Genomic consequences of selection and genome-wide association mapping in soybean

Abstract

Background: Crop improvement always involves selection of specific alleles at genes controlling traits of agronomic importance, likely resulting in detectable signatures of selection within the genome of modern soybean (Glycine max L. Merr.). The identification of these signatures of selection is meaningful from the perspective of evolutionary biology and for uncovering the genetic architecture of agronomic traits.

Results: To this end, two populations of soybean, consisting of 342 landraces and 1062 improved lines, were genotyped with the SoySNP50K Illumina BeadChip containing 52,041 single nucleotide polymorphisms (SNPs), and systematically phenotyped for 9 agronomic traits. A cross-population composite likelihood ratio (XP-CLR) method was used to screen the signals of selective sweeps. A total of 125 candidate selection regions were identified, many of which harbored genes potentially involved in crop improvement. To further investigate whether these candidate regions were in fact enriched for genes affected by selection, genome-wide association studies (GWAS) were conducted on 7 selection traits targeted in soybean breeding (grain yield, plant height, lodging, maturity date, seed coat color, seed protein and oil content) and 2 non-selection traits (pubescence and flower color). Major genomic regions associated with selection traits overlapped with candidate selection regions, whereas no overlap of this kind occurred for the non-selection traits, suggesting that the selection sweeps identified are associated with traits of agronomic importance. Multiple novel loci and refined map locations of known loci related to these traits were also identified.

Conclusions: These findings illustrate that comparative genomic analyses, especially when combined with GWAS, are a promising approach to dissect the genetic architecture of complex traits.

Fig. 1

Genetic divergence of soybean landraces and improved lines. a NJ tree of all soybean accessions tested in this study. Accessions in the neighbor-joining tree are represented by different colors: landraces (blue) and improved lines (red). b Comparison of minor allele frequencies (MAF) between landraces (blue) and improved lines (red). c Genome-wide average LD decay estimated from landraces (blue) and improved lines (red)

Fig. 2

Population structures of soybean landraces and improved lines. a PCA plots of the first two components of 342 accessions of soybean landraces. b NJ tree of soybean landraces. The 6 subgroups identified from the tree are color-coded in a and b. c PCA plots of the first two components of 1062 accessions of improved lines. d NJ tree of improved lines. The 8 subgroups identified from the NJ tree are color-coded in c and d

Fig. 3

Genome-wide visualization of selection during soybean improvement. Each dot represents a non-overlapping window of 20 kb with cross-population composite likelihood ratio (XP-CLR) values indicated along the y axis and physical position indicated along the x axis

Fig. 4

Contributions of identified loci to phenotypic variance (R²) of 9 traits and the corresponding XP-CLR value

Fig. 5

The visualization of the GWAS results and selection signals for selection trait (seed coat color). a Manhattan plots of MLM for seed coat color. The − log10 P-values from a genome-wide scan are plotted against the position on each of the 20 chromosomes. The horizontal red line indicates the genome-wide significance threshold (FDR < 0.05). b Gene diversity (H _i) of genomic regions showing strong association signal on Chromosome 8. c XP-CLR and regional GWAS signals near CHS; gene orientation is indicated by the arrow. d Quantile-quantile (QQ) plot of MLM model for seed coat color

Fig. 6

The visualization of the GWAS results and selection signals for two non-selection traits (pubescence and flower color). a Manhattan plots of MLM for pubescence color. The − log10 P-values from a genome-wide scan are plotted against the position on each of the 20 chromosomes. The horizontal red line indicates the genome-wide significance threshold (FDR < 0.05). b Gene diversity of genomic regions showing strong association signal on Chromosome 6. c XP-CLR and regional GWAS signals near T locus; gene orientation is indicated by the arrow. d Quantile-quantile (QQ) plot of MLM model for pubescence color. e Manhattan plots of MLM for flower color, as in a. f Gene diversity of genomic regions showing strong association signal on Chromosome 13. g XP-CLR and regional GWAS signals near W1 locus; gene orientation is indicated by the arrow. h QQ plot of MLM for flower color