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Identification of candidate genes underlying genic male-sterile msc-1 locus via genome resequencing in Capsicum annuum L.

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Based on genome resequencing, a strong candidate gene Capana02g002096 was identified in this study. Capana02g002096 encodes a homolog of AtDYT1 which is a bHLH transcription factor and involves in the early tapetal development.

Abstract

Genic male-sterile line is an efficient tool for commercial hybrid seed production in pepper; however, so far, only few genes controlling this trait have been cloned. A spontaneous genic male-sterile mutant, msc-1, had been identified and widely used in China, of which the male-sterile trait was proved to be controlled by a single recessive locus. For cloning the gene(s) underlying the msc-1 locus, genome resequencing and comparison analyses were performed between male-sterile and male-fertile lines. According to the genomic variations and genes’ annotations, Capana02g002096 was selected as a candidate gene underlying the msc-1 locus. Capana02g002096 encodes a homolog of AtDYT1, which is a bHLH transcription factor and involves in the early tapetal development. Moreover, a 7-bp deletion was identified in the exon of Capana02g002096, which led to a premature stop codon and may cause a loss-of-function mutation. Further genotyping in the 16C1369AB population containing 1110 plants, a F2 population consisting of 510 plants and 46 inbreed lines revealed that the male-sterile phenotype was co-segregated with the 7-bp deletion. Additionally, real-time PCR analysis revealed that Capana02g002096 was an anther-specific gene and repression of the gene’s expression through VIGS led to male-sterile phenotype. Therefore, based on the evidence at genetic, genomic, transcriptional and posttranscriptional levels, Capana02g002096 was considered as a strong candidate gene underlying the msc-1 locus in pepper and was renamed Msc-1.

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Acknowledgements

This research was supported by The National Key Research and Development Program of China (2017YFD0101903) and the Beijing Fruit Vegetables Innovation Team of Modern Agricultural Industry Technology System (BAIC01-2018).

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Authors and Affiliations

  1. Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China

    Qing Cheng, Peng Wang, Jinqiu Liu, Lang Wu, Zongpeng Zhang, Tiantian Li, Wenjiao Gao, Wencai Yang, Liang Sun & Huolin Shen

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  1. Qing Cheng
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  2. Peng Wang
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Contributions

QC performed most of the experiments, analyzed the data and drafted the manuscript. LS draw the figures and modified the manuscript. PW and QL performed VIGS experiments. LW and ZZ participated in DNA extraction. TL and WG performed the qRT-PCR analysis. WY revised the manuscript. HS and LS designed and directed the entire study. All authors have read and approved the final manuscript.

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Correspondence to Liang Sun or Huolin Shen.

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Communicated by Michael J. Havey.

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Cheng, Q., Wang, P., Liu, J. et al. Identification of candidate genes underlying genic male-sterile msc-1 locus via genome resequencing in Capsicum annuum L.. Theor Appl Genet 131, 1861–1872 (2018). https://doi.org/10.1007/s00122-018-3119-1

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