Genome wide association study of plant height and tiller number in hulless barley

Yixiong Bai,Youhua Yao,Xin Gao,Yong Wang,Likun An,Xiaohong Zhao,Lulu Guan,Zhonghua Wang,Kunlun Wu,Yatao Jia,Xiaohua Yao,Xin Li,Man Li,Aimin Zhang

doi:10.1371/journal.pone.0260723

Yixiong Bai, Youhua Yao + Show 12 more

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https://doi.org/10.1371/journal.pone.0260723

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Abstract

Hulless barley (Hordeum vulgare L. var. nudum), also called naked barley, is a unique variety of cultivated barley. The genome-wide specific length amplified fragment sequencing (SLAF-seq) method is a rapid deep sequencing technology that is used for the selection and identification of genetic loci or markers. In this study, we collected 300 hulless barley accessions and used the SLAF-seq method to identify candidate genes involved in plant height (PH) and tiller number (TN). We obtained a total of 1407 M paired-end reads, and 228,227 SLAF tags were developed. After filtering using an integrity threshold of >0.8 and a minor allele frequency of >0.05, 14,504,892 single-nucleotide polymorphisms (SNP) loci were screened out. The remaining SNPs were used for the construction of a neighbour-joining phylogenetic tree, and the three subcluster members showed no obvious differentiation among regional varieties. We used a genome wide association study approach to identify 1006 and 113 SNPs associated with TN and PH, respectively. Based on best linear unbiased predictors (BLUP), 41 and 29 SNPs associated with TN and PH, respectively. Thus, several of genes, including Hd3a and CKX5, may be useful candidates for the future genetic breeding of hulless barley. Taken together, our results provide insight into the molecular mechanisms controlling barley architecture, which is important for breeding and yield.

Highlights

Hulless barley (Hordeum vulgare L. var. nudum) is a variety of cultivated barley that is known as naked barley because the separation of its grains and glumes creates a ‘naked’ caryopsis [1]
Further analysis of the interaction effects of year, location and genotype, revealed that three factors were significantly correlated to plant height (PH) and tiller number (TN); we found significant interaction effects of L×Y, L×G, L×Y×G (S2 Table), suggesting that the PH and TN traits are modulated by a combination of genetic and non-genetic factors
Based on the results of the association analysis of best linear unbiased predictors (BLUP) values, we screened out 41 and 29 single-nucleotide polymorphisms (SNP) loci related to PH and TN, respectively

Summary

Introduction

Hulless barley (Hordeum vulgare L. var. nudum) is a variety of cultivated barley that is known as naked barley because the separation of its grains and glumes creates a ‘naked’ caryopsis [1]. Nudum) is a variety of cultivated barley that is known as naked barley because the separation of its grains and glumes creates a ‘naked’ caryopsis [1]. Hulless barley is mainly cultivated on the Qinghai–Tibet Plateau [2], because it possesses key adaptations to extreme environments. Approximately 356,000 ha are occupied by hulless barley cultivation in China. Barley is a staple of the Tibetan diet and confers significant nutritional and health benefits. It is widely used in the winemaking and food processing industries, and barley seedlings and straw are used as high-quality forage.

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