State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.
Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai Province, China.
PLoS One. 2021 Dec 2;16(12):e0260723. doi: 10.1371/journal.pone.0260723. eCollection 2021.
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.
裸大麦（Hordeum vulgare L. var. nudum），又称青稞，是一种独特的栽培大麦品种。全基因组特异长度扩增片段测序（SLAF-seq）方法是一种快速的深度测序技术，用于选择和鉴定遗传基因座或标记。在这项研究中，我们收集了 300 份裸大麦品系，并使用 SLAF-seq 方法鉴定与株高（PH）和分蘖数（TN）相关的候选基因。我们总共获得了 1407M 对末端读取，开发了 228227 个 SLAF 标签。使用完整性阈值>0.8 和次要等位基因频率>0.05 进行过滤后，筛选出了 14504892 个单核苷酸多态性（SNP）位点。其余的 SNPs 用于构建邻接聚类进化树，三个亚群成员在区域品种之间没有明显分化。我们使用全基因组关联研究方法鉴定了 1006 个与 TN 相关的 SNP 和 113 个与 PH 相关的 SNP。基于最佳线性无偏预测（BLUP），分别有 41 个和 29 个 SNP 与 TN 和 PH 相关。因此，包括 Hd3a 和 CKX5 在内的几个基因可能是未来裸大麦遗传育种的有用候选基因。总之，我们的研究结果提供了对控制大麦结构的分子机制的深入了解，这对育种和产量具有重要意义。
