Abstract
For genetic identification of soybean [Glycine max (L.) Merrill] cultivars, insertions/deletions (InDel) markers have been preferred currently because they are easy to use, co-dominant and relatively abundant. Despite their biological importance, the investigation of InDels with proven quality and reproducibility has been limited. In this study, we described soybean barcode system approach based on InDel makers, each of which is specific to a dense variation block (dVB) with non-random recombination due to many variations. Firstly, 2,274 VBs were mined by analyzing whole genome data in six soybean cultivars (Backun, Sinpaldal 2, Shingi, Daepoong, Hwangkeum, and Williams 82) for transferability to dVB-specific InDel markers. Secondly, 73,327 putative InDels in the dVB regions were identified for the development of soybean barcode system. Among them, 202 dVB-specific InDels from all soybean cultivars were selected by gel electrophoresis, which were converted as 2D barcode types according to comparing amplicon polymorphisms in the five cultivars to the reference cultivar. Finally, the polymorphism of the markers were assessed in 147 soybean cultivars, and the soybean barcode system that allows a clear distinction among soybean cultivars is also detailed. In addition, the changing of the dVBs in a chromosomal level can be quickly identified due to investigation of the reshuffling pattern of the soybean cultivars with 27 maker sets. Especially, a backcross-inbred offspring, “Singang” and a recurrent parent, “Sowon” were identified by using the 27 InDel markers. These results indicate that the soybean barcode system enables not only the minimal use of molecular markers but also comparing the data from different sources due to no need of exploiting allele binning in new varieties.
Highlights
The task of plant variety and cultivar identification is vital from breeding to cultivar registration, seed production, trade, and inspection
By comparing the dense variation block (dVB) among the genomes for identifying soybean cultivars, two dVBs with ≥99.8% sequence identity as well as ≥0.8 SNV concordance were considered to be of an identical type which were originated from a common parental genome (Kim et al, 2014)
A total of 2,274 dVBs and 73,327 InDels were identified from the six soybean cultivars and these InDels were selected in order to compare with the reference genome to discriminate all genome types in soybean (Table 1)
Summary
The task of plant variety and cultivar identification is vital from breeding to cultivar registration, seed production, trade, and inspection. With the advent of new generation sequencing (NGS) platforms, large volumes of sequencing data are being generated that could be screened with the aid of bioinformatics tools for exploiting molecular markers, including simple sequence repeats (SSRs), single nucleotide polymorphisms (SNPs), and insertion/deletions (InDels) for genetic study in crop plants (Ganal et al, 2009; Deschamps and Campbell, 2010; Hyten et al, 2010b; Kim et al, 2010; Song et al, 2010; Liu et al, 2012; Li et al, 2014; Moghaddam et al, 2014). The SSR-based genotyping in common laboratories has some limitations as follows; a large amount of time and labor would be required because of using polyacrylamide electrophoresis; technical artifacts, such as different allele sizes and different bins depending on analytical systems, would add ambiguity to inter-laboratory analysis; and the relatively high mutation rate of STR loci (∼10−3) would confound the genetic identification of soybean varieties with non-redundant genotypes. SNP-based genotyping is usually complex, expensive, platform-dependent, and hard to be conducted in common laboratories (Lee et al, 2015)
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