Identification of sex determination locus in sea cucumber Apostichopus japonicus using genome-wide association study

doi:10.1186/s12864-022-08632-3

	Identification of sex determination locus in sea cucumber Apostichopus japonicus using genome-wide association study
	Wang, Yixin 1; Yang, Yujia 1; Li, Yulong2 ; Chen, Muyan 1
	2022-05-23
发表期刊	BMC GENOMICS
ISSN	1471-2164
卷号	23 期号:1 页码:14
通讯作者	Yang, Yujia([email protected]) ; Chen, Muyan([email protected])
摘要	Background Sex determination mechanisms are complicated and diverse across taxonomic categories. Sea cucumber Apostichopus japonicus is a benthic echinoderm, which is the closest group of invertebrates to chordate, and important economic and ecologically aquaculture species in China. A. japonicus is dioecious, and no phenotypic differences between males and females can be detected before sexual maturation. Identification of sex determination locus will broaden knowledge about sex-determination mechanism in echinoderms, which allows for the identification of sex-linked markers and increases the efficiency of sea cucumber breeding industry. Results Here, we integrated assembly of a novel chromosome-level genome and resequencing of female and male populations to investigate the sex determination mechanisms of A. japonicus. We built a chromosome-level genome assembly AJH1.0 using Hi-C technology. The assembly AJH1.0 consists of 23 chromosomes ranging from 22.4 to 60.4 Mb. To identify the sex-determination locus of A. japonicus, we conducted genome-wide association study (GWAS) and analyses of distribution characteristics of sex-specific SNPs and fixation index F-ST. The GWAS analysis showed that multiple sex-associated loci were located on several chromosomes, including chromosome 4 (24.8%), followed by chromosome 9 (10.7%), chromosome 17 (10.4%), and chromosome 18 (14.1%). Furthermore, analyzing the homozygous and heterozygous genotypes of plenty of sex-specific SNPs in females and males confirmed that A. japonicus might have a XX/XY sex determination system. As a physical region of 10 Mb on chromosome 4 included the highest number of sex-specific SNPs and higher F-ST values, this region was considered as the candidate sex determination region (SDR) in A. japonicus. Conclusions In the present study, we integrated genome-wide association study and analyses of sex-specific variations to investigate sex determination mechanisms. This will bring novel insights into gene regulation during primitive gonadogenesis and differentiation and identification of master sex determination gene in sea cucumber. In the sea cucumber industry, investigation of molecular mechanisms of sex determination will be helpful for artificial fertilization and precise breeding.
关键词	Sex determination Echinoderm Apostichopus japonicus GWAS Sex-specific SNPs
DOI	10.1186/s12864-022-08632-3
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation China[31972767]
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS类目	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS记录号	WOS:000799259200003
出版者	BMC
引用统计	被引频次：17[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/179282
专题	海洋生态与环境科学重点实验室
通讯作者	Yang, Yujia; Chen, Muyan
作者单位	1.Ocean Univ China, Key Lab Mariculture, Minist Educ, Qingdao, Peoples R China 2.Chinese Acad Sci, Key Lab Marine Ecol & Environm Sci, Inst Oceanol, Qingdao, Peoples R China
推荐引用方式 GB/T 7714	Wang, Yixin,Yang, Yujia,Li, Yulong,et al. Identification of sex determination locus in sea cucumber Apostichopus japonicus using genome-wide association study[J]. BMC GENOMICS,2022,23(1):14.
APA	Wang, Yixin,Yang, Yujia,Li, Yulong,&Chen, Muyan.(2022).Identification of sex determination locus in sea cucumber Apostichopus japonicus using genome-wide association study.BMC GENOMICS,23(1),14.
MLA	Wang, Yixin,et al."Identification of sex determination locus in sea cucumber Apostichopus japonicus using genome-wide association study".BMC GENOMICS 23.1(2022):14.

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