Barcode System for Genetic Identification of Soybean [Glycine max (L.) Merrill] Cultivars Using InDel Markers Specific to Dense Variation Blocks

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.

Genetic Diversity Patterns and Discrimination of 172 Korean Soybean (Glycine max (L.) Merrill) Varieties Based on SSR Analysis

“…Therefore, 202 dVB-specific insertion/deletion (indel) markers have been developed [33]. A barcode system was established, which clearly distinguishes 147 Korean soybean varieties and is regularly updated whenever new varieties are developed [34,35]. The development of DNA markers has been simplified due to the active progression of genome research, but the development of DNA markers through full-length genome analysis in a small-scale laboratory is still difficult.…”

Development of 50 InDel-based barcode system for genetic identification of tartary buckwheat resources

“…More importantly, a wealth of polymorphism data can now be obtained from a massive amount of sequencing data using high-throughput sequencing technologies [ 49 ]. In addition, Sohn et al [ 38 ] reported that the InDel-based barcode system focuses on usability, and provided an efficient resource management system. In addition to the InDel-based barcode system, morphological descriptors are now emerging that aim to identify tartary buckwheat accessions, which can be used to verify key genomic factors that explain or predict major agronomic traits.…”

Development of the chloroplast genome-based InDel markers in Niitaka (Pyrus pyrifolia) and its application

“…SNPs, as well as InDels, were discovered in ndhA and clpP genes at the level of Pyrus species and cultivars. Recently, InDel markers in cp have been used for genetic identification in many crops such as potato, quinoa, ginseng, onion, and soybean (Hong 1 Niitaka TCC CAA AGTTC ----TTT TTT TTT TCA AAT AAA AAAA ---------TTT TAT TTT CAT ATT CTT 2 Whangkeumbae TCC CAA AGTTC ----TTT TTT TTT TCA AAT AAA AAAA ---------TTT TAT TTT CAT ATT CTT 3 Amanogawa TCC CAA AGTTC ----TTT TTT TTT TCA AAT AAA AAAA ---------TTT TAT TTT CAT ATT CTT 4 Gamro TCC CAA AGTTC ----TTT TTT TTT TCA AAT AAA AAAA ---------TTT TAT TTT CAT ATT CTT 5 Sunwhang TCC CAA Joh et al 2017;Lee et al 2017;Sohn et al 2017;Cho et al 2016). It is easy and inexpensive to use (Qiao et al 2016).…”