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

被引：20

作者：

Liu, Feng ^{[1
]}

Zhao, Jiantao ^{[1
,2
]}

Sun, Honghe ^{[2
,3
]}

Xiong, Cheng ^{[1
]}

Sun, Xuepeng ^{[2
,7
]}

Wang, Xin ^{[2
,8
]}

Wang, Zhongyi ^{[1
]}

Jarret, Robert ^{[4
]}

Wang, Jin ^{[1
]}

Tang, Bingqian ^{[1
]}

Xu, Hao ^{[1
]}

Hu, Bowen ^{[1
]}

Suo, Huan ^{[1
]}

Yang, Bozhi ^{[1
]}

Ou, Lijun ^{[1
]}

Li, Xuefeng ^{[5
]}

Zhou, Shudong ^{[5
]}

Yang, Sha ^{[5
]}

Liu, Zhoubing ^{[1
]}

Yuan, Fang ^{[1
]}

Pei, Zhenming ^{[1
]}

Ma, Yanqing ^{[1
]}

Dai, Xiongze ^{[1
]}

Wu, Shan ^{[2
]}

Fei, Zhangjun ^{[2
,6
]}

Zou, Xuexiao ^{[1
]}

机构：

[1] Hunan Agr Univ, Coll Hort, Engn Res Ctr Germplasm Innovat & New Varieties Bre, Key Lab Vegetable Biol Hunan Prov, Changsha, Peoples R China

[2] Boyce Thompson Inst Plant Res, Ithaca, NY 14853 USA

[3] Cornell Univ, Sch Integrat Plant Sci, Plant Biol Sect, Ithaca, NY USA

[4] USDA ARS, Plant Genet Resources Conservat Unit, Griffin, GA USA

[5] Hunan Acad Agr Sci, Inst Vegetable Res, Changsha, Peoples R China

[6] USDA ARS, Robert W Holley Ctr Agr & Hlth, Ithaca, NY 14853 USA

[7] Zhejiang A&F Univ, Coll Hort Sci, Hangzhou, Peoples R China

[8] Huazhong Agr Univ, Coll Hort & Forestry, Dept Vegetable Crops, Wuhan, Peoples R China

来源：

NATURE COMMUNICATIONS | 2023年 / 14卷 / 01期

基金：

美国国家科学基金会; 中国国家自然科学基金;

关键词：

DE-NOVO IDENTIFICATION; PHYLOGENETIC-RELATIONSHIPS; FAMILIES; MODEL; GENE; RESISTANCE; PREDICTION; INFERENCE; ALIGNMENT; DATABASE;

D O I：

10.1038/s41467-023-41251-4

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：14

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