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United States Department of Agriculture

Agricultural Research Service


Location: Dale Bumpers National Rice Research Center

Title: Analysis of genetic and molecular identity among field isolates of the rice blast fungus with an international differential system, rep-PCR and DNA sequencing

item Xing, Junjie
item Jia, Yulin
item Correll, James
item Lee, Fleet
item Cartwright, Richard
item Cao, Mengliang
item Yuan, Longping

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/7/2012
Publication Date: 4/2/2013
Publication URL:
Citation: Xing, J., Jia, Y., Correll, J.C., Lee, F.N., Cartwright, R., Cao, M., Yuan, L. 2013. Analysis of genetic and molecular identity among field isolates of the rice blast fungus with an international differential system, rep-PCR and DNA sequencing. Plant Disease. 97:491-495.

Interpretive Summary: Instability of rice blast resistance unraveled: The genetic identity of 169 blast disease isolates from rice cultivars, with and without the Pi-ta blast resistance gene, were analyzed genotypically and for their disease reaction. The genetic identity of isolates virulent on rice cultivars that carry Pi-ta were determined. This research demonstrated that genetic changes of blast fungus are the major causes of the instability of rice blast resistance.

Technical Abstract: The Pi-ta gene deployed in the Southern US rice germplasm is effective in preventing the infection by strains of Magnaporthe oryzae isolates that carry the avirulence gene AVR-Pita1. In the present study, a total of 169 isolates from rice (Oryza sativa) cultivars, with and without Pi-ta, were analyzed for their genetic identity using an international differential system, repetitive element-based PCR (Rep-PCR), and sequence analysis of PCR products of AVR-Pita1. These isolates belong to the races IA1, IB1, IB17, IC1, and IC17 of M. oryzae. These isolates were further classified into 15 distinct groups by Rep-PCR. There is a predominant group within each race. Pathogenicity assays on rice cultivars Katy (Pi-ta) and M202 (pi-ta) determined that IC1 was virulent to Katy and M202; IB17, IC17 and most of IA1 and IB1were avirulent to Katy and virulent to M202 suggesting the Pi-ta gene in Katy is responsible for preventing infection by these isolates. Consistently, AVR-Pita1 was not amplified from 28 virulent isolates. One AVR-Pita1 allele was amplified by AVR-Pita1-specific primers in 78 avirulent isolates. Interestingly, different AVR-Pita1 alleles were found in each of the 12 avirulent isolates as determined by DNA sequencing. Sequence analysis of 90 PCR products revealed ten AVR-Pita1 haplotypes, four of which were new. A total of 12 amino acid changes were identified in the new variants when compared with the first described AVR-Pita sequence (AF207841). The finding of isolates with altered AVR-Pita1 from rice cultivars with and without Pi-ta suggests that these virulent isolates were adapted to the field environments in the Southern US, further research will be needed to verify this prediction.

Last Modified: 06/24/2017
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