Submitted to: PLoS One
Publication Type: Peer reviewed journal
Publication Acceptance Date: 9/23/2011
Publication Date: 10/17/2011
Citation: Lee, S., Jia, Y., Jia, M.H., Gealy, D.R., Olsen, K.M., Caicedo, A.L. 2011. Molecular evolution of the rice blast resistance gene Pi-ta in invasive weedy rice in the USA. PLoS One. 6(10):e26260. doi:10.1371/journal.pone.0026260. Interpretive Summary: Red rice is a noxious weed that affects production and quality of commercial rice. To determine if a blast resistance gene Pi-ta can be introgressed into deployed rice cultivars, the genomic organization of Pi-ta in invasive weedy rice collected in the USA were analyzed. By analyzing nucleotide sequences and simple sequence repeat data spanning the Pi-ta locus in 58 US weedy rice accessions, 42 wild relatives and 48 cultivars, we found that the genomic region at and around Pi-ta shows low genetic diversity in US weedy rice, and that weeds are more similar to cultivated rice than to wild rice species, Oryza rufipogon, suggesting the possibility of selection for resistance against the rice blast pathogen. In addition, we found evidence suggesting that the susceptible pi-ta allele has been introgressed from US cultivated to weedy rice through outcrossings, but not resistant Pi-ta allele. These findings have significant impact on disease and weed management in rice production.
Technical Abstract: The Pi-ta gene has been effectively used to control rice blast disease caused by Magnaporthe oryzae in many rice growing regions in the world. A number of studies have characterized the molecular evolution of the Pi-ta gene in cultivated rice, O. sativa, and its wild ancestor O. rufipogon; however, information is lacking for the Pi-ta gene in US weedy rice, a major weed of cultivated rice that causes great economic and environmental problems in the US rice farming system. In order to investigate the genome organization of the Pi-ta gene in weedy rice and its relationship to gene flow between cultivated and weedy rice in the USA, we analyzed nucleotide sequences and SSR data in the genomic region of the Pi-ta gene in 58 US weedy rice accessions, as well as 42 wild relatives and 48 cultivars. We found that the genomic region at and around the Pi-ta gene shows low genetic diversity in US weedy rice, and that weeds are more similar to cultivated rice than to wild rice species, Oryza rufipogon. The known resistant Pi-ta allele from cultivated rice was found in the majority of US weedy rice collections, suggesting the possibility of selection for resistance against the rice blast pathogen. Weed accessions containing the resistant Pi-ta allele showed a high level of resistance to two predominantly US blast races IB49 and IC17. In addition, flanking sequences of the Pi-ta gene and SSR markers on rice chromosome 12 revealed that the susceptible pi-ta allele has been introgressed from US cultivated to weedy rice through outcrossings, but not resistant Pi-ta allele. To our knowledge this is the first study of a blast resistance gene in invasive strains of rice. Results of this study should benefit disease and weed management in rice productions worldwide.