Genome-Wide Association of Rice Blast Disease Resistance and Yield-Related Components of Rice.

Robust disease resistance may require an expenditure of energy that may limit crop yield potential. In the present study, a subset of a United States Department of Agriculture rice core collection consisting of 151 accessions was selected using a major blast resistance (R) gene, Pi-ta, marker and was genotyped with 156 simple sequence repeat (SSR) markers. Disease reactions to Magnaporthe oryzae, the causal agent of rice blast disease, were evaluated under greenhouse and field conditions, and heading date, plant height, paddy and brown seed weight in two field environments were analyzed, using an association mapping approach. A total of 21 SSR markers distributed among rice chromosomes 2 to 12 were associated with blast resistance, and 16 SSR markers were associated with seed weight, heading date, and plant height. Most noticeably, shorter plants were significantly correlated with resistance to blast, rice genomes with Pi-ta were associated with lighter seed weights, and the susceptible alleles of RM171 and RM6544 were associated with heavier seed weight. These findings unraveled a complex relationship between disease resistance and yield-related components.

Analysis of Genetic and Molecular Identity Among Field Isolates of the Rice Blast Fungus with an International Differential System, Rep-PCR, and DNA Sequencing.

The Pi-ta gene deployed in southern U.S. rice germplasm is effective in preventing the infection by strains of Magnaporthe oryzae isolates that carry the avirulence (AVR) gene AVR-Pita1. In the present study, 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 polymerase chain reaction (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 was a predominant group within each race. Pathogenicity assays on 'Katy' (Pi-ta) and 'M202' (pi-ta) rice determined that IC1 was virulent to Katy and M202; IB17, IC17, and most of IA1 and IB1 were avirulent to Katy and virulent to M202, suggesting that 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 10 AVR-Pita1 haplotypes, 4 of which were new. In total, 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 United States. Further research will be needed to verify this prediction.

Determination of Resistance Spectra of the Pi-ta and Pi-k Genes to U.S. Races of Magnaporthe oryzae Causing Rice Blast in a Recombinant Inbred Line Population.

Molecular tagged resistance (R) genes are useful for developing improved cultivar resistance using marker-assisted breeding. In the present study, R genes to common races of Magnaporthe oryzae, the causal agent of blast disease of rice (Oryza sativa), were mapped using an F10 recombinant inbred line (RIL) population derived from a cross of tropical japonica cv. Katy with breeding line RU9101001. Katy was resistant to 10 common U.S. races: IA-45, IB-1, IB-45, IB-49, IB-54, IC-17, ID-1, IE-1, IG-1, and IH-1 of M. oryzae. RU9101001 was resistant to races IA-45, IB-45, IB-54, IG-1, and IH-1. Katy and RU9101001 were susceptible to race IE-1k. Twenty-three polymorphic simple sequence repeat (SSR) markers were used to map R genes. Segregation ratios of 1:1 (resistant/susceptible) to races IB-1, IB-49, IC-17, ID-1, and IE-1 indicated the presence of a single dominant R gene in Katy. Ratios of 3:1 (resistant/susceptible) to races IA-45, IB-45, IG-1, and IH-1 indicated that a single R gene was present in Katy and a different R gene was present in RU9101001. Resistance to the abovementioned races was correlated with the presences of the Pi-ta gene and 11 Katy SSR alleles, suggesting that Pi-ta confers resistance to IA-45, IB-1, IB-45, IB-49, IC-17, IG-1, ID-1, IE-1, and IH-1. Katy, RU9101001, and all RILs were resistant to race IB-54, which was consistent with the presence of Pi-ks in Katy and Pi-kh in RU9101001. Resistance to IA-45, IB-45, IG-1, and IH-1 correlated with the presence of Pi-kh, suggesting that Pi-kh confers resistance to IA-45, IB-45, IG-1, and IH-1. These data suggest that Pi-ta and Pi-kh are effective R genes with overlapped resistance to the 10 common races of M. oryzae.

Instability of the Magnaporthe oryzae avirulence gene AVR-Pita alters virulence.

The avirulence gene AVR-Pita of Magnaporthe oryzae determines the efficacy of the resistance gene Pi-ta in rice. The structures of the AVR-Pita alleles in 39 US isolates of M. oryzae were analyzed using polymerase chain reaction. A series of allele-specific primers were developed from the AVR-Pita gene to examine the presence of AVR-Pita. Orthologous alleles of the AVR-Pita gene were amplified from avirulent isolates. Sequence analysis of five alleles revealed three introns at identical positions in the AVR-Pita gene. All five alleles were predicted to encode metalloprotease proteins highly similar to the AVR-Pita protein. In contrast, the same regions of the AVR-Pita alleles were not amplified in the most virulent isolates, and significant variations of DNA sequence at the AVR-Pita allele were verified by Southern blot analysis. A Pot3 transposon was identified in the DNA region encoding the putative protease motif of the AVR-Pita protein from a field isolate B2 collected from a Pi-ta-containing cultivar Banks. These findings show that transposons can contribute to instability of AVR-Pita and is one molecular mechanism for defeating resistance genes in rice cultivar Banks.

Mediation of partial resistance to rice blast through anaerobic induction of ethylene.

ABSTRACT The correlation between anaerobic soil conditions and increased resistance to rice blast disease has long been observed without benefit of an adequate explanation. We researched flood depth, dissolved oxygen (DO), and ethylene relative to expression of partial blast resistance in cvs. M-201, Newbonnet, LaGrue, Mars, and Cypress. Cultivar blast index (BI) and flood DO decreased with increasing flood depth. BIs were positively correlated with DO. Total leaf blast lesions were 3.4 and 3.2 times greater in cvs. M-201 and LaGrue growing in a 5.0-mul liter(-1) DO nutrient solution than when growing in a 0.1-mul liter(-1) DO solution. Treatment with 0.25 mM ethephon, which releases ethylene, lowered BIs of Newbonnet, LaGrue, and Cypress growing upland when applied drench, foliar, or foliar-drench. If flooded, BIs of ethephon-treated cultivars were decreased by drench and foliar-drench applications only. BIs of upland plants were unchanged, whereas BIs of analogous flooded plants increased following treatment with 0.31 mM aminoethoxyvinylglycine (AVG), an ethylene biosynthesis inhibitor. We hypothesize that varying anaerobic conditions mediate production of phytohormones, particularly ethylene, which modify expression of inherent partial blast resistance in these rice cultivars.

Rice Pi-ta gene Confers Resistance to the Major Pathotypes of the Rice Blast Fungus in the United States.

ABSTRACT The Pi-ta gene in rice prevents the infection by Magnaporthe grisea strains containing the AVR-Pita avirulence gene. The presence of Pi-ta in rice cultivars was correlated completely with resistance to two major pathotypes, IB-49 and IC-17, common in the U.S. blast pathogen population. The inheritance of resistance to IC-17 was investigated further using a marker for the resistant Pi-ta allele in an F(2) population of 1,345 progeny from a cross of cv. Katy with experimental line RU9101001 possessing and lacking, respectively, the Pi-ta resistance gene. Resistance to IC-17 was conferred by a single dominant gene and Pi-ta was not detected in susceptible individuals. A second F(2) population of 377 individuals from a reciprocal cross between Katy and RU9101001 was used to verify the conclusion that resistance to IC-17 was conferred by a single dominant gene. In this cross, individuals resistant to IC-17 also were resistant to IB-49. The presence of Pi-ta and resistance to IB-49 also was correlated with additional crosses between 'Kaybonnet' and 'M-204', which also possess and lack Pi-ta, respectively. A pair of primers that specifically amplified a susceptible pi-ta allele was developed to verify the absence of Pi-ta. We suggest that Pi-ta is responsible for resistance to IB-49 and IC-17 and that both races contain AVR-Pita genes.