Abstract
Executive Summary
The research services scheduled for this contract relate to (i) maintenence of a database for descriptive metadata and genetic data for FishGen samples, to (ii) develop a panel of SNPs (single-nucleotide polymorphisms) specific for trout cod (TC) and verify the panel using blind parentage tests, and to (iii) screen Murray cod (MC), golden perch (GP), silver perch (SP) and TC broodstock and wild-caught fish using tissue samples supplied by NSW DPI. A timeline and current status of delivery of scheduled services is outlined in Table 1. At commencement of this contract, the FishGen database contained metadata for 1386 Murray cod, golden perch and silver perch broodstock and wild-caught fish. An additional 761 samples arrived at Flinders in 2019/20 and have now been sorted, labelled and entered into the database, bringing the total number of samples to 2147 (Table 2). The database has also been updated to include information on DNA and sequencing quality for each sample. Broodstock have been received from eight hatcheries (Table 3). The sequencing, bioinformatics and parentage analyses have been completed for 988 GP, 340 MC, 114 SP and 80 TC hatchery broodstock and wild-caught fish. For Murray cod, poor tissue preservation for the majority of samples initially received has reduced the number of successfully genotyped fish, however results have improved for recent samples obtained with the Biomark biopsy system. Tissue preservation for GP, SP and TC was excellent, with DNA extractions for most samples passing quality control and providing high quality sequences. For the GP, MC , SP and TC sequences, bioinformatic processing generated catalogues of 20,895, 13,480, 5,374 and 4,605 high-quality filtered SNP markers for GP, MC , SP and TC respectively. We then carried out further filtering of these catalogues for missing data and genotype repeatability as required for the genetic diversity, parentage and kinship analyses (Table 4).
The research services scheduled for this contract relate to (i) maintenence of a database for descriptive metadata and genetic data for FishGen samples, to (ii) develop a panel of SNPs (single-nucleotide polymorphisms) specific for trout cod (TC) and verify the panel using blind parentage tests, and to (iii) screen Murray cod (MC), golden perch (GP), silver perch (SP) and TC broodstock and wild-caught fish using tissue samples supplied by NSW DPI. A timeline and current status of delivery of scheduled services is outlined in Table 1. At commencement of this contract, the FishGen database contained metadata for 1386 Murray cod, golden perch and silver perch broodstock and wild-caught fish. An additional 761 samples arrived at Flinders in 2019/20 and have now been sorted, labelled and entered into the database, bringing the total number of samples to 2147 (Table 2). The database has also been updated to include information on DNA and sequencing quality for each sample. Broodstock have been received from eight hatcheries (Table 3). The sequencing, bioinformatics and parentage analyses have been completed for 988 GP, 340 MC, 114 SP and 80 TC hatchery broodstock and wild-caught fish. For Murray cod, poor tissue preservation for the majority of samples initially received has reduced the number of successfully genotyped fish, however results have improved for recent samples obtained with the Biomark biopsy system. Tissue preservation for GP, SP and TC was excellent, with DNA extractions for most samples passing quality control and providing high quality sequences. For the GP, MC , SP and TC sequences, bioinformatic processing generated catalogues of 20,895, 13,480, 5,374 and 4,605 high-quality filtered SNP markers for GP, MC , SP and TC respectively. We then carried out further filtering of these catalogues for missing data and genotype repeatability as required for the genetic diversity, parentage and kinship analyses (Table 4).
| Original language | English |
|---|---|
| Place of Publication | Orange, NSW |
| Publisher | Department of Primary Industries |
| Commissioning body | NSW Department of Primary Industries |
| Number of pages | 37 |
| Publication status | Published - 23 Jul 2020 |