Identification of sex‐specific markers and heterogametic XX/XY sex determination system by 2b‐RAD sequencing in redtail catfish (Mystus wyckioides)

Abstract

Sex-specific markers provide significant molecular basis for sex control breeding biotechnology to produce all-male or all-female fish in commercial breeding. Redtail catfish (Mystus wyckioides), one of the commercial bagrid catfishes distributed in Southeast Asian, which have a long sexual maturation period that can last 3-5 years and males have apparent growth advantage over females, but its sex determination system remains unknown. In this study, we first applied 2b-RAD-seq approach to identify three male-specific 2b-RAD-tags and one male heterogametic SNP locus and validated by blast to the genome survey sequences and PCR amplification in both wild and breeding populations. To get longer sex-specific region, we performed genome walking and obtained a 4,630 bp of Y-specific sequence and 4,581 bp of X-specific sequence from the 2b-RADtag ref189950 with 92.19% nucleotide identity between them. And 9,923 bp/3,935 bp of Y-specific sequences and 8,491 bp/5,172 bp of X-specific sequences were also identified with 77.49% and 57.07% nucleotide identity in ref208528 and ref210837, respectively. Subsequently, three different kinds of sex-specific primers with different length products were designed based on the detected highly sex differentiated regions and could be used to distinguish males and females both in wild and artificially bred populations. What is more, the X-specific fragment was discovered to produce the dosage effect association in females and in males. The data suggest that male heterogametic XX/XY sex determination system should exist in the redtail catfish. More significantly, the sex-specific markers are of great value to protect wild resources and improve the efficiency of all-male breeding practices for aquaculture in the redtail catfish.

Identification of Sex-Specific Markers Through 2b-RAD Sequencing in the Sea Urchin (Mesocentrotus nudus)

“…After homologous analysis by BLAST, several ORFs were predicted in these female-specific scaffolds, but no potential genes known for sex determination or differentiation within any scaffold. This phenome is similar to most previously reports that even though the sex-specific markers were extended into long segments within hundreds of genes, no sex related genes have been obtained (Pan et al, 2015;Shi et al, 2018;Zhou et al, 2019;Fang et al, 2020). In the future, we will use genome walking to analyze the differences in sequences between male and female individuals.…”

“…In many animals, sex determination system has been deduced using sexspecific markers which developed by 2b-RAD-seq. In redtail catfish (Mystus wyckioides), some Y-specific fragments and X-specific fragments have been identified by 2b-RAD-seq, and XX/XY sex determination system was deduced because of the X-specific fragment showing dosage effect between females and males (Zhou et al, 2019). In this study, we revealed that all of the identified sex-specific markers were female-specific, and the identified SNP markers were heterozygous in females but homozygous in males (Figures 1, 2), our data suggest that a ZW/ZZ sex-determination system exists in M. nudus.…”

“…Compared to the other traditional RAD-seq methods, 2b-RAD-seq is cost-effective and simple method, and allows for nearly every restriction site in the genome to be screened in parallel (Wang et al, 2012). Some studies have already successfully applied the 2b-RAD approach to explore sexspecific DNA fragments and SNPs in a great diversity of aquatic organisms (Liu et al, 2018;Zhou et al, 2019;Zhu et al, 2021). In addition to quickly identify genetic sex, sexspecific markers also provide insights into the sex-determination system in various animals (Liu et al, 2018).…”

Chromosome-Level Genome Assembly of the Asian Red-Tail Catfish (Hemibagrus wyckioides)

“…Here, it is a famous indigenous fish due to a variety of excellent economic traits such as high protein content, strong disease resistance, easy domestication, and better production performance; it also has ornamental value ( Zhou et al, 2021 ). Therefore, it has recently become an important aquaculture species in China ( Zhou et al, 2019 ; Zhou et al, 2021 ). H. wyckioides exhibits marked sex dimorphism in growth, with the males growing much faster than females.…”

Application of SNP in Genetic Sex Identification and Effect of Estradiol on Gene Expression of Sex-Related Genes in Strongylocentrotus intermedius

“…With the development of next-generation sequencing (NGS) technologies, restriction site-associated DNA sequencing (RADseq) was developed to identify sex-specific markers and discover the mechanisms of sex determination in various species (9)(10)(11). In Mastacembelus armatus, two male-specific DNA fragments and two single nucleotide polymorphisms (SNPs) were identified by RAD-seq, and the Tcl gene was regarded as a candidate sex determination gene (12).…”