Browsing by Author "Ramchiary, Nirala"

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    Genome-wide association study (GWAS) delineates genomic loci for ten nutritional elements in foxtail millet (Setaria italica L.)
    (Elsevier B.V., 2019) Jaiswal, Vandana; Bandyopadhyay, Tirthankar; Gahlaut, Vijay; Gupta, Sarika; Dhaka, Annvi; Ramchiary, Nirala; Prasad, Manoj
    Nutritional deficiency is found to be a major threat to human health, especially in low-income countries. Thus it is essential to improve nutritional qualities of important food crops. Foxtail millet is second largest cultivated millet and 2–5 times nutritionally richer than major cereal crops. During the present study, we identified genetic determinants of ten nutritional elements including potassium, nickel, calcium, boron, magnesium, phosphorus, sulphur, zinc, manganese and iron for the first time in foxtail millet. For this purpose, genome-wide association studies (GWAS) were conducted using 93 diverse accessions and 10 K SNPs (distributed across all the nine foxtail millet chromosomes). Altogether, 74 marker-trait associations (MTAs) were identified to be associated with above mentioned ten elements, out of which ten (10) MTAs (associated with B, Mg, Zn and Fe) showed high confidence [-log(p) > 5.78]. Identified desirable SNP alleles and favourable haplotypes may prove useful in foxtail breeding. Also, significant pyramiding effect suggested that associated elements can be substantially enhanced through combining more than one MTA. Candidate genes residing within or near the association signal may be selected for functional characterization. Superior genotypes identified may prove as a potential donor in foxtail millet breeding assisted through the molecular marker.
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    Genome-wide association study of major agronomic traits in foxtail millet (Setaria italica L.) using ddRAD sequencing
    (Springer Nature, 2019) Jaiswal, Vandana; Gupta, Sarika; Gahlaut, Vijay; Muthamilarasan, Mehanathan; Bandyopadhyay, Tirthankar; Ramchiary, Nirala; Prasad, Manoj
    Foxtail millet (Setaria italica), the second largest cultivated millet crop after pearl millet, is utilized for food and forage globally. Further, it is also considered as a model crop for studying agronomic, nutritional and biofuel traits. In the present study, a genome-wide association study (GWAS) was performed for ten important agronomic traits in 142 foxtail millet core eco-geographically diverse genotypes using 10 K SNPs developed through GBS-ddRAD approach. Number of SNPs on individual chromosome ranged from 844 (chromosome 5) to 2153 (chromosome 8) with an average SNP frequency of 25.9 per Mb. The pairwise linkage disequilibrium (LD) estimated using the squared-allele frequency correlations was found to decay rapidly with the genetic distance of 177 Kb. However, for individual chromosome, LD decay distance ranged from 76 Kb (chromosome 6) to 357 Kb (chromosome 4). GWAS identified 81 MTAs (marker-trait associations) for ten traits across the genome. High confidence MTAs for three important agronomic traits including FLW (flag leaf width), GY (grain yield) and TGW (thousand-grain weight) were identified. Significant pyramiding effect of identified MTAs further supplemented its importance in breeding programs. Desirable alleles and superior genotypes identified in the present study may prove valuable for foxtail millet improvement through marker-assisted selection.