Candidate loci involved in domestication and improvement detected by a published 90K wheat SNP array

Lifeng Gao,Guangyao Zhao,Jizeng Jia,Dawei Huang

doi:10.1038/srep44530

Abstract

Selection is one of the most important forces in crop evolution. Common wheat is a major world food crop and a typical allopolyploid with a huge and complex genome. We applied four approaches to detect loci selected in wheat during domestication and improvement. A total of 7,984 candidate loci were detected, accounting for 23.3% of all 34,317 SNPs analysed, a much higher proportion than estimated in previous reports. We constructed a first generation wheat selection map which revealed the following new insights on genome-wide selection: (1) diversifying selection acted by increasing, decreasing or not affecting gene frequencies; (2) the number of loci under selection during domestication was much higher than that during improvement; (3) the contribution to wheat improvement by the D sub-genome was relatively small due to the bottleneck of hexaploidisation and diversity can be expanded by using synthetic wheat and introgression lines; and (4) clustered selection regions occur throughout the wheat genome, including the centromere regions. This study will not only help future wheat breeding and evolutionary studies, but will also accelerate study of other crops, especially polyploids.

Highlights

Identification of selection signatures and construction of a genome-wide selection map will produce a “treasure map” for breeders
A subset of 82 modern varieties was randomly taken from the 429 modern varieties and 24,588 polymorphic single nucleotide polymorphisms (SNPs) were observed in this subset
The result ascertained that the higher number of polymorphic SNPs in modern cultivars was not due to the difference in sample size

Summary

Introduction

Identification of selection signatures and construction of a genome-wide selection map will produce a “treasure map” for breeders. Detection of selection signatures is a central challenge for both evolutionary biology and crop breeding. Domestication and improvement (post-domestication selection) are important processes of crop evolution whereby selection is the major driver of adaptation to diverse environments in the achievement of high yields. By comparing genomic patterns and levels of variability across populations it is possible to identify selection signatures left by evolutionary forces[4,5]. Genome-wide surveys are important means of detecting deviations from neutrality among loci. A well-known example is Tanksley’s funnel type selection model[14]. By using this approach it was estimated that selected loci accounted for 5% of the maize genome[15,16] and 7% of the sunflower genome[17]. Key Laboratory of Crop Gene Resources and Germplasm Enhancement, MOA, the National Key Facility for Crop www.nature.com/scientificreports/

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