APPLICATION OF PARENTAGE AND RELATEDNESS ANALYSIS TO IMPROVE SELECTIVE BREEDING IN BARRAMUNDI AQUACULTURE

Selecting premium broodstock is fundamental to improving aquaculture productivity, however, the nature of simultaneous broadcast spawning in many species creates difficulties in assigning parentage and relatedness to progeny. One such species is Barramundi (Lates calcarifer) which is farmed extensively in the Australasian tropics and increasingly elsewhere, often with reliance on unimproved broodstock resulting in significant variation in the quality of progeny. Accurate assignment is vital to monitor broodstock performance and reduce the incidence of inbreeding. One effective molecular technique to identify genetic lineage is microsatellite genotyping which targets nucleotide tandem repeats in DNA sequences.

A suite of 16 markers has been developed to amplify microsatellite regions of Barramundi (L. calcarifer) using multiplex PCR reactions. Amplicons are size selected through capillary separation (3100 Genetic Analyzer) and Genemarker® is used to verify allele size. Data is processed using Cervus 3.0.7 where allele frequencies within the population are analysed. Parentage output files assign parents to a particular offspring using a strict confidence level (95%) and no detectable mismatches as a measure of certainty. Cohorts of progeny are then conveniently sorted into family groups with the most dominate females and males being assigned a high value breeding classification. Relatedness analysis is generated using CoAncestory 1.0.1.7 where each individual is compared with all other individuals in a population. Relatedness (Rxy) values range between -1.0 (distantly related) to 1.0 (highly related) and are presented as a coloured heat map for ease when selecting breeding candidates.

These results provide useful information for selection of appropriate broodstock groups prior to spawning events by not only ensuring that mating groups for mass spawning events can be created with minimal inbreeding, but also accounts for spawning success and contribution to progeny cohorts.  The analysis can be modified to suit most aquaculture species and readily integrated into genetic improvement programmes. This technology could become a useful tool in genetic studies to identify important commercial traits and has the potential to compare Genotype by Environment effects which would aid industry in producing consistently high quality seedstock.