Abstract
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.
Highlights
Advancements in technologies like next-generation sequencing (NGS), genotyping-by-sequencing (GBS) and SNP chips further improve the utility of genome-wide association study (GWAS) through the development of high-density genotyping data
Similar variability was observed in other traits including plant height (PH; mean ± SD; 138.4 ± 19.6), tiller number (TN; mean ± SD; 4.3 ± 1.2), flag leaf length (FLL; mean ± SD; 31.4 ± 6.0), flag leaf width (FLW; mean ± SD; 1.8 ± 0.4), peduncle length (PedL; mean ± SD; 19.0 ± 4.4); panicle length (PanL; mean ± SD; 14.6 ± 3.7), tiller maturity (TM; mean ± SD; 87.8 ± 8.0), grain yield (GY; mean ± SD; 12.8 ± 7.8) and thousand grain weight (TGW; mean ± SD; 2.9 ± 0.6)
TGW and GY were negatively correlated to the maximum extent (r2 = −0.716)
Summary
Advancements in technologies like next-generation sequencing (NGS), genotyping-by-sequencing (GBS) and SNP chips further improve the utility of GWAS through the development of high-density genotyping data. To deal with false positives due to population structure and multiple testing in GWAS, statistical tools are being continually developed[27]. High-quality SNPs distributed throughout the foxtail millet genome were mined using Double Digest Restriction Associated DNA (ddRAD) sequencing of 142genotypes. GWAS was performed for ten agronomic traits using 10367 SNPs through FarmCPU approach. Superior alleles and genotypes identified in the present study stand to significantly facilitate the improvement of foxtail millet as a viable and efficient climate resilient crop through marker-assisted selection and other useful crop improvement programmes in the future
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