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

A.S. Mason, J. Zhang, R. Tollenaere, P. Vasquez Teuber, J. Dalton-Morgan, L. Hu, Guijun Yan, Dave Edwards, R. Redden, Jacqueline Batley

Research output: Contribution to journalArticle

  • 13 Citations

Abstract

© 2015 John Wiley & Sons Ltd. 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.
LanguageEnglish
Pages1091-1101
JournalMolecular Ecology Resources
Volume15
Issue number5
Early online date21 Feb 2015
DOIs
StatePublished - Sep 2015

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germplasm
germplasm conservation
genotyping
Single Nucleotide Polymorphism
Research Personnel
Brassicaceae
Costs and Cost Analysis
species diversity
Brassica rapa
Brassica
Chromosomes
single nucleotide polymorphism
Genome
polymorphism
sampling
resource
researchers
Brassica carinata
genetic variation
interspecific hybridization

Cite this

Mason, A. S., Zhang, J., Tollenaere, R., Vasquez Teuber, P., Dalton-Morgan, J., Hu, L., ... Batley, J. (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
Mason, A.S. ; Zhang, J. ; Tollenaere, R. ; Vasquez Teuber, P. ; Dalton-Morgan, J. ; Hu, L. ; Yan, Guijun ; Edwards, Dave ; Redden, R. ; Batley, Jacqueline. / High-throughput genotyping for species identification and diversity assessment in germplasm collections. In: Molecular Ecology Resources. 2015 ; Vol. 15, No. 5. pp. 1091-1101
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Mason, AS, Zhang, J, Tollenaere, R, Vasquez Teuber, P, Dalton-Morgan, J, Hu, L, Yan, G, Edwards, D, Redden, R & Batley, J 2015, 'High-throughput genotyping for species identification and diversity assessment in germplasm collections' Molecular Ecology Resources, vol 15, no. 5, pp. 1091-1101. DOI: 10.1111/1755-0998.12379

High-throughput genotyping for species identification and diversity assessment in germplasm collections. / Mason, A.S.; Zhang, J.; Tollenaere, R.; Vasquez Teuber, P.; Dalton-Morgan, J.; Hu, L.; Yan, Guijun; Edwards, Dave; Redden, R.; Batley, Jacqueline.

In: Molecular Ecology Resources, Vol. 15, No. 5, 09.2015, p. 1091-1101.

Research output: Contribution to journalArticle

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AU - Mason,A.S.

AU - Zhang,J.

AU - Tollenaere,R.

AU - Vasquez Teuber,P.

AU - Dalton-Morgan,J.

AU - Hu,L.

AU - Yan,Guijun

AU - Edwards,Dave

AU - Redden,R.

AU - Batley,Jacqueline

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N2 - © 2015 John Wiley & Sons Ltd. 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.

AB - © 2015 John Wiley & Sons Ltd. 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.

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DO - 10.1111/1755-0998.12379

M3 - Article

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SP - 1091

EP - 1101

JO - Molecular Ecology Notes

T2 - Molecular Ecology Notes

JF - Molecular Ecology Notes

SN - 1755-098X

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ER -

Mason AS, Zhang J, Tollenaere R, Vasquez Teuber P, Dalton-Morgan J, Hu L et al. High-throughput genotyping for species identification and diversity assessment in germplasm collections. Molecular Ecology Resources. 2015 Sep;15(5):1091-1101. Available from, DOI: 10.1111/1755-0998.12379