GENETIC CHARACTERIZATION OF RESISTANCE TO BACTERIAL PANICLE BLIGHT AND SHEATH BLIGHT IN RICE USING QTL LINKAGE ANALYSIS AND QTL-SEQ

Bacterial panicle blight (BPB) and sheath blight (SB) are major diseases of rice causing significant yield reduction in conducive conditions. Few cultivars have shown reliable resistance to these diseases. In this study, a recombinant inbred line (RIL) population derived from the U.S. cultivars Jupiter (moderately resistant) and Trenasse (susceptible) was investigated to identify genomic regions associated with BPB and SB resistance. Phenotypes in BPB and SB, as well as days to heading (DH), of the RIL population were evaluated in the field. DH was found to be correlated to BPB and SB diseases. BPB was also positively correlated to SB. High throughput genotyping was conducted using Kompetitive allele specific polymerase chain reaction (KASP) assays and whole genome sequence (WGS) analyses. A linkage mapping combined with a bulk segregant analysis with whole-genome sequence data (QTL-seq) detected a major QTL on the upper arm of chromosome 3 for BPB, SB and DH traits within the 1.0-1.9Mb position. Additional QTLs for BPB and SB resistance were identified from other chromosomes by QTL-seq. Nine candidate genes were identified within these QTLs, however, sequence analysis revealed only four genes contained polymorphism between the parents. These genes, which are involved in jasmonic acid synthesis, salicylic acid signaling and flowering, also show polymorphism between resistant and susceptible RILs. These findings provide an insight into the complex expression of polygenic resistance for BPB and SB, which may also be closely linked to flowering trait