Signatures of soft sweeps across the Dt1 locus underlying determinate growth habit in soya bean [Glycine max (L.) Merr.]

Abstract

Determinate growth habit is an agronomically important trait associated with domestication in soya bean. Previous studies have demonstrated that the emergence of determinacy is correlated with artificial selection on four nonsynonymous mutations in the Dt1 gene. To better understand the signatures of the soft sweeps across the Dt1 locus and track the origins of the determinate alleles, we examined patterns of nucleotide variation in Dt1 and the surrounding genomic region of approximately 800 kb. Four local, asymmetrical hard sweeps on four determinate alleles, sized approximately 660, 120, 220 and 150 kb, were identified, which constitute the soft sweeps for the adaptation. These variable-sized sweeps substantially reflected the strength and timing of selection and indicated that the selection on the alleles had been completed rapidly within half a century. Statistics of EHH, iHS, H12 and H2/H1 based on haplotype data had the power to detect the soft sweeps, revealing distinct signatures of extensive long-range LD and haplotype homozygosity, and multiple frequent adaptive haplotypes. A haplotype network constructed for Dt1 and a phylogenetic tree based on its extended haplotype block implied independent sources of the adaptive alleles through de novo mutations or rare standing variation in quick succession during the selective phase, strongly supporting multiple origins of the determinacy. We propose that the adaptation of soya bean determinacy is guided by a model of soft sweeps and that this model might be indispensable during crop domestication or evolution.

Genetic association with high‐resolution climate data reveals selection footprints in the genomes of barley landraces across the Iberian Peninsula

“…Recent studies have attempted to reveal associations between environmental traits and genetic polymorphisms. Although the statistical techniques used were developed with a focus on natural populations (Günther & Coop, ; Günther, Lampei, Barilar, & Schmid, ), they are useful to detect meaningful associations in crops as well, using landraces (Abebe, Naz, & Léon, ; Lasky et al, ; Russell et al, ; Zhong et al, ). These studies, and the present one, are a case in point for the usefulness of EAA approaches to study crop adaptation.…”

Targeted resequencing reveals genomic signatures of barley domestication

“…The DRI statistics reveals a severe depletion of nucleotide diversity in the domesticated genotypes at certain loci detected as statistical outliers. All three statistics have frequently been used in the selection scans to reveal domestication sweeps and candidate domestication genes in other crop species (Huang et al, 2012;Lin et al, 2014;Wang et al, 2014;Civ a n et al, 2015;Velasco et al, 2016;Zhong et al, 2017).…”

Selective Sweeps Under Dominance and Inbreeding

“…Many selfing organisms exhibit sweep-like patterns, including Arabidopsis thaliana (Long et al 2013;Huber et al 2014;Fulgione et al 2018;Price et al 2018); Caenorhabditis elegans (Andersen et al 2012); Medicago truncatula (Bonhomme et al 2015); and Microbotryum fungi (Badouin et al 2017). Soft sweeps have also been reported in soya bean (Zhong et al 2017). Detailed analyses of these cases has been hampered by a lack of theory on how hard and soft sweep signatures should manifest themselves under different self-fertilization and dominance levels.…”