Exploring Chromosomes segment substitution lines from inter-specific crosses to decipher the genetics of earliness in rice

Wild introgression lines (ILs) developed from interspecific crosses between the Oryza sativa mega variety Swarna and Oryza nivara accessions, exhibiting significant phenotypic variation for earliness i.e. days to fifty percent flowering (DFF), were subjected to quantitative trait locus sequencing (QTL-seq) to identify genomic regions and sequence variations associated with this trait. Bulked segregant analysis (BSA) was implemented by constructing early- and late-flowering bulks through the selective pooling of DNA from individuals with extreme DFF phenotypes. Whole-genome resequencing of these bulks enabled high-resolution detection of single nucleotide polymorphisms (SNPs) and insertion-deletion (InDel) variations. The SNP-index and delta SNP-index analyses will be calculated to pinpoint candidate genomic regions associated with DFF and putative causal variants. This study provides molecular insights into the genetic basis of flowering time regulation in interspecific rice derivatives, facilitating the identification of potential targets for genetic improvement.