Genome-Wide Association Mapping of Hulless Barely Phenotypes in Drought Environment

Jie Li; Xiaohua Yao; Youhua Yao; Likun An; Zongyun Feng; Kunlun Wu

doi:10.3389/fpls.2022.924892

Genome-Wide Association Mapping of Hulless Barely Phenotypes in Drought Environment

Front Plant Sci. 2022 Jun 23:13:924892. doi: 10.3389/fpls.2022.924892. eCollection 2022.

Authors

Jie Li^{1

2

3

4}, Xiaohua Yao^{2

3

4}, Youhua Yao^{2

3

4}, Likun An^{2

3

4}, Zongyun Feng^{1

5}, Kunlun Wu^{2

3

4}

Affiliations

¹ College of Agronomy Sichuan Agricultural University, Chengdu, China.
² Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, China.
³ Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, China.
⁴ Qinghai Subcenter of National Hulless Barley Improvement, Xining, China.
⁵ State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China.

Abstract

Drought stress is one of the main factors restricting hulless barley (Hordeum vulgare L. var. nudum Hook. f.) yield. Genome-wide association study was performed using 269 lines of hulless barley to identify single-nucleotide polymorphism (SNP) markers associated with drought-resistance traits. The plants were cultured under either normal or drought conditions, and various quantitative traits including shoot fresh weight, shoot dry weight, root fresh weight, root dry weight, leaf fresh weight, leaf saturated fresh weight, leaf dry weight, ratio of root and shoot fresh weight, ratio of root and shoot dry weight, shoot water loss rate, root water loss rate, leaf water content and leaf relative water content, and field phenotypes including main spike length, grain number per plant, grain weight per plant, thousand grain weight (TGW), main spike number, plant height, and effective spike number of plants were collected. After genotyping the plants, a total of 8,936,130 highly consistent population SNP markers were obtained with integrity > 0.5 and minor allele frequency > 0.05. Eight candidate genes potentially contributed to the hulless barley drought resistance were obtained at loci near significant SNPs. For example, EMB506, DCR, and APD2 genes for effective spike number of plants, ABCG11 gene for main spike number (MEN), CLPR2 gene for main spike length, YIP4B gene for root and shoot dry weight (RSWD), and GLYK and BTS genes for TGW. The SNPs and candidate genes identified in this study will be useful in hulless barley breeding under drought resistance.

Keywords: GWAS; SNP; drought resistance; high throughput sequencing; hulless barley; quantitative traits.