Nile tilapia belongs to the second most cultivated group of fish in the world, mainly because of its favorable characteristics for production. Genetic improvement programs and domestication process of Nile tilapia may have modified the genome through selective pressure, leaving signals that can be detected at the molecular level. In this work, signatures of selection were identified using genomewide SNP data, by two haplotype-based (iHS and Rsb) and one F ST based method. Whole-genome re-sequencing of 326 individuals from three strains (A, B and C) of farmed tilapia maintained in Brazil and Costa Rica was carried out using Illumina HiSeq 2500 technology. After applying conventional SNP-calling and quality-control filters, ~ 1.3 M high-quality SNPs were inferred and used as input for the iHS, Rsb and F ST based methods. We detected several candidate genes putatively subjected to selection in each strain. A considerable number of these genes are associated with growth (e.g. NCAPG, KLF3, TBC1D1, TTN), early development (e.g. FGFR3, PFKFB3), and immunity traits (e.g. NLRC3, PIGR, MAP1S). These candidate genes represent putative genomic landmarks that could be associated to traits of biological and commercial interest in farmed nile tilapia. Nile tilapia (Oreochromis niloticus) is a teleost fish of the Cichlidae family native to Africa and the Middle East. The geographic range of the species extends from 8°N to 32°N 1. The first record of domestication is dated around 3,500 years ago as evidenced in paintings at the Theban tombs in Egypt 2. Nowadays, this species is the second most cultivated group of fish in the world 3. Favorable characteristics for production include rapid growth, adaptability to different culture conditions, tolerance to high densities, disease resistance, easy reproduction, and tolerance to low concentrations of oxygen 4. Genetic improvement programs (GIPs) for Nile tilapia began in 1988 as an approach to counteract the production decrease generated by introgressions with Mozambique tilapia (Oreochromis mossambicus) 5,6. Since then, nearly twenty GIPs have been established for Nile tilapia around the world 7,8. GIPs aim to improve traits of commercial interest, such as growth rate, disease resistance, cold and salinity tolerance 7. The GIFT (Genetic Improvement of Farmed Tilapia) 9 Nile tilapia strain was developed by the ICLARM (International Centre for Living Aquatic Resources Management, now the WorldFish Center), in collaboration with the Norwegian Institute of Aquaculture Research (AKVAFORSK, now NOFIMA Marin) 1. The implementation of GIPs for the GIFT population has been successful, because growth rate in Nile tilapia has doubled in five generations, showing that this species had a positive response to selection 1 .

26Nile tilapia (Oreochromis niloticus) is one of the most cultivated and economically important species in 27 world aquaculture. Faster male development during grow-out phase is considered a major problem that 28 generate heterogeneous sizes of fish at harvest. Identifying genomic regions associated with sex 29 determination in Nile tilapia is a research topic of great interest. The objective of this study was to 30 identify genomic variants associated with sex determination in three commercial populations of Nile 31 tilapia. Whole-genome sequencing of 326 individuals was performed, and a total of 2.4 million high-32quality bi-allelic single nucleotide polymorphisms (SNPs) were identified. A genome-wide association 33 study (GWAS) was conducted to identify markers associated with the binary sexual trait (males = 0; 34 females = 1). A mixed logistic regression GWAS model was fitted and a genome-wide significant signal 35 comprising 36 SNPs, located on chromosome 23 spanning a genomic region of 536 kb, was identified. 36Ten out of these 36 genetic variants, intercept the anti-Müllerian hormone gene. Other significant SNPs 37 were located in the neighboring Amh gene region. This gene has been strongly associated with sex 38 determination in several vertebrate species, playing an essential role in the differentiation of male and 39 female reproductive tissue in early stages of development. This finding provides useful information to 40 better understand the genetic mechanisms underlying sex determination in Nile tilapia. 41 42 Keywords: SNP, sex control, quantitative trait loci, WGS, GWAS 43 44 45

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Nile tilapia (Oreochromis niloticus) is one of the most cultivated and economically important species in world aquaculture. Intensive production promotes the use of monosex animals, due to an important dimorphism that favors male growth. Currently, the main mechanism to obtain all-male populations is the use of hormones in feeding during larval and fry phases. Identifying genomic regions associated with sex determination in Nile tilapia is a research topic of great interest. The objective of this study was to identify genomic variants associated with sex determination in three commercial populations of Nile tilapia. Whole-genome sequencing of 326 individuals was performed, and a total of 2.4 million high-quality bi-allelic single nucleotide polymorphisms (SNPs) were identified after quality control. A genome-wide association study (GWAS) was conducted to identify markers associated with the binary sex trait (males = 1; females = 0). A mixed logistic regression GWAS model was fitted and a genome-wide significant signal comprising 36 SNPs, spanning a genomic region of 536 kb in chromosome 23 was identified. Ten out of these 36 genetic variants intercept the anti-Müllerian (Amh) hormone gene. Other significant SNPs were located in the neighboring Amh gene region. This gene has been strongly associated with sex determination in several vertebrate species, playing an essential role in the differentiation of male and female reproductive tissue in early stages of development. This finding provides useful information to better understand the genetic mechanisms underlying sex determination in Nile tilapia.

No abstract