A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits

Guangwei Zhao (1) , Qun Lian (1) , Zhonghua Zhang (2, 3) , Qiushi Fu (1) , Yuhua He (1) , Shuangwu Ma (1) , Valentino Ruggieri (4, 5) , Antonio Monforte (6) , Pingyong Wang (1) , Irene Julca (7, 8, 9) , Huaisong Wang (1) , Junpu Liu (1) , Yong Xu (10) , Runze Wang (11) , Jiabing Ji (1) , Zhihong Xu (1) , Weihu Kong (1) , Yang Zhong (1) , Jianli Shang (1) , Lara Pereira (5, 4) , Jason Argyris (5, 4) , Jian Zhang (12) , Carlos Mayobre (4, 5) , Marta Pujol (4, 5) , Elad Oren (4, 5) , Diandian Ou (1) , Jiming Wang (1) , Dexi Sun (1) , Shengjie Zhao (1) , Yingchun Zhu (1) , Na Li (1) , Nurit Katzir (13) , Amit Gur , Catherine Dogimont (14) , Hanno Schaefer (15) , Wei Fan (16) , Abdelhafid Bendahmane (14) , Zhangjun Fei (17) , Michel Pitrat (14) , Toni Gabaldón (9) , Tao Lin (18) , Jordi Garcia-Mas (4, 5) , Yongyang Xu (1) , Sanwen Huang (1)

1 CAAS - Chinese Academy of Agricultural Sciences
2 Inst Vegetables & Flowers
3 Qingdao Agricultural University
4 IRTA - Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology
5 CRAG - Centre for Research in Agricultural Genomics
6 IBMCP - Instituto de Biologia Molecular y Celular de Plantas
7 UAB - Universitat Autònoma de Barcelona = Autonomous University of Barcelona = Universidad Autónoma de Barcelona
8 CRG - Centre for Genomic Regulation - Centre de Regulació Genòmica [Barcelona]
9 UPF - Universitat Pompeu Fabra [Barcelona]
10 Department of Energy & Materials Engineering - Dongguk University, Seoul
11 State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences
12 Beijing Academy of Agriculture and Forestry Sciences
13 ARO - Agricultural Research Organisation
14 GAFL - Génétique et Amélioration des Fruits et Légumes
15 Plant Biodiversity Research
16 CAS - Chinese Academy of Sciences [Beijing]
17 Boyce Thompson Institute [Ithaca]
18 Department of Fruit Science, College of Horticulture

Melon is an economically important fruit crop that has been cultivated for thousands of years; however, the genetic basis and history of its domestication still remain largely unknown. Here we report a comprehensive map of the genomic variation in melon derived from the resequencing of 1,175 accessions, which represent the global diversity of the species. Our results suggest that three independent domestication events occurred in melon, two in India and one in Africa. We detected two independent sets of domestication sweeps, resulting in diverse characteristics of the two subspecies melo and agrestis during melon breeding. Genome-wide association studies for 16 agronomic traits identified 208 loci significantly associated with fruit mass, quality and morphological characters. This study sheds light on the domestication history of melon and provides a valuable resource for genomics-assisted breeding of this important crop.

Mots clés: cucumber cucumis-sativus; wide association; population-structure; tomato; gene; tool; diversity; cloning; color

Domaines: Sciences de l'Homme et Société

Guangwei Zhao, Qun Lian, Zhonghua Zhang, Qiushi Fu, Yuhua He, et al.. A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits. Nature Genetics, 2019, 51 (11), pp.1607-1615. ⟨10.1038/s41588-019-0522-8⟩. ⟨hal-02527982⟩