A High-Density Genetic Linkage Map of SLAFs and QTL Analysis of Grain Size and Weight in Barley (Hordeum vulgare L.).

Yunxia Fang,Jia Li,Ziling Zhang,Dawei Xue,Hua Wang,Gengwei Wu,Linlin Hou,Xiaoqin Zhang,Xian Zhang,Chunyu Niu,Junjun Zheng,Wenjia Wang,Tao Tong

doi:10.3389/fpls.2020.620922

Abstract

Grain size is an important agronomic trait determines yield in barley, and a high-density genetic map is helpful to accurately detect quantitative trait loci (QTLs) related to grain traits. Using specific-locus amplified fragment sequencing (SLAF-seq) technology, a high-density genetic map was constructed with a population of 134 recombinant inbred lines (RILs) deriving from a cross between Golden Promise (GP) and H602, which contained 12,635 SLAFs with 26,693 SNPs, and spanned 896.74 cM with an average interval of 0.07 cM on seven chromosomes. Based on the map, a total of 16 QTLs for grain length (GL), grain width and thousand-grain weight were detected on 1H, 2H, 4H, 5H, and 6H. Among them, a major QTL locus qGL1, accounting for the max phenotypic variance of 16.7% was located on 1H, which is a new unreported QTL affecting GL. In addition, the other two QTLs, qGL5 and qTGW5, accounting for the max phenotypic variances of 20.7 and 21.1%, respectively, were identified in the same region, and sequencing results showed they are identical to HvDep1 gene. These results indicate that it is a feasible approach to construct a high-quality genetic map for QTL mapping by using SLAF markers, and the detected major QTLs qGL1, qGL5, and qTGW5 are useful for marker-assisted selection (MAS) of grain size in barley breeding.

Highlights

Barley is one of the most important cereal crops in the world, and widely used for animal feed and malting (Baik and Ullrich, 2008; Bond et al, 2015)
Specificlocus amplified fragment sequencing (SLAF-seq) is one version of representation genome sequencing (RRGS) based on special fragment-length, which mainly applied in high-density genetic map construction and gene mapping in many species (Zhang et al, 2013; Li et al, 2014; Hu et al, 2016; Yu et al, 2019; Zhao et al, 2019)
Based on the high-density genetic map, a total of 16 QTLs related to grain size and thousand-grain weight (TGW) were detected on chromosome 1, 2, 4, 5, 6H in consecutive 3 years, and accounted for phenotypic variances ranged from 10.2 to 21.1% (Figure 5 and Table 4)

Summary

Introduction

Barley is one of the most important cereal crops in the world, and widely used for animal feed and malting (Baik and Ullrich, 2008; Bond et al, 2015). Quantitative trait loci mapping has been widely used to identify genomic regions associated with target trait, which mainly subject to the sample size and molecular marker density (Doerge and Rebai, 1996). With the development of high-throughput genotyping and sequencing technology, the massive single nucleotide polymorphisms (SNPs) were extensively identified in different species, which usually used for high-density map construction, genome-wide association analysis, gene mapping, gene chip, MAS, etc. Specificlocus amplified fragment sequencing (SLAF-seq) is one version of RRGS based on special fragment-length, which mainly applied in high-density genetic map construction and gene mapping in many species (Zhang et al, 2013; Li et al, 2014; Hu et al, 2016; Yu et al, 2019; Zhao et al, 2019)

Methods

Results

Conclusion