Assessing Genetic Diversity for a Pre-Breeding Program in Piaractus mesopotamicus by SNPs and SSRs

Abstract

The pacu (Piaractus mesopotamicus) is a Neotropical fish with remarkable productive performance for aquaculture. Knowledge of genetic resources in Neotropical fish is essential for their applications in breeding programs. The aim of this study was to characterize the genetic diversity of seven farmed populations of pacu which will constitute the basis for a broodstock foundation for coming breeding programs in Brazil. Analysis of one wild population (Paraná River) was used as a reference to compare genetic parameters in the farmed populations. The analyses were performed using 32 single-nucleotide polymorphisms (SNP) and 8 simple sequence repeat (SSR) markers. No significant differences in genetic diversity between populations estimated through the number of alleles and allelic richness, observed heterozygosity, expected heterozygosity, and minimum allele frequency were detected (p > 0.05). Low genetic diversity was observed in all farmed stocks and the wild population. Moreover, we detected low genetic structure when comparing farmed and wild populations for SNPs (F_ST = 0.07; K = 3) and SSRs (F_ST = 0.08; K = 2). Analysis of molecular variance (AMOVA) demonstrated that genetic variation was mostly within populations. Kinship analysis showed that most fish farms included related individuals at a proportion of at least 25%. Our results suggest that the basal broodstock for pacu breeding programs should be founded with individuals from different fish farms for higher genetic diversity and to avoid inbreeding risks.

Keywords: aquaculture; breeding programs; genetic variability; inbreeding.

Figure 1

Distribution of kinship values (r_xy) by Wang’s estimator of fish farms (FF1–FF7) in SSR (a) and SNP (b) datasets. Threshold values for kinship analysis: unrelated (r < 0.125), half sibling (0.125 ≤ r ≤ 0.375), and full sibling (r > 0.375) individuals.

Figure 2

ΔK statistics in STRUCTURE analysis as a function of the number of putative genetic clusters (K) for pacu populations. Coefficient of ancestry of pacu individuals collected from seven cultivated stocks (FF1–FF7) and one wild population (WILD), based on 8 SSR (a) and 32 SNP loci (b). Each vertical bar represents an individual. The fish farms are separated by vertical white lines. The color proportions of each bar correspond to individuals’ estimated membership fractions of each of the clusters.