Multi-Locus Genome-Wide Association Studies for 14 Main Agronomic Traits in Barley.

Xin Hu,Genlou Sun,Lipan Liu,Dongfa Sun,Xifeng Ren,Jianfang Zuo,Jibin Wang,Chengdao Li

doi:10.3389/fpls.2018.01683

Abstract

The agronomic traits, including morphological and yield component traits, are important in barley breeding programs. In order to reveal the genetic foundation of agronomic traits of interest, in this study 122 doubled haploid lines from a cross between cultivars “Huaai 11” (six-rowed and dwarf) and “Huadamai 6” (two-rowed) were genotyped by 9680 SNPs and phenotyped 14 agronomic traits in 3 years, and the two datasets were used to conduct multi-locus genome-wide association studies. As a result, 913 quantitative trait nucleotides (QTNs) were identified by five multi-locus GWAS methods to be associated with the above 14 traits and their best linear unbiased predictions. Among these QTNs and their adjacent genes, 39 QTNs (or QTN clusters) were repeatedly detected in various environments and methods, and 10 candidate genes were identified from gene annotation. Nineteen QTNs and two genes (sdw1/denso and Vrs1) were previously reported, and eight candidate genes need to be further validated. The Vrs1 gene, controlling the number of rows in the spike, was found to be associated with spikelet number of main spike, spikelet number per plant, grain number per plant, grain number per spike, and 1,000 grain weight in multiple environments and by multi-locus GWAS methods. Therefore, the above results evidenced the feasibility and reliability of genome-wide association studies in doubled haploid population, and the QTNs and their candidate genes detected in this study are useful for marker-assisted selection breeding, gene cloning, and functional identification in barley.

Highlights

Barley (Hordeum vulgare L, 2n = 2x = 14), one of the first domesticated grains in the Fertile Crescent (Zohary et al, 2012), has been used widely as animal feed, human health foods, and a source of beer
The objectives of this study were to: (a) use genomewide association studies (GWAS) to further dissect the genetic foundations for main agronomic traits in our previous studies of Ren et al (2013, 2014) and Wang et al (2016a), and compare the quantitative trait nucleotide (QTN) results with those in previous studies, (b) evaluate if GWAS is feasible and reliable in the genetic dissection of complex traits in doubled haploid (DH) population, and (c) mine the candidate genes in the regions of the quantitative trait nucleotides (QTNs)
A total of 913 significant QTNs were found to be associated with the 14 agronomic traits in 3 years and their best linear unbiased predictions (BLUPs) values (Table S2)

Summary

Introduction

Its yield and quality are the most important breeding objectives in crop breeding programs Most agronomic traits, such as plant height- and yield-related traits, are controlled by quantitative trait loci (QTLs) in barley, so it is difficult to obtain their genetic foundation and molecular mechanism. A large number of QTLs for plant height related traits were reported to be located on all the seven chromosomes (Sameri et al, 2006; Baghizadeh et al, 2007; Wang et al, 2010; Ren et al, 2014). A huge number of QTLs for yield related traits were detected to be located across all the chromosomes (Li et al, 2005; Sameri et al, 2006; Baghizadeh et al, 2007; Wang et al, 2010, 2016a; Ren et al, 2013)

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Discussion

Conclusion