Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea.
National Academy of Agricultural Science, National Agrobiodiversity Center, Rural Development Administration, Jeonju, 54874, Republic of Korea.
Sci Rep. 2019 Jul 10;9(1):9962. doi: 10.1038/s41598-019-46342-1.
Phytophthora capsici (Leon.) is a globally prevalent, devastating oomycete pathogen that causes root rot in pepper (Capsicum annuum). Several studies have identified quantitative trait loci (QTL) underlying resistance to P. capsici root rot (PcRR). However, breeding for pepper cultivars resistant to PcRR remains challenging due to the complexity of PcRR resistance. Here, we combined traditional QTL mapping with GWAS to broaden our understanding of PcRR resistance in pepper. Three major-effect loci (5.1, 5.2, and 5.3) conferring broad-spectrum resistance to three isolates of P. capsici were mapped to pepper chromosome P5. In addition, QTLs with epistatic interactions and minor effects specific to isolate and environment were detected on other chromosomes. GWAS detected 117 significant SNPs across the genome associated with PcRR resistance, including SNPs on chromosomes P5, P7, and P11 that colocalized with the QTLs identified here and in previous studies. Clusters of candidate nucleotide-binding site-leucine-rich repeat (NBS-LRR) and receptor-like kinase (RLK) genes were predicted within the QTL and GWAS regions; such genes often function in disease resistance. These candidate genes lay the foundation for the molecular dissection of PcRR resistance. SNP markers associated with QTLs for PcRR resistance will be useful for marker-assisted breeding and genomic selection in pepper breeding.
辣椒疫霉（Phytophthora capsici）是一种全球性普遍存在、具有破坏性的卵菌病原体，可导致辣椒（Capsicum annuum）根腐病。已有多项研究鉴定了与辣椒疫霉根腐病（PcRR）抗性相关的数量性状位点（QTL）。然而，由于 PcRR 抗性的复杂性，培育对 PcRR 具有抗性的辣椒品种仍然具有挑战性。在这里，我们将传统的 QTL 作图与 GWAS 相结合，以拓宽我们对辣椒 PcRR 抗性的理解。三个主要效应位点（5.1、5.2 和 5.3）将广谱抗性赋予三种辣椒疫霉菌株，被定位到辣椒染色体 P5 上。此外，在其他染色体上还检测到了与环境具有上位性互作和特定于分离株的微小效应的 QTL。GWAS 在整个基因组中检测到 117 个与 PcRR 抗性相关的显著 SNP，包括染色体 P5、P7 和 P11 上的 SNP，这些 SNP 与这里和以前的研究中鉴定的 QTL 重叠。在 QTL 和 GWAS 区域内预测到了候选核苷酸结合位点-富含亮氨酸重复（NBS-LRR）和受体样激酶（RLK）基因簇；此类基因通常在疾病抗性中发挥作用。这些候选基因为 PcRR 抗性的分子解析奠定了基础。与 PcRR 抗性 QTL 相关的 SNP 标记将有助于辣椒的标记辅助选择和基因组选择育种。
