Screening and characterization of sex-linked DNA markers and marker-assisted selection in the Nile tilapia (Oreochromis niloticus)

Abstract The Nile tilapia is a cultured teleost fish in which males grow faster and larger than females, and mono-sex culturing could avoid unwanted reproduction during grow-out. Sex control in tilapia is an important issue in aquaculture. In the present study, randomly amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) fingerprinting were used to screen pooled and individual DNA samples from XX, XY, and YY fish for sex-linked markers. Four sex-linked markers (Marker-1 from RAPD and Markers-2, -3, and -4 from AFLP) were obtained and mapped to LG23, a small chromosome, by sequence analysis and fluorescence in situ hybridization (FISH). In addition, a total of 32 pairs of primers were designed based on the sequences of scaffolds 7, 29, and 101 on LG23, and these were used to screen genetic differences between X and Y by PCR. One of these (Marker-5) produced a detectable difference between XX, XY, and YY individuals. Eight pairs of primers based on the sequence characterized amplified region (SCAR) were designed and successfully converted to SCAR markers, which were used to sex progeny from different crosses of known genotypes for validation. Subsequently, Markers-4 and -5 were used to sex eight populations of Nile tilapia collected from different fish farms in China, which gave concordance rates that ranged from 76 to 100%. Based on the recombination rate derived from the progeny of XX (♀) × XY (♂), Markers-1, -2, -3, -4, and -5 were estimated to be around 5, 3, 5, 2 and 0 cM away from the sex-determining locus (SD), respectively. Marker-5, which mapped close to the SD reported previously (Eshel et al., 2012), was used for selective breeding of genetic male tilapia (GMT).