A multiplex PCR for rapid identification of species in the triangle of U.

BACKGROUND

Within the Brassicaceae, six species from the genus are widely cultivated throughout the world as oilseed, condiment, fodder or vegetable crops. The genetic relationships among the six species are described by U's triangle model. Extensive shared traits and diverse morphotypes among species make identification and classification based on phenotypic data alone challenging and unreliable, especially when dealing with large germplasm collections. Consequently, a major issue for genebank collections is ensuring the correct identification of species. Molecular genotyping based on simple sequence repeat (SSR) marker sequencing or the Illumina Infinium 60K single nucleotide polymorphism (SNP) array has been used to identify species and assess genetic diversity of collections. However, these methods are technically challenging, expensive and time-consuming, making them unsuitable for routine or rapid screening of accessions for germplasm management. A cheaper, faster and simpler method for species identification is described here.

RESULTS

A multiplex polymerase chain reaction (MPCR) consisting of new and existing primers specific to the A, B and C genomes was able to reliably distinguish all six species in the triangle of U with 16 control samples of known species identity. Further validation against 120 accessions previously genotyped showed that the MPCR is highly accurate and comparable to more advanced techniques such as SSR marker sequencing or the Illumina Infinium 60K SNP array. In addition, the MPCR was sensitive enough to detect seed contaminations in pooled seed samples of accessions.

CONCLUSION

A cheap and fast multiplex PCR assay for identification of species in the triangle of U was developed and validated in this study. The MPCR assay can be readily implemented in any basic molecular laboratory and should prove useful for the management of germplasm collections in genebanks.