Detecting SNPs underlying domestication-related traits in soybean

Abstract

Background: Cultivated soybean (Glycine max) experienced a severe genetic bottleneck during its domestication and a further loss in diversity during its subsequent selection. Here, a panel of 65 wild (G. soja) and 353 cultivated accessions was genotyped at 552 single-nucleotide polymorphism loci to search for signals of selection during and after domestication.

Results: The wild and cultivated populations were well differentiated from one another. Application of the Fst outlier test revealed 64 loci showing evidence for selection. Of these, 35 related to selection during domestication, while the other 29 likely gradually became monomorphic as a result of prolonged selection during post domestication. Two of the SNP locus outliers were associated with testa color.

Conclusions: Identifying genes controlling domestication-related traits is important for maintaining the diversity of crops. SNP locus outliers detected by a combined forward genetics and population genetics approach can provide markers with utility for the conservation of wild accessions and for trait improvement in the cultivated genepool.

Figure 1

The provenance of accessions of G. max and G. soja which formed the germplasm panel. (A) G. soja. (B) G. max landraces. (C) G. max modern cultivars.

Figure 2

The genetic architecture of the 418 accessions of cultivated and wild soybean. (A) A phylogenetic tree constructed from 552 SNP loci. Pink solid circles represent G. soja and green hollow ones for G. max accessions. (B) In the STRUCTURE analysis, the groups formed at K = 2 correspond to G. soja and G. max. For legibility, the names of individual accessions have been omitted.

Figure 3

The detection of SNP locus outliers and related F _st values. The 554 loci have been ordered along the horizontal axis according to their genomic location (Additional file 2). (A) The 35 outlier loci identified in the comparison between wild germplasm and the landraces, (B) The 53 outlier loci identified in the comparison between wild germplasm and the modern cultivars. The outliers associated with a confidence level of >95% have been indicated by open squares. The vertical dotted lines separate the 20 chromosomes from one another.

Figure 4

Allele frequencies at SNP locus outliers. (A) The 24 outliers in common between wild accessions vs landraces and wild accessions vs modern cultivars. (B) The 29 outliers specific to the wild accessions vs modern cultivars comparison. (C) The 11 outliers specific to the wild accessions vs landraces comparison.

Figure 5

SNP locus outliers associated with testa color. (A) The relationship between SNP genotype and testa color in wild accessions, the landraces and the modern cultivars. (B) The frequency of the four haplotype classes based on SNPs within BARC-018681-02991 and BARC-018093-02513.