S02 - Session O3 - Pepper core collection analysis and genome resequence reveals the evens in domestication

Authors: Yacong Cao, Kang Zhang, Hong Zhao, Hailong Yu, Donghui Xu, Shumin Chen, Zhenghai Zhang, Véronique Lefebvre, Paul Bosland, Ilan Paran, Giovanni Giuliano, Feng Cheng, Lihao Wang *

Pepper ( Capsicum spp.) is one of the earliest domesticated crops. We analyzed the genetic diversity of 1904 international accessions conserved at China National Vegetable Germplasm Genebank with 29 simple sequence repeat (SSR) markers to set up a core collection of 248 accessions, capturing 75.6% of the alleles. Three hundred forty-seven pepper accessions, including the core collection from 12 species, were selected for genotyping and phenotyping. Forty-three horticultural traits were investigated in three different locations of China in two years. With Illumina Solexa platform for resequencing and generating 10.1 trillion paired-end reads, the average depth is about 9X. 18,372,022 SNPs and 802,875 InDels were obtained by referencing Zunla-1 2.0 genome. The pepper variome via resequencing data describe the main groups that emerged during domestication and breeding of C. annuum , their relations and temporal succession, and the molecular events underlying the major transitions. The initial differentiation in fruit shape and pungency, increase in fruit weight, the transition from erect to pendent fruits, and the recent appearance of blocky, large, sweet fruits were accompanied by introgressions in chromosomes 9 and 11 derived from distant introgressions, probably of wild C. annuum . Furthermore, we identified contributing genes according to GWAS analysis. Functional proved, Up Capana12g000954 , a key domestication gene controlling erect vs pendant fruit orientation, encoding a BIG GRAIN protein involved in auxin transport. Flip1 (Capana06g001204) , encoding a protein involved in phospholipid flipping, is associated with decreased capsaicinoids content. TRM25 (Capana03g002426) is associated with elongated fruit shape. The function of Up was confirmed by virus-induced gene silencing. These findings constitute a cornerstone for understanding the domestication and differentiation of a key horticultural crop such as the pepper.