Plant & Animal Genomes XVII Conference

January 10-14, 2009
Town & Country Convention Center
San Diego, CA

Intra- And Interspecies SNPs Predicted Using ESTs From Seven Shrimp Species

Danielle M. Gorbach , Zhi-Liang Hu , Zhi-Qiang Du , Max F. Rothschild

  Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA

Shrimp farming is a large industry worldwide. Much research is still needed to enable genetics to play a role in improving shrimp. An initial step is to locate SNPs for creation of a linkage map. Since Litopenaeus vannamei is the most commonly farmed species, it is a primary focus of initial research, but existing data from closely related species may prove useful in unlocking secrets of the L. vannamei genome. By comparing other species’ sequences, we can discover SNPs which distinguish species and may create unique phenotypic characteristics, as well as determining less conserved bases of the shrimp genome, which may segregate within the L. vannamei genome. Publicly available ESTs from seven shrimp species, excluding L. vannamei, were clustered with CAP3, and SNPs were predicted using SNPidentifier and analyzed as to whether the SNPs were intra- or interspecies. A total of 4,597 SNPs were predicted from 4,600 contigs with 735 of these SNPs being interspecies and potentially predictive of species differences while 3,894 SNPs were segregating within at least one species. Researchers also sequenced some homologous regions in 16 L. vannamei to determine if base pair segregation in closely related species could be used to predict SNPs in L. vannamei. Of the 45 bases predicted to segregate within sequenced regions, 9 were intraspecies SNPs and 1 of these was confirmed by sequencing. The intra- and interspecies SNPs predicted may also prove useful for other purposes.
D. M. Gorbach is supported by a USDA-CSREES National Needs fellowship under Grant no. 2007-38420-17767.