Genome-Wide Association Study of Major Agronomic Traits in Foxtail Millet (Setaria italica L.) Using ddRAD Sequencing

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.

Figure 1

Single nucleotide polymorphism (SNP) density on nine foxtail millet chromosomes. The x-axis shows the interval distance in Mb. Window size to calculate SNP density 100 Kb.

Figure 2

Genome-wide linkage disequilibrium (LD) decay plots. x-axis represents distance (base) between SNPs and y-axis represents LD value (r²; 0.0, 0.2, 0.4, 0.6, 0.8, 1.0). Horizontal and vertical lines represent half LD and LD decay distance respectively.

Figure 3

Manhattan plots and quantile-quantile (Q-Q) plots (A and J) of the GWAS results for following 10 traits including Days to flowering (DOF), plant height (PH), tiller number (TN), flag leaf length (FLL), flag leaf width (FLW), peduncle length (PedL), panicle length (PanL), tiller maturity (TM), grain yield (GY), and 1000 grain weight (TGW), respectively. Significant MTA threshold [−log 10 (p) < 10⁻⁰³] and Bonferroni threshold are represented by dash (red) and continuous (grey) lines, respectively. x-axis represents chromosomes.

Figure 4

Linear regression analysis for phenotype (dependent variable) and number of desirable SNP alleles (independent variable). R² = regression coefficient; ***represents 0.0001 level of significance. x-axis represents number of desirable SNP alleles and y-axis represents phenotypic values.