Lin, Ya-Ping, Chen, Hung-Wei, Yeh, Pei-Min, Anand, Shashi S., Lin, Jiunn, Li, Juan, Noble, Thomas, Nair, Ramakrishnan, Schafleitner, Roland, Samsononova, Maria, Bishop-von-Wettberg, Eric, Nuzhdin, Sergey, Ting, Chau-Ti, Lawn, Robert J., and Lee, Cheng-Ruei (2023) Demographic history and distinct selection signatures of two domestication genes in mungbean. Plant Physiology, 193 (2). pp. 1197-1212.

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Abstract

Domestication is the long and complex process underlying the evolution of crops, in which artificial directional selection transformed wild progenitors into the desired form, affecting genomic variation and leaving traces of selection at targeted loci. However, whether genes controlling important domestication traits follow the same evolutionary pattern expected under the standard selective sweep model remains unclear. With whole-genome resequencing of mungbean (Vigna radiata), we investigated this issue by resolving its global demographic history and targeted dissection of the molecular footprints of genes underlying 2 key traits representing different stages of domestication. Mungbean originated in Asia, and the Southeast Asian wild population migrated to Australia about 50 thousand generations ago. Later in Asia, the cultivated form diverged from the wild progenitor. We identified the gene associated with the pod shattering resistance trait, VrMYB26a, with lower expression across cultivars and reduced polymorphism in the promoter region, reflecting a hard selective sweep. On the other hand, the stem determinacy trait was associated with VrDet1. We found that 2 ancient haplotypes of this gene have lower gene expression and exhibited intermediate frequencies in cultivars, consistent with selection favoring independent haplotypes in a soft selective sweep. In mungbean, contrasting signatures of selection were identified from the detailed dissection of 2 important domestication traits. The results suggest complex genetic architecture underlying the seemingly simple process of directional artificial selection and highlight the limitations of genome-scan methods relying on hard selective sweeps.across cultivars and reduced polymorphism in the promoter region, reflecting a hard selective sweep. On the other hand, the stem determinacy trait was associated with VrDet1. We found that 2 ancient haplotypes of this gene have lower gene expression and exhibited intermediate frequencies in cultivars, consistent with selection favoring independent haplotypes in a soft selective sweep. In mungbean, contrasting signatures of selection were identified from the detailed dissection of 2 important domestication traits. The results suggest complex genetic architecture underlying the seemingly simple process of directional artificial selection and highlight the limitations of genome-scan methods relying on hard selective sweeps.

Item ID:	79569
Item Type:	Article (Research - C1)
ISSN:	1532-2548
Keywords:	Genomics; Wild crop relatives; Native Vigna spp; Australian wild mungbean
Copyright Information:	© American Society of Plant Biologists 2023. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com
Date Deposited:	10 Oct 2023 01:57
FoR Codes:	30 AGRICULTURAL, VETERINARY AND FOOD SCIENCES > 3004 Crop and pasture production > 300406 Crop and pasture improvement (incl. selection and breeding) @ 25% 31 BIOLOGICAL SCIENCES > 3105 Genetics > 310509 Genomics @ 50% 31 BIOLOGICAL SCIENCES > 3104 Evolutionary biology > 310499 Evolutionary biology not elsewhere classified @ 25%
SEO Codes:	26 PLANT PRODUCTION AND PLANT PRIMARY PRODUCTS > 2603 Grains and seeds > 260303 Grain legumes @ 100%
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