Development and application of InDel markers based on sudangrass RAD-seq data

Two sudangrass varieties, Sa and S722, were sequenced using restriction site-associated DNA sequencing (RAD-seq) on the Illumina Miniseq platform. After quality control, 920 542 and 892 626 clean reads were obtained for Sa and S722, respectively. Compared with the sorghum reference genome, 2341 and 2123 single nucleotide polymorphisms (SNPs) were obtained from Sa and S722, respectively. A total of 543 and 472 insertion-deletion (InDel) loci were obtained by sequence analysis in Sa and S722, respectively. From these InDel loci, 100 InDels were randomly selected to design InDel markers from Sa and S722. Polymorphism analyses were performed between sorghum Tx623B and Sa and between Tx623B and S722 using the InDel markers. The results showed that the polymorphism between Tx623B and Sa was 85%, and that between Tx623B and S722 was 87%. Diversity analysis was performed using 39 InDel markers for 42 sorghum and 6 sudangrass germplasms. Statistical analyses showed that the Shannon information index was 0.10???1.09 with an average value of 0.54. The polymorphism information content of the InDel markers ranged from 0.04 to 0.66 with an average of 0.35. Two genetic maps of chromosomes 1 and 2 of the Wancao No. 2 recombinant inbred line population were constructed using 16 InDel markers. Thus, it is an effective method to develop InDel markers for sorghum and sudangrass using sudangrass RAD-seq data.