Additional file 1: Figure S1. of Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L.
Screening of DNA polymorphisms in the Gn1a gene using WGS data. Sequencing reads were aligned to the reference genome sequence (IRGSP-1.0). Note that the Gn1a gene lay on the opposite strand of the reference sequence. Screen-captured images of IGV software showed nucleotide variations that were used for marker development. (A) Three SNPs located in the Gn1a promoter region were shown with their genomic location on chromosome 1. Chr1: 5276405, Chr1: 5276521, and Chr1: 5276591 SNPs were used for Gn1a-17SNP/Gn1a-17SNP-FD, Gn1a-18SNP-FD, and Gn1a-19SNP-FD markers, respectively. (B) About a 70-bp deletion (red circles) near the 3â UTR of Gn1a was found in varieties NSIC Rc158 and NSIC Rc238. This indel was used for designing the Gn1a-indel3 marker. (DOC 178 kb
