A single origin and moderate bottleneck during domestication of soybean (Glycine max): implications from microsatellites and nucleotide sequences

Abstract

Background and Aims It is essential to illuminate the evolutionary history of crop domestication in order to understand further the origin and development of modern cultivation and agronomy; however, despite being one of the most important crops, the domestication origin and bottleneck of soybean (Glycine max) are poorly understood. In the present study, microsatellites and nucleotide sequences were employed to elucidate the domestication genetics of soybean. Methods The genomes of 79 landrace soybeans (endemic cultivated soybeans) and 231 wild soybeans (G. soja) that represented the species-wide distribution of wild soybean in East Asia were scanned with 56 microsatellites to identify the genetic structure and domestication origin of soybean. To understand better the domestication bottleneck, four nucleotide sequences were selected to simulate the domestication bottleneck. Key Results Model-based analysis revealed that most of the landrace genotypes were assigned to the inferred wild soybean cluster of south China, South Korea and Japan. Phylogeny for wild and landrace soybeans showed that all landrace soybeans formed a single cluster supporting a monophyletic origin of all the cultivars. The populations of the nearest branches which were basal to the cultivar lineage were wild soybeans from south China. The coalescent simulation detected a bottleneck severity of K' = 2 during soybean domestication, which could be explained by a foundation population of 6000 individuals if domestication duration lasted 3000 years. Conclusions As a result of integrating geographic distribution with microsatellite genotype assignment and phylogeny between landrace and wild soybeans, a single origin of soybean in south China is proposed. The coalescent simulation revealed a moderate genetic bottleneck with an effective wild soybean population used for domestication estimated to be approximately 2 % of the total number of ancestral wild soybeans. Wild soybeans in Asia, especially in south China, contain tremendous genetic resources for cultivar improvement.

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

“…Together with principal component analysis (PCA) (Fig. 1c), these results support the hypothesis that all currently grown domesticated soybeans originated from a single domestication event 16 . Then the domesticated accessions were grouped into two main clades, designated as group I and group II.…”

Investigation of the domestication of common bean (Phaseolus vulgaris) using multilocus sequence data

“…In this study we evaluated multilocus sequence data from a diverse group of landrace genotypes to assess nucleotide diversity, population differentiation and demography of the species. These results have implications for understanding the history of domestication of common bean, which itself contributes to our understanding of the origin and development of modern cultivation and agronomy (Guo et al 2010). This study also enhances our understanding of the factors that contribute to LD in present day cultivars which, in turn, has implications for association mapping studies.…”

“…These estimates are higher than those proposed by Buckler et al (2001), who suggested that 60-80% of variability is retained in the domesticated crops. The loss of variability in other crops is within that range: grasses (66%, Buckler et al 2001), soybean (50%, Hyten et al 2007;Guo et al 2010) and rice (70%, Li et al 2009). In the present study, a high level of loss of diversity is not evident from nucleotide diversity or SNP density data.…”

Legume Crops Phylogeny and Genetic Diversity for Science and Breeding

“…Based on 14 C radiocarbon dating, these soybean remains are more than 2,590 years old. However, the exact site of domestication has not been identified until now, although several candidate locations have been proposed, including the Huanghuai Region (Yellow River valley) (Li et al, 2010a;Li et al, 2013a;Guo et al, 2010).…”

“…Major traits of agricultural importance, including yield and stress tolerance, are polygenic, and the presence of these favorable alleles in G. soja will help breeding programs introduce beneficial traits into soybean (Tanksley and McCouch 1997;. Therefore, wild soybeans are important sources of novel alleles that can be used to broaden the genetic base of cultivated soybean, which is necessary due to the fact that diversity in soybean has been greatly reduced by the genetic bottleneck of domestication (Guo et al, 2010;Lam et al, 2010;Li et al, 2010).…”