GWAS Reveal Novel Sex-Related Markers and Candidate Genes in Sea Urchin Mesocentrotus nudus

Wang, Quanchao; Liu, Ying; Wang, Yanxia; Shao-yu, Jiang; Zhang, Chuanxin; Li, Baoquan

doi:10.1007/s10126-021-10084-x

Cited by 7 publications

(2 citation statements)

References 30 publications

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“…Sex-specific genes are located on the heterogametic sex chromosomes, and they are prerequisites for revealing the sex determination mechanisms, identifying sex-specific markers, and actualizing sex-controlled breeding [20][21][22]. 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.…”

Section: Introductionmentioning

confidence: 99%

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)

Zhu,

Wang,

Chen

et al. 2024

IJMS

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Male and female Chinese soft-shelled turtles (Pelodiscus sinensis) have sex-dimorphic growth patterns, and males have higher commercial value because of their larger size and thicker calipash. Thus, developing sex-specific markers is beneficial to studies on all-male breeding in P. sinensis. Here, we developed an accurate and efficient workflow for the screening of sex-specific sequences with ZW or XY sex determination systems. Based on this workflow, female and male P. sinensis reference genomes of 2.23 Gb and 2.26 Gb were obtained using de novo assembly. After aligning and filtering, 4.01 Mb female-specific sequences were finally identified. Subsequently, the seven developed sex-specific primer pairs were 100% accurate in preliminary, population, and embryonic validation. The presence and absence of bands for the primers of P44, P45, P66, P67, P68, and P69, as well as two and one bands for the PB1 primer, indicate that the embryos are genetically female and male, respectively. NR and functional annotations identified several sex-determining candidate genes and related pathways, including Ran, Eif4et, and Crkl genes, and the insulin signaling pathway and the cAMP signaling pathway, respectively. Collectively, our results reveal that a ZW-type sex-determination system is present in P. sinensis and provide novel insights for the screening of sex-specific markers, sex-control breeding, and the studies of the sex determination mechanism of P. sinensis.

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Section: Introductionmentioning

confidence: 99%

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)

Zhu,

Wang,

Chen

et al. 2024

IJMS

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“…An approximate GWAS result by ddRAD sequencing has also been obtained in a random breeding population of Larimichthys crocea, some candidate genes (i.e., dmrt1 , dmrt3 , piwil2 , fam102a , and odf2 ) and some others (i.e., axl , cyp2a10 , and cyp2g1 ) were detected separately to be involved in sex determination and GSI traits ( Lin et al, 2021 ). Furthermore, a GWAS was conducted to reveal novel sex-related candidate genes (i.e., trap1 and fryl ) involved in sex determination and differentiation in Mesocentrotus nudus using the genotyping-by-sequencing method ( Wang et al, 2022 ). In addition, similar studies have been carried out on Cynoglossus semilaevis ( Zhang et al, 2020 ), Salmo salar ( Gutierrez et al, 2015 ; Gabián et al, 2019 ), and Scophthalmus maximus ( Martínez et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association study reveals genomic loci of sex differentiation and gonadal development in Plectropomus leopardus

Gao,

Wang,

Liu

et al. 2023

Front. Genet.

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Introduction:Plectropomus leopardus, a commercially significant marine fish, is primarily found in the Western Pacific regions and along the coast of Southeast Asia. A thorough analysis of the molecular mechanisms involved in sex differentiation is crucial for gaining a comprehensive understanding of gonadal development and improving sex control breeding. However, the relevant fundamental studies of P. leopardus are relatively lacking.Methods: In this study, a genome-wide association study (GWAS) was conducted to investigate the genetic basis mechanism of sex differentiation and gonadal developmental traits in P. leopardus utilizing about 6,850,000 high-quality single-nucleotide polymorphisms (SNPs) derived from 168 individuals (including 126 females and 42 males) by the genome-wide efficient mixed-model association (GEMMA) algorithm.Results: The results of these single-trait GWASs showed that 46 SNP loci (-log10p > 7) significantly associated with sex differentiation, and gonadal development traits were distributed in multiple different chromosomes, which suggested the analyzed traits were all complex traits under multi-locus control. A total of 1,838 potential candidate genes were obtained by considering a less-stringent threshold (-log10p > 6) and ±100 kb regions surrounding the significant genomic loci. Moreover, 31 candidate genes were identified through a comprehensive analysis of significant GWAS peaks, gene ontology (GO) annotations, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, including taf7, ddx6, apoeb, sgk1, a2m, usf1, hsd3b7, dll4, xbp1, tet3, esr1, and gli3. These trait-associated genes have been shown to be involved in germline development, male sex differentiation, gonad morphogenesis, hormone receptor binding, oocyte development, male gonad development, steroidogenesis, estrogen-synthetic pathway, etc.Discussion: In the present study, multiple genomic loci of P. leopardus associated with sex differentiation and gonadal development traits were identified for the first time by using GWAS, providing a valuable resource for further research on the molecular genetic mechanism and sex control in P. leopardus. Our results also can contribute to understanding the genetic basis of the sex differentiation mechanism and gonadal development process in grouper fish.

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Characterization and sexual dimorphic expression of Cytochrome P450 genes in gonads of the sea urchin (Mesocentrotus nudus)

Su,

Meng,

Kong

et al. 2024

Aquaculture Reports

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GWAS Reveal Novel Sex-Related Markers and Candidate Genes in Sea Urchin Mesocentrotus nudus

Cited by 7 publications

References 30 publications

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)

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)

Genome-wide association study reveals genomic loci of sex differentiation and gonadal development in Plectropomus leopardus

Characterization and sexual dimorphic expression of Cytochrome P450 genes in gonads of the sea urchin (Mesocentrotus nudus)

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