ARS | Publication request: Characterization of Pi-ta Blast resistance gene in an international rice core collection

Submitted to: Plant Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 2, 2009
Publication Date: October 1, 2010
Citation: Wang, X., Fjellstrom, R.G., Jia, Y., Yan, W., Jia, M.H., Scheffler, B.E., Wu, D., Shu, Q., McClung, A.M. 2010. Characterization of Pi-ta Blast resistance gene in an international rice core collection. Plant Breeding. 129(5):491-501.

Interpretive Summary: Identification and characterization of blast resistance (R) genes are critical tasks to determine the presence of new virulent pathogen races. R genes to rice pathogens are predicted to be distributed among rice germplasm worldwide. The major blast R gene Pi-ta has been effectively deployed to control disease caused by all major races of the blast pathogen in the Southern US since 1990. However a virulent pathogen race (IE-1k) overcoming Pi-ta was found and reported to cause significant crop losses in several commercial rice fields. In the present study, a subset consisting of 193 world accessions was assembled to identify rice germplasm that contain the Pi-ta gene and germplasm that contain R gene to the race IE-1k. The Pi-ta gene was initially identified in 159 genetically diverse germplasm using an indel marker for Pi-ta. The intron and carboxyl terminus of the Pi-ta gene were also sequenced in the 193 accessions to verify the existence of the Pi-ta gene. The results showed that all 159 accessions contain the Pi-ta gene and a single amino acid alanine at the 918 position of the Pi-ta protein was confirmed to determine resistance specificity. In addition, a new single nucleotide polymorphism (SNP) in the intron region of the Pi-ta gene was identified to correlate with resistance. Ultimately, 83 accessions were identified to contain resistance genes not found in the US cultivars and which conferred resistance to race IE-1k. These accessions are useful as the resistance donors for rice improvement in the southern US.

Technical Abstract: The Pi-ta gene in rice prevents infections by races of Magnaporthe oryzae containing AVR-Pita. In the present study, 1,790 accessions were characterized for Pi-ta, and the Pi-ta independent resistance genes using marker analysis, disease evaluation with the race IB-49 carrying AVR-Pita, and IE-1k not carrying AVR-Pita and sequence analysis. A total of 183 accessions were identified using a Pi-ta indel marker from the intron region. Sequence analysis revealed that resistance functional nucleotide polymorphism (FNP) was present in 163 accessions including reference cultivars. Among them, 89 were resistant to IB-49 and susceptible to IE-1k indicating that these accessions contain the Pi-ta R alleles. Four accessions susceptible to IB-49 suggest that components were not intact in Pi-ta mediated resistance. In contrast, 14 accessions with the susceptible FNP were resistant to IB-49 suggesting these 14 accessions may contain the Pi-ta independent new R gene. Together, 87 accessions were identified that contain the new R gene to IE-1k. These accessions were genetically distinct determined by SSR markers. The results could impact breeding for blast resistance worldwide.