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

• Published in: Genes Vol. 11; no. 9; p. 1017
• Main Authors: Triay, Cécile, Conte, Matthew A, Baroiller, Jean-François, Bezault, Etienne, Clark, Frances E, Penman, David J, Kocher, Thomas D, D'Cotta, Helena
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 29.08.2020; MDPI
• Subjects: amh; Animal genetics; Animals; Breakpoints; Chromosome Mapping; Chromosomes; Cichlids - genetics; Deoxyribonucleic acid; DNA; DNA sequencing; Domestication; Female; Females; Fish; Genetic analysis; Genetic diversity; Genetic Linkage; Genetic Markers; Genetic testing; Genetics; Genomes; Insertion; Life Sciences; Male; male duplication; Males; Mammals; Nile tilapia; Nonsense mutation; Oreochromis niloticus; Polymorphism, Single Nucleotide; Populations and Evolution; Quantitative Trait Loci; Sequence Analysis, DNA; Sex chromosomes; Sex determination; Sex Determination Processes - genetics; Sex linkage; sex-determinant; Stop codon; Tilapia; Whole Genome Sequencing; Y-chromosome; Ghana; Lake Malawi; Lake Volta; Ethiopia; East Africa; Y-chromosome; Nile tilapia; male duplication; amh; sex-determinant
• ISSN: 2073-4425; 2073-4425
• DOI: 10.3390/genes11091017

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 duplication in LG23 in both populations and determined its breakpoints between the and genes. We found two common deletions of ~5 kb in males and confirmed the presence of both and 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 .