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Sexual dimorphism of aquaculture traits is common for farmed fish. The Nile tilapia is the second most important farmed species with a production 6 million tons in 2020. Intensive farming relies on the production of all-males due to males' higher growth rate, and as a way to avoid uncontrolled reproductions. Currently the large majority of the all-male productions are obtained through androgen treatments. We aim to use more sustainable procedures to produce all-males such as the use of YY males. Until now, the use of YY males has not been reliable. This is because sex determination in Nile tilapia is complex and controlled by several factors. Although sex determinism follows an XX/XY system, the linkage group (LG) carrying the major sex determinant gene has been assigned to either LG1 or LG23, depending on the domesticated strain. Minor parental factors can also be implicated and in addition, high temperatures can override the genetic determinism. It is not clear to what extent these differences in sex determination are due to natural diversity in the mechanisms of sex determination or due to processes of domestication. It is therefore necessary to better understand the genetic basis of sex determinism in order to use this approach to generate all-males. For this, we decided to work on wild populations in Africa that have not suffered domestic manipulations. We underwent a study of sex determination in several wild populations from West (Lake Volta, Lake Kou) and East Africa (Lake Koka and Lake Hora). We used complementary genomic approaches of ddRAD, whole genome sequencing and long Nanopore reads. We were able to determine that the amh region present on LG23 is the major sex-determining region in most of these populations. Nevertheless, our results also show that there is high polymorphism in this SD region. Furthermore, there are populations that lack the male-specific amh duplication on LG23. Hence, there are no universal Y markers for Nile tilapia. It is necess

In domesticated strains of the Nile tilapia, phenotypic sex has been linked to genetic variants on linkage groups 1, 20 and 23. This diversity of sex-loci might reflect a naturally polymorphic sex determination system in Nile tilapia, or it might be an artefact arising from the process of domestication. Here, we searched for sex-determiners in wild populations from Kpandu, Lake Volta (Ghana-West Africa), and from Lake Koka (Ethiopia-East Africa) that have not been subjected to any genetic manipulation. We analysed lab-reared families using double-digest Restriction Associated DNA sequencing (ddRAD) and analysed wild-caught males and females with pooled whole-genome sequencing (WGS). Strong sex-linked signals were found on LG23 in both populations, and sex-linked signals with LG3 were observed in Kpandu samples. WGS uncovered blocks of high sequence coverage, suggesting the presence of B chromosomes. We confirmed the existence of a tandem amh duplication in LG23 in both populations and determined its breakpoints between the oaz1 and dot1l genes. We found two common deletions of ~5 kb in males and confirmed the presence of both amhY and amh∆Y genes. Males from Lake Koka lack both the previously reported 234 bp deletion and the 5 bp frameshift-insertion that creates a premature stop codon in amh∆Y.

Tilapias (family Cichlidae) are of importance in aquaculture and fisheries. Hybridisation and introgression are common within tilapia genera but are difficult to analyse due to limited numbers of species-specific genetic markers. We tested the potential of double digested restriction-site associated DNA (ddRAD) sequencing for discovering single nucleotide polymorphism (SNP) markers to distinguish between 10 tilapia species. Analysis of ddRAD data revealed 1,371 shared SNPs in the de novo-based analysis and 1,204 SNPs in the reference-based analysis. Phylogenetic trees based on these two analyses were very similar. A total of 57 species-specific SNP markers were found among the samples analysed of the 10 tilapia species. Another set of 62 species-specific SNP markers was identified from a subset of four species which have often been involved in hybridisation in aquaculture: 13 for Oreochromis niloticus, 23 for O. aureus, 12 for O. mossambicus and 14 for O. u. hornorum. A panel of 24 SNPs was selected to distinguish among these four species and validated using 91 individuals. Larger numbers of SNP markers were found that could distinguish between the pairs of species within this subset. This technique offers potential for the investigation of hybridisation and introgression among tilapia species in aquaculture and in wild populations.

Nile tilapia, Oreochromis niloticus, is a major farmed fish in which the farming of all-male offspring is the best way to avoid unwanted reproduction during the grow-out period and to optimize the production since males grow faster than females. Currently, the most sustainable method for producing all-male offspring is based on the use of YY males. However, the classic procedure to produce YY males is tedious because XY females and YY males cannot be identified before sexual maturity, and consequently YY males have been produced in very few strains. The recent identified sex markers could optimize this process. Nevertheless studies have shown that sex is linked to at least 2 linkage groups LG1 and LG23, depending on the strains as well as the wild populations. Therefore, it is necessary to develop a specific protocol for YYmales' production assisted by these markers for each farmed strain. The aim of the present study was to analyse and apply these sex markers to produce YY males in a wild population from Burkina Faso (Bama, Lake Kou) during its domestication process. In our study, we used the amh genes (located on LG23) identified in a Japanese Oreochromis niloticus strain containing several insertions and deletions located in the promoter, exon VI and exon VII. Ninety one O. niloticus wild caught breeders from Lake Kou were genotyped using these amh genes' markers. According to progeny testing results, amh markers correctly assigned the genotype for 82% of the G0 XY males. This suggests that in the remaining males, sex was not linked to LG23. The markers formally identified all G0 females including XX and XY genotypes which were also confirmed by progeny testing. To obtain G1 XY females, 34 progenies were treated with ethynyl-estradiol during the sex differentiating period. We subsequently identified precociously with the amh markers 58 XY females sampled amongst these progenies. The genotypes of three of the XY females out of 58 were confirmed by progeny testing

Background Inversions and other structural polymorphisms often reduce the rate of recombination between sex chromosomes, making it impossible to fine map sex-determination loci using traditional genetic mapping techniques. Here we compare distantly related species of tilapia that each segregate an XY system of sex-determination on linkage group 1. We use whole genome sequencing to identify shared sex-patterned polymorphisms, which are candidates for the ancestral sex-determination mutation. Results We found that Sarotherodon melanotheron segregates an XY system on LG1 in the same region identified in Oreochromis niloticus. Both species have higher densities of sex-patterned SNPs, as well as elevated number of ancestral copy number variants in this region when compared to the rest of the genome, but the pattern of differentiation along LG1 differs between species. The number of sex-patterned SNPs shared by the two species is small, but larger than expected by chance, suggesting that a novel Y-chromosome arose just before the divergence of the two species. We identified a shared sex-patterned SNP that alters a Gata4 binding site near Wilms tumor protein that might be responsible for sex-determination. Conclusions Shared sex-patterned SNPs, insertions and deletions suggest an ancestral sex-determination system that is common to both S. melanotheron and O. niloticus. Functional analyses are needed to evaluate shared SNPs near candidate genes that might play a role in sex-determination of these species. Interspecific variation in the sex chromosomes of tilapia species provides an excellent model system for understanding the evolution of vertebrate sex chromosomes.

A role for GH and IGF-I in the modulation of the immune system has been under discussion for decades. Generally, GH is considered a stimulator of innate immune parameters in mammals and teleost fish. The stimulatory effects in humans as well as in bony fish often appear to be correlated with elevated endocrine IGF-I (liver-derived), which has also been shown to be suppressed during infection in some studies. Nevertheless, data are still fragmentary. Some studies point to an important role of GH and IGF-I particularly during immune organ development and constitution. Even less is known about the potential relevance of local (autocrine/paracrine) IGF-I within adult and developing immune organs, and the distinct localization of IGF-I in immune cells and tissues of mammals and fish has not been systematically defined. Thus far, IGF-I has been localized in different mammalian immune cell types, particularly macrophages and granulocytes, and in supporting cells, but not in T-lymphocytes. In the present study, we detected IGF-I in phagocytic cells isolated from rainbow trout head kidney and, in contrast to some findings in mammals, in T-cells of a channel catfish cell line. Thus, although numerous analogies among mammals and teleosts exist not only for the GH/IGF-system, but also for the immune system, there are differences that should be further investigated. For instance, it is unclear whether the primarily reported role of GH/IGF-I in the innate immune response is due to the lack of studies focusing on the adaptive immune system, or whether it truly preferentially concerns innate immune parameters. Infectious challenges in combination with GH/IGF-I manipulations are another important topic that has not been sufficiently addressed to date, particularly with respect to developmental and environmental influences on fish growth and health.