Table 1.
The re-sequencing information of 20 rice varieties.
Fig 1.
Distribution of InDels in Oryza sativa ssp. indica and Oryza sativa spp. javanica on each chromosome with a window size of 100 kb.
The outermost circle represents 12 rice chromosomes; the middle circle represents the distribution of common InDels in the 10 indica rice varieties with Nipponbare as a reference; the innermost circle indicates the distribution of 10 javanica common InDels on each chromosome with a window size of 100 kb, orange line indicates the indica common InDel number per 100kb, cyan-blue line suggests the javanica common InDel number per 100kb.
Fig 2.
The number and density of InDels in javanica rice varieties.
A: the common InDels identified on each chromosome from the 10 Oryza sativa ssp. javanica sequences with Nipponbare as a reference. B: the density of the InDels (n/Mb) of the 10 Oryza sativa ssp. javanica accessions.
Fig 3.
Four representative InDel markers show more than two alleles but can distinguish the two subspecies.
The 30 samples on the left and 30 samples on the right show the Oryza sativa ssp. javanica varieties and Oryza sativa ssp. indica accessions, respectively. The detailed information is presented in S2 Table.
Fig 4.
Application of the newly developed InDel markers in 60 rice varieties, including each 30 indica and javanica accessions.
The 30 samples on the left (javanica) exhibited single bands different from the 30 samples on the right (indica).
Fig 5.
The physical map of 85 available InDel markers.
The position of each marker is indicated on the reference genome (Nipponbare-IRGSP-1.0) with a horizontal bar.