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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: Sequence variation at the rice blast resistance gene Pi-km locus: Implications for the development of allele specific markers

Authors
item Costanzo, Stefano
item Jia, Yulin

Submitted to: Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 20, 2010
Publication Date: February 24, 2010
Repository URL: http://handle.nal.usda.gov/10113/42901
Citation: Costanzo, S., Jia, Y. 2010. Sequence variation at the rice blast resistance gene Pi-km locus: Implications for the development of allele specific markers. Plant Science. 178-523-530.

Interpretive Summary: Recently a new blast resistance (R) gene Pi-km has been cloned that protects rice crops against specific races of the fungal pathogen Magnaporthe oryzae. The use of blast R genes remains the most cost-effective method for an integrated disease management strategy. To facilitate rice breeding we developed a Pi-km specific DNA marker. For this purpose, we explored the existing sequence diversity, within several US cultivars for alleles of the two genes responsible for the Pi-km specificity. Based on our findings, specific primer sets have been designed to discriminate among the various Pi-km alleles. The new markers should simplify the introgression of the valuable blast resistance associated with the complex Pi-k locus into rice cultivars.

Technical Abstract: The recently cloned blast resistance (R) gene Pi-km protects rice crops against specific races of the fungal pathogen Magnaporthe oryzae in a gene-for-gene manner. The use of blast R genes remains the most cost-effective method for an integrated disease management strategy. To facilitate rice breeding we developed a Pi-km specific DNA marker. For this purpose, we initially explored the existing sequence diversity for alleles of the two genes responsible for the Pi-km specificity. The analysis of 15 rice cultivars revealed that the majority of nucleotide polymorphisms were 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 isolates, 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 discriminate among the various Pi-km alleles. The new markers should simplify the introgression of the valuable blast resistance associated with the complex Pi-k locus into rice cultivars.

Last Modified: 12/22/2014
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