Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation

Feng Liu, Jiantao Zhao, Honghe Sun, Cheng Xiong, Xuepeng Sun, Xin Wang, Zhongyi Wang, Robert Jarret, Jin Wang, Bingqian Tang, Hao Xu, Bowen Hu, Huan Suo, Bozhi Yang, Lijun Ou, Xuefeng Li, Shudong Zhou, Sha Yang, Zhoubing Liu, Fang Yuan, Zhenming Pei, Yanqing Ma, Xiongze Dai, Shan Wu (), Zhangjun Fei () and Xuexiao Zou ()
Additional contact information
Feng Liu: Hunan Agricultural University
Jiantao Zhao: Hunan Agricultural University
Honghe Sun: Boyce Thompson Institute
Cheng Xiong: Hunan Agricultural University
Xuepeng Sun: Boyce Thompson Institute
Xin Wang: Boyce Thompson Institute
Zhongyi Wang: Hunan Agricultural University
Robert Jarret: Plant Genetic Resources Conservation Unit
Jin Wang: Hunan Agricultural University
Bingqian Tang: Hunan Agricultural University
Hao Xu: Hunan Agricultural University
Bowen Hu: Hunan Agricultural University
Huan Suo: Hunan Agricultural University
Bozhi Yang: Hunan Agricultural University
Lijun Ou: Hunan Agricultural University
Xuefeng Li: Institute of Vegetable Research, Hunan Academy of Agricultural Science
Shudong Zhou: Institute of Vegetable Research, Hunan Academy of Agricultural Science
Sha Yang: Institute of Vegetable Research, Hunan Academy of Agricultural Science
Zhoubing Liu: Hunan Agricultural University
Fang Yuan: Hunan Agricultural University
Zhenming Pei: Hunan Agricultural University
Yanqing Ma: Hunan Agricultural University
Xiongze Dai: Hunan Agricultural University
Shan Wu: Boyce Thompson Institute
Zhangjun Fei: Boyce Thompson Institute
Xuexiao Zou: Hunan Agricultural University

Nature Communications, 2023, vol. 14, issue 1, 1-14

Abstract: Abstract Pepper (Capsicum spp.) is one of the earliest cultivated crops and includes five domesticated species, C. annuum var. annuum, C. chinense, C. frutescens, C. baccatum var. pendulum and C. pubescens. Here, we report a pepper graph pan-genome and a genome variation map of 500 accessions from the five domesticated Capsicum species and close wild relatives. We identify highly differentiated genomic regions among the domesticated peppers that underlie their natural variations in flowering time, characteristic flavors, and unique resistances to biotic and abiotic stresses. Domestication sweeps detected in C. annuum var. annuum and C. baccatum var. pendulum are mostly different, and the common domestication traits, including fruit size, shape and pungency, are achieved mainly through the selection of distinct genomic regions between these two cultivated species. Introgressions from C. baccatum into C. chinense and C. frutescens are detected, including those providing genetic sources for various biotic and abiotic stress tolerances.

Date: 2023
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-41251-4

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DOI: 10.1038/s41467-023-41251-4

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