Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation
Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation
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DOI：
10.1111/pbi.13262
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发表时间：
2020-04-01
影响因子：
13.8
通讯作者：
Batley, Jacqueline
中科院分区：
文献类型：
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作者：
Dolatabadian, Aria;Bayer, Philipp E.;Batley, Jacqueline
基于单核苷酸多态性（SNP）、拷贝数变异（CNV）和存在/不存在变异（PAV）发现的方法为研究基因结构和进化提供了宝贵的资源。然而，由于这些结构变异，单个参考基因组无法涵盖一个物种的全部基因内容。因此，需要进行泛基因组学分析以确保物种内的基因组多样性得到充分体现。甘蓝型油菜是世界上最重要的油料作物之一，不同品种的抗性基因表现出差异。在这里，我们描述了 50 个甘蓝型油菜品系的抗性基因分布。我们总共鉴定了 1749 个抗性基因类似物 (RGAs)，其中 996 个是核心基因，753 个是可变基因，其中 368 个不存在于参考基因组 (cv. Darmor-bzh) 中。此外，在1030个RGA中总共预测了15 318个SNP。结果表明，核心 R 基因比可变基因含有更多的 SNP。与单基因相比，更多的富含核苷酸结合位点的亮氨酸重复序列（NBS-LRR）基因位于簇中，并且更可能在簇中发现可变基因。我们鉴定了 106 个与黑胫病抗性数量性状基因座 (QTL) 相关的 RGA 候选者。这项研究提供了对抗性基因的更好理解，以实现基于基因组学的改进和提高抗病性。
Methods based on single nucleotide polymorphism (SNP), copy number variation (CNV) and presence/absence variation (PAV) discovery provide a valuable resource to study gene structure and evolution. However, as a result of these structural variations, a single reference genome is unable to cover the entire gene content of a species. Therefore, pangenomics analysis is needed to ensure that the genomic diversity within a species is fully represented. Brassica napus is one of the most important oilseed crops in the world and exhibits variability in its resistance genes across different cultivars. Here, we characterized resistance gene distribution across 50 B. napus lines. We identified a total of 1749 resistance gene analogs (RGAs), of which 996 are core and 753 are variable, 368 of which are not present in the reference genome (cv. Darmor-bzh). In addition, a total of 15 318 SNPs were predicted within 1030 of the RGAs. The results showed that core R-genes harbour more SNPs than variable genes. More nucleotide binding site-leucine-rich repeat (NBS-LRR) genes were located in clusters than as singletons, with variable genes more likely to be found in clusters. We identified 106 RGA candidates linked to blackleg resistance quantitative trait locus (QTL). This study provides a better understanding of resistance genes to target for genomics-based improvement and improved disease resistance.