Genome-Wide Association Study of Leaf Blast Resistance in MAGIC indica Population of Rice (Oryza sativa L.)

Rice blast is one of the most widespread diseases threatening rice production and crop damage accounts for a major loss to rice farmers worldwide. To identify genetic regions associated with leaf blast resistance, a genome-wide association study was performed with 391 MAGIC indica plus rice accessions developed at IRRI, Philippines. Evaluation of leaf blast severity was performed in the uniform blast nursery (UBN) during 2016 and 2017 at ICAR-IIRR, Hyderabad, India. Genome-Wide Association Study was performed using six different statistical models with GBS data on 27041 single nucleotide polymorphisms (SNPs) distributed on all 12 rice chromosomes. A total of 130 associated SNP were detected and only seven common SNPs were identified with all the models on chromosome 3, 8, and 12. Farm CPU and Blink gave similar results and detected 31 associated SNPs on chromosome 3, 8, and 12. The highest number of annotated genes were identified on chromosome 12 followed by 8 and 3. Chromosome 12 harboring a major cluster of blast resistant genes and at least 20 blast resistant genes were mapped on this chromosome. Candidate genes identified in associated SNP regions on chromosome 12 in our study are encoding disease resistance genes; stripe rust resistance protein, MLA12, NBS-LRR disease resistance protein, NB-ARC domain-containing protein, CC-NBS-LRR resistance protein MLA13, indicating the possibility of developing casual SNPs/QTNs for leaf blast resistance in rice from these regions.