Mining and Identification of Functional Novel Alleles of Pi2/9 locus From Rice 3K Germplasm Against Rice Blast, Magnaporthe oryzae via Genome Wide Association Study (GWAS) Pipeline
C. CHAIPANYA (1), J. Divina (1), F. Borja (1), J. Yanoria (1), R. Mauleon (1), R. Opulencia (1), C. Jantasuriyarat (2), B. Zhou (1) (1) International Rice Research Institute, Philippines; (2) Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand

Rice blast caused by fungal Magnaporthe oryzae is known to be the most devastating biotic stress affecting rice farmers globally, causing severe economic losses and threatening food chain supply. We report mining of R alleles at the Pi2/9 locus from the sequenced 3K rice germplasm via GWAS approach. A set of blast differential isolates was used to differentiate novel alleles from known ones at the Pi2/9 locus. Phenotypic-genotypic association was explored utilizing PLINK-1.07 along PLINK-1.9 program with confounding population structure determination and correction through PCA was performed via EIGENSOFT-v6.0.1. Shortlisted candidate lines harboring 10 most significant alleles were retrieved and exposed to 4 additional blast strains. Of the 27 lines, 8 lines were resistant towards all of IRRI's differential isolate set. cDNA was derived from these lines and subsequently shipped for sequencing. Clustering via MEGA-v.5 indicates 5 different sequence patterns from sequenced lines wherein 1 is a known Piz-t allele and 4 are putatively new alleles. 6 different clusters were observed from phylogenetic tree derived from 539 lines based on the 100 kb window genomic region at the Pi2/9 locus. Together, GWAS pipeline has been shown to be efficient in identifying and delimiting candidate lines containing putative R alleles from selected region. Derived F2 population from retrieved lines will be subjected for functional gene validation via bulk segregation analysis.

Abstract Number: P17-506
Session Type: Poster