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

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.

An ex vivo Approach to Study Hormonal Control of Spermatogenesis in the Teleost Oreochromis niloticus

“…Amh is an important regulator of spermatogenesis in teleost fish and in some tilapia strains a tandem duplication (amh∆Y and amhY) carries the task of a male sex determining factor (90)(91)(92). One of these copies (amh∆Y) is not present in our fish line ( Figure S7), but whether the second copy (amhY) exists or not in our strain is under investigation.…”

Multi-trait GWAS using imputed high-density genotypes from whole-genome sequencing identifies genes associated with body traits in Nile tilapia

“…The availability of a chromosome-level reference genome assembly [15] and high-throughput whole-genome sequencing (WGS) methods [16,17], have allowed for the assessment of genetic variation of different Nile tilapia populations at a genome-wide level and the recent development of single nucleotide polymorphism (SNP) panels [18,19]. The availability of Nile tilapia SNP panels made it possible to use modern molecular breeding approaches; including mapping of quantitative trait loci (QTL) through genome-wide association studies (GWAS), marker-assisted selection (MAS) and genomic selection [20,21].…”

Development of Disease-Resistance-Associated Microsatellite DNA Markers for Selective Breeding of Tilapia (Oreochromis spp.) Farmed in Taiwan

“…Relative to the aquaculture industry, modern genome-based strategies (e.g., marker-assisted selection and genomic selection breeding) have been widely using in agriculture and animal industries. Even though marker-assisted selection has only begun to be applied in the aquaculture industry in recent years, some cases of aquaculture studies can be found; for instance, high growth rate, cold resistance, and disease resistance in flatfish [ 69 , 70 ], rainbow trout [ 73 , 74 , 75 , 76 , 77 ], and carp [ 78 , 79 ]. Thus far, most of the current research of marker-assisted selection has focused on developing massive SNPs, SSRs, and deletions in Nile tilapia [ 80 ] for sex determination [ 81 ], population structure analysis [ 82 ], improvement of growth and fillet yield [ 83 , 84 ], and cold stress [ 85 ].…”