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

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