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Resequencing of Rosa rugosa accessions revealed the history of population dynamics, breed origin, and domestication pathways

Authors :
Fengqi Zang
Yan Ma
Qichao Wu
Xiaolong Tu
Xiaoman Xie
Ping Huang
Boqiang Tong
Yongqi Zheng
Dekui Zang
Source :
BMC Plant Biology, Vol 23, Iss 1, Pp 1-12 (2023)
Publication Year :
2023
Publisher :
BMC, 2023.

Abstract

Abstract Background Rosa rugosa is a shrub that originated in China and has economic and ecological value. However, during the development of R. rugosa, the genetic background was chaotic, and the genetic structure among different wild populations was unclear, as well as wild and cultivated accessions. Here, we report whole-genome resequencing of wild and cultivated R. rugosa accessions. Results A total of 19,041,284 SNPs were identified in 188 R. rugosa accessions and 3 R. chinensis accessions by resequencing. Population genetic analysis revealed that cultivated and wild groups were separated very early. All R. rugosa accessions were divided into 8 categories based on genetic structure: (1) Weihai, Yantai, and Liaoning category, (2) Jilin category, and (3) Hammonasset category (above three are wild); (4) traditional varieties, (5) hybrids between R. rugosa and R. chinensis, (6) Zizhi Rose, (7) Kushui Rose, (8) hybrids between R. rugosa and R. multiflora. We found that the heterozygosity and genetic diversity of wild accessions were generally lower than those of cultivated individuals. The genes that were selected during cultivation were identified, and it was found that these genes were mainly related to environmental adaptation and growth. Conclusions The Jilin population was the oldest population and later migrated to Liaoning and then migrated to Yantai and Weihai by sea regression in the Bohai Basin. The Hammonasset naturalized population probably originated from the Jilin population and then experienced separate differentiation. The long-term asexual reproduction pattern of R. rugosa decreased genetic diversity in the wild population. During R. rugosa cultivation, the ancestors of the Jilin population were involved in breeding traditional varieties, after which almost no wild individuals were engaged in breeding. However, in recent decades, cross breeding of R. rugosa started the utilization of wild germplasms. In comparison, some other species play important roles in variety formation. Few genes related to economic traits were selected, suggesting no directional domestication in the R. rugosa cultivation process.

Details

Language :
English
ISSN :
14712229
Volume :
23
Issue :
1
Database :
Directory of Open Access Journals
Journal :
BMC Plant Biology
Publication Type :
Academic Journal
Accession number :
edsdoj.b1c882bb25c848028547da78ee745ce7
Document Type :
article
Full Text :
https://doi.org/10.1186/s12870-023-04244-5