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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 X 1 , Waiho K 1 , Li X 2 , Ikhwanuddin M 3 , Miao G 1 , Lin F 1 Show all authors , Zhang Y 1 , Li S 1 , Zheng H 1 , Liu W 1 , Aweya JJ 1 , Azmie G 3 , Baylon JC 4 , Quinitio ET 5 , Ma H 6

Affiliations 

  • 1 Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063, China
  • 2 East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, China
  • 3 Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Malaysia
  • 4 Division of Biological Sciences, College of Arts and Sciences, University of the Philippines, Visayas, 5023, Miagao, Philippines
  • 5 Aquaculture Department, Southeast Asian Fisheries Development Center, 5021, Tigbauan, Philippines
  • 6 Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063, China. [email protected]
BMC Genomics, 2018 Dec 29;19(1):981.
PMID: 30594128 DOI: 10.1186/s12864-018-5380-8

Abstract

BACKGROUND: Mud 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.

RESULTS: Restriction-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.

CONCLUSIONS: Sex-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.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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