InDel Markers Based on 3K Whole-Genome Re-Sequencing Data Characterise the Subspecies of Rice (Oryza sativa L.)

A molecular marker is a valuable tool in genetic research. Insertions–deletions (InDels) are commonly used polymorphisms gene mapping, analysing diversity, marker-assisted breeding, and phylogenetics. The 3000 Rice Genome Project, re-sequencing project, discovered millions of genome-wide InDels. We found that the proportion >50-bp long InDels (699,475) total (1,248,503) 56.02%. number on each chromosome was consistent with corresponding length. maximum were 1 (78,935), minimum 9 (41,752), an average density 1.87 InDels/kb (range: 1.50–2.36 InDels/kb). Furthermore, 96 about 3.98 Mb/InDel selected to detect polymorphism. results exhibited ideal performance 2% agarose gel electrophoresis. Phylogenetic analysis InDel markers had excellent between rice varieties japonica indica, could be classified based statistical their polymorphisms. applied identify recombinant inbred lines population. These reveal high-density help us examine functional species variation, map-based cloning.