Dissection of QTL alleles for blast resistance based on linkage and linkage disequilibrium mapping in japonica rice seedlings

Rice blast is one of the major fungal diseases that badly reduce rice production in China and worldwide. Molecular markers tightly linked to resistant genes can be used for marker-assisted and/or genomic selection. In this study, linkage mapping and association mapping were used to identify the QTLs for the disease index of 7 and 14 days after inoculation (DI7 and DI14) conferring resistance against two highly pathogenic and locally predominant isolates (DB22 and DB77) in japonica rice at the seedling stage. The recombinant inbred line (RIL) population with 114 SSR markers derived from Dongnong 415 (resistant to rice blast) as the male parent and Lijiangxintuanheigu (LTH, susceptible to rice blast) as the female parent was used for linkage mapping. A total of 10 QTLs were identified by the inclusive composite interval mapping method (ICIM), explaining 7.89-33.75 % of the total phenotypic variance. This study was supplemented with association mapping, which was conducted using a panel of 227 japonica rice cultivars released in Northeastern China during the past 50 years with 118 selected SSR markers. A total of 13 significant marker-trait associations (P a parts per thousand currency signaEuro parts per thousand 0.01) involving 10 markers were identified using the MLM (Q + K) models in TASSEL 3.0. Among them, 8 of the SSR markers confirmed or narrowed the genomic regions for blast resistance that were reported in linkage studies, including five QTLs identified during the present study. Phenotypic effects of each allele of the 8 stable markers were compared, and 12 resistant alleles were identified. These resistant alleles could be used to design parental combinations and the expected results would be obtained by pyramiding or substituting the resistant alleles per QTL (apart from possible epistatic effects). The results should increase our understanding of the genetic basis of blast resistance and facilitate future resistant breeding in rice.