Zeng Bing, Yan Haidong, Liu Xinchun, Zang Wenjing, Zhang Ailing, Zhou Sifan, Huang Linkai, Liu Jinping
Department of Animal Science, Southwest University, Rongchang, Chongqing, 402460 China.
Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China.
Hereditas. 2017 Feb 23;154:5. doi: 10.1186/s41065-017-0027-3. eCollection 2017.
While orchardgrass ( L.) is a well-known perennial forage species, rust diseases cause serious reductions in the yield and quality of orchardgrass; however, genetic mechanisms of rust resistance are not well understood in orchardgrass.
In this study, a genome-wide association study (GWAS) was performed using specific-locus amplified fragment sequencing (SLAF-seq) technology in orchardgrass. A total of 2,334,889 SLAF tags were generated to produce 2,309,777 SNPs. ADMIXTURE analysis revealed unstructured subpopulations for 33 accessions, indicating that this orchardgrass population could be used for association analysis. Linkage disequilibrium (LD) analysis revealed an average r of 0.4 across all SNP pairs, indicating a high extent of LD in these samples. Through GWAS, a total of 4,604 SNPs were found to be significantly ( < 0.01) associated with the rust trait. The bulk analysis discovered a number of 5,211 SNPs related to rust trait. Two candidate genes, including cytochrome P450, and prolamin were implicated in disease resistance through prediction of functional genes surrounding each high-quality SNP ( < 0.01) associated with rust traits based on GWAS analysis and bulk analysis.
The large number of SNPs associated with rust traits and these two candidate genes may provide the basis for further research on rust resistance mechanisms and marker-assisted selection (MAS) for rust-resistant lineages.
虽然鸭茅是一种著名的多年生牧草品种，但锈病会导致鸭茅的产量和品质严重下降；然而，鸭茅抗锈病的遗传机制尚未得到充分了解。
在本研究中，利用特异性位点扩增片段测序（SLAF-seq）技术对鸭茅进行了全基因组关联研究（GWAS）。共产生了2334889个SLAF标签，以生成2309777个单核苷酸多态性（SNP）。群体结构分析显示33份材料的亚群结构不明显，表明该鸭茅群体可用于关联分析。连锁不平衡（LD）分析显示，所有SNP对的平均r值为0.4，表明这些样本中LD程度较高。通过GWAS，共发现4604个SNP与锈病性状显著相关（<0.01）。混合分组分析发现了5211个与锈病性状相关的SNP。基于GWAS分析和混合分组分析，通过预测与锈病性状相关的每个高质量SNP（<0.01）周围的功能基因，发现两个候选基因，包括细胞色素P450和醇溶蛋白与抗病性有关。
大量与锈病性状相关的SNP和这两个候选基因可能为进一步研究抗锈病机制和抗锈病品系的标记辅助选择（MAS）提供基础。
