Abstract
BackgroundTilapias (Family Cichlidae) are the second most important group of aquaculture species in the world. They have been the subject of much research on sex determination due to problems caused by early maturation in culture and their complex sex-determining systems. Different sex-determining loci (linkage group 1, 20 and 23) have been detected in various tilapia stocks. The ‘genetically improved farmed tilapia’ (GIFT) stock, founded from multiple Nile tilapia (Oreochromis niloticus) populations, with some likely to have been introgressed with O. mossambicus, is a key resource for tilapia aquaculture. The sex-determining mechanism in the GIFT stock was unknown, but potentially complicated due to its multiple origins.ResultsA bulk segregant analysis (BSA) version of double-digest restriction-site associated DNA sequencing (BSA-ddRADseq) was developed and used to detect and position sex-linked single nucleotide polymorphism (SNP) markers in 19 families from the GIFT strain breeding nucleus and two Stirling families as controls (a single XY locus had been previously mapped to LG1 in the latter). About 1500 SNPs per family were detected across the genome. Phenotypic sex in Stirling families showed strong association with LG1, whereas only SNPs located in LG23 showed clear association with sex in the majority of the GIFT families. No other genomic regions linked to sex determination were apparent. This region was validated using a series of LG23-specific DNA markers (five SNPs with highest association to sex from this study, the LG23 sex-associated microsatellite UNH898 and ARO172, and the recently isolated amhy marker for individual fish (n = 284).ConclusionsPerhaps surprisingly given its multiple origins, sex determination in the GIFT strain breeding nucleus was associated only with a locus in LG23. BSA-ddRADseq allowed cost-effective analysis of multiple families, strengthening this conclusion. This technique has potential to be applied to other complex traits. The sex-linked SNP markers identified will be useful for potential marker-assisted selection (MAS) to control sex-ratio in GIFT tilapia to suppress unwanted reproduction during growout.
Highlights
Tilapias (Family Cichlidae) are the second most important group of aquaculture species in the world
These two Stirling Nile tilapia families were used as positive controls for the BSAddRADseq analysis
We developed a powerful extension of Bulk segregant analysis (BSA) and ddRADseq by applying preextraction pooling of tissue samples to ddRADseq for the analysis and identification of sex-determining region(s) in genetically improved farmed tilapia’ (GIFT) families, followed by the verification of the identified region with different molecular marker analyses
Summary
Tilapias (Family Cichlidae) are the second most important group of aquaculture species in the world They have been the subject of much research on sex determination due to problems caused by early maturation in culture and their complex sex-determining systems. Fish are an extremely diverse group of organisms, with the underlying mechanisms of sex determination not being strongly conserved among taxa. These can vary among closely related species, and even show intraspecific variation. Different components of the transforming growth factor beta (TGF-β) have been identified as strong candidates for master sexdetermining genes in different fish species - Amhy in Odontesthes hatcheri [9], Amhr in Takifugu rubripes [10] and Amhy in the Nile tilapia, Oreochromis niloticus [11, 12]. A sexually dimorphic immune-related gene only present on the Y chromosome (sdY) is the master sexdetermining gene in the rainbow trout, Oncorhynchus mykiss [13] and this male-specific gene have been found to be conserved across the salmonids [14]
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