A duplication of the Anti-Müllerian hormone gene is associated with genetic sex determination of different Oreochromis niloticus strains

Abstract

Sex determination (SD) mechanisms are ancient and conserved, yet much diversity is exhibited in primary sex-determining signals that trigger male or female development. In O. niloticus, SD is associated with a male-specific locus on linkage group (LG) 23 which harbors the Y-linked Anti-Müllerian hormone (amh) gene, and a truncated duplication, denoted amhΔy. We have evaluated the possible role of identified indels and SNPs in the amh gene on SD, based on conservation in different O. niloticus strains. A fluorescent assay for the detection of a 5 bp insertion in amhΔy exon VI, efficiently discriminated between XX, XY, and YY genotypes. Concordance rate between amhΔy and sex varied in six Oreochromis strains, from 100% (Ghana) through 90% (Swansea) to 85% (Thai-Chitralada). The association of amhΔy with sex was found to be conserved in all tested O. niloticus strains, and thus supports its key role in SD. However, the previously identified missense SNP (C/T) in amh exon II was found only in the Swansea strain, thus excluding its candidacy for the causal variation of SD across all strains. Effects of markers on LGs 1, 3, and 23 (amhΔy) fully explained sex distribution in one Thai-Chitralada family (R 2 = 1.0), whereas in another family only the major effect of LG23 (amhΔy) was significant (R 2 = 0.37). Thus, amhΔy on LG23 is associated with genetic SD, either as a single causal gene in different O. niloticus strains, or in combination with segregating genes on LGs 1 and 3 in the Thai-Chitralada hybrid strain.

Estimating Copy-Number Proportions: The Comeback of Sanger Sequencing

“…CNVs are common variations in chromosomal structure that play an important role in phenotypic variation and genetic disease; SNP genotyping methods that offer independent fluorescence intensities for two alleles can be used to estimate copy-number proportions between copies of segmental duplications [ 37 ]. Thus, using Sanger sequencing (AB1) or fragment analysis (FSA) trace files, investigation of peak-height ratio of SNPs within base strings that do not induce peak-ratio bias has been reported as an accurate tool for quantifying gene copy-number proportions [ 38 , 39 , 40 ]. As demonstrated in Figure 1 , peak-calling programs and web tools designed to quantify CRISPR-Cas9 base editing from Sanger sequencing can readily be used to estimate copy-number proportions in CNVs.…”

Preferential Mapping of Sex-Biased Differentially-Expressed Genes of Larvae to the Sex-Determining Region of Flathead Grey Mullet (Mugil cephalus)

“…Such master genes of SD frequently have truncated copies of the original genes i.e., AMH , DMRT1 , SOX3 , IRF9 , AMHR2 , and GSDF ( Li and Gui, 2018 ; Matsuda, 2018 ). The truncated copies may be located in tandem, adjacent to the original genes, like the AMHY and AMH in Nile tilapia ( Eshel et al, 2014 ; Li et al, 2015 ; Curzon et al, in press ), or in different chromosomes, like DMRTY and DMRT1 in medaka ( Matsuda et al, 2002 ). Likewise, the mammalian master SD regulator SRY is probably a male-specific copy of SOX3 ( Waters et al, 2007 ).…”

“…In our previous study, we generated the first draft of linkage map of the gray mullet and found synteny relationships between flathead gray mullet and Nile tilapia linkage groups (LGs) ( Dor et al, 2016 ). Segregating markers on LGs 1, 3, and 23 were associated with sex in different tilapia species ( Curzon et al, in press ). Nevertheless, we located a single SDR on mullet LG9, orthologous to tilapia LG8 (tLG8), with evidence for XX/XY SD mechanism ( Dor et al, 2016 ).…”

All‐male production by marker‐assisted selection for sex determining loci of admixed Oreochromis niloticus and Oreochromis aureus stocks

“…Production of all-male populations is essential for effective aquaculture and can be accomplished by crossing Oreochromis niloticus (On) XX females and Oreochromis aureus (Oa) ZZ males (Fishelson 1962;Beardmore et al 2001), which possess an XX/XY SD system mapped to LG23 (Eshel et al 2014) and a WZ/ZZ SD system mapped to LG3 (Lee et al 2004), respectively. Involvement of the XX/XY SD mechanism on LG1 in On 9 Oa hybrids has been also reported, and may be a result of a polygenic SD mechanism within these species (Lee et al 2003), or the emergence of additional SD genes caused by admixture (Curzon et al 2020). Indeed, Trombka & Avtalion (1993) observed the complete absence of females in an all-male cross of Oa from the Dead Sea region with Ghanaian On.…”

“…In purebred species Oa and On alleles, LG3-UNH168 170 and LG23-UNH898 414 (or LG23-ILL2 209), are strongly associated with W and Y chromosomes, respectively (Eshel et al 2014;Curzon et al 2020). The interaction of Oa W and On Y alleles in Oa males indicates that LG23-Y is dominant to LG3-W.…”