Abstract
BackgroundRice blast disease is one of the most serious and recurrent problems in rice-growing regions worldwide. Most resistance genes were identified by linkage mapping using genetic populations. We extensively examined 16 rice blast strains and a further genome-wide association study based on genotyping 0.8 million single nucleotide polymorphism variants across 366 diverse indica accessions.ResultsTotally, thirty associated loci were identified. The strongest signal (Chr11_6526998, P =1.17 × 10−17) was located within the gene Os11g0225100, one of the rice Pia-blast resistance gene. Another association signal (Chr11_30606558) was detected around the QTL Pif. Our study identified the gene Os11g0704100, a disease resistance protein containing nucleotide binding site-leucine rich repeat domain, as the main candidate gene of Pif. In order to explore the potential mechanism underlying the blast resistance, we further examined a locus in chromosome 12, which was associated with CH149 (P =7.53 × 10−15). The genes, Os12g0424700 and Os12g0427000, both described as kinase-like domain containing protein, were presumed to be required for the full function of this locus. Furthermore, we found some association on chromosome 3, in which it has not been reported any loci associated with rice blast resistance. In addition, we identified novel functional candidate genes, which might participate in the resistance regulation.ConclusionsThis work provides the basis of further study of the potential function of these candidate genes. A subset of true associations would be weakly associated with outcome in any given GWAS; therefore, large-scale replication is necessary to confirm our results. Future research will focus on validating the effects of these candidate genes and their functional variants using genetic transformation and transferred DNA insertion mutant screens, to verify that these genes engender resistance to blast disease in rice.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0311-6) contains supplementary material, which is available to authorized users.
Highlights
Rice blast disease is one of the most serious and recurrent problems in rice-growing regions worldwide
The correlation coefficient indicated that diseased leaf area (DLA) by blast strains CH131, CH154 and CH159 was significantly associated with latitude while DLA by CH251 was associated with longitude (r = −0.27, P =1.6 × 10−7) (Additional file 1: Figure S1)
Based on the SharedAllele distance [23] using the unweighted pair-group method with arithmetic mean (UPGMA) [24], the set of strains could be divided into two groups: one group only consisted of the strains CH131, CH212, CH362 and CH193, which have the weaker pathogenicity, and the other comprised the remaining 12 strains, which have the stronger pathogenicity (Additional file 2: Figure S2)
Summary
Rice blast disease is one of the most serious and recurrent problems in rice-growing regions worldwide. The strongest signal (Chr11_6526998, P =1.17 × 10−17) was located within the gene Os11g0225100, one of the rice Pia-blast resistance gene Another association signal (Chr11_30606558) was detected around the QTL Pif. Our study identified the gene Os11g0704100, a disease resistance protein containing nucleotide binding site-leucine rich repeat domain, as the main candidate gene of Pif. In order to explore the potential mechanism underlying the blast resistance, we further examined a locus in chromosome 12, which was associated with CH149 (P =7.53 × 10−15). About 180 R genes have been isolated to the disease caused by a pathogen infection (http://www.ricedata.cn/ontology). More than 68 loci, involved in rice blast resistance, referring to 83 major blast resistance genes, have been identified, and at least 24 resistance genes have been cloned (http://www.ricedata.cn/gene). Cultivating rice varieties with highly efficient, durable resistance to blast is still the most economically feasible and environmentally sound management approach in most blast-prone rice ecosystems
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