Meiotic maps of sockeye salmon derived from massively parallel DNA sequencing

BMC Genomics

Research Article

Michael R Miller¹  James E Seeb²  Meredith V Everett² 

[1] Institute of Molecular Biology and Institute of Neuroscience, 1229 University of Oregon, 97403-1229, Eugene, OR, USA;School of Aquatic and Fishery Sciences, University of Washington, Box 355020, 98195-5020, Seattle, WA, USA;

关键词: RAD sequencing;    Meiotic map;    Linkage map;    SNP;   

DOI  :  10.1186/1471-2164-13-521

 received in 2012-02-21, accepted in 2012-09-23,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundMeiotic maps are a key tool for comparative genomics and association mapping studies. Next-generation sequencing and genotyping by sequencing are speeding the processes of SNP discovery and the development of new genetic tools, including meiotic maps for numerous species. Currently there are limited genetic resources for sockeye salmon, Oncorhynchus nerka. We develop the first dense meiotic map for sockeye salmon using a combination of novel SNPs found in restriction site associated DNA (RAD tags) and SNPs available from existing expressed sequence tag (EST) based assays.ResultsWe discovered and genotyped putative SNPs in 3,430 RAD tags. We removed paralogous sequence variants leaving 1,672 SNPs; these were combined with 53 EST-based SNP genotypes for linkage mapping. The map contained 29 male and female linkage groups, consistent with the haploid chromosome number expected for sockeye salmon. The female map contains 1,057 loci spanning 4,896 cM, and the male map contains 1,118 loci spanning 4,220 cM. Regions of conservation with rainbow trout and synteny between the RAD based rainbow trout map and the sockeye salmon map were established.ConclusionsUsing RAD sequencing and EST-based SNP assays we successfully generated the first high density linkage map for sockeye salmon.

【 授权许可】

CC BY   
© Everett et al.; licensee BioMed Central Ltd. 2012