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

Huang, Shunmou, Deng, Linbin, Guan, Mei, Li, Jiana, Lu, Kun, Wang, Hanzhong, Fu, Donghui, Mason, Annaliese S., Liu, Shengyi and Hua, Wei (2013) Identification of genome-wide single nucleotide polymorphisms in allopolyploid crop Brassica napus. BMC Genomics, 14 717: 1-21. doi:10.1186/1471-2164-14-717

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Author Huang, Shunmou
Deng, Linbin
Guan, Mei
Li, Jiana
Lu, Kun
Wang, Hanzhong
Fu, Donghui
Mason, Annaliese S.
Liu, Shengyi
Hua, Wei
Title Identification of genome-wide single nucleotide polymorphisms in allopolyploid crop Brassica napus
Journal name BMC Genomics   Check publisher's open access policy
ISSN 1471-2164
Publication date 2013-10-20
Sub-type Article (original research)
DOI 10.1186/1471-2164-14-717
Open Access Status DOI
Volume 14
Issue 717
Start page 1
End page 21
Total pages 21
Place of publication London, United Kingdom
Publisher BioMed Central
Collection year 2014
Language eng
Formatted 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.
Keyword Brassica napus
Non-synonymous SNP
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Centre for Integrative Legume Research Publications
School of Agriculture and Food Sciences
Official 2014 Collection
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Citation counts: TR Web of Science Citation Count  Cited 12 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 14 times in Scopus Article | Citations
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Created: Mon, 28 Oct 2013, 11:44:40 EST by Annaliese Mason on behalf of Centre for Integrative Legume Research