Genotyping by sequencing (GBS) is the recent approach of next-generation sequencing technique for discovering and genotyping single nucleotide polymorphisms (SNPs) in crop species. Genotypic variation studies (SNPs and insertion-deletions/InDels) were performed using four rice lines based on GBS data by aligning to the reference genome Nipponbare. Local aromatic rice landrace Tulaipanji was crossed with Ranjit, and two distinct lines were identified from the progenies: one line with awns and aroma traits and the other without awns and aroma. Total number of SNPs and InDels identified were 52810 and 4327 at read depth 10, respectively. Out of the total polymorphic SNPs/InDels, 16490 were intergeneric, 7812 were inside gene, and 4435 were intronic. Phylogenetically, Tulaipanji was closer to the reference genome nipponbare. Based on recurrent parent genome analysis, out of 10013 alleles, 92.52% was introgressed into progeny-awn from Tulaipanji and 7.48% from Ranjit, whereas progeny-awnless carried 89.19% alleles from Ranjit and only 10.81% alleles from Tulaipanji. In addition, progeny-awn was the highest heterozygous (83.88%) and progeny-awnless was the least (2.24%) at this fifth generation of recombinant inbred lines. These SNP variations may be linked to the phenotypic traits and can be utilized in crop improvement through linkage mapping. These results suggest that adding a high density of SNP markers to a mapping or breeding population through GBS has a great value for numerous applications in rice breeding and genetics research.
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