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

作者：Shunmou Huang, Linbin Deng, Mei Guan, Jiana Li, Kun Lu, Hanzhong Wang, Donghui Fu, Annaliese S. Mason, Shengyi Liu, Wei Hua · 发表于：BMC Genomics · 年份：2013 · DOI：10.1186/1471-2164-14-717 · 被引用次数：63 · 研究领域：Nitrogen and Sulfur Effects on Brassica、Genetic diversity and population structure、Lipid metabolism and biosynthesis

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....