A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes

Dalton-Morgan, Jessica, Hayward, Alice, Alamery, Salman, Tollenaere, Reece, Mason, Annaliese S., Campbell, Emma, Patel, Dhwani, Lorenc, Michał T., Yi, Bin, Long, Yan, Meng, Jinling, Raman, Rosy, Raman, Harsh, Lawley, Cindy, Edwards, David and Batley, Jacqueline (2014) A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes. Functional and Integrative Genomics, 14 4: 643-655. doi:10.1007/s10142-014-0391-2

Author Dalton-Morgan, Jessica
Hayward, Alice
Alamery, Salman
Tollenaere, Reece
Mason, Annaliese S.
Campbell, Emma
Patel, Dhwani
Lorenc, Michał T.
Yi, Bin
Long, Yan
Meng, Jinling
Raman, Rosy
Raman, Harsh
Lawley, Cindy
Edwards, David
Batley, Jacqueline
Title A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes
Journal name Functional and Integrative Genomics   Check publisher's open access policy
ISSN 1438-793X
Publication date 2014-08-22
Year available 2014
Sub-type Article (original research)
DOI 10.1007/s10142-014-0391-2
Open Access Status
Volume 14
Issue 4
Start page 643
End page 655
Total pages 13
Place of publication Heidelberg, Germany
Publisher Springer
Collection year 2015
Language eng
Formatted abstract
Single-nucleotide polymorphisms (SNPs)are molecular markers based on nucleotide variation and can be used for genotyping assays across populations and to track genomic inheritance. SNPs offer a comprehensive genotyping alternative to whole-genome sequencing for both agricultural and research purposes including molecular breeding and diagnostics, genome evolution and genetic diversity analyses, genetic mapping, and trait association studies. Here genomic SNPs were discovered between four cultivars of the important amphidiploid oilseed species Brassica napus and used to develop a B. napus Infinium™ array containing 5,306 SNPs randomly dispersed across the genome. Assay success was high, with >94 % of these producing a reproducible, polymorphic genotype in the 1,070 samples screened. Although the assay was designed to B. napus, successful SNP amplification was achieved in the B. napus progenitor species, Brassica rapa and Brassica oleracea, and to a lesser extent in the related species Brassica nigra. Phylogenetic analysis was consistent with the expected relationships between B. napus individuals. This study presents an efficient custom SNP assay development pipeline in the complex polyploid Brassica genome and demonstrates the utility of the array for high-throughput genotyping in a number of related Brassica species. It also demonstrates the utility of this assay in genotyping resistance genes on chromosome A7, which segregate amongst the 1,070 samples.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: School of Agriculture and Food Sciences
Official 2015 Collection
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Citation counts: TR Web of Science Citation Count  Cited 9 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 5 times in Scopus Article | Citations
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Created: Tue, 26 Aug 2014, 21:21:45 EST by Dr Alice Hayward on behalf of Centre for Plant Science