Abstract:
Recent advances in next generation sequencing have created opportunities to directly
identify genetic loci and candidate genes for abiotic stress responses in plants. With the objective of
identifying candidate genes within the previously identified QTL-hotspots, the whole genomes of two
divergent cultivars for salt responses, namely At 354 and Bg 352, were re-sequenced using Illumina
Hiseq 2500 100PE platform and mapped to Nipponbare and R498 genomes. The sequencing results
revealed approximately 2.4 million SNPs and 0.2 million InDels with reference to Nipponbare while
1.3 million and 0.07 million with reference to R498 in two parents. In total, 32,914 genes were reported
across all rice chromosomes of this study. Gene mining within QTL hotspots revealed 1236 genes, out
of which 106 genes were related to abiotic stress. In addition, 27 abiotic stress-related genes were
identified in non-QTL regions. Altogether, 32 genes were identified as potential genes containing
polymorphic non-synonymous SNPs or InDels between two parents. Out of 10 genes detected
with InDels, tolerant haplotypes of Os01g0581400, Os10g0107000, Os11g0655900, Os12g0622500, and
Os12g0624200 were found in the known salinity tolerant donor varieties. Our findings on different
haplotypes would be useful in developing resilient rice varieties for abiotic stress by haplotype-based
breeding studies.
