Molecular selection tools for the Australian crocodile industry

Summary

To remain internationally competitive, the Australian saltwater crocodile industry must develop efficient selection tools for identifying superior breeding animals to improve their herds and products. CrocPLAN (RIRDC Project US109A) was developed in recognition of this fact. Developments in CrocPLAN are now focused on incorporating DNA genotypes into the selection process to permit more accurate and expeditious genetic improvement, overcoming the long generation impediment to traditional selection of crocodiles, and making selection for difficult to measure and sexlimited traits possible. Recent research efforts have provided the basic genomic resources, namely a genetic marker map, permitting preliminary searches of the crocodile genome for genes underlying phenotypic variation for three traits of economic importance in the crocodile industry (RIRDC Project US139A). This proof of principle has motivated further extensive genome scans and the development of even better genetic selection tools arising from recent developments in molecular genomics, namely high density single nucleotide polymorphism (SNP) resources. High density marker resources, in conjunction with larger animal pedigrees, will permit far more exhaustive and sensitive genome scans to identify genomic regions associated with a whole range of economically important traits, which will ultimately be incorporated into CrocPLAN. We propose to identify quantitative trait loci (QTL) for traits associated with skin quality, animal survival, animal behaviour, growth and reproductive success in farmed saltwater crocodiles. In addition to QTL scans, we propose to develop further genomic resources which will position the Australian crocodile industry at the forefront for the development of genetic selection tools.

Program

New and Emerging Animal Industries

Research Organisation

The University of Sydney

Objective Summary

First we will identify further production traits for incorporation into CrocPLAN, particularly those affecting skin quality and juvenile survival/mortality. We will estimate relevant genetic and phenotypic parameters (heritability, repeatability and correlation), and perform QTL scans for those traits where there is a significant genetic component to identify genomic regions harbouring the genes that underpin phenotypic variation for each trait. This large scale QTL mapping objective will realise the full potential of the genetic resources recently generated through RIRDC project US139A. Second we will develop a large single nucleotide polymorphism (SNP) marker resource for the saltwater crocodile. This marker resource will be used for fine mapping of QTL, whole genome association analyses and the development of molecular genetic selection tools. This will involve the construction of normalised cDNA libraries for the saltwater crocodile, nextgeneration 454 sequencing of normalised cDNA libraries and capture of SNP information using cutting edge bioinformatic techniques. Finally we will design a SNP genotyping array and conduct a pilot experiment to assess the feasibility of SNP genotyping methods for the development of an industry selection tool.