BAC‐based upgrading and physical integration of a genetic SNP map in Atlantic salmon

Abstract

A better understanding of the genotype-phenotype correlation of Atlantic salmon is of key importance for a whole range of production, life history and conservation biology issues attached to this species. High-density linkage maps integrated with physical maps and covering the complete genome are needed to identify economically important genes and to study the genome architecture. Linkage maps of moderate density and a physical bacterial artificial chromosome (BAC) fingerprint map for the Atlantic salmon have already been generated. Here, we describe a strategy to combine the linkage mapping with the physical integration of newly identified single nucleotide polymorphisms (SNPs). We resequenced 284 BAC-ends by PCR in 14 individuals and detected 180 putative SNPs. After successful validation of 152 sequence variations, genotyping and genetic mapping were performed in eight salmon families comprising 376 individuals. Among these, 110 SNPs were positioned on a previously constructed linkage map containing SNPs derived from expressed sequence tag (EST) sequences. Tracing the SNP markers back to the BACs enabled the integration of the genetic and physical maps by assigning 73 BAC contigs to Atlantic salmon linkage groups.

Temporal change in genetic integrity suggests loss of local adaptation in a wild Atlantic salmon (Salmo salar) population following introgression by farmed escapees

“…Table 3 presents a summary of these markers, including their names, known linkage group used from Boulding et al (2008) and Lorenz et al (2010), as well as gene annotation when available. Three outliers (Contig14899_0107, Contig15610_550 and Contig16686_0431) identified in the genome scan involving WILD-1992, were also identified in comparisons with WILD-1995_96 and/or WILD-1998_99.…”

“…In total, a panel of 388 Atlantic salmon SNPs were genotyped in 16 different multiplexes, with multiplexing levels ranging from 12 to 36. The 13 multiplexes with the highest number of SNPs from Moen et al (2008) as well as the 3 multiplexes with the highest number of SNPs from Lorenz et al (2010) were selected for genotyping. PCR and extension primers were designed with the software MassARRAY AssayDesign v3.1 (Sequenom).…”

Genomics and Genome Sequencing: Benefits for Finfish Aquaculture

“…For example, the 207,869 BAC-end sequences for the Atlantic salmon BAC library cover approximately 3.5% of the whole genome sequence. This glance into a genome is very powerful, as it can provide information about the complexity of the genome (i.e., repeat content), and the BACend sequences can be a source of molecular markers (as described above for Atlantic salmon Lorenz et al, 2010)). Finally, the BAC-end sequences can be used for comparative synteny analyses by aligning them against other, fully sequenced genomes, which can provide insight into the gene content of the BACs, thus providing a partial, putative annotation of segments of the genome (Sarropoulou et al, 2007).…”

“…It was not until large EST databases became available that an intensive search was undertaken for SNPs that could be tied to actual genes . Resequencing BAC-end sequences (described below) was another approach taken to identify SNPs for Atlantic salmon (Lorenz et al, 2010), but this process was highly labor intensive relative to the information gained. A next generation sequencing strategy (Van Tassell et al, 2008) has also been used to identify SNPs in Atlantic salmon; however, the repetitive nature of the genome made it difficult to distinguish between putative SNPs arising from duplicated regions and those from a unique locus.…”

“…The number of microsatellite markers was expanded to approximately 2,000 thanks to BAC-end sequencing, and a relatively dense genetic map covering the 29 pairs of chromosomes in the European strain of Atlantic salmon was built . Additional maps were constructed using SNPs derived from ESTs (Moen et al, 2008a) and BAC-end sequences (Lorenz et al, 2010), and these were incorporated into a dense SNP map comprising ~5,600 SNPs . In terms of other salmonids, linkage maps have been constructed for rainbow trout Nichols et al, 2003;Rexroad et al, 2005;Sakamoto et al, 2000), brown trout (Gharbi et al, 2006), coho salmon (Oncorhynchus kisutch) (McClelland & Naish, 2008), and Arctic charr .…”