BACKGROUND 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. 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. RESULTS A 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). CONCLUSIONS Perhaps 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.

中文翻译：

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罗非鱼GIFT菌株中的性别确定受连锁组23中一个基因座的控制。

背景罗非鱼（丽鱼科）是世界上第二重要的水产养殖物种。由于文化早期成熟及其复杂的性别决定系统而引起的问题，它们已成为关于性别决定的许多研究的主题。在各种罗非鱼种群中发现了不同的性别决定基因座（连锁群1、20和23）。由多个尼罗罗非鱼（Oreochromis niloticus）种群建立的“基因改良养殖罗非鱼”（GIFT）种群是罗非鱼水产养殖的重要资源，其中有些可能已被莫桑比克梭菌（O. mossambicus）渗入。GIFT种群中的性别决定机制尚不清楚，但由于其起源多而可能很复杂。结果开发了双消化限制性位点相关DNA测序（BSA-ddRADseq）的本体分离分析（BSA）版本，并用于检测和定位GIFT菌株育种的19个科中的性连锁单核苷酸多态性（SNP）标记核和两个斯特林家族作为对照（单个XY基因座先前已映射到LG1中的LG1）。每个家庭在整个基因组中检测到约1500个SNP。斯特灵家族中的表型性表现出与LG1的强烈关联，而在大多数GIFT家庭中，只有LG23中的SNP表现出明显的性关联。没有其他与性别决定有关的基因组区域明显。使用一系列LG23特异性DNA标记（该研究中与性相关性最高的5个SNP，LG23与性相关的微卫星UNH898和ARO172，以及最近分离出的单个鱼类的amhy标记（n = 284）。结论也许令人惊讶的是，鉴于其起源多种多样，GIFT菌株繁殖核中的性别决定仅与LG23中的一个基因座有关。BSA-ddRADseq允许对多个家族进行经济高效的分析，从而加强了这一结论。该技术有可能应用于其他复杂性状。鉴定出的与性别相关的SNP标记物可用于潜在的标记物辅助选择（MAS），以控制GIFT罗非鱼的性别比，从而抑制成年期不必要的繁殖。GIFT菌株繁殖核中的性别决定仅与LG23中的基因座相关。BSA-ddRADseq允许对多个家族进行具有成本效益的分析，从而加强了这一结论。该技术有潜力应用于其他复杂性状。鉴定出的与性别相关的SNP标记物可用于潜在的标记物辅助选择（MAS），以控制GIFT罗非鱼的性别比，从而抑制成年期不必要的繁殖。GIFT菌株繁殖核中的性别决定仅与LG23中的基因座相关。BSA-ddRADseq允许对多个家族进行具有成本效益的分析，从而加强了这一结论。该技术有潜力应用于其他复杂性状。鉴定出的与性别相关的SNP标记物可用于潜在的标记物辅助选择（MAS），以控制GIFT罗非鱼的性别比，从而抑制成年期不必要的繁殖。