Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome

被引:41
作者
Tsai, Hsin Y. [1 ]
Robledo, Diego [1 ,2 ]
Lowe, Natalie R. [1 ]
Bekaert, Michael [3 ]
Taggart, John B. [3 ]
Bron, James E. [3 ]
Houston, Ross D. [1 ]
机构
[1] Univ Edinburgh, Sch Vet Studies, Roslin Inst & Royal Dick, Roslin EH25 9RG, Midlothian, Scotland
[2] Univ Santiago de Compostela, Fac Biol, Dept Genet, Santiago De Compostela 15782, Spain
[3] Univ Stirling, Sch Nat Sci, Inst Aquaculture, Stirling FK9 4LA, Scotland
基金
英国医学研究理事会; 英国生物技术与生命科学研究理事会; 英国自然环境研究理事会;
关键词
Salmo salar; linkage map; SNP array; recombination; RNA-Seq; SINGLE NUCLEOTIDE POLYMORPHISMS; SEX-SPECIFIC RECOMBINATION; WIDE ASSOCIATION; REVEALS; PREDICTION; GENE; POPULATION; GENERATION; RESISTANCE; ALIGNMENT;
D O I
10.1534/g3.116.029009
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
High density linkage maps are useful tools for fine-scale mapping of quantitative trait loci, and characterization of the recombination landscape of a species' genome. Genomic resources for Atlantic salmon (Salmo salar) include a well-assembled reference genome, and high density single nucleotide polymorphism (SNP) arrays. Our aim was to create a high density linkage map, and to align it with the reference genome assembly. Over 96,000 SNPs were mapped and ordered on the 29 salmon linkage groups using a pedigreed population comprising 622 fish from 60 nuclear families, all genotyped with the 'ssalar01' high density SNP array. The number of SNPs per group showed a high positive correlation with physical chromosome length (r = 0.95). While the order of markers on the genetic and physical maps was generally consistent, areas of discrepancy were identified. Approximately 6.5% of the previously unmapped reference genome sequence was assigned to chromosomes using the linkage map. Male recombination rate was lower than females across the vast majority of the genome, but with a notable peak in subtelomeric regions. Finally, using RNA-Seq data to annotate the reference genome, the mapped SNPs were categorized according to their predicted function, including annotation of similar to 2500 putative nonsynonymous variants. The highest density SNP linkage map for any salmonid species has been created, annotated, and integrated with the Atlantic salmon reference genome assembly. This map highlights the marked heterochiasmy of salmon, and provides a useful resource for salmonid genetics and genomics research.
引用
收藏
页码:2173 / 2179
页数:7
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