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Article

Genome-Wide Correlation of 36 Agronomic Traits in the 287 Pepper (Capsicum) Accessions Obtained from the SLAF-seq-Based GWAS

by
Lang Wu
1,2,†,
Peng Wang
1,2,†,
Yihao Wang
1,2,
Qing Cheng
1,2,
Qiaohua Lu
1,2,
Jinqiu Liu
1,2,
Ting Li
1,2,
Yixin Ai
1,2,
Wencai Yang
1,2,
Liang Sun
1,2,* and
Huolin Shen
1,2,*
1
Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
2
Department of Vegetable Science, College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Int. J. Mol. Sci. 2019, 20(22), 5675; https://doi.org/10.3390/ijms20225675
Submission received: 5 October 2019 / Revised: 29 October 2019 / Accepted: 4 November 2019 / Published: 13 November 2019
(This article belongs to the Section Molecular Genetics and Genomics)
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Abstract

There are many agronomic traits of pepper (Capsicum L.) with abundant phenotypes that can benefit pepper growth. Using specific-locus amplified fragment sequencing (SLAF-seq), a genome-wide association study (GWAS) of 36 agronomic traits was carried out for 287 representative pepper accessions. To ensure the accuracy and reliability of the GWAS results, we analyzed the genetic diversity, distribution of labels (SLAF tags and single nucleotide polymorphisms (SNPs)) and population differentiation and determined the optimal statistical model. In our study, 1487 SNPs were highly significantly associated with 26 agronomic traits, and 2126 candidate genes were detected in the 100-kb region up- and down-stream near these SNPs. Furthermore, 13 major association peaks were identified for 11 key agronomic traits. Then we examined the correlations among the 36 agronomic traits and analyzed SNP distribution and found 37 SNP polymerization regions (total size: 264.69 Mbp) that could be selected areas in pepper breeding. We found that the stronger the correlation between the two traits, the greater the possibility of them being in more than one polymerization region, suggesting that they may be linked or that one pleiotropic gene controls them. These results provide a theoretical foundation for future multi-trait pyramid breeding of pepper. Finally, we found that the GWAS signals were highly consistent with those from the nuclear restorer-of-fertility (Rf) gene for cytoplasmic male sterility (CMS), verifying their reliability. We further identified Capana06g002967 and Capana06g002969 as Rf candidate genes by functional annotation and expression analysis, which provided a reference for the study of cytoplasmic male sterility in Capsicum.
Keywords: pepper; agronomic traits; genome-wide association study (GWAS); specific-locus amplified fragment sequencing (SLAF-seq); multi-trait pyramid breeding; restorer-of-fertility (Rf) gene pepper; agronomic traits; genome-wide association study (GWAS); specific-locus amplified fragment sequencing (SLAF-seq); multi-trait pyramid breeding; restorer-of-fertility (Rf) gene

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MDPI and ACS Style

Wu, L.; Wang, P.; Wang, Y.; Cheng, Q.; Lu, Q.; Liu, J.; Li, T.; Ai, Y.; Yang, W.; Sun, L.; et al. Genome-Wide Correlation of 36 Agronomic Traits in the 287 Pepper (Capsicum) Accessions Obtained from the SLAF-seq-Based GWAS. Int. J. Mol. Sci. 2019, 20, 5675. https://doi.org/10.3390/ijms20225675

AMA Style

Wu L, Wang P, Wang Y, Cheng Q, Lu Q, Liu J, Li T, Ai Y, Yang W, Sun L, et al. Genome-Wide Correlation of 36 Agronomic Traits in the 287 Pepper (Capsicum) Accessions Obtained from the SLAF-seq-Based GWAS. International Journal of Molecular Sciences. 2019; 20(22):5675. https://doi.org/10.3390/ijms20225675

Chicago/Turabian Style

Wu, Lang, Peng Wang, Yihao Wang, Qing Cheng, Qiaohua Lu, Jinqiu Liu, Ting Li, Yixin Ai, Wencai Yang, Liang Sun, and et al. 2019. "Genome-Wide Correlation of 36 Agronomic Traits in the 287 Pepper (Capsicum) Accessions Obtained from the SLAF-seq-Based GWAS" International Journal of Molecular Sciences 20, no. 22: 5675. https://doi.org/10.3390/ijms20225675

APA Style

Wu, L., Wang, P., Wang, Y., Cheng, Q., Lu, Q., Liu, J., Li, T., Ai, Y., Yang, W., Sun, L., & Shen, H. (2019). Genome-Wide Correlation of 36 Agronomic Traits in the 287 Pepper (Capsicum) Accessions Obtained from the SLAF-seq-Based GWAS. International Journal of Molecular Sciences, 20(22), 5675. https://doi.org/10.3390/ijms20225675

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