Absence of Gene Is Concordant with Femaleness in Cichlids Harboring the LG1 Sex-Determination System.

has been used as a reference genome for studies of tilapia sex determination (SD) revealing segregating genetic loci on linkage groups (LGs) 1, 3, and 23. The master key regulator genes (MKR) underlying the SD regions on LGs 3 and 23 have been already found. To identify the MKR in fish that segregate for the LG1 XX/XY SD-system, we applied short variant discovery within the sequence reads of the genomic libraries of the hybrid stock, and , which were aligned to a 3-Mbp-region of the genome. We obtained 66,372 variants of which six were concordant with the XX/XY model of SD and were conserved across these species, disclosing the male specific gene. We further validated this observation in and in the hybrid stock. Genome alignment of the 1252-bp transcript showed that the gene's size was 2664 bp, and that its three exons were capable of encoding 99 amino acids including a 45-amino-acid basic helix-loop-helix domain that is typical of the ovary development regulator- (). In gonads, the gene was exclusively expressed in testes. Thus, the genomic presence determines male fate by interrupting the female developmental program. This indicates that the gene is the long-sought SD MKR on LG1.