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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #257064

Title: Screening and association mapping of rice blast disease resistance using a diverse collection of rice germplasm

item ALI, M. LIAKAT - Arkansas Agricultural Experiment Station
item ZHAO, KEYAN - Cornell University
item TUNG, CHIH-WEI - Cornell University
item WRIGHT, MARK - Cornell University
item REYNOLDS, ANDY - Cornell University
item BUSTAMANTE, CARLOS - Cornell University
item McClung, Anna
item MCCOUCH, SUSAN - Cornell University
item Eizenga, Georgia

Submitted to: Symposium Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 7/16/2010
Publication Date: 8/12/2010
Citation: Ali, M.L., Zhao, K., Tung, C., Wright, M., Reynolds, A., Bustamante, C.D., Mcclung, A.M., Mccouch, S.R., Eizenga, G.C. 2010. Screening and association mapping of rice blast disease resistance using a diverse collection of rice germplasm. p. 96. In: Proc. 5th Int. Rice Blast Conf. 12-14 Aug. 2010. Little Rock, Arkansas USA.

Interpretive Summary:

Technical Abstract: Rice blast, caused by the fungus Magnaporthe oryzae B. Couch, is a very serious disease in rice (Oryza sativa L.) worldwide. Incorporation of new blast resistance genes into breeding lines is an important objective of many rice breeding programs. A diverse collection of 409 O. sativa accessions described as the “Rice Diversity Panel” was purified by single plant selection for two generations and genotyped with SSR markers and 44,000 SNP markers. Based on SSR markers, the five rice subpopulation groups represented in this panel are aus (59 accessions), indica (90), temperate japonica (108), tropical japonica (104), and aromatic/ GroupV (15), as well as, admixture groups representing the Indica (11 accessions) and Japonica (22) varietal groups. The objectives of this study were to 1) rate the Diversity Panel for reaction to blast disease, 2) identify new germplasm as a source of blast resistance using SSR/SNP markers associated with Pi-genes, and 3) discover novel “marker-blast trait” associations. The diversity panel was scored on a “0” (no disease) to “9” (dead) scale for reaction to M. oryzae, after field inoculation with a mixture of the U.S. blast races, IB-49, IC-17 and IE-1K. Accessions in the indica subpopulation were the most resistant (mean=3.0) to these races while temperate japonica was the most susceptible (mean=7.0). The Pi-b resistance gene on chromosome 2 confers resistance to races IC-17 and IE-1K. Only 16 accessions, mostly indica, carried the Pi-b allele and rated < 3.0. Similarly for Pi-ta on chromosome 12, only 30 accessions, mostly indica, carried Pi-ta resistance allele and 23 of the 30 accessions rated < 3.0. The Pi-ta gene confers resistance to races IB-49 and IC-17. A Genome Wide Association (GWA) scan using genotypes from the 44,000 SNP array identified marker-blast trait associations in the complete diversity panel and only within four of the five subpopulation groups (aus, indica, tropical and temperate japonica). Physical positions of these associations were compared with the position of approx. 12 cloned blast resistance genes located on chromosomes 1, 2, 4, 6, 8, 9, 11 and 12 using the TIGR/MSU v6 sequence annotation. There was strong signal around the Pi-ta gene in the GWA scan and SNPs in the neighboring regions of some of the other cloned genes. Different sets of Pi-genes were identified across the different subpopulations illustrating the genetic heterogeneity of blast resistance. Further investigation of these marker-blast trait associations should identify new SNP markers linked to the blast resistance and possibly new germplasm sources of resistance genes. Both the new SNP markers and novel candidate Pi-genes could be used to incorporate blast resistance into new rice cultivars.