Genome-wide association mapping of bakanae disease resistance in rice

Bakanae, a disease of rice caused by Fusarium spp. affects different growth stages of the plant and can result in heavy losses in crop yields. The objectives of this study were to identify quantitative trait loci (QTLs), and subsequently candidate genes, with a role in bakanae disease resistance. A total of 201 rice cultivars from the Bengal and Assam Aus Panel (BAAP) were screened for resistance to F. fujikuroi VAE5, allowing the identification of cultivars with moderate-to-high levels of resistance to bakanae. Seedlings were observed for symptoms of bakanae disease; plant heights were recorded 28 days after inoculation and plants harvested to determine shoot biomass. Genome-wide association mapping was conducted on bakanae indices traits. A total of 38 QTLs and 34 candidate genes were identified for resistance to bakanae disease. The haplotype variants of thirteen candidate genes (OsWRKY77; OsPP2C06; OsAC07; OsBgal3; OsPRX22; RING-H2; LOC_Os02g50820; OsRFPH2-15; GLP; OsLTPd3; LOC_Os12g07150; Coiled-coil; LOC_Os12g07550) are discussed. The accessions with the rare allele of genes OsWRKY77 and OsPP2C06 for QTL qBK1_3 had the lowest disease index (<10 %) when compared to the more common alleles. Bakanae resistant rice cultivars, QTLs/genes, and superior haplotypes found here will be relevant for future research on the genetics and breeding of bakanae resistant rice.