Genome-Wide SNP Analysis of Hybrid Clariid Fish Reflects the Existence of Polygenic Sex-Determination in the Lineage

Abstract

The African catfish (Clarias gariepinus) may exhibit the co-existence of XX/XY and ZZ/ZW sex-determination systems (SDSs). However, the SDS of African catfish might be influenced by a polygenic sex-determination (PSD) system, comprising multiple independently segregating sex “switch” loci to determine sex within a species. Here, we aimed to detect the existence of PSD using hybrid. The hybrid produced by crossing male African catfish with female bighead catfish (C. macrocephalus, XX/XY) is a good animal model to study SDSs. Determining the SDS of hybrid catfish can help in understanding the interactions between these two complex SDS systems. Using the genotyping-by-sequencing “DART-seq” approach, we detected seven moderately male-linked loci and seventeen female-linked loci across all the examined hybrid specimens. Most of these loci were not sex-linked in the parental species, suggesting that the hybrid exhibits a combination of different alleles. Annotation of the identified sex-linked loci revealed the presence of one female-linked locus homologous with the B4GALNT1 gene, which is involved in the spermatogenesis pathway and hatchability. However, this locus was not sex-linked in the parental species, and the African catfish might also exhibit PSD.

Something Fishy about Siamese Fighting Fish (Betta splendens) Sex: Polygenic Sex Determination or a Newly Emerged Sex-Determining Region?

“…Perhaps, it is simply the combination of multiple and independent “switch” loci or alleles specifying the segregation of sex within a species, known as polygenic sex determination (PSD). PSD can occur by modifying current sex chromosomes to generate a third functional sex chromosome at the same locus, or by modifying autosomal loci in other regions of the genome to generate a novel process for gonad development regulation [ 16 , 17 , 18 , 109 ], resulting in the generation of multiple phenotypic or reproductive types within one sex. Such multiple classes may promote fitness benefits for natural selection in the population.…”

“…However, this information was derived from the analysis of only one commercial stock [ 14 ]. Teleosts with different geological populations, ecotypes, or varieties are reported to have different SDSs and/or sex determination regions (SDRs) [ 15 , 16 , 17 , 18 ]. Studies on more Siamese fighting fish populations are required to confirm this.…”

“…Recent next-generation sequencing technologies have facilitated the discovery of numerous genetic markers in any organism at affordable costs, facilitating investigations of genetic diversity within and between populations [ 27 ]. Only a fraction of homologous regions in the genomes of non-model species can be sequenced and genotyped for single-nucleotide polymorphisms (SNPs) to identify the genomic regions of sex-determining loci [ 16 , 17 , 18 , 28 , 29 , 30 , 31 ]. In this study, we addressed our first hypothesis using a genome-wide SNP approach to identify novel SNP loci in captive-bred individuals with known phenotypic sex assignment and determine associated regions in Siamese fighting fish.…”

Haplotype-resolved assembly of the African catfish (Clarias gariepinus) provides insights for semi-terrestrial adaptation of airbreathing catfishes

“…As a result, the African catfish is considered an excellent biological model for studying amphibious traits (i.e., bimodal breathing) and terrestrial transition [16][17][18] . However, current genomics research has primarily focused on phylogenetic and domestication studies 9,[19][20][21] , as well as on sex-chromosome and karyotype evolution utilizing only a limited panel of molecular markers [22][23][24] .Clarias gariepinus genome is made up of 2n = 2x = 56 chromosomes (18 m + 20 sm + 18 st/a) 25 with a fundamental number (NF) of 94. Its chromosome system has historically been contentious.…”

“…Previous findings suggested a XX/XY male heterogametic chromosomal system [26][27][28][29] , while others pointed to a ZZ/ZW female heterogametic sex determination system (SDS) 30,31 . However, recent research using high-throughput sequencing data have shown that both systems coexist in C.gariepinus 22,23 . The coexistence of both SDSs is most likely heavily influenced by environmental and social factors, as well as geographical habitat: the ZZ/ZW system is indicated in African wild ecotypes 25,30 , XX/XY system is observed in some anthropogenically introduced populations in Europe and China 27,28,32 , and both systems were evidenced within the same population in Thailand 22,33 .…”