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United States Department of Agriculture

Agricultural Research Service


Location: Dale Bumpers National Rice Research Center

Title: New insight for two major rice blast R genes: Pi-ta and Pi-km)

item Costanzo, Stefano
item Yang, Y
item Jia, Yulin

Submitted to: Symposium Proceedings
Publication Type: Abstract only
Publication Acceptance Date: 8/5/2010
Publication Date: 8/12/2010
Citation: Costanzo, S., Yang, Y., Jia, Y. 2010. New insight for two major rice blast R genes: Pi-ta and Pi-km [abstract]. 5th International Rice Blast Conference, August 12-14, 2010, Little Rock, Arkansas. Abstract II-CO-84.

Interpretive Summary:

Technical Abstract: In rice breeding programs across the world, the introgression of major resistance (R) genes remains the most cost-effective method to control blast epidemics caused by the fungal pathogen Magnaporthe oryzae. During the last two years, we have examined two loci, on chromosome 12 and 11, which harbor previously characterized R genes Pi-ta and Pi-km, respectively. At the Pi-ta locus, we studied the gene expression, and identified new alternative splicing events as well as new introns and novel differentially spliced sites. A total of 12 transcript variants were predicted with open reading frames ranging from 945 to 3099 bp and encoding 11 distinct putative products between 315 and 1033 amino acids. Among them, five preserved complete nucleotide binding sites-leucine rich repeats (NBS-LRR) domains and two couple the original NBS-LRR domain of the Pi-ta protein with a C-terminal thioredoxin domain. These post-transcriptional modifications of Pi-ta produce a series of transcript isoforms that could have a significant role in R gene regulation and/or may increase protein diversity. Next, we explored the sequence variation for this locus. Proximal to the Pi-ta promoter region we discovered a 3364 bp fragment encoding a predicted transposase consistently associated with the resistance phenotype. Additionally, a previously un-characterized NBS-LRR gene located 10 kb (3–prime) from the Pi-ta locus was cloned and transformed in a rice cv. Kitake. Preliminary inoculation tests suggest this gene may contribute to enhanced blast resistance. At the Pi-km locus, we initially explored the existing sequence diversity for alleles of the two genes responsible for resistance specificity of this gene. The analysis of 15 rice cultivars revealed that the majority of nucleotide polymorphisms were only associated with the Pi-km1 gene. Interestingly, the correspondent amino acid variation was localized within the predicted coiled-coil domain of the putative Pi-km1 protein. In contrast, the sequence of Pi-km2 alleles was highly conserved even within distantly related cultivars. Furthermore, disease reactions of the selected cultivars to five M. oryzae races, as well as their determined Pi-km1 allele, showed a good correlation with the known Pi-k genes (-k/-kh/-km/-ks/-kp) historically reported for these cultivars. Based on these findings, specific primer sets have been designed to successfully discriminate among the various Pi-km alleles. The new information obtained from our studies has contributed to a better understanding of the gene-for-gene complex mechanisms regulating this plant-pathogen interaction as well as simplifying resistance breeding efforts by introducing more selective tools for marker assisted selection. References: 1. Costanzo, S. and Jia, Y. 2010. Sequence variation at the rice blast resistance gene Pi-km locus: Implications for the development of allele specific markers. Plant Sci. 178:523-530. 2. Lee, S., Costanzo, S., Jia, Y., Olsen, K.M. and Caicedo, A.L. 2009. Evolutionary dynamics of the genomic region around the blast resistance gene Pi-ta in AA genome oryza species. Genetics, 183:1315-1325. 3. Costanzo, S. and Jia, Y. 2009. Alternatively spliced transcripts of Pi-ta blast resistance gene in Oryza sativa. Plant Sci. 177:468-478.

Last Modified: 8/24/2016
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