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Peer-reviewedCC BY 4.0Frontiers in Plant Science

Genome-wide association study of yield and yield-related traits in pepper (Capsicum annuum L.)

  • Xiaocui Chen1
  • Xiaowei Zhang1
  • Shichao Sun2
  • Hong Yang3
  • Cheng Qin1
  • Dan Zhou1
  • Di Peng1
  • Qingqing Li1
  • Xiaosong Gou1
  • Ao Wang1
  1. 1Zunyi Academy of Agricultural Sciences
  2. 2State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences
  3. 3Guizhou Academy of Agricultural Sciences
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Abstract

Fruit morphology and yield are major determinants of pepper market value and productivity, but the genetic basis of these traits remains incompletely resolved. In this study, we evaluated 195 Capsicum annuum accessions for six fruit morphology and yield-related traits in two environments. The traits showed substantial variation, with coefficients of variation of 40.43-57.09% and broad-sense heritability of 0.59-0.97. Reduced-representation sequencing generated 76,418 high-quality single nucleotide polymorphisms, and population analyses resolved eight genetic subgroups. Genome-wide association analysis detected 23 significant loci, comprising 12 loci for fruit morphology and 11 loci for yield-related traits. These loci contained 318 unique genes. Notably, the major fruit-length loci qFL2 and qFL5 contained gibberellin 20 oxidase 1 ( GA20ox1 ) and an OVATE family protein gene corresponding to the functionally characterized pepper fruit-elongation regulator CaOFP20 , respectively. These loci, allele-trait associations, and putative candidate genes provide a basis for further validation and marker development in pepper breeding.

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Cite

BibTeXRIS
BibTeX
@article{chen2026genomewide,
  title = {{Genome-wide association study of yield and yield-related traits in pepper (Capsicum annuum L.)}},
  author = {Xiaocui Chen and Xiaowei Zhang and Shichao Sun and Hong Yang and Cheng Qin and Dan Zhou and Di Peng and Qingqing Li and Xiaosong Gou and Ao Wang},
  journal = {Frontiers in Plant Science},
  year = {2026},
  month = oct,
  doi = {10.3389/fpls.2026.1926954},
  url = {https://www.frontiersin.org/articles/10.3389/fpls.2026.1926954/full},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Genome-wide association study of yield and yield-related traits in pepper (Capsicum annuum L.)
AU  - Xiaocui Chen
AU  - Xiaowei Zhang
AU  - Shichao Sun
AU  - Hong Yang
AU  - Cheng Qin
AU  - Dan Zhou
AU  - Di Peng
AU  - Qingqing Li
AU  - Xiaosong Gou
AU  - Ao Wang
PY  - 2026
DA  - 2026/10/22
JO  - Frontiers in Plant Science
DO  - 10.3389/fpls.2026.1926954
UR  - https://www.frontiersin.org/articles/10.3389/fpls.2026.1926954/full
AB  - Fruit morphology and yield are major determinants of pepper market value and productivity, but the genetic basis of these traits remains incompletely resolved. In this study, we evaluated 195 Capsicum annuum accessions for six fruit morphology and yield-related traits in two environments. The traits showed substantial variation, with coefficients of variation of 40.43-57.09% and broad-sense heritability of 0.59-0.97. Reduced-representation sequencing generated 76,418 high-quality single nucleotide polymorphisms, and population analyses resolved eight genetic subgroups. Genome-wide association analysis detected 23 significant loci, comprising 12 loci for fruit morphology and 11 loci for yield-related traits. These loci contained 318 unique genes. Notably, the major fruit-length loci qFL2 and qFL5 contained gibberellin 20 oxidase 1 ( GA20ox1 ) and an OVATE family protein gene corresponding to the functionally characterized pepper fruit-elongation regulator CaOFP20 , respectively. These loci, allele-trait associations, and putative candidate genes provide a basis for further validation and marker development in pepper breeding.
SN  - 1664-462X
ER  -