ddRADseq reveals determinants for temperature-dependent sex reversal in Nile tilapia on LG23

Abstract

BackgroundIn Nile tilapia sex determination is governed by a male heterogametic system XX/XY either on LG1 or LG23. The latter carries a Y-specific duplicate of the amh gene, which is a testis-determining factor. Allelic variants in the amh gene demonstrated to be major triggers for autosomal and temperature-dependent sex reversal. Further, QTL on LG23 and LG20 show a temperature-responsiveness with influence on the phenotypic sex relative to the sex chromosomes. Here we present a ddRADseq based approach to identify genomic regions that show unusual large differentiation in terms of fixation index (FST) between temperature-treated pseudomales and non-masculinized females using a comparative genome-scan. Genome-wide associations were identified for the temperature-dependent sex using a genetically all-female population devoid of amh-ΔY.ResultsTwenty-two thousand three hundred ninety-two SNPs were interrogated for the comparison of temperature-treated pseudomales and females, which revealed the largest differentiation on LG23. Outlier FST-values (0.35–0.44) were determined for six SNPs in the genomic interval (9,190,077–11,065,693) harbouring the amh gene (9,602,693–9,605,808), exceeding the genome-wide low FST of 0.013. Association analysis with a set of 9104 selected SNPs confirmed that the same genomic region on LG23 exerts a significant effect on the temperature-dependent sex.ConclusionsThis study highlights the role of LG23 in sex determination, harbouring major determinants for temperature-dependent sex reversal in Nile tilapia. Furthermore FST outlier detection proves a powerful tool for detection of sex-determining regions in fish genomes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3930-0) contains supplementary material, which is available to authorized users.

Structure and Sequence of the Sex Determining Locus in Two Wild Populations of Nile Tilapia

“…In the Nile tilapia, markers on LGs 1, 3, 20 and 23 have all been found associated with phenotypic sex in various domesticated strains [ 29 , 30 , 34 , 35 , 36 , 39 , 40 , 44 , 65 ]. To overcome possible artefacts due to the process of domestication, we have searched for the genetic basis of sex determination (SD) in wild populations of Nile tilapia and studied whether there are population differences.…”

“…Our family ddRAD results reveal that LG23 is an XY sex chromosome in both the Kpandu and Koka populations. LG23 has already been reported to be the sex chromosome in some domesticated Nile tilapia [ 41 , 43 , 44 , 65 ]. Among the significant sex-variants between 24 and 40 Mb on LG23, one is common to both populations: the anti-Müllerian hormone gene ( amh ).…”

“…The amh gene has a primary role in the sex differentiation pathway of vertebrates including fish [ 69 ] and is implicated in germ cell proliferation in teleost fish (reviewed by Mullen et al [ 70 ]). Amhy also appears to be the sex-determiner in several domesticated strains of Nile tilapia [ 40 , 41 , 42 , 43 , 44 , 65 ]. A recent study of a wild Lake Kou population (Burkina Faso) of Nile tilapia also showed that sex was linked to LG23 but the amh gene alone was not sufficient to explain all the sex-ratios observed [ 47 ].…”

Population Structure and Genetic Diversity of Nile Tilapia (Oreochromis niloticus) Strains Cultured in Tanzania

“…Several studies have applied ddRAD-seq sequencing to generate high-density linkage maps (Brown et al, 2016;Manousaki et al, 2016) and estimate genetic diversity (Antoniou et al, 2017;Hosoya et al, 2018). Furthermore, ddRADseq has been utilized in several tilapia studies for evaluating the suitability of DNA from skin mucus swabs (Taslima et al, 2017), identification of sex determining regions (Wessels et al, 2017), and quantitative trait loci (QTL) analysis (Li et al, 2017).…”

miRTil: An Extensive Repository for Nile Tilapia microRNA Next Generation Sequencing Data

“…Due to its economic potential, the scientific community is interested in revealing the molecular mechanisms underlying economically interesting genotypes. Some traits include sexual differentiation, muscle growth, lipogenesis, and disease resistance [4][5][6][7]. Data from the plant science community have shown that economically interesting traits, such as disease resistance, biomass production, plant development, and environmental biotic or abiotic stress, can be altered by manipulation of microRNAs (miRNAs) [8][9][10].…”