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Article|28 Feb 2022|OPEN
Genomic population structure and local adaptation of the wild strawberry Fragaria nilgerrensis
Yuxi Hu1,2 , Chao Feng1 , Lihua Yang1 and Patrick P. Edger3 , Ming Kang,1,4 ,
1Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
2University of Chinese Academy of Sciences, Beijing 100049, China
3Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
4Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
*Corresponding author. E-mail: mingkang@scbg.ac.cn

Horticulture Research 9,
Article number: uhab059 (2022)
doi: https://doi.org/10.1093/hr/uhab059
Views: 331

Received: 22 Jul 2021
Revised: 10 Apr 2022
Accepted: 15 Oct 2021
Published online: 28 Feb 2022

Abstract

The crop wild relative Fragaria nilgerrensis is adapted to a variety of diverse habitats across its native range in China. Thus, discoveries made in this species could serve as a useful guide in the development of new superior strawberry cultivars that are resilient to new or variable environments. However, the genetic diversity and genetic architecture of traits in this species underlying important adaptive traits remain poorly understood. Here, we used whole-genome resequencing data from 193 F. nilgerrensis individuals spanning the distribution range in China to investigate the genetic diversity, population structure and genomic basis of local adaptation. We identified four genetic groups, with the western group located in Hengduan Mountains exhibiting the highest genetic diversity. Redundancy analysis suggested that both environment and geographic variables shaped a significant proportion of the genomic variation. Our analyses revealed that the environmental difference explains more of the observed genetic variation than geographic distance. This suggests that adaptation to distinct habitats, which present a unique combination of abiotic factors, likely drove genetic differentiation. Lastly, by implementing selective sweep scans and genome–environment association analysis throughout the genome, we identified the genetic variation associated with local adaptation and investigated the functions of putative candidate genes in F. nilgerrensis.