Identification of Sex-Linked SNPs and Sex-Determining Regions in the Yellowtail Genome

Abstract

Unlike the conservation of sex-determining (SD) modes seen in most mammals and birds, teleost fishes exhibit a wide variety of SD systems and genes. Hence, the study of SD genes and sex chromosome turnover in fish is one of the most interesting topics in evolutionary biology. To increase resolution of the SD gene evolutionary trajectory in fish, identification of the SD gene in more fish species is necessary. In this study, we focused on the yellowtail, a species widely cultivated in Japan. It is a member of family Carangidae in which no heteromorphic sex chromosome has been observed, and no SD gene has been identified to date. By performing linkage analysis and BAC walking, we identified a genomic region and SNPs with complete linkage to yellowtail sex. Comparative genome analysis revealed the yellowtail SD region ancestral chromosome structure as medaka-fugu. Two inversions occurred in the yellowtail linage after it diverged from the yellowtail-medaka ancestor. An association study using wild yellowtails and the SNPs developed from BAC ends identified two SNPs that can reasonably distinguish the sexes. Therefore, these will be useful genetic markers for yellowtail breeding. Based on a comparative study, it was suggested that a PDZ domain containing the GIPC protein might be involved in yellowtail sex determination. The homomorphic sex chromosomes widely observed in the Carangidae suggest that this family could be a suitable marine fish model to investigate the early stages of sex chromosome evolution, for which our results provide a good starting point.

A novel PDZ domain-containing gene is essential for male sex differentiation and maintenance in yellow catfish (Pelteobagrus fulvidraco)

“…GOPC, Atg7 or PICK1 knockout mice did not have reproductive ability due to the defects in acrosome formation, similar to the phenotypes of human globozoospermia [28][29][30]. Comparative genome analysis indicated that GIPC, a PDZ protein was located in the sex-determining regions and might be involved in sex determination of yellowtail [31].…”

Full genome survey and dynamics of gene expression in the greater amberjack Seriola dumerili

“…Like the chromosome number in the Japanese yellowtail, previous cytogenetic analysis determined the haploid number of chromosomes in the greater amberjack to be 24 [ 12 ]. Applying a comparative mapping approach based on previously published genetic linkage and RH maps of Japanese yellowtail [ 13 , 14 , 22 ] as well as the medaka genome, the generated greater amberjack scaffolds were clustered successfully to 24 in silico groups (Table 2 , Fig. 2b ).…”

“…3a , Additional file 8 ), although in neither case have these been reported as sex-determining chromosomes [ 23 , 24 ]. In the Japanese yellowtail, the sex-linked locus was without doubt linked to LG12, but despite this and the generation of a second, increased-resolution genetic linkage map [ 14 ], the sex-determining genes known to date have not been identified in the sex-determining region of the Japanese yellowtail. The authors speculated that the PDZ domain containing GIPC1 protein, found in the SD region of LG12, may be of importance in determining sex in the Japanese yellowtail.…”

Genetic Polymorphisms in Aromatase (<b><i>cyp19a1</i></b>) Are Not Associated with Gonadal Phenotypes in Red-Eared Slider Turtle Hatchlings Developed at a Pivotal Temperature

“…One of the biggest developmental debates in discussing sex determination in species with no apparent heteromorphic chromosomes, but clearly having genetic cues, is whether embryonic sex is determined by a single gene, a few loci or a combination of a large number of genes. Several species of fish, such as European sea bass ( Dicentrarchus labrax ) and yellowtail ( Seriola quinqueradiata ), lack a major sex-determining gene or set of genetic markers, but rather seem to have a polygenic sex-determining system [Koyama et al, 2015;Palaiokostas et al, 2015]. In some cases, however, a single SNP in a certain gene can be associated with phenotypic sex.…”