Oryza sativa cultivar:BPT 5204 Raw sequence reads

Characterization of strong culm Samba Mahsuri mutants and identification of candidate gene associated with strong culm. A strong culm mutant of high grain and cooking quality mega variety, BPT 5204 (pushing resistance - 15.00 g/ stem) was identified and named as TI-17 (pushing resistance - 29.67 g/ stem). To map the genomic regions/ genes/ SNPs associated with strong culm phenotype, MutMap QTL-seq strategy was deployed. The strong culm mutant, TI-17 was crossed with the wild type parent BPT 5204 for developing F2 mapping population (252). The F2 mapping population was thoroughly phenotyped for strong culm using Vernier Calipers and Prostrate tester. Extreme phenotype individuals 15 each - strong culm like TI-17 (pushing resistance - 29.00 to 33.00 g/ stem) and weak culm like BPT 5204 (pushing resistance - 12.50 to 15.00 g/ stem) were selected and pooled as one sample in equimolar DNA concentration. The DNA of two extreme bulks and two parents TI-17 and BPT 5204 were whole genome resequenced using Illumina 2500 platform. The pipeline (MutMap: https://github.com/YuSugihara/MutMap, QTL-seq: https://github.com/YuSugihara/QTL-seq) was followed for MutMap QTL-seq analysis. The SNP index and delta SNP index were calculated accordingly.