J Syst Evol ›› 2021, Vol. 59 ›› Issue (2): 316-325.DOI: 10.1111/jse.12565

• Research Articles • Previous Articles     Next Articles

Origins of weedy rice revealed by polymorphisms of chloroplast DNA sequences and nuclear microsatellites

Nan Yao1†, Zhe Wang1†‡, Zhuo-Jun Song1, Lei Wang1, Yong-Sheng Liu2, Ying Bao3*, and Bao-Rong Lu1*   

  1. 1Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, Department of Ecology and Evolutionary Biology, Fudan University, Shanghai 200438, China
    2School of Horticulture, Anhui Agricultural University, Hefei 230036, China
    3School of Life Sciences, Qufu Normal University, Qufu 273165, Shandong, China
  • Received:2019-04-14 Accepted:2019-11-14 Online:2020-01-05 Published:2021-03-01

Abstract: Conspecific weeds that permanently infest worldwide agroecosystems are evolved from their crop species. These weeds cause substantial problems for crop production by competing for resources in agricultural fields. Weedy rice represents such a conspecific weed infesting rice ecosystems, and causing tremendous rice yield losses owing to its strong competitiveness and abundant genetic diversity, likely resulted from its complex origins. Here, we report the use of chloroplast DNA (cpDNA) fingerprints to determine whether weedy rice is evolved from its wild (exo‐feral) or cultivated (endo‐feral) rice progenitor as the maternal donor in recent hybridization events. In addition, we also applied nuclear simple sequence repeat (SSR) markers to confirm the exo‐feral or endo‐feral origins of weedy rice accessions determined by the cpDNA fingerprints. We found that the studied weedy rice accessions evolved either from their wild or cultivated rice progenitor, as the maternal donor, based on the cpDNA network and structure analyses. Combined analyses of cpDNA and nuclear SSR markers indicated that a much greater proportion of weedy rice accessions had the endo‐feral origin. In addition, results from the genetic structure of nuclear SSR markers indicated that weedy rice accessions from the endo‐feral pathway are distinctly associated with either indica or japonica rice cultivars, suggesting their complex origins through crop–weed introgression. The complex pathways of origin and evolution could greatly promote genetic diversity of weedy rice. Therefore, innovative methods should be developed for effective weedy rice control.

Key words: genetic structure, molecular markers, Networking analysis, Oryza sativa f. spontanea, weed evolution, wild relatives