title: A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes.
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.
authors.affiliation: Centre for Integrative Legume Research and School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia.
authors.forename: Jessica
authors.initials: J
authors.lastname: Dalton-Morgan
authors.forename: Alice
authors.initials: A
authors.lastname: Hayward
authors.forename: Salman
authors.initials: S
authors.lastname: Alamery
authors.forename: Reece
authors.initials: R
authors.lastname: Tollenaere
authors.forename: Annaliese S
authors.initials: AS
authors.lastname: Mason
authors.forename: Emma
authors.initials: E
authors.lastname: Campbell
authors.forename: Dhwani
authors.initials: D
authors.lastname: Patel
authors.forename: Michał T
authors.initials: MT
authors.lastname: Lorenc
authors.forename: Bin
authors.initials: B
authors.lastname: Yi
authors.forename: Yan
authors.initials: Y
authors.lastname: Long
authors.forename: Jinling
authors.initials: J
authors.lastname: Meng
authors.forename: Rosy
authors.initials: R
authors.lastname: Raman
authors.forename: Harsh
authors.initials: H
authors.lastname: Raman
authors.forename: Cindy
authors.initials: C
authors.lastname: Lawley
authors.forename: David
authors.initials: D
authors.lastname: Edwards
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Batley
mesh_terms: D029688:Brassica napus / Q000235:genetics*; D032461:Chromosomes, Plant / Q000235:genetics; D004171:Diploidy; D060467:Disease Resistance / Q000235:genetics*; D017343:Genes, Plant; D056426:Genetic Loci; D014644:Genetic Variation; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D015810:Linkage Disequilibrium / Q000235:genetics; D010935:Plant Diseases / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015203:Reproducibility of Results