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High-throughput genotyping for species identification and diversity assessment in germplasm collections
- Source :
- Molecular Ecology Resources. 15:1091-1101
- Publication Year :
- 2015
- Publisher :
- Wiley, 2015.
-
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.
- Subjects :
- 2. Zero hunger
Germplasm
Genetic diversity
Genotyping Techniques
business.industry
Australia
High-Throughput Nucleotide Sequencing
food and beverages
Single-nucleotide polymorphism
Biology
Polymorphism, Single Nucleotide
Genome
Biotechnology
Interspecific hybridization
Seed Bank
Evolutionary biology
Brassicaceae
Genetics
SNP
business
Genotyping
Ecology, Evolution, Behavior and Systematics
SNP array
Subjects
Details
- ISSN :
- 1755098X
- Volume :
- 15
- Database :
- OpenAIRE
- Journal :
- Molecular Ecology Resources
- Accession number :
- edsair.doi.dedup.....c0f4931935ed748ae3b810ab40e5389f