Abstract
BackgroundEvidence of introgression, the transfer of genetic material, between crops and their wild relatives through spontaneous hybridization and subsequent backcrossing has been documented; however, the evolutionary patterns and consequences of introgression and its influence on the processes of crop domestication and varietal diversification are poorly understood.ResultsWe investigate the genomic landscape and evolution of putative crop-wild-relative introgression by analyzing the nuclear and chloroplast genomes from a panel of wild (Glycine soja) and domesticated (Glycine max) soybeans. Our data suggest that naturally occurring introgression between wild and domesticated soybeans was widespread and that introgressed variation in both wild and domesticated soybeans was selected against throughout the genomes and preferentially removed from the genomic regions underlying selective sweeps and domestication quantitative trait locus (QTL). In both taxa, putative introgression was preferentially retained in recombination-repressed pericentromeric regions that exhibit lower gene densities, reflecting potential roles of recombination in purging introgression. Despite extensive removal of introgressed variation by recurrent selection for domestication-related QTL and associated genomic regions, spontaneous interspecific hybridization during soybean domestication appear to have contributed to a rapid varietal diversification with high levels of genetic diversity and asymmetric evolution between the nuclear and chloroplast genomes.ConclusionsThis work reveals the evolutionary forces, patterns, and consequences of putative genomic introgression between crops and their wild relatives, and the effects of introgression on the processes of crop domestication and varietal diversification. We envision that interspecific introgression serves as an important mechanism for counteracting the reduction of genetic diversity in domesticated crops, particularly the ones under single domestication.
Highlights
Evidence of introgression, the transfer of genetic material, between crops and their wild relatives through spontaneous hybridization and subsequent backcrossing has been documented; the evolutionary patterns and consequences of introgression and its influence on the processes of crop domestication and varietal diversification are poorly understood
These samples were distributed in most major phylogenetical clades/groups of 18,480 domesticated soybean accessions and 1168 wild soybean accessions collected from 84 countries or developed in the USA that are deposited in the US Department of Agriculture (USDA) Soybean Germplasm Collection [6] and considered to be very representative of soybean genetic diversity
We first identified local regional haplotypes in each of the 62 G. soja and 240 G. max accessions that were identical by descent (IBD) to individuals within the G. soja and G. max subpopulations using all Single nucleotide polymorphism (SNP) data from the 302 accessions following an approach previously described [27]
Summary
The transfer of genetic material, between crops and their wild relatives through spontaneous hybridization and subsequent backcrossing has been documented; the evolutionary patterns and consequences of introgression and its influence on the processes of crop domestication and varietal diversification are poorly understood. It has been widely accepted that soybean was domesticated from its annual wild relative Glycine soja in China approximately ~ 6000–9000 years ago [2, 3], resulting in dramatic morphological and physiological modifications often referred to as the “domestication syndrome” [4]. This process was followed by varietal diversification, forming a multitude of soybean landraces adapted to diverse eco-regions for cultivation in agricultural systems. At each of the two domestication loci, the causal mutation responsible for the domestication transition was shared by phylogenetically defined major groups of landraces that are representative of the cultivated soybean population
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