Final report for the Murray-Darling Basin Fisheries Genetic Resource Program (FishGen 2)

The research services scheduled for this contract relate to (i) delivery of a database for descriptive metadata and genetic data for FishGen samples, (ii) screen Murray cod (MC) and golden perch (GP) broodstock and wild-caught fish using tissue samples supplied by NSW DPI, and to (iii) develop a panel of SNPs (single-nucleotide polymorphisms) specific for silver perch (SP) and verify the panel using blind parentage tests. Delivery of the database and a short progress report were completed on the 25th of January 2019 and a progress report updating results for the SP verification and GP parentage was submitted in June 2019 (Table 1). A Microsoft Access database has been established to manage FishGen sample metadata and genetic data. To date, metadata for 1386 Murray cod, golden perch and silver perch broodstock and wild-caught fish provided by NSW DPI and SARDI has been entered. DNA extractions for most (~96%) golden perch brood stock and wild-caught fish were successful. The sequencing, bioinformatics and parentage analysis has been completed for 718 golden perch. For Murray cod, poor tissue preservation for the majority of samples initially received substantially reduced the success rate of DNA extractions (~14% after repeated extractions). This issue was previously identified during the FishGen verification round, where up to 15 repeat extractions were required to obtain enough DNA from many MC samples. On the other hand, for this round sequencing for 115 MC samples (40% of 282 MC) has been completed and, due to the increased tissue quality of more recent samples, we expect this number to improve in the next round. Tissue preservation for SP was excellent, with DNA extractions for all 94samples passing quality control and providing high quality sequences. For the SP, GP and MC sequences, bioinformatic processing generated catalogues of 3,252, 11,506 and 3,498 high-quality filtered SNP markers for SP, GP and MC, respectively. We then carried out further filtering of these catalogues for missing data and genotype repeatability. This strict filtering produced 752 SNP markers for the SP parentage verification, 2,711 and 1,086 SNPs for GP and MC genetic diversity statistics and kinship analyses, and 527 and 414 SNPs for the GP and MC parentage analyses.