W033 From SNP Discovery to SNP Associations: Using Next-generation Sequencing and Custom Arrays to Create A High Density Genetic Linkage Map for the Silver Lipped Pearl Oyster, Pinctada maxima

Date: Saturday, January 14, 2012
Time: 9:35 AM
Room: Royal Palm Salons 3-4
David B. Jones , Centre for Sustainable Fisheries and Aquaculture, James Cook University, Townsville, Australia
Kyall R. Zenger , Centre for Sustainable Fisheries and Aquaculture, James Cook University, Townsville, Australia
Dean R. Jerry , Centre for Sustainable Fisheries and Aquaculture, James Cook University, Townsville, Australia
Pearls are an important export commodity for the Australian aquaculture industry with a production value of ~$113 million per annum. However, due to the large variation in pearl quality, there is the need for product improvement. Marker Assisted Selection (MAS) is one genetic approach that has great potential to increase the number of highly valuable pearls and therefore industry productivity. However, before MAS programs can be implemented, knowledge of trait and DNA marker associations must be established. To achieve this, comprehensive genomic resources including a high-density genetic linkage map of the silver-lipped pearl oyster (Pinctada maxima) needs to be established. Using next-generation sequencing, a large EST sequence database for P. maxima (1.3 million sequences, 4Gb, equivalent 5x genome coverage) was generated, assembled and annotated. From this database, genes associated with nacre biomineralization were identified, as well as 25,000+ high-quality single nucleotide polymorphism (SNP) markers. The best 3,000 SNPs have been incorporated into a high-density Illumina Infinium custom genotyping array. Using this array, more than 1100 family individuals have been genotyped to construct a comprehensive genetic linkage map. To date, we have mapped 924 SNPs over a total map distance of 1059.2 cM, covering an estimated 96.76% of the genome (14 linkage groups), at an average interval distance of 1.5cM. This genomics resource will not only provide important information on the genomic structure of a model bivalve species, but will also become a vital resource for the identification of pearl trait / DNA marker associations.