Bakanae or foot rot disease caused by Fusarium fujikuroi [teleomorph: Gibberella fujikuroi (Sawada) Ito] is emerging as a serious disease in rice. The disease causes both quantitative and qualitative losses to the grains under the field conditions. Breeding for resistance to Bakanae disease is a promising strategy to manage this emerging disease. In this study, we used a population of 168 F14 recombinant inbred lines (RILs) derived from two indica rice parents Pusa 1342, a highly resistant variety and Pusa Basmati 1121, a highly susceptible variety to map quantitative trait loci (QTLs) governing resistance against Bakanae disease. The disease reaction of 168 F14 RILs were measured on the seedlings inoculated using Fusarium fujikuroi culture using high-throughput screening protocol under glasshouse conditions. Utilizing inclusive composite interval mapping, three QTLs governing resistance to Bakanae were identified, namely qBK1.1, qBK1.2 and qBK1.3 which accounted 4.76, 24.74 and 6.49 % of phenotypic variation, respectively. The major effect QTL designated qBK1.2 was mapped in 0.26 Mb region between RM5336 and RM10153. A total of 55 annotated genes were identified within the identified QTL region qBK1.2. The novel QTLs identified in this study are useful resource for efficiently breeding rice cultivars resistant to Bakanae disease. This is the first report on identification of QTLs governing resistance against Bakanae in rice using inclusive composite interval mapping strategy in a RIL population.

Rice germplasm is a rich resource for discovering genes associated with salt tolerance. In the current study, a set of 96 accessions were evaluated for seedling stage salinity tolerance and its component traits. Significant phenotypic variation was observed among the genotypes for all the measured traits and eleven accessions with high level of salt tolerance at seedling stage were identified. The germplasm set comprised of three sub-populations and genome-wide association study (GWAS) identified a total of 23 marker–trait associations (MTAs) for traits studied. These MTAs were located on rice chromosomes 1, 2, 5, 6, 7, 9, and 12 and explained the trait phenotypic variances ranging from 13.98 to 29.88 %. Twenty-one MTAs identified in this study were located either in or near the previously reported quantitative trait loci (QTLs), while two MTAs namely, qSDW2.1 and qSNC5 were novel. A total of 18 and 13 putative annotated candidate genes were identified in a genomic region spanning ~200 kb around the MTAs qSDW2.1 and qSNC5, respectively. Some of the important genes underlying the novel MTAs were OsFBA1,OsFBL7, and mTERF which are known to be associated with salinity tolerance in crops. These MTAs pave way for combining salinity tolerance with high yield in rice genotypes through molecular breeding.