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Long-read bitter gourd (Momordica charantia) genome and the genomic architecture of nonclassic domestication

Matsumura, Hideo Hsiao, Min-Chien Lin, Ya-Ping Toyoda, Atsushi Taniai, Naoki Tarora, Kazuhiko Urasaki, Naoya Anand, Shashi S. Dhillon, Narinder P. S. Schafleitner, Roland 信州大学 DOI:32461376

2022.01.27

概要

The genetic architecture of quantitative traits is determined by both Mendelian and polygenic factors, yet classic examples of plant domestication focused on selective sweep of newly mutated Mendelian genes. Here we report the chromosome-level genome assembly and the genomic investigation of a nonclassic domesti- cation example, bitter gourd (Momordica charantia), an important Asian vegetable and medicinal plant of the family Cucurbitaceae. Population resequencing revealed the divergence between wild and South Asian cultivars about 6,000 y ago, followed by the sep- aration of the Southeast Asian cultivars about 800 y ago, with the latter exhibiting more extreme trait divergence from wild progen- itors and stronger signs of selection on fruit traits. Unlike some crops where the largest phenotypic changes and traces of selec- tion happened between wild and cultivar groups, in bitter gourd large differences exist between two regional cultivar groups, likely reflecting the distinct consumer preferences in different countries. Despite breeding efforts toward increasing female flower proportion, a gynoecy locus exhibits complex patterns of balanced polymorphism among haplogroups, with potential signs of selective sweep within haplogroups likely reflecting artificial selection and introgression from cultivars back to wild accessions. Our study highlights the importance to investigate such nonclassic example of domestication showing signs of balancing selection and polygenic trait architecture in addition to classic selective sweep in Mendelian factors.

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