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

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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.

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Acknowledgments

The authors would like to acknowledge funding support from the Australian Research Council (Projects LP0882095, LP0883462, LP0989200, LP110100200 and DP0985953). Support from the Australian Genome Research Facility (AGRF), the Queensland Cyber Infrastructure Foundation (QCIF) and the Australian Partnership for Advanced Computing (APAC) is gratefully acknowledged. Rowan Bunch is gratefully acknowledged for HiScanSQ 6 K SNP chip scanning.

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Authors and Affiliations

  1. Centre for Integrative Legume Research and School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia

    Jessica Dalton-Morgan, Alice Hayward, Salman Alamery, Reece Tollenaere, Annaliese S. Mason, Emma Campbell, Dhwani Patel, Michał T. Lorenc, David Edwards & Jacqueline Batley

  2. Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia

    Michał T. Lorenc & David Edwards

  3. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China

    Bin Yi, Yan Long & Jinling Meng

  4. NSW Agricultural Genomics Centre, NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, PMB, Wagga Wagga, NSW, 2650, Australia

    Rosy Raman & Harsh Raman

  5. Illumina Inc., Hayward, CA, USA

    Cindy Lawley

  6. School of Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia

    Jacqueline Batley

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  1. Jessica Dalton-Morgan
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Corresponding author

Correspondence to Jacqueline Batley.

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Suppl. Figure 1

Representative samples from the observed cluster types with Brassica napus SNPs based on the GenomeStudio software. Genotype calls are represented by different coloured regions: AA is red, BB is blue and AB is purple. (a) Locus produces well defined clusters which segregates on the A genome and fails on the C genome. (b) Locus produces well defined clusters which segregates on the C genome and fails on the A genome. (c) Locus is monomorphic within all samples run on 6 K chip. (d) Locus is monomorphic on C genome and has failed on the A genome. Individuals from diploid species are identified by the colour scheme: B. rapa: green; B. oleracea:cyan; B. nigra: pink. (GIF 334 kb)

High resolution image (TIFF 761 kb)

Suppl. Figure 2

Principle component analysis on the 71 informative B. napus genotypes plus individuals from the progenitor species (46 B. rapa, four B. oleracea). (GIF 17 kb)

High resolution image (TIFF 3439 kb)

Suppl. Figure 3

Principle component analysis on the 71 informative B. napus genotypes. (GIF 16 kb)

High resolution image (TIFF 3439 kb)

Suppl. Figure 4

Heatmap displaying pairwise Linkage disequilibrium between polymorphic SNPs (PNG 1420 kb)

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Dalton-Morgan, J., Hayward, A., Alamery, S. et al. A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes. Funct Integr Genomics 14, 643–655 (2014). https://doi.org/10.1007/s10142-014-0391-2

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