Identification of sex-linked DNA markers by AFLP in Portunus trituberculatus

Lai, Xiaofang; Gao, Huan; Yan, Binlun; Yan, Wenhua; Shan-rui, Shen

doi:10.1016/j.gene.2014.04.034

Cited by 7 publications

(2 citation statements)

References 21 publications

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“…Over the last few decades, various genetic approaches have been successfully applied to identify sex-specific DNA sequences or markers in a range of aquaculture fish and crustacean species. For example, random amplified polymorphic DNA (RAPD) for turbot ( Scophthalmus maximus ) [17], amplified fragment length polymorphism (AFLP) for swimming crab ( Portunus trituberculatus ) [18] and Pacific bluefin tuna ( Thunnus orientalis ) [19], as well as simple sequence repeat (SSR) markers for half-smooth tongue sole ( Cynoglossus semilaevis ) [20, 21] and rock bream ( Oplegnathus fasciatus ) [22]. Currently, with the rapid development of next-generation sequencing (NGS) technologies, some novel methods have been developed for exploring sex-associated DNA markers [3, 23].…”

Section: Introductionmentioning

confidence: 99%

Female-specific SNP markers provide insights into a WZ/ZZ sex determination system for mud crabs Scylla paramamosain, S. tranquebarica and S. serrata with a rapid method for genetic sex identification

Shi

Waiho

et al. 2018

BMC Genomics

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BackgroundMud crabs, Scylla spp., are commercially important large-size marine crustaceans in the Indo-West Pacific region. As females have the higher growth rate and economic value, the production of all female stocks is extremely essential in aquaculture. However, the sex determination mechanism is still unclear. Development of sex-specific genetic markers based on next-generation sequencing proved to be an effective tool for discovering sex determination system in various animals.ResultsRestriction-site associated DNA sequencing (RAD-seq) was employed to isolate sex-specific SNP markers for S. paramamosain. A total of 335.6 million raw reads were obtained from 20 individuals, of which 204.7 million were from 10 females and 130.9 million from 10 males. After sequence assembly and female-male comparison, 20 SNP markers were identified to be sex-specific. Furthermore, ten SNPs in a short sequence (285 bp) were confirmed heterozygous in females and homozygous in males in a large population by PCR amplification and sequencing. Subsequently, a female-specific primer was successfully designed according to the female-specific nucleotide which could amplify an expected band from females but not from males. Thus, a rapid and effective method for molecular sexing in S. paramamosain was developed, meanwhile, this method could successfully identify the sex of S. tranquebarica and S. serrata. Finally, nine and four female-specific SNP markers were detected in S. tranquebarica and S. serrata, respectively.ConclusionsSex-specific SNP markers were firstly identified in crab species and showed female heterogamety and male homogamety, which provided strong genetic evidence for a WZ/ZZ sex determination system in mud crabs S. paramamosain, S. tranquebarica and S. serrata. These findings will lay a solid foundation for the study of sex determination mechanism, sex chromosome evolution, and the development of mono-sex population in crustaceans.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5380-8) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Female-specific SNP markers provide insights into a WZ/ZZ sex determination system for mud crabs Scylla paramamosain, S. tranquebarica and S. serrata with a rapid method for genetic sex identification

Shi

Waiho

et al. 2018

BMC Genomics

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“…With the decrease of sequencing cost, next-generation sequencing (NGS) has been used to explore or confirm the sex determination system of some species in recent years ( Shi X. et al, 2018 ). In addition, SNP and InDel markers obtained by NGS are more efficient, economical, simple, and comprehensive than previous RAPD ( Xia et al, 2011 ; Vale et al, 2014 ) and AFLP ( Xu et al, 2013 ; Lai et al, 2014 ) methods. SNP and InDel markers reduced the possibility of failure in the development of trait association markers and provided new insights into the sex determination system ( Shi X. et al, 2018 ; Fang et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Exploration of an XX/XY Sex Determination System and Development of PCR-Based Sex-specific Markers in Procambarus clarkii Based on Next-Generation Sequencing Data

Shen

Wang

et al. 2022

Front. Genet.

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Many economic crustacean species have sex dimorphisms during their growth. Exploring the sex determination system and developing sex-specific molecular marker(s) are very helpful for carrying out sex control breeding, and next-generation sequencing has been used as an efficient way to explore them in recent years. In this study, first, the genetic sex determination system of P. clarkii was explored as an XX/XY system by analyzing the 2b-RAD sequencing data. Furthermore, DNA samples of male and female individuals from a P. clarkii family were pooled separately for whole-genome resequencing. Based on the data of whole-genome resequencing, the 9,163 male- and female-specific bias sites with higher feasibility were obtained based on the assumption of the XX/XY sex determination system, and four sites were selected to design the sex-specific marker primers. One efficient sex-specific marker was identified with a sex discrimination rate of 99.49% (195/196) when applied to five different geographical groups with 196 individuals. The results of this study would provide a foundation for the realization of P. clarkii sex control and could provide some reference for investigating the sex determination system and sex molecular marker(s) of other crustacean species based on next-generation sequencing data.

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Identification of sex-specific DNA markers: Providing molecular evidence for the ZW sex determination system in the redclaw crayfish (Cherax quadricarinatus)

et al. 2022

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Identification of sex-linked DNA markers by AFLP in Portunus trituberculatus

Cited by 7 publications

References 21 publications

Female-specific SNP markers provide insights into a WZ/ZZ sex determination system for mud crabs Scylla paramamosain, S. tranquebarica and S. serrata with a rapid method for genetic sex identification

Female-specific SNP markers provide insights into a WZ/ZZ sex determination system for mud crabs Scylla paramamosain, S. tranquebarica and S. serrata with a rapid method for genetic sex identification

Exploration of an XX/XY Sex Determination System and Development of PCR-Based Sex-specific Markers in Procambarus clarkii Based on Next-Generation Sequencing Data

Identification of sex-specific DNA markers: Providing molecular evidence for the ZW sex determination system in the redclaw crayfish (Cherax quadricarinatus)

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