Research articles
ScienceAsia 48 (2022):ID 491-495 |doi:
10.2306/scienceasia1513-1874.2022.065
Development and application of InDel markers based on
sudangrass RAD-seq data
Lihua Wanga,b, Jieqin Lib, Qiuwen Zhanb, Yixin Shena,*
ABSTRACT: 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.
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| a |
College Of Agro-Grassland Science, Nanjing Agricultural University, NanJing 210095 China |
| b |
Anhui Science and Technology University, Fengyang 233100 China |
* Corresponding author, E-mail: yxshen@njau.edu.cn
Received 19 Jul 2021, Accepted 12 Feb 2022
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