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

Abstract

Sex-specific markers play an important role in revealing sex-determination mechanism. Sea urchin (Mesocentrotus nudus) is an economically important mariculture species in several Asian countries and its gonads are the sole edible parts for people. However, growth rate and immunocompetence differ by sex in this species, sex-specific markers have not been identified, and the sex-determination mechanism of sea urchin remains undetermined. In this study, type IIB endonuclease restriction-site associated DNA sequencing (2b-RAD-seq) and a genome survey of M. nudus were performed, and three female-specific markers and three female heterogametic single nucleotide polymorphism (SNP) loci were identified. We validated these sex-specific markers via PCR amplification in a large number of individuals, including wild and artificially bred populations. Several open reading frames (ORFs) were predicted, although there are no potential genes known for sex determination and sex differentiation within the scaffold in which the sex-specific markers are located. Importantly, the female-specific sequences and female heterozygous SNP loci indicate that a female heterogametic and male homogametic ZW/ZZ sex-determination system should exist in M. nudus. The results provide a solid basis for revealing the sex-determination mechanism of this species, and open up new possibilities for developing sex-control breeding in sea urchin.

Identification of Sex-Specific Markers and Candidate Genes Using WGS Sequencing Reveals a ZW-Type Sex-Determination System in the Chinese Soft-Shell Turtle (Pelodiscus sinensis)

“…In traditional methods, restriction fragment length polymorphism (RFLP) [23,24], the random amplification of polymorphic DNA (RAPD) [25,26], and amplified fragment length polymorphism (AFLP) [27,28] are frequently used to develop sex-specific DNA molecular markers. However, they are gradually being phased out of the historical stage due to their complicated experimental workflow and expensive costs [29,30]. With the development of molecular biotechnology, it has become increasingly popular to develop sex-specific marker methods based on next-generation sequencing, including restriction site-associated DNA sequencing (RADseq) [31,32], double-digest restriction-site associated DNA sequencing (ddRAD-seq) [33,34], and type IIB endonucleases restriction-site associated DNA sequencing (2bRAD-seq) [35,36].…”

Identification of sex determination locus in sea cucumber Apostichopus japonicus using genome-wide association study

“…However, several features of echinoderm genome render sequence assembly difficult, including large genome size, a large number of low frequency repeats, high heterozygosity, and high genome sequence variation [ 24 , 25 ]. Besides, the knowledge of sex determination in echinoderms is still very limited, mainly focusing on karyotype analysis [ 26 – 28 ], sex-associated markers [ 29 , 30 ], linkage-mapping analysis [ 31 – 33 ], and gonadal transcriptome [ 34 – 37 ].…”

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

“…As previously described, the gonads of sea urchins are classified into four stages, namely, intergametogenesis and nutritive phagocyte (NP) phagocytosis (stage 1), pregametogenesis and NP renewal (stage 2), gametogenesis and NP utilization (stage 3), and the end of gametogenesis, NP exhaustion, and spawning (stage 4) ( 5 ). Recently, three female-specific markers were identified and could be used to identify the genetic sex of Mesocentrotus nudus ( 6 ). In addition, the number of genes and micro-RNAs associated with sex determination and sex differentiation have been identified by RNA sequencing ( 7 , 8 ).…”