The pepper restorer-of-fertility (CaRf) gene was fine mapped based on conjoint analysis of recombinants and collinearity between the two pepper reference genomes. Capana06g003028, encoding an Rf-like PPR protein, was proposed as the strongest candidate for pepper CaRf based on sequence comparison and expression analysis. The cytoplasmic male sterility (CMS)/restorer-of-fertility (Rf) system not only provides an excellent model to dissect genetic interactions between the mitochondria and nucleus but also plays a vital role in high-efficiency hybrid seed production in crops including pepper (Capsicum spp.). Although two important CMS candidate genes, orf507 and Ψatp6-2, have previously been suggested, the pepper Rf gene (CaRf) has not yet been isolated. In this study, a high-density genetic map comprising 7566 SNP markers in 1944 bins was first constructed with the array genotyping results from 317 F2 individuals. Based on this map, the CaRf gene was preliminarily mapped to a region of 1.15 Mb in length at the end of chromosome P6. Then, by means of a conjoint analysis of recombinants and collinearity between the two pepper reference genomes, an important candidate interval with 270.10 kb in length was delimited for CaRf. Finally, Capana06g003028, which encodes an Rf-like PPR protein, was proposed as the strongest candidate for CaRf based on sequence analysis and expression characteristics in sterile and fertile plants. The high-density genetic map and fine mapping results provided here lay a foundation for the application of molecular breeding, as well as cloning and functional analysis of CaRf, in pepper.

中文翻译：

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基于辣椒（Capsicum annuum L.）高密度遗传作图和共线性分析的生育力恢复基因精细定位。

基于重组体的联合分析和两个辣椒参考基因组之间的共线性，辣椒恢复力 (CaRf) 基因被精细定位。基于序列比较和表达分析，Capana06g003028 编码一种 Rf 样 PPR 蛋白，被认为是辣椒 CaRf 的最强候选者。细胞质雄性不育（CMS）/生育力恢复器（Rf）系统不仅为剖析线粒体和细胞核之间的遗传相互作用提供了一个极好的模型，而且在包括辣椒在内的作物的高效杂交种子生产中发挥着至关重要的作用。辣椒属）。尽管之前已经提出了两个重要的 CMS 候选基因 orf507 和 Ψatp6-2，但辣椒 Rf 基因 (CaRf) 尚未被分离出来。在这项研究中，首先使用来自 317 个 F2 个体的阵列基因分型结果构建了包含 1944 个 bin 中的 7566 个 SNP 标记的高密度遗传图谱。根据该图谱，初步将CaRf基因定位在P6染色体末端1.15 Mb长的区域。然后，通过对两个辣椒参考基因组之间的重组子和共线性进行联合分析，为 CaRf 划定了一个长度为 270.10 kb 的重要候选区间。最后，基于不育和可育植物中的序列分析和表达特征，提出了编码 Rf 样 PPR 蛋白的 Capana06g003028 作为 CaRf 的最强候选者。此处提供的高密度遗传图谱和精细定位结果为辣椒分子育种的应用以及CaRf的克隆和功能分析奠定了基础。