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

MASTROCHIRICO-FILHO, VITO ANTONIO; DEL PAZO, FELIPE; HATA, MILENE ELISSA; VILLANOVA, GABRIELA VANINA; FORESTI, FAUSTO; VERA, MANUEL; MARTÍNEZ, PAULINO; PORTO-FORESTI, FÁBIO; HASHIMOTO, DIOGO TERUO

Genes

mdpi

Lugar: Basel; Año: 2019 vol. 10

Abstract: The pacu (Piaractus mesopotamicus) is a Neotropical fish with remarkable productiveperformance for aquaculture. Knowledge of genetic resources in Neotropical fish is essential for theirapplications in breeding programs. The aim of this study was to characterize the genetic diversity ofseven farmed populations of pacu which will constitute the basis for a broodstock foundation forcoming breeding programs in Brazil. Analysis of one wild population (Paraná River) was used as areference to compare genetic parameters in the farmed populations. The analyses were performedusing 32 single-nucleotide polymorphisms (SNP) and 8 simple sequence repeat (SSR) markers.No significant differences in genetic diversity between populations estimated through the number ofalleles and allelic richness, observed heterozygosity, expected heterozygosity, and minimum allelefrequency were detected (p > 0.05). Low genetic diversity was observed in all farmed stocks and thewild population. Moreover, we detected low genetic structure when comparing farmed and wildpopulations for SNPs (FST = 0.07; K = 3) and SSRs (FST = 0.08; K = 2). Analysis of molecular variance(AMOVA) demonstrated that genetic variation was mostly within populations. Kinship analysisshowed that most fish farms included related individuals at a proportion of at least 25%. Our resultssuggest that the basal broodstock for pacu breeding programs should be founded with individualsfrom different fish farms for higher genetic diversity and to avoid inbreeding risks.