1College of Horticulture, South China Agricultural University/State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/ Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, 510642 Guangzhou, China 2Tropical Crop Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, 571737 Danzhou, China 3Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, 510640 Guangzhou, China 4BGI Genomics, BGI-Shenzhen, 518083 Shenzhen, China 5Vegetable Research Institute, Guangxi Academy of Agricultural Sciences, 530007 Nanning, China 6Crop Research Institute, Fujian Academy of Agricultural Sciences, 350013 Fuzhou, China 7Institute of Vegetable Research, Hunan Academy of Agricultural Sciences, 410125 Changsha, China 8Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, 330200 Nanchang, China 9World Vegetable Center, East and Southeast Asia, Research and Training Station, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand *Corresponding author. E-mail: hewm@genomics.cn,narinder.dhillon@worldveg.org,hukailin@scau.edu.cn
Received: 04 Feb 2020 Revised: 14 Mar 2020 Accepted: 23 Mar 2020 Published online: 01 Jun 2020
Abstract
Bitter gourd (Momordica charantia) is a popular cultivated vegetable in Asian and African countries. To reveal the characteristics of the genomic structure, evolutionary trajectory, and genetic basis underlying the domestication of bitter gourd, we performed whole-genome sequencing of the cultivar Dali-11 and the wild small-fruited line TR and resequencing of 187 bitter gourd germplasms from 16 countries. The major gene clusters (Bi clusters) for the biosynthesis of cucurbitane triterpenoids, which confer a bitter taste, are highly conserved in cucumber, melon, and watermelon. Comparative analysis among cucurbit genomes revealed that the Bi cluster involved in cucurbitane triterpenoid biosynthesis is absent in bitter gourd. Phylogenetic analysis revealed that the TR group, including 21 bitter gourd germplasms, may belong to a new species or subspecies independent from M. charantia. Furthermore, we found that the remaining 166 M. charantia germplasms are geographically differentiated, and we identified 710, 412, and 290 candidate domestication genes in the South Asia, Southeast Asia, and China populations, respectively. This study provides new insights into bitter gourd genetic diversity and domestication and will facilitate the future genomics-enabled improvement of bitter gourd.
, Narinder P. S. Dhillon9 ,
