Chloroplast and whole-genome sequencing shed light on the evolutionary history and phenotypic diversification of peanuts
Zheng Zheng, Ziqi Sun, Feiyan Qi, Yuanjin Fang, Ke Lin, Stefano Pavan, Bingyan Huang, Wenzhao Dong, Pei Du, Mengdi Tian, Lei Shi, Jing Xu, Suoyi Han, Huan Liu, Qin Li, Zhongxin Zhang, Xiaodong Dai, Lijuan Miao, Ruifang Zhao, Juan Wang, Yan-Lin Liao, Alun Li, Jue Ruan, Chiara Delvento, Riccardo Aiese Cigliano, Chris Maliepaard, Yuling Bai, Richard G. F. Visser, Xinyou Zhang
Abstract
Cultivated peanut (Arachis hypogaea L.) is a widely grown oilseed crop worldwide; however, the events leading to its origin and diversification are not fully understood. Here by combining chloroplast and whole-genome sequence data from a large germplasm collection, we show that the two subspecies of A. hypogaea (hypogaea and fastigiata) likely arose from distinct allopolyploidization and domestication events. Peanut genetic clusters were then differentiated in relation to dissemination routes and breeding efforts. A combination of linkage mapping and genome-wide association studies allowed us to characterize genes and genomic regions related to main peanut morpho-agronomic traits, namely flowering pattern, inner tegument color, growth habit, pod/seed weight and oil content. Together, our findings shed light on the evolutionary history and phenotypic diversification of peanuts and might be of broad interest to plant breeders.