A genetic linkage map of the threatened catfish Lophiosilurus alexandri: Inferences on effective population size

We report the first genetic linkage map of the catfish Lophiosilurus alexandri, a South American threatened and promising aquaculture catfish species. Using the progeny of three full-sib families, with 141, 74, and 49 offspring, respectively, we could genotype 2351 SNP markers using the ddRAD technology, shared by the male and the female maps constructed. The averaged, female and male maps spanned a total length of 2201.3 cM, 2481.9 cM, and 1872.8 cM, respectively, and comprehended the expected 27 linkage groups according to the karyotype information of the species (2n = 54). The recombination rate was nearly twice higher in the female than in the male map. The average map was used to estimate the historical effective population size (Ne) of the species from linkage disequilibrium between pairs of SNPs using parental individuals and revealed a remarkable drop in Ne about 20–25 generations in the past. The construction of the biggest artificial reservoir in Latin America and associated nutrient retention is pointed as a possible reason for such a reduction and suggests a reevaluation of the conservation status of the species. The current map lays the groundwork for understanding the genetic basis of economically important traits in breeding programs and will be useful for the genome assembly of this important commercial species.