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Open Access Highly Accessed Research article

Identification of genome-wide single nucleotide polymorphisms in allopolyploid crop Brassica napus

Shunmou Huang1, Linbin Deng1, Mei Guan2, Jiana Li3, Kun Lu3, Hanzhong Wang1, Donghui Fu4, Annaliese S Mason5, Shengyi Liu1* and Wei Hua1*

Author Affiliations

1 Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, Hubei, People’s Republic of China

2 The Oilseed Crop Institute, Hunan Agricultural University, National Oilseed Crop Improvement Center, Changsha 410128, Hunan, People’s Republic of China

3 Chongqing Rapeseed Technology Research Center, Chongqing Key Laboratory of Crop Quality Improvement, Key Laboratory of Biotechnology and Crop Quality Improvement of Ministry of Agriculture, College of Agronomy and Biotechnology, Southwest University, 216 Tiansheng Road, Beibei, Chongqing 400716, People’s Republic of China

4 Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China

5 Centre for Integrative Legume Research and School of Agriculture and Food Sciences, The University of Queensland, Brisbane 4072, Australia

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BMC Genomics 2013, 14:717  doi:10.1186/1471-2164-14-717

Published: 20 October 2013

Abstract

Background

Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation. Identification of large numbers of SNPs is helpful for genetic diversity analysis, map-based cloning, genome-wide association analyses and marker-assisted breeding. Recently, identifying genome-wide SNPs in allopolyploid Brassica napus (rapeseed, canola) by resequencing many accessions has become feasible, due to the availability of reference genomes of Brassica rapa (2n = AA) and Brassica oleracea (2n = CC), which are the progenitor species of B. napus (2n = AACC). Although many SNPs in B. napus have been released, the objective in the present study was to produce a larger, more informative set of SNPs for large-scale and efficient genotypic screening. Hence, short-read genome sequencing was conducted on ten elite B. napus accessions for SNP discovery. A subset of these SNPs was randomly selected for sequence validation and for genotyping efficiency testing using the Illumina GoldenGate assay.

Results

A total of 892,536 bi-allelic SNPs were discovered throughout the B. napus genome. A total of 36,458 putative amino acid variants were located in 13,552 protein-coding genes, which were predicted to have enriched binding and catalytic activity as a result. Using the GoldenGate genotyping platform, 94 of 96 SNPs sampled could effectively distinguish genotypes of 130 lines from two mapping populations, with an average call rate of 92%.

Conclusions

Despite the polyploid nature of B. napus, nearly 900,000 simple SNPs were identified by whole genome resequencing. These SNPs were predicted to be effective in high-throughput genotyping assays (51% polymorphic SNPs, 92% average call rate using the GoldenGate assay, leading to an estimated >450 000 useful SNPs). Hence, the development of a much larger genotyping array of informative SNPs is feasible. SNPs identified in this study to cause non-synonymous amino acid substitutions can also be utilized to directly identify causal genes in association studies.

Keywords:
Brassica napus; Allopolyploid; Resequencing; Genotyping; GoldenGate; Non-synonymous SNP