Abstract
The Pi-ta gene in rice has been effectively used to control rice blast disease caused by Magnaporthe oryzae worldwide. Despite a number of studies that reported the Pi-ta gene in domesticated rice and wild species, little is known about how the Pi-ta gene has evolved in US weedy rice, a major weed of rice. 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 US, we analyzed nucleotide sequence variation at the Pi-ta gene and its surrounding 2 Mb region in 156 weedy, domesticated and wild rice relatives. We found that the region at and around the Pi-ta gene shows very low genetic diversity in US weedy rice. The patterns of molecular diversity in weeds are more similar to cultivated rice (indica and aus), which have never been cultivated in the US, rather than the wild rice species, Oryza rufipogon. In addition, the resistant Pi-ta allele (Pi-ta) found in the majority of US weedy rice belongs to the weedy group strawhull awnless (SH), suggesting a single source of origin for Pi-ta. Weeds with Pi-ta were resistant to two M. oryzae races, IC17 and IB49, except for three accessions, suggesting that component(s) required for the Pi-ta mediated resistance may be missing in these accessions. Signatures of flanking sequences of the Pi-ta gene and SSR markers on chromosome 12 suggest that the susceptible pi-ta allele (pi-ta), not Pi-ta, has been introgressed from cultivated to weedy rice by out-crossing.
Highlights
Weedy rice is commonly found in cultivated rice fields and shares traits with both cultivated and wild rice
We found that nucleotide diversity at and around the Pi-ta locus in US weedy rice is exceptionally low when compared with that in other Oryza species
This result indicates the occurrence of genetic bottlenecks during the establishment of weedy rice in the US that is consistent with a few other reports [2,3,5,6]
Summary
Weedy rice is commonly found in cultivated rice fields and shares traits with both cultivated and wild rice. A few studies have been reported for more precise understanding the genomic diversity of US weedy rice and molecular evolution of important traits (shattering, red pigmentation, and phenol reaction locus Ph1) in weedy rice [2,3,5,6] In these studies, the research groups generated a large DNA sequence dataset for the target locus by sequencing at and flanking region of the locus. The research groups generated a large DNA sequence dataset for the target locus by sequencing at and flanking region of the locus This approach for genome-wide survey of nucleotide polymorphisms has enhanced our understanding of the molecular evolution and evolutionary origin of the gene in US weedy rice
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