0.37 cM) intra-specific chickpea genetic linkage maps. One of these constructed high-resolution genetic map has potential to identify 33 major genomic regions harbouring 35 robust QTLs (PVE: 17.9-39.7%) associated with three agronomic traits, which were mapped within <1 cM mean marker intervals on desi chromosomes. The extended LD (linkage disequilibrium) decay (~15 cM) in chromosomes of genetic maps have encouraged us to use a rapid integrated approach (comparative QTL mapping, QTL-region specific haplotype/LD-based trait association analysis, expression profiling and gene haplotype-based association mapping) rather than a traditional QTL map-based cloning method ...
A rapid high-resolution genome-wide strategy for molecular mapping of major QTL(s)/gene(s) regula... more A rapid high-resolution genome-wide strategy for molecular mapping of major QTL(s)/gene(s) regulating important agronomic traits is vital for in-depth dissection of complex quantitative traits and genetic enhancement in chickpea. The present study for the first time employed a NGS-based whole-genome QTL-seq strategy to identify one major genomic region harbouring a robust 100-seed weight QTL using an intra-specific 221 chickpea mapping population (desi cv. ICC 7184 × desi cv. ICC 15061). The QTL-seq-derived major SW QTL (CaqSW1.1) was further validated by single-nucleotide polymorphism (SNP) and simple sequence repeat (SSR) marker-based traditional QTL mapping (47.6% R 2 at higher LOD >19). This reflects the reliability and efficacy of QTL-seq as a strategy for rapid genome-wide scanning and fine mapping of major trait regulatory QTLs in chickpea. The use of QTL-seq and classical QTL mapping in combination narrowed down the 1.37 Mb (comprising 177 genes) major SW QTL (CaqSW1.1) region into a 35 kb genomic interval on desi chickpea chromosome 1 containing six genes. One coding SNP (G/A)-carrying constitutive photomorphogenic9 (COP9) signalosome complex subunit 8 (CSN8) gene of these exhibited seed-specific expression, including pronounced differential up-/down-regulation in low and high seed weight mapping parents and homozygous individuals during seed development. The coding SNP mined in this potential seed weight-governing candidate CSN8 gene was found to be present exclusively in all cultivated species/ genotypes, but not in any wild species/genotypes of primary, secondary and tertiary gene pools. This indicates the effect of strong artificial and/or natural selection pressure on target SW locus during chickpea domestication. The proposed QTL-seq-driven integrated genome-wide strategy has potential to delineate major candidate gene(s) harbouring a robust trait regulatory QTL rapidly with optimal use of resources. This will further assist us to extrapolate the molecular mechanism underlying complex quantitative traits at a genome-wide scale leading to fast-paced marker-assisted genetic improvement in diverse crop plants, including chickpea.
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 1981
Two experiments, each including the same 30 homozygous varieties of spring wheat plus one separat... more Two experiments, each including the same 30 homozygous varieties of spring wheat plus one separate tester variety, were conducted in order to detect epistasis and to test and estimate the additive and dominance components of genetic variation for five quantitative traits: final plant height, spike length, number of spikelets per spike, 100-kernel weight and grain yield per plant. Epistasis played a significant role in the control of 100-kernel weight and yield per plant. There was a gratifyingly good agreement between the two independent methods (2¯B1i - ¯f1i - ¯Pi and 2¯Bci - ¯F1i) used to test the presence of epistasis. In both experiments, there was a remarkably uniform high dominance ratio for most of the traits studied indicating that this test cross design is equally sensitive to both additive and dominance genetic variation.
Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic di... more Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea.
High experimental validation/genotyping success rate (94-96%) and intra-specific polymorphic pote... more High experimental validation/genotyping success rate (94-96%) and intra-specific polymorphic potential (82-96%) of 1536 SNP and 472 SSR markers showing in silico polymorphism between desi ICC 4958 and kabuli ICC 12968 chickpea was obtained in a 190 mapping population (ICC 4958 × ICC 12968) and 92 diverse desi and kabuli genotypes. A high-density 2001 marker-based intra-specific genetic linkage map comprising of eight LGs constructed is comparatively much saturated (mean map-density: 0.94 cM) in contrast to existing intra-specific genetic maps in chickpea. Fifteen robust QTLs (PVE: 8.8-25.8% with LOD: 7.0-13.8) associated with pod and seed number/plant (PN and SN) and 100 seed weight (SW) were identified and mapped on 10 major genomic regions of eight LGs. One of 126.8 kb major genomic region harbouring a strong SW-associated robust QTL (Caq'SW1.1: 169.1-171.3 cM) has been delineated by integrating high-resolution QTL mapping with comprehensive marker-based comparative genome map...
Finger millet (Eleusine coracana L. Gaertn.) ranks third in production among the dry land cereals... more Finger millet (Eleusine coracana L. Gaertn.) ranks third in production among the dry land cereals. It is widely cultivated in Africa and South Asia where soil salinization is a major production constraint. It is a potential crop for salt affected soils. To identify salt tolerant germplasm, the minicore finger millet germplasm (n = 80) was screened for grain yield performance in a soil saturated with NaCl solution of 100 or 125 mM. Genotype effect was significant for most traits, while salinity × genotype interaction was significant only in one year. Salinity delayed phenology, marginally reduced shoot biomass and grain yield. There was a large range of genotypic variation in grain yield under salinity and other traits. The yield loss was higher in accessions with prolific growth and yield potential was associated with saline yields. Based on saline yields, accessions were grouped in to four groups and the top tolerant group had 22 accessions with IE 4797 remaining at the top. Salinity had no adverse impact on grain yield of five accessions. Root anatomy in selected genotype of pearl and finger millet showed presence of porous cortex and well fortified endodermis in finger millet that can exclude Na + and enhance N absorption.
Groundnut (Arachis hypogaea L.) is an important oilseed crop cultivated in 96 countries of world.... more Groundnut (Arachis hypogaea L.) is an important oilseed crop cultivated in 96 countries of world.World crop productivity (1.30 t ha-1) is low. The available large variability contained in the germplasm accessions has not been adequately utilized in the crop improvement programs and most groundnut cultivars stand on a very narrow genetic base. This is due to lack of information on
The heat conduction equation has been solved for evaluation of thermal conductivity of soil by ov... more The heat conduction equation has been solved for evaluation of thermal conductivity of soil by overspecifying the usual boundary conditions in terms of heat flux at the boundary surface. For the determination of thermal conductivity, heat flux needs to be measured at any one time instant ‘t0’ and the variation of the boundary temperature with time. With the knowledge of the heat capacity of soil, thermal conductivity value is explicitly obtained.
The cost of potato cultivation has been found 17 to 24 per cent higher under contract farming ove... more The cost of potato cultivation has been found 17 to 24 per cent higher under contract farming over various costs than under non-contract system, mainly due to high investments on seeds, fertilizers and machine power. Yield has been found 255.78 quintals per ha in the contract farms, which is 8.84 per cent higher over the potato yield obtained from the non-contract farms. Gross income has been Rs 99753 per ha in the contract farms as against Rs 41572 per ha in non-contract system. The sale price of potato has been found much higher (Rs 390/q) for contract than non-contract farms (Rs 177 /q). The net return over operational cost (cost 'A1') has been found as Rs 11882 per ha in non-contract farms, which increased more than five-times under contract farming system, it being Rs 62982 per ha. Similarly, the net return has been found five-and-a-half times more in contract than non-contract system over cost C1 (without rental value of the land). The net return over cost C2 has been ...
A field experiment was conducted during the year 2007–08 and 2008–09 to find out the most remuner... more A field experiment was conducted during the year 2007–08 and 2008–09 to find out the most remunerative winter vegetables grown as intercrops with autumn planted sugarcane. Six treatments formulated with intercropping i.e. sugarcane sole, sugarcane+ radish, sugarcane+ onion, sugarcane+ fenugreek, sugarcane+ Frenchbean and sugarcane+ potato in randomized block design. Based on the two years study, onion intercropping was selected as most remunerative in autumn cane with the highest cane equivalent yield (147.9 t/ha) and net return (Rs. 192340) among all the intercropping systems. Sugarcane + potato intercropping was also found comparable with sugarcane+onion produced cane equivalent yield of 147.0 t/ha and net return (Rs. 188680/ha). Whereas, lowest cane equivalent yield and net return recorded under sugarcane+ fenugreek intercropping system among the vegetables.
The study identified 9045 high-quality SNPs employing both genome-wide GBS-and candidate gene-bas... more The study identified 9045 high-quality SNPs employing both genome-wide GBS-and candidate gene-based SNP genotyping assays in 172, including 93 cultivated (desi and kabuli) and 79 wild chickpea accessions. The GWAS in a structured population of 93 sequenced accessions detected 15 major genomic loci exhibiting significant association with seed coat color. Five seed color-associated major genomic loci underlying robust QTLs mapped on a high-density intra-specific genetic linkage map were validated by QTL mapping. The integration of association and QTL mapping with gene haplotype-specific LD mapping and transcript profiling identified novel allelic variants (non-synonymous SNPs) and haplotypes in a MATE secondary transporter gene regulating light/yellow brown and beige seed coat color differentiation in chickpea. The down-regulation and decreased transcript expression of beige seed coat color-associated MATE gene haplotype was correlated with reduced proanthocyanidins accumulation in the mature seed coats of beige than light/yellow brown seed colored desi and kabuli accessions for their coloration/pigmentation. This seed color-regulating MATE gene revealed strong purifying selection pressure primarily in LB/YB seed colored desi and wild Cicer reticulatum accessions compared with the BE seed colored kabuli accessions. The functionally relevant molecular tags identified have potential to decipher the complex transcriptional regulatory gene function of seed coat coloration and for understanding the selective sweep-based seed color trait evolutionary pattern in cultivated and wild accessions during chickpea domestication. The genome-wide integrated approach employed will expedite marker-assisted genetic enhancement for developing cultivars with desirable seed coat color types in chickpea.
DNA research : an international journal for rapid publication of reports on genes and genomes, Jan 17, 2015
We developed 21,499 genome-wide insertion-deletion (InDel) markers (2- to 54-bp in silico fragmen... more We developed 21,499 genome-wide insertion-deletion (InDel) markers (2- to 54-bp in silico fragment length polymorphism) by comparing the genomic sequences of four (desi, kabuli and wild C. reticulatum) chickpea [Cicer arietinum (L.)] accessions. InDel markers showing 2- to 6-bp fragment length polymorphism among accessions were abundant (76.8%) in the chickpea genome. The physically mapped 7,643 and 13,856 markers on eight chromosomes and unanchored scaffolds, respectively, were structurally and functionally annotated. The 4,506 coding (23% large-effect frameshift mutations) and regulatory InDel markers were identified from 3,228 genes (representing 11.7% of total 27,571 desi genes), suggesting their functional relevance for trait association/genetic mapping. High amplification (97%) and intra-specific polymorphic (60-83%) potential and wider genetic diversity (15-89%) were detected by genome-wide 6,254 InDel markers among desi, kabuli and wild accessions using even a simpler cost-e...
Grain legumes are the primary sources of oil, fiber, and protein-rich food and feed. Crops adapta... more Grain legumes are the primary sources of oil, fiber, and protein-rich food and feed. Crops adaptation to climate change is one of the major challenges to scientific community in the 21st century. Grain legumes have narrow genetic base due to bottlenecks associated with domestication. Genes for desirable traits are embedded in biodiversity. ICRISAT genebank holds 49,819 accessions of its mandate grain legumes. Core/mini core collections have been suggested as resource to discover new sources of variations for enhanced use of germplasm in crop breeding. Using mini core approach trait-specific genetically diverse germplasm for resistance to drought, salinity, water logging, heat stress, pest, diseases, herbicide, and for agronomic and nutritional traits have been identified. The evidence to date suggests increased use of germplasm in legumes breeding at ICRISAT since formation of mini core collections. The crops have moved from orphan to genomic resources rich crops. The chickpea and p...
We identified 44844 high-quality SNPs by sequencing 92 diverse chickpea accessions belonging to a... more We identified 44844 high-quality SNPs by sequencing 92 diverse chickpea accessions belonging to a seed and pod trait-specific association panel using reference genome-and de novo-based GBS (genotyping-by-sequencing) assays. A GWAS (genome-wide association study) in an association panel of 211, including the 92 sequenced accessions, identified 22 major genomic loci showing significant association (explaining 23-47% phenotypic variation) with pod and seed number/plant and 100-seed weight. Eighteen trait-regulatory major genomic loci underlying 13 robust QTLs were validated and mapped on an intra-specific genetic linkage map by QTL mapping. A combinatorial approach of GWAS, QTL mapping and gene haplotype-specific LD mapping and transcript profiling uncovered one superior haplotype and favourable natural allelic variants in the upstream regulatory region of a CesA-type cellulose synthase (Ca_Kabuli_CesA3) gene regulating high pod and seed number/ plant (explaining 47% phenotypic variation) in chickpea. The up-regulation of this superior gene haplotype correlated with increased transcript expression of Ca_Kabuli_CesA3 gene in the pollen and pod of high pod/seed number accession, resulting in higher cellulose accumulation for normal pollen and pollen tube growth. A rapid combinatorial genome-wide SNP genotyping-based approach has potential to dissect complex quantitative agronomic traits and delineate trait-regulatory genomic loci (candidate genes) for genetic enhancement in crop plants, including chickpea. Chickpea (Cicer arietinum L.), a member of family Fabaceae is an annual, diploid, self-pollinated crop species with a very small genome size of ~740 Mbp. It is the most cultivated food legume/pulse crop worldwide that serves as an important dietary source of protein with essential amino acids for human. The seed and pod characters are major yield contributing traits of chickpea and vary widely across global germplasm collections, landraces and cultivated desi and kabuli accessions. Considering the agronomic importance of seed and pod traits, multiple efforts have been made for molecular mapping of quantitative trait loci (QTLs) governing major seed and pod yield contributing traits, including seed and pod number, double podding and seed weight in chickpea 1-31. Unfortunately, due to lack of requisite intra-specific polymorphism in chickpea, no such robust genes/QTLs associated with seed and pod traits have been identified/fine mapped hitherto, which can be utilized for marker-assisted genetic
Foxtail millet (Setaria italica (L.) P. Beauv.) is an ideal crop for changing climates and stress... more Foxtail millet (Setaria italica (L.) P. Beauv.) is an ideal crop for changing climates and stressed environments due to its short duration, high photosynthetic efficiency and good level of resistance to pest and diseases. Soil salinisation is an increasing problem, with 23% of the global cultivated land already affected. Foxtail millet has potential as a crop for salt-affected soils, with its high tolerance to salinity. The foxtail millet core collection (n = 155) was screened in a soil saturated once with 100 mm NaCl and in a non-saline control in 2008 and a subset (n = 84) in 2009 in a partly controlled environment using Alfisol to identify the best salt-tolerant germplasm. Plants were grown in pots and protected from rain. The salinity response was measured as grain yield per pot. Genotype and salinity × genotype interaction effects were significant for most traits, and there was a large range of yield and biomass variation across accessions. Salinity delayed panicle emergence an...
We discovered 26785 and 16573 high-quality SNPs differentiating two parental genotypes of a RIL m... more We discovered 26785 and 16573 high-quality SNPs differentiating two parental genotypes of a RIL mapping population using reference desi and kabuli genome-based GBS assay. Of these, 3625 and 2177 SNPs have been integrated into eight desi and kabuli chromosomes, respectively in order to construct ultra-high density (0.20-0.37 cM) intra-specific chickpea genetic linkage maps. One of these constructed high-resolution genetic map has potential to identify 33 major genomic regions harbouring 35 robust QTLs (PVE: 17.9-39.7%) associated with three agronomic traits, which were mapped within <1 cM mean marker intervals on desi chromosomes. The extended LD (linkage disequilibrium) decay (~15 cM) in chromosomes of genetic maps have encouraged us to use a rapid integrated approach (comparative QTL mapping, QTL-region specific haplotype/LD-based trait association analysis, expression profiling and gene haplotype-based association mapping) rather than a traditional QTL map-based cloning method ...
A rapid high-resolution genome-wide strategy for molecular mapping of major QTL(s)/gene(s) regula... more A rapid high-resolution genome-wide strategy for molecular mapping of major QTL(s)/gene(s) regulating important agronomic traits is vital for in-depth dissection of complex quantitative traits and genetic enhancement in chickpea. The present study for the first time employed a NGS-based whole-genome QTL-seq strategy to identify one major genomic region harbouring a robust 100-seed weight QTL using an intra-specific 221 chickpea mapping population (desi cv. ICC 7184 × desi cv. ICC 15061). The QTL-seq-derived major SW QTL (CaqSW1.1) was further validated by single-nucleotide polymorphism (SNP) and simple sequence repeat (SSR) marker-based traditional QTL mapping (47.6% R 2 at higher LOD >19). This reflects the reliability and efficacy of QTL-seq as a strategy for rapid genome-wide scanning and fine mapping of major trait regulatory QTLs in chickpea. The use of QTL-seq and classical QTL mapping in combination narrowed down the 1.37 Mb (comprising 177 genes) major SW QTL (CaqSW1.1) region into a 35 kb genomic interval on desi chickpea chromosome 1 containing six genes. One coding SNP (G/A)-carrying constitutive photomorphogenic9 (COP9) signalosome complex subunit 8 (CSN8) gene of these exhibited seed-specific expression, including pronounced differential up-/down-regulation in low and high seed weight mapping parents and homozygous individuals during seed development. The coding SNP mined in this potential seed weight-governing candidate CSN8 gene was found to be present exclusively in all cultivated species/ genotypes, but not in any wild species/genotypes of primary, secondary and tertiary gene pools. This indicates the effect of strong artificial and/or natural selection pressure on target SW locus during chickpea domestication. The proposed QTL-seq-driven integrated genome-wide strategy has potential to delineate major candidate gene(s) harbouring a robust trait regulatory QTL rapidly with optimal use of resources. This will further assist us to extrapolate the molecular mechanism underlying complex quantitative traits at a genome-wide scale leading to fast-paced marker-assisted genetic improvement in diverse crop plants, including chickpea.
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 1981
Two experiments, each including the same 30 homozygous varieties of spring wheat plus one separat... more Two experiments, each including the same 30 homozygous varieties of spring wheat plus one separate tester variety, were conducted in order to detect epistasis and to test and estimate the additive and dominance components of genetic variation for five quantitative traits: final plant height, spike length, number of spikelets per spike, 100-kernel weight and grain yield per plant. Epistasis played a significant role in the control of 100-kernel weight and yield per plant. There was a gratifyingly good agreement between the two independent methods (2¯B1i - ¯f1i - ¯Pi and 2¯Bci - ¯F1i) used to test the presence of epistasis. In both experiments, there was a remarkably uniform high dominance ratio for most of the traits studied indicating that this test cross design is equally sensitive to both additive and dominance genetic variation.
Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic di... more Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea.
High experimental validation/genotyping success rate (94-96%) and intra-specific polymorphic pote... more High experimental validation/genotyping success rate (94-96%) and intra-specific polymorphic potential (82-96%) of 1536 SNP and 472 SSR markers showing in silico polymorphism between desi ICC 4958 and kabuli ICC 12968 chickpea was obtained in a 190 mapping population (ICC 4958 × ICC 12968) and 92 diverse desi and kabuli genotypes. A high-density 2001 marker-based intra-specific genetic linkage map comprising of eight LGs constructed is comparatively much saturated (mean map-density: 0.94 cM) in contrast to existing intra-specific genetic maps in chickpea. Fifteen robust QTLs (PVE: 8.8-25.8% with LOD: 7.0-13.8) associated with pod and seed number/plant (PN and SN) and 100 seed weight (SW) were identified and mapped on 10 major genomic regions of eight LGs. One of 126.8 kb major genomic region harbouring a strong SW-associated robust QTL (Caq'SW1.1: 169.1-171.3 cM) has been delineated by integrating high-resolution QTL mapping with comprehensive marker-based comparative genome map...
Finger millet (Eleusine coracana L. Gaertn.) ranks third in production among the dry land cereals... more Finger millet (Eleusine coracana L. Gaertn.) ranks third in production among the dry land cereals. It is widely cultivated in Africa and South Asia where soil salinization is a major production constraint. It is a potential crop for salt affected soils. To identify salt tolerant germplasm, the minicore finger millet germplasm (n = 80) was screened for grain yield performance in a soil saturated with NaCl solution of 100 or 125 mM. Genotype effect was significant for most traits, while salinity × genotype interaction was significant only in one year. Salinity delayed phenology, marginally reduced shoot biomass and grain yield. There was a large range of genotypic variation in grain yield under salinity and other traits. The yield loss was higher in accessions with prolific growth and yield potential was associated with saline yields. Based on saline yields, accessions were grouped in to four groups and the top tolerant group had 22 accessions with IE 4797 remaining at the top. Salinity had no adverse impact on grain yield of five accessions. Root anatomy in selected genotype of pearl and finger millet showed presence of porous cortex and well fortified endodermis in finger millet that can exclude Na + and enhance N absorption.
Groundnut (Arachis hypogaea L.) is an important oilseed crop cultivated in 96 countries of world.... more Groundnut (Arachis hypogaea L.) is an important oilseed crop cultivated in 96 countries of world.World crop productivity (1.30 t ha-1) is low. The available large variability contained in the germplasm accessions has not been adequately utilized in the crop improvement programs and most groundnut cultivars stand on a very narrow genetic base. This is due to lack of information on
The heat conduction equation has been solved for evaluation of thermal conductivity of soil by ov... more The heat conduction equation has been solved for evaluation of thermal conductivity of soil by overspecifying the usual boundary conditions in terms of heat flux at the boundary surface. For the determination of thermal conductivity, heat flux needs to be measured at any one time instant ‘t0’ and the variation of the boundary temperature with time. With the knowledge of the heat capacity of soil, thermal conductivity value is explicitly obtained.
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Papers by Dr. Sube Singh