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

Springer Science and Business Media LLC - Tập 14 - Trang 643-655 - 2014
Jessica Dalton-Morgan1, Alice Hayward1, Salman Alamery1, Reece Tollenaere1, Annaliese S. Mason1, Emma Campbell1, Dhwani Patel1, Michał T. Lorenc1,2, Bin Yi3, Yan Long3, Jinling Meng3, Rosy Raman4, Harsh Raman4, Cindy Lawley5, David Edwards1,2, Jacqueline Batley1,6
1Centre for Integrative Legume Research and School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia
2Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia
3National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
4NSW Agricultural Genomics Centre, NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, PMB, Wagga Wagga, Australia
5Illumina Inc., Hayward, USA
6School of Plant Biology, University of Western Australia, Crawley, Australia

Tóm tắt

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.

Tài liệu tham khảo

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