U. S. shrimp breeding companies play a major role in driving genetic progress in global shrimp genetics and productivity as industry based genetic diversity (GD) underpins genetic progress. To date an assessment within and among companies has not been performed. Quantifying GD aids in future selection options and guides gene banks in germplasm collection strategies.
For this study, we obtained 878 animal samples from three corporations, denoted as C1 (n = 278), C2 (n = 300), C3 (n = 300). DNA extraction and genotyping were performed using 192 SNP evenly spaced across the shrimp genome. Quality control of a call rate threshold of 80% (SNP and animals) and a minor allele frequency of < 0.05, left 171 SNP and 878 animals for analysis. Data analyses included: principal component analysis, STRUCTURE, effective population and Fst.
First and second principal components (PC), accounting for 19.5% of the variation, and suggested corporate populations were genetically distinct. This finding was supported by estimates of Fst (Table 1) and STRUCTURE results (Figure 1). STRUCTURE analysis suggested within company substructure for C2 and C3. Low Ne for C1 and C2 (Table 1) suggest future management of GD is needed to preserve selection options.
Our findings suggest corporate lines are genetically diverse from each other. Within corporation GD based upon Ne estimates suggest vigilance should be employed to minimize inbreeding and genetic relationship.