Fine mapping using whole-genome sequencing confirms anti-Müllerian hormone as a major gene for sex determination in farmed Nile tilapia (Oreochromis niloticus L.)

Abstract

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

Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus)

“…Genetic diversity (H e , H o and π) was low and similar between all strains of Nile tilapia. These results are in agreement with those reported by previous works (H e ranging from 0.2 to 0.4 [30][31][32][33][34] ). Low genetic diversity is expected in domesticated populations, compared to their wild conspecifics as these populations can lose genetic diversity due to selective breeding and the absence of gene flow with other populations 35 .…”

“…DNA from all individuals was purified from fin-clip samples using a Wizard Genomic DNA purification kit (Promega). The DNA libraries were prepared and sequenced using an Illumina HiSeq 2500 machine (Illumina, USA) as described by Cáceres et al 33 and Yáñez et al 73 . Reads were aligned to the Nile tilapia reference genome (O_niloticus_UMD, GCA_000188235.2) with BWA MEM 74 .…”

High-throughput single nucleotide polymorphism (SNP) discovery and validation through whole-genome resequencing of hundreds of individuals in Nile tilapia (Oreochromis niloticus)

“…The SNP panel presented here provides an excellent resource for the development of genome-scale studies of biologically and economically important traits. For instance, a recent genome-wide association study using a subset 2.4 million SNPs derived from the 29.9 million SNPs available from the present study, confirmed the anti-Müllerian hormone as a major gene associated with sex determination in different populations of farmed Nile tilapia (Caceres et al 2019). This information could assist future strategies aiming at generating monosex (all-male) Nile tilapia populations for farming purposes without using hormones, to better exploit the sexual dimorphism present in the species, in which male individuals growth faster than females (Baroiller and D’Cotta 2001; Alcantar et al 2014).…”

High-quality chromosome-level genomes of two tilapia species reveal their evolution of repeat sequences and sex chromosomes

“…The repetitive nature of this part of LG3, together with its extremely low recombination, may have contributed to the difficulty of finding genetic markers to anchor a large portion of LG3 in the ONEg assembly [22]. Later QTL mapping and genomic analyses, however confirmed that LG1 or LG23 is the sex chromosome of ON [22, 26], while LG3 has been frequently adopted as the sex chromosome in other tilapia species [22, 45].…”

“…The rapid transition of sex chromosome system between the two species OA and ON occurred within only 5 MY. More strikingly, another study has mapped the male SD gene in a Japanese strain of ON ( ONJp ) onto LG23 rather than LG1 [23-26]. The Y-linked male SD gene is a duplicated copy of anti-Mullerian hormone ( Amhy ), and its disruption by CRISPR/Cas9 causes male-to-female sex reversal [25].…”