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United States Department of Agriculture

Agricultural Research Service

Research Project: RESPONSE OF DIVERSE RICE GERMPLASM TO BIOTIC AND ABIOTIC STRESSES Title: Evolutionary dynamics and structure of the rice blast resistance locus Pi-ta in wild, cultivated, and US weedy rice

item Lee, S -
item Costanzo, Stefano
item Olsen, Kenneth -
item Caicedo, A -

Submitted to: Symposium Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: August 5, 2010
Publication Date: August 12, 2010
Citation: Lee, S., Jia, Y., Costanzo, S., Olsen, K.M., Caicedo, A., Gealy, D.R., Jia, M.H. 2010. Evolutionary dynamics and structure of the rice blast resistance locus Pi-ta in wild, cultivated, and US weedy rice [abstract]. 5th International Rice Blast Conference, August 12-14, 2010, Little Rock, Arkansas. Abstract II-CO-85.

Technical Abstract: The Pi-ta gene in rice has been used to control rice blast pathogen, Magnaporthe oryza, in rice growing areas worldwide for decades. To understand the evolutionary process and natural selection of Pi-ta during rice domestication, we first examined sequences of the genomic region of Pi-ta in geographically diverse rice accessions of AA genome Oryza species: O. sativa, O. rufipogon, O. nivara, O. meridionalis, O, barthii, O. glaberrima, and O. glumaepatula. A single amino acid change at position 918 of the Pi-ta protein known to determine resistance specificity was consistently found in O. sativa and O. rufipogon. Interestingly, a 3364 bp fragment encoding a predicted transposon was also consistently found in the proximity of the Pi-ta promoter region associated with the resistance phenotype. In O. rufipogon, patterns potentially consistent with recent directional selection were found in the Pi-ta region, while no significant deviation from neutral evolution was found in O. sativa groups. Results of sequence variation in flanking regions around Pi-ta in O. sativa suggest that the size of the resistance Pi-ta introgressed block was at least 5.4 Mb in all elite resistant cultivars, but not in the cultivars without Pi-ta, suggesting that the Pi-ta region has evolved under extensive selection pressure during crop breeding. In a complementary study, in order to understand the evolutionary dynamics of the Pi-ta locus in US weedy rice, we analyzed nucleotide sequences and SSR markers at/around the Pi-ta genomic region in US weedy rice samples. The level of genetic diversity in the US weedy rice population was low compared with that in cultivated and wild rice groups. The same resistant Pi-ta in cultivated rice was found in the majority of US weedy rice. Phylogenetic relationships of Pi-ta in weedy red rice suggest that they are genetically closer to both Asian and US cultivated rice than to O. rufipogon. Evidence for direct gene flow of Pi-ta between US cultivars and US weedy rice was not found, but possible evidence of natural hybridization at the Pi-ta locus was observed between three weedy rice accessions (1025-01, 1214-02, and TX4) and three US cultivars (Edith, Carolina Gold, and Blue Rose). In addition, the Pi-ta genomic region (8 Mb) in the weedy rice accession 2002-2-pot 21 was identical to that of Lemont, Cypress, Delitus, Rexoro, CL121, and CL161, presenting the evidence of hybridization events occurring at the pi-ta locus between cultivated and weedy rice. Details and significance of these new findings will be presented. References: 1. Lee, S., Costanzo, S., Olsen, K.M., Caicedo, A.L. and Jia, Y. 2009. Evolutionary dynamics of the blast resistance gene Pi-ta in AA genome group of Oryza species during domestication. Genetics 183: 1315-1325. 2. Jia, Y., Liu, G., Costanzo, S., Lee, S., and Dai, Y. 2009. Current progress on genetic interactions of rice with rice blast and sheath blight. Frontier of Agriculture in China 3(3): 231-239.

Last Modified: 8/3/2015
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