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Front Genet
2021 Jan 01;12:717538. doi: 10.3389/fgene.2021.717538.
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Identification of Sex-Specific Markers Through 2b-RAD Sequencing in the Sea Urchin (Mesocentrotus nudus).
Cui Z
,
Zhang J
,
Sun Z
,
Liu B
,
Zhao C
,
Chang Y
.
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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.
FIGURE 1. Validation of three candidate female-specific 2b-RAD-tags in 10 females and 9 males. Label M represents the DL2,000 DNA marker.
FIGURE 2. Validation of candidate sex-specific SNP loci in 10 females and 9 males. (A) Three female-specific SNP markers in the sequencing chromatograms of the sex-related sequence of M. nudus. (B) Statistics of sexual phenotype and SNP genotype of the 10 females and 9 males.
FIGURE 3. Identification of 38 females by histological detection of gonads in the breeding population. NP, nutritive phagocytes; Oo, oogonia.
FIGURE 4. Identification of 57 males by histological detection of gonads in the breeding population. NP, nutritive phagocytes; SPC, spermatocyte.
FIGURE 5. Identification of 10 females and 9 males by histological detection of gonads in the wild population. NP, nutritive phagocytes; Oo, oogonia; SPC, spermatocyte.
FIGURE 6. Electrophoretogram of the amplified products using female-tag 3 for genotypic sex identification in M. nudus. Label M represents the DL2,000 DNA marker (500 and 250 bp DNA ladder are shown).
FIGURE 7. Electrophoretogram of the amplified products using female-tag 7 for genotypic sex identification in M. nudus. Label M represents the DL2,000 DNA marker (500 and 250 bp DNA ladder are shown).
FIGURE 8. Electrophoretogram of the amplified products using female-tag 8 for genotypic sex identification in M. nudus. Label M represents the DL2,000 DNA marker (500 and 250 bp DNA ladder are shown).
FIGURE 9. Annotation of sex-specific sequences obtained in M. nudus. Poly A, poly adenylic acid; CDS, coding sequence; TSS, transcriptional start site. (A) Annotation ofscaffold 655827. (B) Annotation of scaffold 439353.
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