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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #306819

Title: Characterization of resistance genes to rice blast fungus Magnaporthe oryzae in a “Green Revolution” rice variety

Author
item LIU, YAN - University Of Arkansas
item QI, XINSHUAI - Washington University
item YOUNG, NELSON - University Of Massachusetts
item OLSEN, KENNETH - Washington University
item CAICEDO, ANA - University Of Massachusetts
item Jia, Yulin

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/7/2014
Publication Date: 1/24/2015
Publication URL: http://handle.nal.usda.gov/10113/60686
Citation: Liu, Y., Qi, X., Young, N.D., Olsen, K.M., Caicedo, A.L., Jia, Y. 2015. Characterization of resistance genes to rice blast fungus magnaporthe oryzae in a “Green Revolution” rice variety. Molecular Breeding. 35:52. DOI 10.1007/s11032-015-0256-y.

Interpretive Summary: Presently, most of blast resistance genes have been identified from indica rice germplasm worldwide. In the present study, we identified a blast resistance gene from the indica rice Dee Geo Woo Gen (DGWG), one of the major sources of the semi dwarf gene (SD1). SD1 has been used to reduce the stature of rice that played a critical role in the green revolution. The blast resistance gene named as Pi66(t) was identified using one field isolate of rice blast from the southern US, and DGWG was used as one parent to create two mapping populations consisting of 399 individuals. Approximately, 30-50 X of the genomes of three parents were sequenced using next generation sequencing to identify 20561 polymorphic single nucleotide polymorphisms (SNPs) for the construction of linkage maps. All individuals were genotyped with genotyping by sequencing and two linkage maps with over 20000 genetic markers were constructed. Consequently, Pi66(t) was delimited by two SNPs to a 129 kb region with six candidate genes on rice chromosome 11 which was close to nine known R genes. Analysis of an integrated physical map of these R genes and their blast resistance spectra suggested that Pi66(t) is a novel blast R gene. The closely linked SNPs can be readily used to tag Pi66(t) for breeding for improved blast resistance, and subsequently for positional cloning.

Technical Abstract: The indica rice variety Dee Geo Woo Gen (DGWG) was the source of the semi-dwarf gene (SD1) which played an important role in the Green Revolution. In the present study, resistance (R) genes to the U.S. race (isolate) IB54 of Magnaporthe oryzae, causal agent of rice blast disease, was investigated. Two recombinant inbred line (RIL) mapping populations, consisting of 175 and 224 individuals derived from crosses of DGWG with the straw hull weedy rice type PI653435 (AR-2001-1135; S population) and the black hull type PI653419 (MS-1996-9; B population), respectively, were used for mapping blast R genes and quantitative trait loci (QTLs). Two high resolution linkage maps with 6,179 (S population) and 14,382 (B Population) single nucleotide polymorphic (SNP) markers derived from genotyping-by-sequencing (GBS) data were used to map R genes. Two partial resistance QTLs, qBR1.1 and qBR6.1, and one major resistance QTL, qBR11.1, were identified in the B population. One partial resistance QTL, qBR6.1, and one major resistance QTL, qBR11.1, were confirmed with the S population. The total phenotypic variation of three resistance QTLs was 51 %, ranging from 1.12 % to 47.62 %, in the B population. All three resistance QTLs were localized to relatively small genomic regions. The major resistance QTL, qBR11.1, was mapped to a 129 kb region on chromosome 11 near nine known blast R genes. Analysis of an integrated physical map of these R genes and their blast resistance spectra suggested that Pi66(t) is a novel blast R gene. Within this 129 kb region, three genes encoding putative nucleotide-binding site (NBS) and leucine rich repeat (LRR) disease resistance proteins and three genes encoding WRKY transcription factors WRKY61, WRKY63, and WRKY41 were identified as candidate genes of qBR11.1 and tentatively designated as Pi66(t). Identification of blast R genes in DGWG should help continued deployment of useful genes for improving crop productivity and resistance to rice blast disease.