Recently, Wang Lihao's research team and Cheng Feng's research team from the Institute of Vegetables and Flowers of the Chinese Academy of Agricultural Sciences published a cooperative research result titled Pepper variety reveals the history and key loci associated with fruit domestication and diversity in Molecular Plant (IF: 21.949). The study resequencing of 347 portions of pepper germplasm resource from 12 pepper species, constructing a whole genome variation map of annually cultivated pepper species, revealing its process of domestication selection and breeding improvement, and at the same time identifying the genetic regulatory sites and population selection characteristics of important traits such as capsicum fruit orientation, fruit shape, and spicy taste. The research results have greatly deepened our understanding of the transmission and type diversification process of cultivated peppers, and provided strong support for the genetic improvement of pepper varieties.
pepper originated in Central and South America and is widely planted around the world. my country's pepper sowing area and output value rank first among all kinds of vegetables, and has important industrial value. The cultivar types of peppers are extremely rich, but the process of domestication selection, characteristics and genetic basis of important traits of peppers so far is not clear.
This study resequencing and variant analysis of 347 pepper germplasm resources collected from all over the world, and constructed a map of pepper variants containing 18,372,022 SNPs and 802,875 InDels. Based on genetic variation, combined with geographical origins, fruit type and other characteristics, the annual pepper population was divided into 9 main groups (Figure 1), namely: 1) wild/ancestral groups, including wild and more primitive materials; 2) local populations; 3) breeding improvement resource groups; 4) and 6) bell pepper group; 5) breeding varieties with different origins and diverse fruit shapes; 7) pepper resource groups in northwestern and northern China; 8) pepper resource groups in central China; 9) resource groups in high-altitude areas such as Yunnan, Guizhou, Sichuan and Tibet in southwestern China.
, through the comparison of variations in different groups and the genetic diversity of , revealed the domestication and improvement process of peppers from wild/ancestral species, local varieties to modern cultivars with diverse types from genome level (Figure 1). It was first proposed that the evolution of the pepper cultivation group underwent two steps of domestication: the first group of fruits were small, the first step of domestication made the capsicum fruits longer and spicy, forming the second group mainly based on local varieties; the second step of domestication made the capsicum fruits further longer and larger, and increasing the fruit weight, while the spicy rate was significantly reduced, forming the third group of breeding improved. The two-step domestication process of peppers is accompanied by strong domestication choices with different types of gene sets. At the same time, the study revealed that the domestication history of bell peppers in groups 4 and 6 was relatively short, and for the first time, the key infiltration events of two wild genomic fragments located on chromosomes 9 and 11 and the strong selection clearance of the capsaicin regulatory gene Pun1 was closely related to the formation of the large fruit bell pepper (bell pepper). In particular, the study also found that the 9th group had the highest genetic diversity among Chinese pepper groups, suggesting that southwestern China may be an area with early introduction of peppers and abundant sources, with certain characteristics of secondary origin or diversification centers.
Figure 1 Chili group division and two-step domestication and improvement process
Based on the mutation group data, GWAS analysis of pepper population was further carried out. Combined with genetic localization and other studies, the key domestication gene Up that controls the orientation of the fruit was identified and verified in plants for the first time. The Up gene encodes a protein associated with auxin transport, and there is a 579 bp structural variant (SV, missing) in the upstream region of its gene. Through experiments such as transcriptome , VIGS, etc., it was found that the expression difference of this gene in different fruit orientation materials was completely related to its fruit orientation (Figure 2). It was also found that the 579 bp variant is located in a repetitive sequence of the retroposon type (LINE). Based on the methylation experimental data, it was speculated that the existence of its sequence affected the methylation intensity of transposon silencing inhibition of , resulting in differences in the expression of Up gene. In addition, this study also locates multiple gene loci related to important traits of capsicum fruit, such as FSI that regulates the shape of the fruit, Punv that regulates the spicy taste, etc.
Figure 2 Up gene that determines the orientation of capsicum fruits. Based on the above results, this study proposes an evolutionary model that dominated the process of domestication, differentiation and type diversification of pepper cultivation species by key gene loci at important traits of pepper. The combination of domestication choices for the fruit orientation gene Up, fruit shape regulation gene FSI, spicy flavor regulation gene Pun1 and punv, as well as two wild infiltration fragments, are the key genetic basis for the formation of diversified types of bell peppers with large fruit bell peppers and narrow fruit (or long) peppers (Figure 3). In summary, the study constructed a data set of variation groups of pepper cultivation populations, revealing the genome selection characteristics and key gene loci in the process of domestication and diversification of capsicum fruits. The analysis of genetic loci and regulatory mechanisms of important traits such as fruit shape, spicyity and fruit orientation has laid an important foundation for the study of pepper functional genomics , and also provides an important theoretical basis for pepper molecular breeding and genetic improvement.
Figure 3 Key events affecting the domestication and diversification of capsicum fruits
This study takes from the Institute of Vegetable and Flowers of the Chinese Academy of Agricultural Sciences as the first completion unit, and assistant researchers Cao Yacong, Zhang Kang, Yu Hailong, Chen Shumin and Xu Donghui are the first authors of the paper, and researcher Cheng Feng, Wang Lihao and Professor Giovanni Giuliano from the Italian National Center for New Technology, Energy and Sustainable Economic Development are the joint corresponding author . The research was supported by projects such as the National Key R&D Plan, the Chinese Academy of Agricultural Sciences Science and Technology Innovation Project, the technology system of the bulk vegetable industry, and the National Natural Science Foundation. (Zhang Kang)
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