Impacts of nucleotide fixation during soybean domestication and improvement

Weiming He,Hon-Ming Lam,Shancen Zhao,Shengkai Pan,Haiyang Wu,Fengya Zheng

doi:10.1186/s12870-015-0463-z

Abstract

BackgroundPlant domestication involves complex morphological and physiological modification of wild species to meet human needs. Artificial selection during soybean domestication and improvement results in substantial phenotypic divergence between wild and cultivated soybeans. Strong selective pressure on beneficial phenotypes could cause nucleotide fixations in the founder population of soybean cultivars in quite a short time.ResultsAnalysis of available sequencing accessions estimates that ~5.3 million single nucleotide variations reach saturation in cultivars, and then ~9.8 million in soybean germplasm. Selective sweeps defined by loss of genetic diversity reveal 2,255 and 1,051 genes were involved in domestication and subsequent improvement, respectively. Both processes introduced ~0.1 million nucleotide fixations, which contributed to the divergence of wild and cultivated soybeans. Meta-analysis of reported quantitative trait loci (QTL) and selective signals with nucleotide fixation identifies a series of putative candidate genes responsible for 13 agronomically important traits. Nucleotide fixation mediated by artificial selection affected diverse molecular functions and biological reactions that associated with soybean morphological and physiological changes. Of them, plant-pathogen interactions are of particular relevance as selective nucleotide fixations happened in disease resistance genes, cyclic nucleotide-gated ion channels and terpene synthases.ConclusionsOur analysis provides insights into the impacts of nucleotide fixation during soybean domestication and improvement, which would facilitate future QTL mapping and molecular breeding practice.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0463-z) contains supplementary material, which is available to authorized users.

Highlights

Plant domestication involves complex morphological and physiological modification of wild species to meet human needs
Estimation of single nucleotide variations among soybean populations Recently, a set of diverse soybean individuals was sequenced and reported based on NGS platforms [7,8,10]. These soybeans, representing wild and cultivars that mainly consist of landrace and modern elite accessions in East Asia, were selected based on intensive molecular and phenotypic analysis to maximally reflect the genetic diversity of soybeans (Additional file 1: Table S1)
We downloaded all the short reads of sequencing soybeans from NCBI Short Read Archive under accession numbers SRA020131, SRA009252, SRP015830, and ERP002622. These reads were aligned to the soybean reference genome Glycine max (Phytozome v9) with SOAP2 [15], and were subsequently used to detect Single nucleotide variation (SNV) with SOAPsnp pipeline [16]

Summary

Introduction

Plant domestication involves complex morphological and physiological modification of wild species to meet human needs. Artificial selection during soybean domestication and improvement results in substantial phenotypic divergence between wild and cultivated soybeans. Strong selective pressure on beneficial phenotypes could cause nucleotide fixations in the founder population of soybean cultivars in quite a short time. Modern soybean cultivars were originally domesticated from its wild progenitor A variety of morphological and physiological changes except for reproductive isolation have occurred that distinguish soybean. Heritable changes occurred during plant domestication are being revealed by gene mapping and genomic analyses [5]. Re-sequenced soybeans representing wild and cultivated accessions revealed the nature and extent of genetic diversity in both populations [7,8,9]. Another research reported a reservoir of genes that were affected by early domestication

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