Phylogenetic origin and dispersal pattern of Taiwan weedy rice.

Authors: WU, DONG-HONG - Taiwan Agricultural Research Institute; Gealy, David; Jia, Melissa; Edwards, Jeremy; LAI, MING-HSIN - Agricultural Research Institute Of Taiwan; McClung, Anna

Submitted to: Pest Management Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/12/2019
Publication Date: 11/12/2019
Citation: Wu, D., Gealy, D.R., Jia, M.H., Edwards, J., Lai, M., McClung, A.M. 2019. Phylogenetic origin and dispersal pattern of Taiwan weedy rice. Pest Management Science. https://doi.org/10.1002/ps.5683.
DOI: https://doi.org/10.1002/ps.5683

Interpretive Summary: Weedy red rice is a severe pest of rice in both the southern USA and Taiwan, reducing crop productivity and grain quality. In a large-scale cooperative project between rice scientists of Taiwan and the USDA, detailed DNA analyses showed that most weedy red rice in Taiwan rice fields was genetically similar to cultivated rice that had been produced in these fields in the distant past. By contrast, most weedy rice in the USA is genetically similar to rice that has never been cultivated in USA rice fields. An evaluation of population genetics revealed that most Taiwan weedy rice types had originated from intercrossing in the distant past between old cultivated red-bran rice landraces and an old Indica variety, ‘Dee-Geo-Woo-Gen’, although crosses with more modern Indica varieties have also occurred. An analysis combining knowledge of the ancestral backgrounds of weedy rice types with their geographic locations suggested that the distribution of weed contamination resulted from long-distance transport of seed at planting time across Taiwan, often from warmer, earlier-planted regions to cooler, later-planted regions and not from short-distance movement of pollen. Even though there had been extensive efforts before 1945 to remove red-bran landraces from paddy fields, cropping practices that include ratooning and allowing volunteer rice plants from the first crop to serve as the second crop have contributed to the persistence of weedy rice contamination observed in Taiwan rice fields.

Technical Abstract: Weedy red rice is a severe pest of rice in both the southern USA and Taiwan. In a large-scale cooperative project between rice scientists of Taiwan and the USA, principal coordinates analysis (PCoA) was used to show that most weedy red rice of Taiwan was genetically similar to Indica cultivars or old landraces from Taiwan, contrasting with the USA where weedy rice was genetically intermediate between Indica and AUS rice subpopulations. The inbreeding coefficient of the Taiwan weedy red rice (TWR) population was high (>0.8) and similar to that of the inbred temperate Japonica and Indica cultivars of Taiwan, which suggests that Taiwan weedy rice was derived from multiple generations of self-pollination that occurred following much earlier outcrossing events. A combined analysis of the ancestry coefficients and geographic locations of weedy rice suggests a dispersal pattern of long-distance and seed-mediated contamination across Taiwan, often from warmer, earlier-planted regions to cooler, later-planted regions. Parentage analysis of Taiwan weedy rice revealed that Indica landraces, Indica cultivars, and temperate Japonica populations were present in the weedy rice gene pool. The results indicated the two main clusters of Taiwan weedy rice were derived from red bran Indica landraces crossed with cultivars derived from ‘Dee-Geo-Woo-Gen (DGWG) / D. S. Wied’ or ‘DGWG / Ling-Ho’. Two other clusters were very similar to modern Indica cultivars such as ‘Taichung sen 10’ or ‘Taichung sen waxy 2’. Few weedy rice accessions (3%) appear to be derived from hybridization between Indica and Japonica rice. Based on these results, the phylogenetic origin of most Taiwan weedy rice appears to be from hybrid progenies of old cultivated red rice accessions crossed with ‘DGWG’ derived cultivars. The inbreeding coefficient trend of the six TWR clusters suggests a temporal shift from “old” red-bran Indica landraces with a high inbreeding coefficient to modern Indica varieties with a low inbreeding coefficient. Although there were sustained efforts to remove these old red rice accessions from paddy fields before 1945, some farmers continued to use contaminated seed sources for planting. This practice, along with cultivation of volunteer rice in the second cropping season, apparently facilitated seed-mediated contamination of rice seed, and the increase in weedy rice in paddy soils.