title: High-throughput genotyping for species identification and diversity assessment in germplasm collections.
abstract: Germplasm collections provide an extremely valuable resource for breeders and researchers. However, misclassification of accessions by species often hinders the effective use of these collections. We propose that use of high-throughput genotyping tools can provide a fast, efficient and cost-effective way of confirming species in germplasm collections, as well as providing valuable genetic diversity data. We genotyped 180 Brassicaceae samples sourced from the Australian Grains Genebank across the recently released Illumina Infinium Brassica 60K SNP array. Of these, 76 were provided on the basis of suspected misclassification and another 104 were sourced independently from the germplasm collection. Presence of the A- and C-genomes combined with principle components analysis clearly separated Brassica rapa, B. oleracea, B. napus, B. carinata and B. juncea samples into distinct species groups. Several lines were further validated using chromosome counts. Overall, 18% of samples (32/180) were misclassified on the basis of species. Within these 180 samples, 23/76 (30%) supplied on the basis of suspected misclassification were misclassified, and 9/105 (9%) of the samples randomly sourced from the Australian Grains Genebank were misclassified. Surprisingly, several individuals were also found to be the product of interspecific hybridization events. The SNP (single nucleotide polymorphism) array proved effective at confirming species, and provided useful information related to genetic diversity. As similar genomic resources become available for different crops, high-throughput molecular genotyping will offer an efficient and cost-effective method to screen germplasm collections worldwide, facilitating more effective use of these valuable resources by breeders and researchers.
authors: School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.|Centre for Integrative Legume Research, The University of Queensland, Brisbane, QLD, 4072, Australia.
authors: Annaliese S
authors: AS
authors: Mason
authors: Ministry of Agriculture (MOA) key laboratory of Huazhong Crop Physiology, Ecology and Production, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.|Faculty of Science, School of Plant Biology, The University of Western Australia, Perth, WA, 6009, Australia.
authors: Jing
authors: J
authors: Zhang
authors: School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.|Centre for Integrative Legume Research, The University of Queensland, Brisbane, QLD, 4072, Australia.
authors: Reece
authors: R
authors: Tollenaere
authors: School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.|Centre for Integrative Legume Research, The University of Queensland, Brisbane, QLD, 4072, Australia.
authors: Paula
authors: P
authors: Vasquez Teuber
authors: School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.|Centre for Integrative Legume Research, The University of Queensland, Brisbane, QLD, 4072, Australia.
authors: Jessica
authors: J
authors: Dalton-Morgan
authors: Ministry of Agriculture (MOA) key laboratory of Huazhong Crop Physiology, Ecology and Production, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.
authors: Liyong
authors: L
authors: Hu
authors: Faculty of Science, School of Plant Biology, The University of Western Australia, Perth, WA, 6009, Australia.|The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
authors: Guijun
authors: G
authors: Yan
authors: School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.|Faculty of Science, School of Plant Biology, The University of Western Australia, Perth, WA, 6009, Australia.
authors: David
authors: D
authors: Edwards
authors: Department of Environment and Primary Industries, Australian Grains Genebank, Horsham, VIC, 3401, Australia.
authors: Robert
authors: R
authors: Redden
authors: School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.|Centre for Integrative Legume Research, The University of Queensland, Brisbane, QLD, 4072, Australia.|Faculty of Science, School of Plant Biology, The University of Western Australia, Perth, WA, 6009, Australia.
authors: Jacqueline
authors: J
authors: Batley
mesh_terms: D001315:Australia; D019607:Brassicaceae / Q000145:classification* / Q000235:genetics*; D060005:Genotyping Techniques / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D000068098:Seed Bank
keywords: Brassicaceae; Illumina Infinium SNP array; genebanks; genetic resources; germplasm collections; molecular genotyping