Yacong Cao
Kang Zhang
Hailong Yu
Shumin Chen
Donghui Xu
Hong Zhao
Zhenghai Zhang
Yinqing Yang
Xiaozhen Gu
Xinyan Liu
Haiping Wang
Yaxin Jing
Yajie Mei
Xiang Wang
Véronique Lefebvre
Weili Zhang
Yuan Jin
Dongliang An
Risheng Wang
Paul Bosland
Xixiang Li
Ilan Paran
Baoxi Zhang
Giovanni Giuliano
Lihao Wang
Feng Cheng

Pepper (Capsicum spp.) is an important vegetable crop, providing a unique pungent sensation when eaten. Through the construction of the pepper variome map, we describe the main groups that emerged during domestication and breeding of C. annuum, their relations and temporal succession, and the molecular events underlying the main transitions. The initial differentiation in fruit shape and pungency, increase in fruit weight, and transition from erect to pendent fruits, and the recent appearance of blocky, large, sweet fruits (bell peppers), were accompanied by strong selection/fixation of key alleles and introgressions in two large genomic regions. Furthermore, we describe the identification of Up, a key domestication gene controlling erect vs pendent fruit orientation, encoding a BIG GRAIN protein involved in auxin transport. The up gene gained increased expression especially in the fruit pedicel through a 579 bp sequence deletion in its 5' upstream region, resulting in the phenotype of pendent fruit. 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.