Genome-wide association studies and expression analysis of GA-related genes for exploring foot rot resistance in rice germplasm

A diverse set of 275 rice germplasm lines including 159 lines from global rice diversity panel, 10 Oryza glaberrima Steud accessions; 22 basmati and non-basmati varieties, 67 aromatic germplasm lines and 17 advanced breeding lines were screened along with susceptible and resistant checks for foot rot disease caused by Fusarium moniliforme Sheldon through artificial inoculation. The screening was conducted in trays under less humid condition (50% RH) in April 2019 (referred as E1) and in the field under high humid condition (72% RH) in July 2019 (referred as E2). The susceptible plants showed stunting in E1 and elongation in E2. Based on screening in E1 and E2, thirty-three lines including eighteen of global rice diversity panel, five of O. glabberrima, two aromatic and ten released varieties showed complete resistance to foot rot. Multi-locus GWAS using 159 lines of global rice diversity panel identified 11 QTLs on seven different chromosomes. In the 11 QTL regions, 40 putative genes were identified based on stringent filtering and relevance to the disease. The QTL present on chromosome 1 (qbk1) that co-localized with many studies is proposed for further studies. In addition, the expression analysis of GA-related genes, viz. OsXTH8, OsGAE1, EUI, G-alpha-(D1), GID1, GID2 and SLR1, showed no association with foot rot resistance/susceptibility. However, 24 DAS was identified as the most important stage for expression analysis. The highly resistant lines are suggested to use in the rice breeding program particularly basmati rice. Besides, the genomic region flanking the associated SNPs and the candidate genes within them could be studied further to identify underlying genes and markers associated with foot rot resistance.