The Institute of Vegetables and Flowers of the Chinese Academy of Agricultural Sciences reveals the genetic basis of the selection characteristics of chili pepper domestication and important traits of fruit

Recently, the research team of Wang Lihao and Cheng Feng of the Institute of Vegetables and Flowers of the Chinese Academy of Agricultural Sciences published collaborative research results
entitled Pepper variome reveals the history and key loci associated with fruit domestication and diversification at Molecular Plant (IF: 21.
949).
。 In this study, 347 pepper germplasm resources from 12 pepper species were resequenced, and the whole genome variation map of annually cultivated pepper species was constructed, revealing the process of domestication selection and breeding improvement, and identifying the genetic regulation loci and population selection characteristics
of important traits such as 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, widely cultivated in the world, China's pepper sown area and output value are ranked first in all kinds of vegetables, has important industrial value
.
The types of cultivars cultivated in pepper are extremely rich, but the genetic basis for the domestication selection process and characteristics and important traits of peppers is not clear
so far.

 

In this study, 347 pepper germplasm resources collected from around the world were resequenced and variationally analyzed, and a map
of pepper variants containing 18,372,022 SNPs and 802,875 InDels was constructed 。 Based on genetic variation, combined with geographical origin, fruit type and other characteristics, the annual pepper population is divided into 9 main groups (Figure 1), namely: 1) wild/ancestral groups, including wild and more primitive materials; 2) local populations; 3) Breeding and improvement resource groups; 4) and 6) for the group of bell peppers; 5) Breeding variety groups with different origins and diverse fruit shapes; 7) Pepper resource groups in northwest and northern China; 8) Central China pepper resource group; 9) Resource groups
in high-altitude areas such as Yunnan-Guizhou-Sichuan-Tibet in southwest China.

 

Through the comparison of variation and genetic diversity in different groups, the domestication and improvement process
of pepper from wild/ancestral species, local varieties to modern cultivated varieties with diverse types was revealed from the whole genome level.
For the first time, it is proposed that the evolution of pepper cultivation groups has undergone a two-step domestication process: the first group has small fruits, and the first step of domestication has made the pepper fruits longer and more spicy, forming a second group dominated by local varieties; The second step of domestication led to further lengthening and enlargement of the pepper fruit, an increase in fruit weight, and a significant decrease in spiciness, forming a breeding improvement group
3.
The two-step domestication process of peppers is strongly selected
for domestication along with different types of gene sets.
At the same time, the study revealed a relatively short history of domestication of groups 4 and 6 of bell peppers, with the first discovery of key infiltration events of two wild genomic fragments located on chromosomes 9 and 11 and the strong selective clearance of the capsaicin regulatory gene Pun1 that is closely related
to the formation of big-fruit bell peppers (bell peppers).
In particular, the study also found that Group 9 had the highest genetic diversity in the Chinese pepper taxa, suggesting that southwestern China may be an area of earlier and abundant sources of chili peppers, characterized by some secondary origin or diversification centers
.

 

Based on the variome data, the GWAS analysis of pepper populations was further carried out, combined with genetic mapping and other studies, and the key domestication gene Up that controlled fruit orientation was identified and verified in plants for the
first time.
The Up gene encodes a protein associated with auxin transport with a 579 bp structural variant (SV, deletion)
in the upstream region of its gene.
Through transcriptome, VIGS and other experiments, it was found that the expression difference of this gene in different fruit-oriented materials was completely related
to its fruit orientation.
It was found that the 579 bp variant was located in a repeat sequence of the reverse seat type (LINE), and combined with the methylation experimental data, it was speculated that the presence of its sequence affected the methylation intensity of transposon silencing inhibition, resulting in differences
in the expression of the Up gene.
In addition, this study also locates multiple gene loci related to important traits of pepper fruit, such as FSI that regulates fruit shape and punv that regulates spicy taste
.

 

Based on the above results, this study proposes an evolutionary model
of the process of domestication, differentiation and type diversification of pepper cultivars dominated by key gene loci of important properties of pepper.
The different combination of domestication selections for the fruit orientation gene Up, the fruit-shaped regulatory gene fsi, the spicy taste regulatory genes Pun1 and punv, and 2 wild involution fragments are the key genetic basis for
the formation of diversified types of large-fruit bell pepper and narrow-fruit (or long-shaped) pepper 。 In summary, this study constructs the variome dataset of pepper cultivar populations, reveals the genome selection characteristics and key gene loci in the process of pepper fruit domestication and diversification, and the analysis of the genetic loci and regulatory mechanisms of important traits such as fruit shape, spiciness and fruit orientation lays an important foundation for the study of pepper functional genomics, and also provides an important theoretical basis
for molecular breeding and genetic improvement of pepper.

 

The study was completed first by the Institute of Vegetables and Flowers of the Chinese Academy of Agricultural Sciences, with assistant researchers Cao Yacong, Zhang Kang, Yu Hailong, Chen Shumin and Xu Donghui as the first authors of the paper, and Professor Cheng Feng, Wang Lihao and Professor Giovanni Giuliano of the Italian National Center for New Technology, Energy and Sustainable Economic Development as co-corresponding authors
.
The research is supported
by the National Key R&D Program, the Science and Technology Innovation Project of the Chinese Academy of Agricultural Sciences, the Technology System of the Bulk Vegetable Industry, and the National Natural Science Foundation of China.

 

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