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

Joshua C O Koh; Denise M Barbulescu; Sally Norton; Bob Redden; Phil A Salisbury; Sukhjiwan Kaur; Noel Cogan; Anthony T Slater

doi:10.1186/s13007-017-0200-8

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

Plant Methods. 2017 Jun 15:13:49. doi: 10.1186/s13007-017-0200-8. eCollection 2017.

Authors

Joshua C O Koh¹, Denise M Barbulescu¹, Sally Norton², Bob Redden², Phil A Salisbury^{3

4}, Sukhjiwan Kaur⁴, Noel Cogan⁴, Anthony T Slater⁴

Affiliations

¹ Department of Economic Development, Jobs, Transport and Resources, Grains Innovation Park, 110 Natimuk Rd, Horsham, VIC 3401 Australia.
² Department of Economic Development, Jobs, Transport and Resources, Australian Grains Genebank, Private Bag 260, Horsham, VIC 3401 Australia.
³ Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC 3010 Australia.
⁴ Department of Economic Development, Jobs, Transport and Resources, AgriBio, Centre for AgriBioscience, La Trobe University, 5 Ring Road, Bundoora, VIC 3083 Australia.

Abstract

Background: Within the Brassicaceae, six species from the genus Brassica are widely cultivated throughout the world as oilseed, condiment, fodder or vegetable crops. The genetic relationships among the six Brassica species are described by U's triangle model. Extensive shared traits and diverse morphotypes among Brassica 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 Brassica napus 60K single nucleotide polymorphism (SNP) array has been used to identify species and assess genetic diversity of Brassica collections. However, these methods are technically challenging, expensive and time-consuming, making them unsuitable for routine or rapid screening of Brassica accessions for germplasm management. A cheaper, faster and simpler method for Brassica species identification is described here.

Results: A multiplex polymerase chain reaction (MPCR) consisting of new and existing primers specific to the Brassica A, B and C genomes was able to reliably distinguish all six Brassica species in the triangle of U with 16 control samples of known species identity. Further validation against 120 Brassica 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 B. napus 60K SNP array. In addition, the MPCR was sensitive enough to detect seed contaminations in pooled seed samples of Brassica accessions.

Conclusion: A cheap and fast multiplex PCR assay for identification of Brassica 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 Brassica germplasm collections in genebanks.

Keywords: Brassica; Brassicaceae; Genebank; Germplasm management; Species identification; Triangle of U.