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

Authors: LIU, FENG - Hunan Agricultural University; ZHAO, JIANTAO - Hunan Agricultural University; SUN, HONGHE - Boyce Thompson Institute; XIONG, CHENG - Hunan Agricultural University; SUN, XUEPENG - Boyce Thompson Institute; WANG, XIN - Boyce Thompson Institute; WANG, ZHONGYI - Hunan Agricultural University; Jarret, Robert - Bob; WANG, JIN - Hunan Agricultural University; TANG, BINGQIAN - Hunan Agricultural University; XU, HAO - Hunan Agricultural University; HU, BOWEN - Hunan Agricultural University; SUO, HUAN - Hunan Agricultural University; YANG, BOZHI - Hunan Agricultural University; OU, LIJUN - Hunan Agricultural University; LI, XUEFENG - Hunan Academy Of Agricultural Sciences; ZHOU, SHUDONG - Hunan Academy Of Agricultural Sciences; YANG, SHA - Hunan Academy Of Agricultural Sciences; LIU, ZHOUBING - Hunan Agricultural University; YUAN, FANG - Hunan Agricultural University; PEI, ZHENMING - Hunan Agricultural University; MA, YANQING - Hunan Agricultural University; DAI, XIONGZE - Hunan Agricultural University; WU, SHAN - Boyce Thompson Institute; FEI, ZHANGJUN - Boyce Thompson Institute; ZOU, XUEXIAO - Hunan Agricultural University

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/28/2023
Publication Date: 9/7/2023
Citation: Liu, F., Zhao, J., Sun, H., Xiong, C., Sun, X., Wang, X., Wang, Z., Jarret, R.L., Wang, J., Tang, B., Xu, H., Hu, B., Suo, H., Yang, B., Ou, L., Li, X., Zhou, S., Yang, S., Liu, Z., Yuan, F., Pei, Z., Ma, Y., Dai, X., Wu, S., Fei, Z., Zou, X. 2023. Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation. Nature Communications. 14(5487):1-14. https://doi.org/10.1038/s41467-023-41251-4.
DOI: https://doi.org/10.1038/s41467-023-41251-4

Interpretive Summary: Garden pepper is an important and valuable crop in the USA, and elsewhere in the world. Fundamental in efforts to improve this crop is a thorough knowledge and understanding of the genetic basis that accounts for the many traits that contribute to pepper productivity and fruit edibility and desirability. These include characteristics such as yield, fruit shape and taste, resistance to diseases and insects, etc. A new and higher quality DNA sequence of the entire pepper genome is presented. This study provides a more detailed analysis of the total genome (genetic makeup) of pepper (several types) than has previously been obtained. This improved DNA sequence was used successfully to classify various types of peppers into distinct groups that permits their classification as an aid to the management of pepper genetic resources. Unique areas within this DNA sequence provided useful information on how the various pepper types evolved and identified areas that are associated with resistance characteristics. In summary, this improved DNA sequence, and the tools that will be developed from it, contribute to our ability to understand the basis for the diversity of pepper types and characteristics, thus our ability to develop improved varieties of this important crop.

Technical Abstract: Pepper (Capsicum spp.) is one of the most ancient domesticated 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 high-quality genome of C. annuum var. annuum and a genome variation map of 500 accessions from the five domesticated Capsicum species and closely-related wild species. 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. The common domesticated traits in C. annuum var. annuum and C. baccatum var. pendulum such as enlarged fruit size and pungency are likely achieved mainly through the selection of different genomic regions, whereas diverse fruit shapes are likely the results of selection of both common and unique genomic regions. Introgression from C. baccatum into C. chinense and C. frutescens provides genetic sources for various biotic and abiotic stress resistances. This study improves our understanding of pepper diversity and domestication and offers valuable genomic resources.