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Fine mapping of restorer-of-fertility gene based on high-density genetic mapping and collinearity analysis in pepper (Capsicum annuum L.)

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Abstract

Key message

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.

Abstract

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.

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (31372076, 31672162 and 31701921), the Guangzhou Science and Technology Plan Projects (201704020019), the Natural Science Foundation of Guangdong Province (2019A1515011784) and the Opening Project (No. 011) of the Key Laboratory of Urban Agriculture in South China, Ministry of Agriculture and Rural Affairs. We acknowledge Mrs. Cuiling Zhong for her kind help in manuscript preparation. We thank the reviewers for their insightful and constructive comments to improve our manuscript.

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  1. Jiaowen Cheng and Yijian Chen have contributed equally to this work.

Authors and Affiliations

  1. College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China

    Jiaowen Cheng, Yijian Chen, Yafei Hu, Ziyan Zhou, Fang Hu, Jichi Dong, Weili Chen & Kailin Hu

  2. Department of Horticulture, College of Food Science and Engineering, Foshan University, Foshan, 528200, Guangdong, China

    Junjie Cui

  3. College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China

    Zhiming Wu

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  1. Jiaowen Cheng
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Contributions

JWC and KLH conceived and designed the experiments; JWC, YJC, ZYZ, FH, JCD and JJC performed the experiments; JWC, YFH, ZMW and KLH analysed the data; JWC and KLH wrote the manuscript. All authors reviewed and approved the manuscript.

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Correspondence to Kailin Hu.

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Cheng, J., Chen, Y., Hu, Y. et al. Fine mapping of restorer-of-fertility gene based on high-density genetic mapping and collinearity analysis in pepper (Capsicum annuum L.). Theor Appl Genet 133, 889–902 (2020). https://doi.org/10.1007/s00122-019-03513-y

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