Abstract:

The objective of this work was to develop novel,convenient,and reliable molecular marker in soybean.Twelve soybean germplasm accessions from different geography region were used to develop large-size InDel markers based on 10 depth genomic re-sequencing.Developed InDel markers were used to construct DNA fingerprint of 96 varieties in Huanghuaihai Uniform Test in 2018.The results showed that a total of 66 561 InDel markers,with insertion/deletion fragment size larger than 20 bp,were discovered among the 12 accessions.The distribution pattern among the genome of these InDel markers were also illustrated.The ratio of the InDel in intron,upstream of the gene,downstream of the gene,intergenic region,intragenic region,5'-UTR and 3'-UTR were 12.35%,25.83%,20.44%,34.39%,0.19%,0.93%,1.51%,respectively.There were 42 453 InDels yield insertion/deletion fragment size between 20 to 40 bp,13 044 InDels between 41—60 bp,5 034 InDels between 61—80 bp,2 285 InDels between 81—100 bp,and 2 413 InDels larger than 100 bp.Then,160 InDel markers were randomly selected according to the insertion/deletion fragment size throughout the whole genome.As results,thirty-two InDel markers,that only yield 2 alleles in for each locus and could be distinguished easily on agarose gel,were developed and validated through primer design,PCR and agarose gel electrophoresis.Additionally,DNA fingerprint of 96 varieties in Huanghuaihai Uniform Test in 2018,were constructed using the 32 developed InDel markers.As results,the average purity of the tested soybean varieties was 96.84%,and no varieties shared the same name.The InDel markers developed in this study were stable,reliable and user friendly.They could be used to construct DNA fingerprint and test seed purity of soybean.

Key words: Soybean, Molecular markers, Large size insertion/deletion marker, Genetic diversity analysis