Assessment of SNP Genotyping for Genetic Differentiation
Liu, S. et al. "Assessment of genetic differentiation and genetic assignment of commercial rainbow trout strains using a SNP panel." Aquaculture (2017)
Objective: characterize genetic differentiation of commercial rainbow trout strains in breeders and population fish
Utilization of Standard BioTools™ products: • EP1™ system
• IFC Controller HX
• 96.96 Dynamic Array™ IFCs
Conclusions: • 97.1% correct self-assignment to eight breeder populations
• 98.2% correct assignment of production fish
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TROUT CASE STUDY
Objective: The objective of this study was to measure gene expression levels of Hemocyte immune response genes when exposed to White Spot Syndrome Virus (WSSV) and Fusarium solani (fungal) in order to understand the molecular mechanisms driving shrimp-pathogen interactions to develop strategies to control disease outbreaks in shrimp production systems with L. vannamei. Utilization of Standard BioTools products: Biomark SystemNanoFlex 4-IFC Controller96.96 dynamic arraysReal-Time PCR Analysis Software Conclusions: Genes that were monitored showed up regulation and down regulation over the time course study. Results reported can serve as immunomarkers for mortality events and could help reduce the loss in shrimp production systems
Results and conclusions
• 97.1% correct assignment of breeders to self-assigned populations
• 98.2% of known origin production fish assigned to correct breeding populations
• CN farm fish assigned to Troutlodge breeding populations, which matched purchasing records.
• 98.4% of non-Troutlodge fish excluded as Troutlodge fish
Confirmed SNP panel for parentage assignment and the panel
has sufficient power for genetic assignment of commercial
rainbow trait strains used.
Background and methods
Utilized rainbow trout SNP panel from Liu et al. (2016) and EP1 system
Objectives of the study:
• Characterize eight Troutlodge breeding populations
• Evaluate accuracy of genetic assignment of the eight populations using the SNP panel