Early Intergenerational Changes in Genetic Diversity During Domestication of Procambarus acanthophorus Using Mitochondrial and Nuclear DNA Markers

Abstract

Procambarus acanthophorus is a freshwater crayfish species endemic to Mexico with high aquaculture potential. Monitoring genetic diversity during the early stages of domestication is crucial to avoid the erosion of adaptive potential and ensure the success of breeding programmes. This study analysed changes in genetic variability across four consecutive populations: a wild founder population (G0) and three captive-bred generations (G1, G2, G3), using five mitochondrial markers (COI, COII, COIII, tRNA-Asn/12S and D-loop) and one nuclear marker (elongation factor 2, EF-2). A total of 21 haplotypes were detected, with decreasing haplotype richness from G0 (n = 10) to G3 (n = 5), although haplotype and nucleotide diversity remained within moderate to high ranges (Hd = 0.65–0.90; π = 0.0020–0.0466), consistent with diversity levels reported in other early-stage domestication studies. AMOVA revealed that 68% of the total genetic variation was among generations, and pairwise Fst values confirmed progressive differentiation. These findings suggest that while some genetic erosion is occurring, the implemented breeding practices have preserved a substantial portion of genetic diversity during early domestication. This study provides a preliminary genetic baseline for the management of P. acanthophorus breeding programmes and underscores the need for continued monitoring using complementary nuclear markers.