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Front. Plant Sci. | doi: 10.3389/fpls.2018.01683

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

Xin Hu1,  Jianfang Zuo1, Jibin Wang1, Lipan Liu1,  Genlou Sun2,  Chengdao Li3, 4, Xifeng Ren1* and  Dongfa Sun4, 5*
  • 1College of Plant Science and Technology, Huazhong Agricultural University, China
  • 2Department of Biology, Saint Mary’s University, Canada
  • 3School of Veterinary and Life Sciences, Murdoch University, Australia
  • 4Hubei Collaborative Innovation Center for Grain Industry, China
  • 5College of Plant Science and Technology, Huazhong Agricultural University, China

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 three 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 ten 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 1000 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.

Keywords: GWAS, barley, DH population, quantitative trait loci (QTL);, quantitative trait nucleotides (QTNs), candidate gene

Received: 30 Jul 2018; Accepted: 29 Oct 2018.

Edited by:

Zhenyu Jia, University of California, Riverside, United States

Reviewed by:

Yin-Gang Hu, Northwest A&F University
Yang Xu, Yangzhou University, China  

Copyright: © 2018 Hu, Zuo, Wang, Liu, Sun, Li, Ren and Sun. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Dr. Xifeng Ren, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China, renxifeng@mail.hzau.edu.cn
Prof. Dongfa Sun, Huazhong Agricultural University, College of Plant Science and Technology, Wuhan, China, sundongfa1@mail.hzau.edu.cn