Abstract
Executive Summary
The research services scheduled for this contract relate to (i) develop panels of SNPs (single-nucleotide polymorphisms) specific for Murray Cod (MC) and for Golden Perch (GP), and to (ii) carry out blind parentage tests using the SNP panels for MC and GP on tissue samples supplied by NSW DPI. Results were
expected to be communicated to NSW DPI in a short report by the 15th of June 2018. We implemented an approach based on next-generation sequencing technology and a series of bioinformatics filtering steps that generated two powerful and highly effective SNP panels for parentage analyses; one for MC and one for GP. Briefly, DNA extractions were carried out for all MC and GP samples, and genomic libraries for a total of 90 individuals (48 MC and 42 GP) were sequenced in a genome platform, which generated ~480 million DNA sequences. Following bioinformatic processing of all these sequences, we generated catalogues of 24,460 and 25,935 high-quality filtered SNP markers for MC and GP, respectively. These catalogues are the largest sets of SNP markers ever reported for MC and for GP, providing unparalleled power for addressing a range of questions in fisheries management. We then carried out further filtering of
these catalogues for no missing data across all individuals (a conservative procedure appropriate for exclusion-based methods of parentage). This strict filtering produced 1268 SNP markers for MC and 2318 SNP markers for GP. Multiple complementary statistical analyses of the large and the strict SNP datasets were used to infer parentage using a blind test framework based on three categories: potential parents, non-parent adults and larvae. Both likelihood-based and exclusion-based parentage methods unambiguously produced the same results for each species: they identified the same parent-pair for each offspring. Using 10,000 simulated offspring for each species, we assessed the power for the SNP panels to correctly assign parents. We found that we obtained 100% correct assignments for both species based on the simulations. The parentage results were also fully consistent with results from two other analytical methods that use multivariate approaches to infer the number of clusters of genetically related individuals. In addition to the details of methods implemented, our final report includes a list of parent-pair for each
offspring, as well as comments about some issues encountered during DNA extraction due to poor preservation of tissue samples and other findings relevant to fisheries management. The work and results reported here conclusively attest to the power of the SNP-based approach and the resulting SNP catalogues to assign parentage in both captive-born and wild-caught MC and GP.
The research services scheduled for this contract relate to (i) develop panels of SNPs (single-nucleotide polymorphisms) specific for Murray Cod (MC) and for Golden Perch (GP), and to (ii) carry out blind parentage tests using the SNP panels for MC and GP on tissue samples supplied by NSW DPI. Results were
expected to be communicated to NSW DPI in a short report by the 15th of June 2018. We implemented an approach based on next-generation sequencing technology and a series of bioinformatics filtering steps that generated two powerful and highly effective SNP panels for parentage analyses; one for MC and one for GP. Briefly, DNA extractions were carried out for all MC and GP samples, and genomic libraries for a total of 90 individuals (48 MC and 42 GP) were sequenced in a genome platform, which generated ~480 million DNA sequences. Following bioinformatic processing of all these sequences, we generated catalogues of 24,460 and 25,935 high-quality filtered SNP markers for MC and GP, respectively. These catalogues are the largest sets of SNP markers ever reported for MC and for GP, providing unparalleled power for addressing a range of questions in fisheries management. We then carried out further filtering of
these catalogues for no missing data across all individuals (a conservative procedure appropriate for exclusion-based methods of parentage). This strict filtering produced 1268 SNP markers for MC and 2318 SNP markers for GP. Multiple complementary statistical analyses of the large and the strict SNP datasets were used to infer parentage using a blind test framework based on three categories: potential parents, non-parent adults and larvae. Both likelihood-based and exclusion-based parentage methods unambiguously produced the same results for each species: they identified the same parent-pair for each offspring. Using 10,000 simulated offspring for each species, we assessed the power for the SNP panels to correctly assign parents. We found that we obtained 100% correct assignments for both species based on the simulations. The parentage results were also fully consistent with results from two other analytical methods that use multivariate approaches to infer the number of clusters of genetically related individuals. In addition to the details of methods implemented, our final report includes a list of parent-pair for each
offspring, as well as comments about some issues encountered during DNA extraction due to poor preservation of tissue samples and other findings relevant to fisheries management. The work and results reported here conclusively attest to the power of the SNP-based approach and the resulting SNP catalogues to assign parentage in both captive-born and wild-caught MC and GP.
| Original language | English |
|---|---|
| Place of Publication | Orange, NSW |
| Publisher | Department of Primary Industries |
| Commissioning body | NSW Department of Primary Industries |
| Number of pages | 10 |
| Publication status | Published - 14 Jun 2018 |