Ning Weidong, Wang Wenzheng, Liu Zijian, Xie Weibo, Chen Hanchen, Hong Dengfeng, Yang Qing-Yong, Cheng Shifeng, Guo Liang
Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 China.
Yazhouwan National Laboratory, Sanya, 572025 Hainan China.
Mol Breed. 2024 Dec 18;44(12):2. doi: 10.1007/s11032-024-01522-4. eCollection 2024 Dec.
, a globally significant oilseed crop, exhibits a wide distribution across diverse climatic zones. is being increasingly susceptible to distinct diseases, such as blackleg, clubroot and sclerotinia stem rot, leading to substantial reductions in yield. Nucleotide-binding site leucine-rich repeat genes (), the most pivotal family of resistance genes, can be effectively harnessed by identifying and uncovering their diversity to acquire premium disease-resistant gene resources. Here, we collected the genomes of 23 accessions and established the first comprehensive pan-NLRome in by leveraging multiple genomic resources. We observe significant variation in the number of genes across different accessions, ranging from 189 to 474. Notably, (TIR-NBS-LRR) genes constitute approximately half of the total count, indicating their predominant presence in . The number of in the C subgenome is significantly higher than that in the A subgenome, and chromosome C09 exhibits the highest density of genes with featuring multiple clusters. Domain analysis reveals that the integrated domains significantly enhance the diversity of NLRs, with B3 DNA binding, VQ, and zinc fingers being the most prevalent integrated domains. Pan-genomic analysis reveals that the core type of genes, which is present in most accessions, constitutes approximately 58% of the total . Furthermore, we conduct a comparative analysis of the diversity of genes across distinct ecotypes, leading to the identification of ecotype-specific NLRs and their integrated domains. In conclusion, our study effectively addresses the limitations of a single reference genome and provides valuable insights into the diversity of genes in , thereby contributing to disease resistance breeding.
[作物名称]是一种具有全球重要意义的油料作物，广泛分布于不同的气候区。它越来越容易受到多种病害的侵袭，如黑胫病、根肿病和菌核病，导致产量大幅下降。核苷酸结合位点富含亮氨酸重复序列基因（NLRs）是抗性基因中最关键的家族，通过识别和揭示其多样性，可以有效地利用这些基因来获取优质的抗病基因资源。在此，我们收集了23个种质的基因组，并利用多种基因组资源构建了首个全面的[作物名称]泛NLRome。我们观察到不同[作物名称]种质中NLR基因数量存在显著差异，范围从189个到474个。值得注意的是，TIR-NBS-LRR基因约占总数的一半，表明它们在[作物名称]中占主导地位。C亚基因组中的NLR数量显著高于A亚基因组，并且C09染色体上的NLR基因密度最高，具有多个NLR簇。结构域分析表明，整合结构域显著增强了NLRs的多样性，其中B3 DNA结合结构域、VQ结构域和锌指结构域最为普遍。泛基因组分析表明，大多数种质中存在的核心类型的NLR基因约占总数的58%。此外，我们对不同生态型的NLR基因多样性进行了比较分析，鉴定出了生态型特异性的NLR及其整合结构域。总之，我们的研究有效地解决了单一参考基因组的局限性，为[作物名称]中NLR基因的多样性提供了有价值的见解，从而有助于抗病育种。
