Department of Horticulture, Division of Applied Life Science (BK21 Four Program), Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea.
BMC Plant Biol. 2024 Nov 1;24(1):1036. doi: 10.1186/s12870-024-05742-w.
Bacterial wilt (BW), caused by Ralstonia solanacearum (Ral), results in substantial yield losses in pepper crops. Developing resistant pepper varieties through breeding is the most effective strategy for managing BW. To achieve this, a thorough understanding of the genetic information connected with resistance traits is essential. Despite identifying three major QTLs for bacterial wilt resistance in pepper, Bw1 on chromosome 8, qRRs-10.1 on chromosome 10, and pBWR-1 on chromosome 1, the genetic information of related BW pepper varieties has not been sufficiently studied. Here, we resequenced two pepper inbred lines, C. annuum 'MC4' (resistant) and C. annuum 'Subicho' (susceptible), and analyzed genomic variations through SNPs and Indels to identify candidate genes for BW resistance.
An average of 139.5 Gb was generated among the two cultivars, with coverage ranging from 44.94X to 46.13X. A total of 8,815,889 SNPs was obtained between 'MC4' and 'Subicho'. Among them, 31,190 (0.35%) were non-synonymous SNPs (nsSNPs) corresponding to 10,926 genes, and these genes were assigned to 142 Gene Ontology (GO) terms across the two cultivars. We focused on three known BW QTL regions by identifying genes with sequence variants through gene set enrichment analysis and securing those belonging to high significant GO terms. Additionally, we found 310 NLR genes with nsSNP variants between 'MC4' (R) and 'Subicho' (S) within these regions. Also, we performed an Indel analysis on these genes. By integrating all this data, we identified eight candidate BW resistance genes, including two NLR genes with nsSNPs variations in qRRs-10.1 on chromosome 10.
We identified genomic variations in the form of SNPs and Indels by re-sequencing two pepper cultivars with contrasting traits for bacterial wilt. Specifically, the four genes associated with pBWR-1 and Bw1 that exhibit both nsSNP and Indel variations simultaneously in 'Subicho', along with the two NLR genes linked to qRRs-10.1, which are known for their direct involvement in immune responses, are identified as most likely BW resistance genes. These variants in leading candidate genes associated with BW resistance can be used as important markers for breeding pepper varieties.
由丁香假单胞菌引起的细菌性萎蔫病（BW）会导致辣椒作物产量大幅损失。通过育种培育抗病辣椒品种是管理 BW 的最有效策略。为此，必须深入了解与抗性性状相关的遗传信息。尽管已经在辣椒中鉴定出三个与细菌性萎蔫病抗性相关的主要 QTL，即第 8 号染色体上的 Bw1、第 10 号染色体上的 qRRs-10.1 和第 1 号染色体上的 pBWR-1，但相关 BW 辣椒品种的遗传信息尚未得到充分研究。在这里，我们对两个辣椒自交系 C. annuum 'MC4'（抗性）和 C. annuum 'Subicho'（敏感）进行了重测序，并通过 SNPs 和 Indels 分析了基因组变异，以鉴定 BW 抗性的候选基因。
两个品种共产生了 139.5 Gb 的平均数据，覆盖度为 44.94X 至 46.13X。'MC4'和'Subicho'之间共获得了 8815889 个 SNPs。其中，31190 个（0.35%）是非同义 SNPs（nsSNPs），对应于 10926 个基因，这些基因被分配到两个品种的 142 个基因本体论（GO）术语中。通过基因集富集分析鉴定具有序列变异的基因，并确定属于高显著 GO 术语的基因，我们重点关注了三个已知的 BW QTL 区域。此外，我们在这些区域内发现了 310 个具有 nsSNP 变异的 NLR 基因，在'MC4'（R）和'Subicho'（S）之间。我们还对这些基因进行了 Indel 分析。通过整合所有这些数据，我们鉴定出了 8 个候选 BW 抗性基因，包括 2 个在 10 号染色体上 qRRs-10.1 中具有 nsSNP 变异的 NLR 基因。
我们通过对具有 BW 性状差异的两个辣椒品种进行重测序，鉴定出 SNP 和 Indel 形式的基因组变异。具体来说，在 'Subicho'中同时具有 nsSNP 和 Indel 变异的与 pBWR-1 和 Bw1 相关的四个基因，以及与 qRRs-10.1 相关的两个 NLR 基因，它们直接参与免疫反应，被认为是最有可能的 BW 抗性基因。这些与 BW 抗性相关的主要候选基因中的变异可以作为辣椒品种选育的重要标记。
