Creation of a Genomic Resource and Quantitative Trait Loci Detection in Pacific Whiteleg Shrimp Litopenaeus vannamei for Selective Breeding Applications

The Pacific whiteleg shrimp (Litopenaeus vannamei) is the world’s most widely farmed penaeid (~75% global shrimp production) with a global production value at approximately $US8.1 billion. Despite its importance, knowledge of its genome structure and the genetic basis underlying important production traits (eg., disease resistance and growth) and their interaction are scarce. This project aims to use high-throughput DNA sequencing / genotyping to provide detailed information on both of these important areas of research. Using Illumina GAxII sequencing technology, the L. vannamei transcriptome was sequenced to an average genome depth of 15x coverage. Sequence reads were assembled into 76,789 contigs with a N50 of 2,375 bp and a maximum length of 16,552 bp. Based on BLAST and GO analyses, these contigs represent a significant proportion of unique genes and gene ontology pathways. From this dataset, more than 256,000 high-quality SNPs have been identified, with the 10,000 most informative constructed into a whole-genome SNP genotyping array. Currently, more than 2,500 individuals are being genotyped for the purpose of genomic map construction and whole-genome trait association studies. Phenotype data on disease resistance (eg., WSSV), growth rates and salinity tolerance is being generated from 280+ families. These individuals have been selected to represent much of the genetic and phenotypic diversity found within the farmed L. vannamei industry. The development of these genetic resources will not only be used to identify QTLs influencing commercially important traits, but will also considerably increase our understanding of genome structure and its evolution in crustaceans in general.