Identification of male-specific SNP markers and development of PCR-based genetic sex identification technique in crucifix crab (Charybdis feriatus) with implication of an XX/XY sex determination system

Shaobin Fang; Yin Zhang; Xi Shi; Huaiping Zheng; Shengkang Li; Yueling Zhang; Hanafiah Fazhan; Khor Waiho; Huaqiang Tan; Mhd Ikhwanuddin; Hongyu Ma

doi:10.1016/j.ygeno.2019.03.003

Identification of male-specific SNP markers and development of PCR-based genetic sex identification technique in crucifix crab (Charybdis feriatus) with implication of an XX/XY sex determination system

Genomics. 2020 Jan;112(1):404-411. doi: 10.1016/j.ygeno.2019.03.003. Epub 2019 Mar 7.

Authors

Affiliations

¹ Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
² Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China.
³ STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China; Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu 21030, Malaysia.
⁴ Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China. Electronic address: mahy@stu.edu.cn.

PMID: 30851358
DOI: 10.1016/j.ygeno.2019.03.003

Abstract

In this study, we first identified male-specific SNP markers using restriction site-associated DNA sequencing, and further developed a PCR-based sex identification technique for Charybdis feriatus. A total of 296.96 million clean reads were obtained, with 114.95 and 182.01 million from females and males. After assembly and alignment, 10 SNP markers were identified being heterozygous in males but homozygous in females. Five markers were further confirmed to be male-specific in a large number of individuals. Moreover, two male-specific sense primers and a common antisense primer were designed, using which, a PCR-based genetic sex identification method was successfully developed and used to identify the sex of 103 individuals, with a result of 49 females and 54 males. The presence of male-specific SNP markers suggests an XX/XY sex determination system for C. feriatus. These findings should be helpful for better understanding sex determination mechanism, and drafting artificial breeding program in crustaceans.

Keywords: Charybdis feriatus; RAD-seq; Sex identification; Sex-specific SNP marker; XX/XY sex determination system.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Brachyura / genetics*
Female
Genetic Markers
Male
Polymerase Chain Reaction / methods*
Polymorphism, Single Nucleotide*
Sequence Analysis, DNA
Sex Determination Analysis / methods*

Substances

Genetic Markers