High-throughput genotyping for species identification and diversity assessment in germplasm collections

Mason, Annaliese S, Zhang, Jing, Tollenaere, Reece, Vasquez Teuber, Paula, Dalton-Morgan, Jessica, Hu, Liyong, Yan, Guijun, Edwards, David, Redden, Robert and Batley, Jacqueline (2015) High-throughput genotyping for species identification and diversity assessment in germplasm collections. Molecular Ecology Resources, 15 5: 1091-1101. doi:10.1111/1755-0998.12379

Author Mason, Annaliese S
Zhang, Jing
Tollenaere, Reece
Vasquez Teuber, Paula
Dalton-Morgan, Jessica
Hu, Liyong
Yan, Guijun
Edwards, David
Redden, Robert
Batley, Jacqueline
Title High-throughput genotyping for species identification and diversity assessment in germplasm collections
Journal name Molecular Ecology Resources   Check publisher's open access policy
ISSN 1755-0998
Publication date 2015-02-21
Year available 2015
Sub-type Article (original research)
DOI 10.1111/1755-0998.12379
Open Access Status
Volume 15
Issue 5
Start page 1091
End page 1101
Total pages 11
Place of publication Oxford, United Kingdom
Publisher Wiley-Blackwell Publishing Ltd.
Collection year 2016
Language eng
Formatted 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.
Keyword Brassicaceae
Genetic resources
Germplasm collections
Illumina Infinium SNP array
Molecular genotyping
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Centre for Integrative Legume Research Publications
School of Agriculture and Food Sciences
Official 2016 Collection
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Citation counts: TR Web of Science Citation Count  Cited 3 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 1 times in Scopus Article | Citations
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