1
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Garcia BF, Mastrochirico-Filho VA, Gallardo-Hidalgo J, Campos-Montes GR, Medrano-Mendoza T, Rivero-Martínez PV, Caballero-Zamora A, Hashimoto DT, Yáñez JM. A high-density linkage map and sex-determination loci in Pacific white shrimp (Litopenaeus vannamei). BMC Genomics 2024; 25:565. [PMID: 38840101 PMCID: PMC11155064 DOI: 10.1186/s12864-024-10431-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 05/20/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Expansion of genomic resources for the Pacific white shrimp (Litopenaeus vannamei), such as the construction of dense genetic linkage maps, is crucial for the application of genomic tools in order to improve economically relevant traits. Sexual dimorphism exists in Pacific white shrimp, and the mapping of the sex-determination region in this species may help in future reproductive applications. We have constructed male, female, and sex-averaged high-density genetic maps using a 50 K single-nucleotide polymorphism (SNP) array, followed by a genome-wide association study (GWAS) to identify genomic regions associated with sex in white shrimp. RESULTS The genetic map yielded 15,256 SNPs assigned to 44 linkage groups (LG). The lengths of the male, female, and sex-averaged maps were 5,741.36, 5,461.20 and 5,525.26 cM, respectively. LG18 was found to be the largest for both sexes, whereas LG44 was the shortest for males and LG31 for females. A sex-determining region was found in LG31 with 21 statistically significant SNPs. The most important SNP was previously identified as a sex-linked marker and was able to identify 99% of the males and 88% of the females. Although other significant markers had a lower ability to determine sex, putative genes were intercepted or close to them. The oplophorus-luciferin 2-monooxygenase, serine/arginine repetitive matrix protein and spermine oxidase genes were identified as candidates with possible participation in important processes of sexual differentiation in shrimp. CONCLUSIONS Our results provide novel genomic resources for shrimp, including a high-density linkage map and new insights into the sex-determining region in L. vannamei, which may be usefulfor future genetics and reproduction applications.
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Affiliation(s)
- Baltasar F Garcia
- São Paulo State University (Unesp), Aquaculture Center of UNESP, Jaboticabal, SP, 14884-900, Brazil
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, 8820000, Chile
| | - Vito A Mastrochirico-Filho
- São Paulo State University (Unesp), Aquaculture Center of UNESP, Jaboticabal, SP, 14884-900, Brazil
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, 8820000, Chile
| | | | - Gabriel R Campos-Montes
- Departamento de El Hombre y su Ambiente, Universidad Autónoma Metropolitana, Unidad Xochimilco, Calzada del Hueso 1100, Coyoacán, CDMX, C.P. 04960, México
| | - Thania Medrano-Mendoza
- Doctorado en Ciencias Agropecuarias, Universidad Autónoma Metropolitana, Unidad Xochimilco, Calzada del Hueso 1100, Coyoacán, CDMX, C.P. 04960, México
| | - Psique Victoria Rivero-Martínez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana, Unidad Xochimilco, Calzada del Hueso 1100, Coyoacán, CDMX, C.P. 04960, México
| | - Alejandra Caballero-Zamora
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana, Unidad Xochimilco, Calzada del Hueso 1100, Coyoacán, CDMX, C.P. 04960, México
| | - Diogo T Hashimoto
- São Paulo State University (Unesp), Aquaculture Center of UNESP, Jaboticabal, SP, 14884-900, Brazil
| | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, 8820000, Chile.
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2
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Zhang X, Xiang J, Yuan J, Li F. Penaeid Shrimp Chromosome Studies Entering the Post-Genomic Era. Genes (Basel) 2023; 14:2050. [PMID: 38002993 PMCID: PMC10671375 DOI: 10.3390/genes14112050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Chromosome studies provide the foundation for comprehending inheritance, variation, systematics, and evolution. Penaeid shrimps are a group of crustaceans with great economic importance. Basic cytogenetic information obtained from these shrimps can be used to study their genome structure, chromosome relationships, chromosome variation, polyploidy manipulation, and breeding. The study of shrimp chromosomes experienced significant growth in the 1990s and has been closely linked to the progress of genome research since the application of next-generation sequencing technology. To date, the genome sequences of five penaeid shrimp species have been published. The availability of these genomes has ushered the study of shrimp chromosomes into the post-genomic era. Currently, research on shrimp cytogenetics not only involves chromosome counting and karyotyping, but also extends to investigating submicroscopic changes; exploring genome structure and regulation during various cell divisions; and contributing to the understanding of mechanisms related to growth, sexual control, stress resistance, and genome evolution. In this article, we provide an overview of the progress made in chromosome research on penaeid shrimp. We emphasize the mutual promotion between studies on chromosome structure and genome research and highlight the impact of chromosome-level assembly on studies of genome structure and function. Additionally, we summarize the emerging trends in post-genomic-era shrimp chromosome research.
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Affiliation(s)
- Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (J.Y.)
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianhai Xiang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (J.Y.)
| | - Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (J.Y.)
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (J.Y.)
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Li XY, Mei J, Ge CT, Liu XL, Gui JF. Sex determination mechanisms and sex control approaches in aquaculture animals. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1091-1122. [PMID: 35583710 DOI: 10.1007/s11427-021-2075-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/14/2022] [Indexed: 01/21/2023]
Abstract
Aquaculture is one of the most efficient modes of animal protein production and plays an important role in global food security. Aquaculture animals exhibit extraordinarily diverse sexual phenotypes and underlying mechanisms, providing an ideal system to perform sex determination research, one of the important areas in life science. Moreover, sex is also one of the most valuable traits because sexual dimorphism in growth, size, and other economic characteristics commonly exist in aquaculture animals. Here, we synthesize current knowledge of sex determination mechanisms, sex chromosome evolution, reproduction strategies, and sexual dimorphism, and also review several approaches for sex control in aquaculture animals, including artificial gynogenesis, application of sex-specific or sex chromosome-linked markers, artificial sex reversal, as well as gene editing. We anticipate that better understanding of sex determination mechanisms and innovation of sex control approaches will facilitate sustainable development of aquaculture.
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Affiliation(s)
- Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jie Mei
- College of Fisheries, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chu-Tian Ge
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, China
| | - Xiao-Li Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan, 430072, China.
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4
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Li Z, Xu Y. Bulk segregation analysis in the NGS era: a review of its teenage years. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1355-1374. [PMID: 34931728 DOI: 10.1111/tpj.15646] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/27/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Bulk segregation analysis (BSA) utilizes a strategy of pooling individuals with extreme phenotypes to conduct economical and rapidly linked marker screening or quantitative trait locus (QTL) mapping. With the development of next-generation sequencing (NGS) technology in the past 10 years, BSA methods and technical systems have been gradually developed and improved. At the same time, the ever-decreasing costs of sequencing accelerate NGS-based BSA application in different species, including eukaryotic yeast, grain crops, economic crops, horticultural crops, trees, aquatic animals, and insects. This paper provides a landscape of BSA methods and reviews the BSA development process in the past decade, including the sequencing method for BSA, different populations, different mapping algorithms, associated region threshold determination, and factors affecting BSA mapping. Finally, we summarize related strategies in QTL fine mapping combining BSA.
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Affiliation(s)
- Zhiqiang Li
- Adsen Biotechnology Co., Ltd., Urumchi, 830022, China
| | - Yuhui Xu
- Adsen Biotechnology Co., Ltd., Urumchi, 830022, China
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5
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Wang Q, Liu Y, Wang Y, Jiang S, Zhang C, Li B. GWAS Reveal Novel Sex-Related Markers and Candidate Genes in Sea Urchin Mesocentrotus nudus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:32-39. [PMID: 34812992 DOI: 10.1007/s10126-021-10084-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
Mesocentrotus nudus is an economically important mariculture species. Identification of sex-related markers and candidate genes has potential implications for sex-control breeding of Mesocentrotus nudus. The aim of this study was to identify the molecular markers and genes associated with the sex of M. nudus. Initial GWAS analysis based on 80 individuals genotyped by using GBS identified 22 sex-related SNPs located on 9 GBS tags. Further targeted sequencing in another population of 124 individuals confirmed that 7 SNPs located on 7 GBS tags displayed complete associations with sex, suggesting a ZW/ZZ sex-determination system in M. nudus. Besides, genome and transcriptome annotations presented that the heat shock protein 75 kDa, mitochondrial (trap1), and protein furry homolog-like (fryl) may be important candidate genes involved in sex determination and differentiation in M. nudus. However, further studies are needed to elucidate the functions of these genes. Overall, the current results not only provide molecular markers that may contribute to the sex-control breeding for M. nudus, but also provide new insights to understand the regulatory mechanism of sea urchin sex.
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Affiliation(s)
- Quanchao Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Ying Liu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanxia Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shaoyu Jiang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuanxin Zhang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Baoquan Li
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
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6
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Zhang Y, Zhang C, Yao N, Huang J, Sun X, Zhao B, Li H. Construction of a high-density linkage map and detection of sex-specific markers in Penaeus japonicus. PeerJ 2021; 9:e12390. [PMID: 34760384 PMCID: PMC8559604 DOI: 10.7717/peerj.12390] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/05/2021] [Indexed: 12/13/2022] Open
Abstract
Penaeus japonicus is one of the most important farmed shrimp species in many countries. Sexual dimorphism is observed in P. japonicus, in which females grow faster and larger than males; therefore, a unisexual female culture of P. japonicus could improve the efficiency of productivity. However, the genetic mechanisms underlying sex determination in P. japonicus are unclear. In this study, we constructed a high-density genetic linkage map of P. japonicus using genotyping-by-sequencing (GBS) technology in a full-sib family. The final map was 3,481.98 cM in length and contained 29,757 single nucleotide polymorphisms (SNPs). These SNPs were distributed on 41 sex-averaged linkage groups, with an average inter-marker distance of 0.123 cM. One haplotype, harboring five sex-specific SNPs, was detected in linkage group 1 (LG1), and its corresponding confidence interval ranged from 211.840 to 212.592 cM. Therefore, this high-density genetic linkage map will be informative for genome assembly and marker-assisted breeding, and the sex-linked SNPs will be helpful for further studies on molecular mechanisms of sex determination and unisexual culture of P. japonicus in the future.
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Affiliation(s)
- Yaqun Zhang
- Chinese Academy of Fishery Sciences, Beijing, China
| | - Chuantao Zhang
- Xiaying Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Weifang, Shandong, China
| | - Na Yao
- Chinese Academy of Fishery Sciences, Beijing, China
| | - Jingxian Huang
- Xiaying Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Weifang, Shandong, China
| | - Xiangshan Sun
- Xiaying Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Weifang, Shandong, China
| | - Bingran Zhao
- Xiaying Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Weifang, Shandong, China
| | - Hengde Li
- Chinese Academy of Fishery Sciences, Beijing, China
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7
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Toyota K, Miyakawa H, Hiruta C, Sato T, Katayama H, Ohira T, Iguchi T. Sex Determination and Differentiation in Decapod and Cladoceran Crustaceans: An Overview of Endocrine Regulation. Genes (Basel) 2021; 12:genes12020305. [PMID: 33669984 PMCID: PMC7924870 DOI: 10.3390/genes12020305] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 02/07/2023] Open
Abstract
Mechanisms underlying sex determination and differentiation in animals are known to encompass a diverse array of molecular clues. Recent innovations in high-throughput sequencing and mass spectrometry technologies have been widely applied in non-model organisms without reference genomes. Crustaceans are no exception. They are particularly diverse among the Arthropoda and contain a wide variety of commercially important fishery species such as shrimps, lobsters and crabs (Order Decapoda), and keystone species of aquatic ecosystems such as water fleas (Order Branchiopoda). In terms of decapod sex determination and differentiation, previous approaches have attempted to elucidate their molecular components, to establish mono-sex breeding technology. Here, we overview reports describing the physiological functions of sex hormones regulating masculinization and feminization, and gene discovery by transcriptomics in decapod species. Moreover, this review summarizes the recent progresses of studies on the juvenile hormone-driven sex determination system of the branchiopod genus Daphnia, and then compares sex determination and endocrine systems between decapods and branchiopods. This review provides not only substantial insights for aquaculture research, but also the opportunity to re-organize the current and future trends of this field.
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Affiliation(s)
- Kenji Toyota
- Marine Biological Station, Sado Center for Ecological Sustainability, Niigata University, Sado, Niigata 952-2135, Japan
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Hiratsuka, Kanagawa 259-1293, Japan;
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Katsushika, Tokyo 125-8585, Japan
- Correspondence: (K.T.); (T.S.); (T.I.)
| | - Hitoshi Miyakawa
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi 321-8505, Japan;
| | - Chizue Hiruta
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan;
| | - Tomomi Sato
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa 236-0027, Japan
- Correspondence: (K.T.); (T.S.); (T.I.)
| | - Hidekazu Katayama
- Department of Applied Biochemistry, School of Engineering, Tokai University, Kanagawa 259-1292, Japan;
| | - Tsuyoshi Ohira
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Hiratsuka, Kanagawa 259-1293, Japan;
| | - Taisen Iguchi
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa 236-0027, Japan
- Correspondence: (K.T.); (T.S.); (T.I.)
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8
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Zeng D, Yang C, Li Q, Zhu W, Chen X, Peng M, Chen X, Lin Y, Wang H, Liu H, Liang J, Liu Q, Zhao Y. Identification of a quantitative trait loci (QTL) associated with ammonia tolerance in the Pacific white shrimp (Litopenaeus vannamei). BMC Genomics 2020; 21:857. [PMID: 33267780 PMCID: PMC7709431 DOI: 10.1186/s12864-020-07254-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 11/18/2020] [Indexed: 12/18/2022] Open
Abstract
Background Ammonia is one of the most common toxicological environment factors affecting shrimp health. Although ammonia tolerance in shrimp is closely related to successful industrial production, few genetic studies of this trait are available. Results In this study, we constructed a high-density genetic map of the Pacific white shrimp (Litopenaeus vannamei) using specific length amplified fragment sequencing (SLAF-seq). The constructed genetic map contained 17,338 polymorphic markers spanning 44 linkage groups, with a total distance of 6360.12 centimorgans (cM) and an average distance of 0.37 cM. Using this genetic map, we identified a quantitative trait locus (QTL) that explained 7.41–8.46% of the phenotypic variance in L. vannamei survival time under acute ammonia stress. We then sequenced the transcriptomes of the most ammonia-tolerant and the most ammonia-sensitive individuals from each of four genetically distinct L. vannamei families. We found that 7546 genes were differentially expressed between the ammonia-tolerant and ammonia-sensitive individuals. Using QTL analysis and the transcriptomes, we identified one candidate gene (annotated as an ATP synthase g subunit) associated with ammonia tolerance. Conclusions In this study, we constructed a high-density genetic map of L. vannamei and identified a QTL for ammonia tolerance. By combining QTL and transcriptome analyses, we identified a candidate gene associated with ammonia tolerance. Our work provides the basis for future genetic studies focused on molecular marker-assisted selective breeding. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07254-x.
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Affiliation(s)
- Digang Zeng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Chunling Yang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Qiangyong Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Weilin Zhu
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Min Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Xiaohan Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Yong Lin
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Huanling Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agriculture University, Wuhan, 430070, China
| | - Hong Liu
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agriculture University, Wuhan, 430070, China
| | - Jingzhen Liang
- Life Science Research Institute, Guangxi University, Nanning, 530004, China
| | - Qingyun Liu
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China.
| | - Yongzhen Zhao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China.
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9
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Mangabeira-Silva IS, Soares PET, Lanza DCF. Single nucleotide polymorphism associated with disease resistance in Penaeus vannamei. J Invertebr Pathol 2020; 177:107498. [PMID: 33137318 DOI: 10.1016/j.jip.2020.107498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 10/23/2022]
Abstract
Despite the considerable number of genetic markers published for Penaeus vannamei, the classification of these markers and their standardization in specific databases is still insufficient. As a consequence, access to these markers is difficult, hampering their application in genetic association studies. In this study, all previously described single nucleotide polymorphisms (SNPs) related to resistance for P. vannamei were revised, and 512 SNPs were identified and classified in detail. We observed that most of the SNPs occurred in the proteins including Toll like receptors 1 and 3, hemocyanin large and small subunits, and anti-lipopolysaccharide factors 1 and 2, allowing to propose to use them as targets in association studies involving resistance in P. vannamei. Additionally, the potential effects of the most frequent non-synonymous coding SNPs in the secondary structure of the main target proteins were evaluated using an in silico approach. These data can serve as the starting point for the development of new genetic and computational tools as well as for the design of new association studies that involve resistance in P. vannamei.
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Affiliation(s)
- Iasmim Santos Mangabeira-Silva
- Laboratório de Biologia Molecular Aplicada - LAPLIC, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil; Programa de Pós-Graduação em Biotecnologia, RENORBIO, Brazil
| | - Paulo Eduardo Toscano Soares
- Laboratório de Biologia Molecular Aplicada - LAPLIC, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil; Programa de Pós-Graduação em Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Daniel Carlos Ferreira Lanza
- Laboratório de Biologia Molecular Aplicada - LAPLIC, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil; Programa de Pós-Graduação em Biotecnologia, RENORBIO, Brazil; Programa de Pós-Graduação em Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil.
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10
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Lv J, Lu X, Ti X, Liu P, Li J, Li J. QTL mapping and marker identification for sex determination in the ridgetail white prawn, Exopalaemon carinicauda. Genomics 2020; 112:5240-5247. [PMID: 32956845 DOI: 10.1016/j.ygeno.2020.09.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 11/25/2022]
Abstract
Sex determination is an important and intriguing research topic in the field of evolutionary and developmental biology. Quantitative trait locus (QTL) mapping for sex is helpful in clarifying the sex determination system of species. In this study, a second high-resolution genetic linkage map was constructed for the ridgetail white prawn, Exopalaemon carinicauda, which included 9280 markers, covering 99.98% of the complete genome. Based on the linkage map, a highly significant sex-related QTL was first mapped to a single linkage group (LG3, LOD > 55.6). Fifty-two markers in the QTL region were significantly associated with sex (p ≤ 10-40), of which heterogametic genotypes in females supported the ZW sex determination mechanism. Six markers were verified to be significantly associated with sex in the wild population. Some sex-related genes were identified, including phospholipase D, protein kinase shaggy, and longitudinals lacking protein. These results inform our understanding of the mechanisms of sex determination in E. carinicauda.
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Affiliation(s)
- Jianjian Lv
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, P.R. China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Xuan Lu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, P.R. China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xingbin Ti
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, P.R. China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Ping Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, P.R. China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Jitao Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, P.R. China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Jian Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, P.R. China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
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11
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Levy T, Sagi A. The "IAG-Switch"-A Key Controlling Element in Decapod Crustacean Sex Differentiation. Front Endocrinol (Lausanne) 2020; 11:651. [PMID: 33013714 PMCID: PMC7511715 DOI: 10.3389/fendo.2020.00651] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/11/2020] [Indexed: 12/12/2022] Open
Abstract
The androgenic gland (AG)-a unique crustacean endocrine organ that secretes factors such as the insulin-like androgenic gland (IAG) hormone-is a key player in crustacean sex differentiation processes. IAG expression induces masculinization, while the absence of the AG or a deficiency in IAG expression results in feminization. Therefore, by virtue of its universal role as a master regulator of crustacean sexual development, the IAG hormone may be regarded as the sexual "IAG-switch." The switch functions within an endocrine axis governed by neuropeptides secreted from the eyestalks, and interacts downstream with specific insulin receptors at its target organs. In recent years, IAG hormones have been found-and sequenced-in dozens of decapod crustacean species, including crabs, prawns, crayfish and shrimps, bearing different types of reproductive strategies-from gonochorism, through hermaphroditism and intersexuality, to parthenogenesis. The IAG-switch has thus been the focus of efforts to manipulate sex developmental processes in crustaceans. Most sex manipulations were performed using AG ablation or knock-down of the IAG gene in males in order to sex reverse them into "neo-females," or using AG implantation/injecting AG extracts or cells into females to produce "neo-males." These manipulations have highlighted the striking crustacean sexual plasticity in different species and have permitted the manifestation of either maleness or femaleness without altering the genotype of the animals. Furthermore, these sex manipulations have not only facilitated fundamental studies of crustacean sexual mechanisms, but have also enabled the development of the first IAG-switch-based monosex population biotechnologies, primarily for aquaculture but also for pest control. Here, we review the crustacean IAG-switch, a unique crustacean endocrine mechanism, from the early discoveries of the AG and the IAG hormone to recent IAG-switch-based manipulations. Moreover, we discuss this unique early pancrustacean insulin-based sexual differentiation control mechanism in contrast to the extensively studied mechanisms in vertebrates, which are based on sex steroids.
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Affiliation(s)
- Tom Levy
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Amir Sagi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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12
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Wang Q, Yu Y, Zhang Q, Luo Z, Zhang X, Xiang J, Li F. The Polymorphism of LvMMD2 and Its Association with Growth Traits in Litopenaeus vannamei. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:564-571. [PMID: 32578061 DOI: 10.1007/s10126-020-09977-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 05/11/2020] [Indexed: 06/11/2023]
Abstract
The Pacific white shrimp Litopenaeus vannamei is one of the major economic aquaculture species. The growth trait is considered as the most important trait in L. vannamei aquaculture. Identification of the genetic components underlying growth-related traits in L. vannamei could be useful for the selective breeding of growth trait. Our previous work identified several growth-related SNPs by genome-wide association study (GWAS). Based on the assembled genome, we identified a new candidate gene (LvMMD2) beside the associated marker. This gene encodes the progestin and AdipoQ receptor 10 (PAQR10) protein. We further investigate the polymorphisms of LvMMD2 and their association with body weight of L. vannamei. By resequencing the coding region of LvMMD2, a total of 8 SNPs were identified, including 6 synonymous mutations and 2 nonsynonymous mutations. Association analyses based on a population of 322 individuals revealed that several SNPs located in the coding region of LvMMD2 were significantly associated with the body weight, especially the nonsynonymous mutation named as MMD_5 contributed the most association to the trait and it could explain 10.5% of phenotypic variance. In addition, several genes involved in growth and development have been identified as LvMMD2-interacting genes. These findings strongly suggested that LvMMD2 might be an important gene regulating the shrimp growth. More importantly, the MMD_5 could be a promising candidate locus for marker-assisted selection (MAS) of the body weight in L. vannamei.
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Affiliation(s)
- Quanchao Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yang Yu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Qian Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zheng Luo
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaojun Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Fuhua Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, China.
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13
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Zhang B, Zhao N, Peng K, He X, Chen CX, Liu H, Liu K, Jia L, Bao B. A combination of genome-wide association study screening and SNaPshot for detecting sex-related SNPs and genes in Cynoglossus semilaevis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 35:100711. [PMID: 32683285 DOI: 10.1016/j.cbd.2020.100711] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/02/2020] [Accepted: 07/04/2020] [Indexed: 11/16/2022]
Abstract
Chinese tongue sole (Cynoglossus semilaevis) males and females exhibit great differences in growth rate and appearance. The species is heterogametic (ZW/ZZ) and has sex-reversed "pseudomales" that are genetically female and physiologically male. In this study, we identified eight sex-specific single nucleotide polymorphism (SNP) markers for the sex identification of C. semilaevis by using a combination of genome-wide association study (GWAS) screening and SnaPshot validation. Candidate SNPs were screened using genotyping by sequencing to perform GWAS of the differential SNPs between the sexes of C. semilaevis. The SNP loci were amplified using a multiplex PCR system and detected via SNaPshot, which enables multiplexing of up to 30-40 SNPs in a single assay and ensures high accuracy of the results. The molecular markers detected in our study were used to successfully identify normal males and pseudomales from 45 caught and 40 cultured C. semilaevis specimens. Linkage disequilibrium analysis showed that the eight SNP loci were related to each other, with a strong linkage. Moreover, we investigated the expression of prdm6 mRNA containing a missense SNP and confirmed that the gene is differentially expressed in the gonads of the different sexes of C. semilaevis; the expression of prdm6 mRNA was significantly higher in the males than in the females and pseudomales. This means prdm6 may be related to sex differentiation in C. semilaevis.
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Affiliation(s)
- Bo Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Tianjin Fisheries Research Institute, Tianjin, China
| | - Na Zhao
- Tianjin Medicine Biotechnology Co, Ltd, Tianjin, China
| | - Kangkang Peng
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Xiaoxu He
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Chun Xiu Chen
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Hao Liu
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Kefeng Liu
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Lei Jia
- Tianjin Fisheries Research Institute, Tianjin, China.
| | - Baolong Bao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.
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14
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Cai L, Zheng J, Jia Y, Gu Z, Liu S, Chi M, Cheng S. Molecular Characterization and Expression Profiling of Three Transformer-2 Splice Isoforms in the Redclaw Crayfish, Cherax quadricarinatus. Front Physiol 2020; 11:631. [PMID: 32733260 PMCID: PMC7363937 DOI: 10.3389/fphys.2020.00631] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 05/18/2020] [Indexed: 12/02/2022] Open
Abstract
Sex determination/sex differentiation is determined by genetics, environmental factors, or the interactions of the two. The Transformer-2 (Tra-2) gene plays an important role in the sex determination cascade signal pathway in insects. In this study, the Tra-2 gene was isolated and characterized from the cDNA library of gonad tissues in the redclaw crayfish, Cherax quadricarinatus. Three splice variants were identified, designated as CqTra-2A, CqTra-2B, and CqTra-2C, and sequence analysis showed that they had a highly conserved RRM domain. Phylogenetic analysis was performed by the NJ method, and the results revealed that the Tra-2 protein of the redclaw crayfish was very closely related to those of Macrobrachium rosenbergii, Fenneropenaeus chinensis, and Macrobrachium nipponense. Real-time PCR analysis showed that the three isoforms were predominantly expressed in the ovary and gradually increased with embryonic development. Additionally, the expression pattern of CqTra-2 at different developmental stages was analyzed by qPCR and revealed that the phase of having a body length of 3 cm may be the key period for the sex differentiation of C. quadricarinatus. RNAi-targeting gene silencing further confirmed the function of CqTra-2 in sexual differentiation in redclaw crayfish. Our experimental data will contribute to understanding the mechanism of sex determination in crustaceans.
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Affiliation(s)
- Lina Cai
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Engineering Research Center of Aquaculture, National Demonstration Center for Experimental Fisheries Science Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China.,Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Jianbo Zheng
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Yongyi Jia
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Zhimin Gu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Engineering Research Center of Aquaculture, National Demonstration Center for Experimental Fisheries Science Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China.,Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Shili Liu
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Meili Chi
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Shun Cheng
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
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15
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Wang Y, Yu Y, Li S, Zhang X, Xiang J, Li F. Sex-Specific Transcriptome Sequencing of Zoea I Larvae and Identification of Sex-Linked Genes Using Bulked Segregant Analysis in Pacific White Shrimp Litopenaeus vannamei. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:423-432. [PMID: 32281012 DOI: 10.1007/s10126-020-09962-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 02/27/2020] [Indexed: 06/11/2023]
Abstract
In order to learn the sex determination and differentiation process in shrimp, we performed sex-specific transcriptome sequencing of the Zoea I larvae in Litopenaeus vannamei (L. vannamei) using a DNA/RNA co-extraction method. The sex-specific genes and the sex-linked SNPs were identified. De novo assembly of all the clean reads generated 41,270 unigenes with an average length of 1026 bp and an N50 of 1922 bp. A total of 60 differentially expressed genes (DEGs) between females and males at Zoea I stage were obtained, in which 41 unigenes had annotations. DEGs that might be related to sex development in L. vannamei were analyzed. Besides, paralogous genes of some known sex-related genes in model organisms such as sex-lethal (Sxl) showed no sex-biased difference, which indicated they may not play roles in sex development at Zoea I stage. Candidate sex-linked SNPs were validated in six populations of L. vannamei, and SNPs in Unigene0020898 and Unigene0020336 were fully linked to genders, suggesting the two genes located in the sex-determining region of L. vannamei. Our report provided the sex-specific gene expression in early developmental stage of L. vannamei, and found some sex-biased genes that may participate in the sex development process. We also detected two sex-linked genes which may be located in the sex determination region of L. vannamei through bulked segregant analysis, and the SNPs on these genes also provided a method for genetic sex identification at transcriptional level. Our findings will facilitate further researches on molecular mechanism of sex determination and differentiation in shrimps.
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Affiliation(s)
- Yue Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Yu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Shihao Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Xiaojun Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Fuhua Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
- The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, People's Republic of China.
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16
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Astorkia M, Hernández M, Bocs S, Ponce K, León O, Morales S, Quezada N, Orellana F, Wendra F, Sembiring Z, Asmono D, Ritter E. Detection of significant SNP associated with production and oil quality traits in interspecific oil palm hybrids using RARSeq. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 291:110366. [PMID: 31928673 DOI: 10.1016/j.plantsci.2019.110366] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/28/2019] [Accepted: 11/30/2019] [Indexed: 06/10/2023]
Abstract
A RARSeq based Association mapping study was performed in a population of 104 Elaeis oleifera x E. guineensis hybrids of five origins with the aim of finding functional markers associated to six productive and 19 oil quality traits. For this purpose mRNA of each genotype was isolated and double stranded cDNA was synthesized. Following digestion with two restriction enzymes and adapter ligation, a size selected pool of barcoded amplicons was produced and sequenced using Illumina MiSeq. The obtained sequences were processed with a "snakemake" pipeline, filtered and missing values were imputed. For all traits except two significant effects of the origin was observed. Genetic diversity analyses revealed high variability within origins and an excess of heterozygosity in the population. Two GLM models with Q matrix or PCA matrix as covariates and two MLM models incorporating in addition a Kinship matrix were tested for genotype-phenotype associations using GAPIT software. Using unadjusted p values (< 0.01) 78 potential associations were detected involving 25 SNP and 20 traits. When applying FDR multiple testing with p < 0.05, 25 significant associations remained involving eight SNP and six quality traits. Four SNP were located in genes with a potential relevant biological meaning.
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Affiliation(s)
- Maider Astorkia
- NEIKER Tecnalia, Campus Agroalimentario De Arkaute, Apdo 46. 01080 Vitoria-Gasteiz, Spain.
| | - Mónica Hernández
- NEIKER Tecnalia, Campus Agroalimentario De Arkaute, Apdo 46. 01080 Vitoria-Gasteiz, Spain
| | - Stéphanie Bocs
- CIRAD, UMR AGAP, F-34398, Montpellier, France; AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France; South Green Bioinformatics Platform, Bioversity, CIRAD, INRA, IRD, Montpellier, France
| | - Kevin Ponce
- La Fabril SA, Km 5.5 via Manta, Montecristi, Avenida 113, 130902, Manta, Ecuador
| | - Olga León
- Energy & Palma SA, Av. Atahualpa E3-49 y Juan Gonzales, Ed. Fundación Pérez Pallarez, Officina 4ª, 170507, Quito, Ecuador
| | - Shone Morales
- La Fabril SA, Km 5.5 via Manta, Montecristi, Avenida 113, 130902, Manta, Ecuador
| | - Nathalie Quezada
- La Fabril SA, Km 5.5 via Manta, Montecristi, Avenida 113, 130902, Manta, Ecuador
| | - Francisco Orellana
- Energy & Palma SA, Av. Atahualpa E3-49 y Juan Gonzales, Ed. Fundación Pérez Pallarez, Officina 4ª, 170507, Quito, Ecuador
| | - Fahmi Wendra
- Department of Research & Development, PT Sampoerna Agro Tbk., Jl. Basuki Rahmat No. 788, Palembang, 30127, Indonesia
| | - Zulhermana Sembiring
- Department of Research & Development, PT Sampoerna Agro Tbk., Jl. Basuki Rahmat No. 788, Palembang, 30127, Indonesia
| | - Dwi Asmono
- Department of Research & Development, PT Sampoerna Agro Tbk., Jl. Basuki Rahmat No. 788, Palembang, 30127, Indonesia
| | - Enrique Ritter
- NEIKER Tecnalia, Campus Agroalimentario De Arkaute, Apdo 46. 01080 Vitoria-Gasteiz, Spain
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17
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Improvement of the Pacific bluefin tuna (Thunnus orientalis) reference genome and development of male-specific DNA markers. Sci Rep 2019; 9:14450. [PMID: 31595011 PMCID: PMC6783451 DOI: 10.1038/s41598-019-50978-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/17/2019] [Indexed: 12/30/2022] Open
Abstract
The Pacific bluefin tuna, Thunnus orientalis, is a highly migratory species that is widely distributed in the North Pacific Ocean. Like other marine species, T. orientalis has no external sexual dimorphism; thus, identifying sex-specific variants from whole genome sequence data is a useful approach to develop an effective sex identification method. Here, we report an improved draft genome of T. orientalis and male-specific DNA markers. Combining PacBio long reads and Illumina short reads sufficiently improved genome assembly, with a 38-fold increase in scaffold contiguity (to 444 scaffolds) compared to the first published draft genome. Through analysing re-sequence data of 15 males and 16 females, 250 male-specific SNPs were identified from more than 30 million polymorphisms. All male-specific variants were male-heterozygous, suggesting that T. orientalis has a male heterogametic sex-determination system. The largest linkage disequilibrium block (3,174 bp on scaffold_064) contained 51 male-specific variants. PCR primers and a PCR-based sex identification assay were developed using these male-specific variants. The sex of 115 individuals (56 males and 59 females; sex was diagnosed by visual examination of the gonads) was identified with high accuracy using the assay. This easy, accurate, and practical technique facilitates the control of sex ratios in tuna farms. Furthermore, this method could be used to estimate the sex ratio and/or the sex-specific growth rate of natural populations.
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18
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Wang L, Chua E, Sun F, Wan ZY, Ye B, Pang H, Wen Y, Yue GH. Mapping and Validating QTL for Fatty Acid Compositions and Growth Traits in Asian Seabass. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:643-654. [PMID: 31273567 DOI: 10.1007/s10126-019-09909-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/17/2019] [Indexed: 06/09/2023]
Abstract
Asian seabass is an important food fish species. While improving growth, increasing the nutritional value is important, omega-3 fatty acids are indispensable to human health. Identifying and validating DNA markers associated with traits is the first step towards marker-assisted selection (MAS). We quantified 13 different fatty acids and three growth traits in 213 F2 Asian seabass from a family at the age 270 days post hatch, and screened QTL for these traits. The content of total fatty acids in 100 g flesh was 2.57 ± 0.80 g, while the proportions of docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) were 16.96 ± 2.20% and 5.42 ± 0.90%, respectively. A linkage map with 2424 SNPs was constructed and used for QTL mapping. For fatty acid compositions, 14 significant QTL were identified on three linkage groups (LG5, LG11 and LG14), with phenotypic variance explained (PVE) from 12.8 to 24.6%. Thirty-nine suggestive QTL were detected on 16 LGs. Two significant QTL for EPA were identified on LG5 and LG14, with PVE of 15.2% and 15.1%, respectively. No significant QTL was identified for DHA. For growth traits, six significant and 13 suggestive QTL were identified on two and seven LGs, respectively. Only a few significant QTL for fatty acids overlapped with previously mapped QTL for these traits, suggesting that most QTL detected in a family are family-specific and could only be used in MAS in the family per se. To facilitate population-wide molecular breeding, more powerful methods (e.g. GWAS) should be used to identify SNPs for genomic selection.
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Affiliation(s)
- Le Wang
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Elaine Chua
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Fei Sun
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Zi Yi Wan
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Baoqing Ye
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Hongyan Pang
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Yanfei Wen
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Gen Hua Yue
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.
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19
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Levy T, Rosen O, Manor R, Dotan S, Azulay D, Abramov A, Sklarz MY, Chalifa-Caspi V, Baruch K, Shechter A, Sagi A. Production of WW males lacking the masculine Z chromosome and mining the Macrobrachium rosenbergii genome for sex-chromosomes. Sci Rep 2019; 9:12408. [PMID: 31455815 PMCID: PMC6712010 DOI: 10.1038/s41598-019-47509-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 07/09/2019] [Indexed: 11/30/2022] Open
Abstract
The cultivation of monosex populations is common in animal husbandry. However, preselecting the desired gender remains a major biotechnological and ethical challenge. To achieve an efficient biotechnology for all-female aquaculture in the economically important prawn (Macrobrachium rosenbergii), we achieved – for the first time – WW males using androgenic gland cells transplantation which caused full sex-reversal of WW females to functional males. Crossing the WW males with WW females yielded all-female progeny lacking the Z chromosome. We now have the ability to manipulate – by non-genomic means – all possible genotype combinations (ZZ, WZ and WW) to retain either male or female phenotypes and hence to produce monosex populations of either gender. This calls for a study of the genomic basis underlying this striking sexual plasticity, questioning the content of the W and Z chromosomes. Here, we report on the sequencing of a high-quality genome exhibiting distinguishable paternal and maternal sequences. This assembly covers ~ 87.5% of the genome and yielded a remarkable N50 value of ~ 20 × 106 bp. Genomic sex markers were used to initiate the identification and validation of parts of the W and Z chromosomes for the first time in arthropods.
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Affiliation(s)
- Tom Levy
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer Sheva, 8410501, Israel
| | - Ohad Rosen
- Enzootic HK, Ltd., Unit 1109, 11/F, Kowloon Centre, 33 Ashley Road, Tsimshatsui, Kowloon, Hong Kong
| | - Rivka Manor
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer Sheva, 8410501, Israel
| | - Shahar Dotan
- Enzootic HK, Ltd., Unit 1109, 11/F, Kowloon Centre, 33 Ashley Road, Tsimshatsui, Kowloon, Hong Kong
| | - Dudu Azulay
- Enzootic HK, Ltd., Unit 1109, 11/F, Kowloon Centre, 33 Ashley Road, Tsimshatsui, Kowloon, Hong Kong
| | - Anna Abramov
- Enzootic HK, Ltd., Unit 1109, 11/F, Kowloon Centre, 33 Ashley Road, Tsimshatsui, Kowloon, Hong Kong
| | - Menachem Y Sklarz
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O. Box 653, Beer Sheva, 8410501, Israel
| | - Vered Chalifa-Caspi
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O. Box 653, Beer Sheva, 8410501, Israel
| | | | - Assaf Shechter
- Enzootic HK, Ltd., Unit 1109, 11/F, Kowloon Centre, 33 Ashley Road, Tsimshatsui, Kowloon, Hong Kong
| | - Amir Sagi
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer Sheva, 8410501, Israel. .,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O. Box 653, Beer Sheva, 8410501, Israel.
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20
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Waiho K, Fazhan H, Zhang Y, Zhang Y, Li S, Zheng H, Liu W, Ikhwanuddin M, Ma H. Gonadal microRNA Expression Profiles and Their Potential Role in Sex Differentiation and Gonadal Maturation of Mud Crab Scylla paramamosain. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:320-334. [PMID: 30835008 DOI: 10.1007/s10126-019-09882-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
Although the sexual dimorphism in terms of gonadal development and gametogenesis of mud crab has been described, the internal regulating mechanism and sex differentiation process remain unclear. A comparative gonadal miRNA transcriptomic study was conducted to identify miRNAs that are differentially expressed between testes and ovaries, and potentially uncover miRNAs that might be involved in sex differentiation and gonadal maturation mechanisms of mud crabs (Scylla paramamosain). A total of 10 known miRNAs and 130 novel miRNAs were identified, among which 54 were differentially expressed. Target gene prediction revealed a significant enrichment in 30 KEGG pathways, including some reproduction-related pathways, e.g. phosphatidylinositol signalling system and inositol phosphate metabolism pathways. Further analysis on six differentially expressed known miRNAs, six differentially expressed novel miRNAs and their reproduction-related putative target genes shows that both miRNAs and putative target genes showed stage-specific expression during gonadal maturation, suggesting their potential regulatory roles in sex differentiation and reproductive development. This study reveals the sex-biased miRNA profile and establishes a solid foundation for understanding the sex differentiation and gonadal maturation mechanisms of S. paramamosain.
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Affiliation(s)
- Khor Waiho
- 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
| | - Hanafiah Fazhan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Yin Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Yueling Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Huaiping Zheng
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Wenhua Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Mhd Ikhwanuddin
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.
- Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Malaysia.
| | - Hongyu Ma
- 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.
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21
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Li BJ, Zhu ZX, Gu XH, Lin HR, Xia JH. QTL Mapping for Red Blotches in Malaysia Red Tilapia (Oreochromis spp.). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:384-395. [PMID: 30863905 DOI: 10.1007/s10126-019-09888-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 02/21/2019] [Indexed: 06/09/2023]
Abstract
Body color is an interesting economic trait in fish. Red tilapia with red blotches may decrease its commercial values. Conventional selection of pure red color lines is a time-consuming and labor-intensive process. To accelerate selection of pure lines through marker-assisted selection, in this study, double-digest restriction site-associated DNA sequencing (ddRAD-seq) technology was applied to genotype a full-sib mapping family of Malaysia red tilapia (Oreochromis spp.) (N = 192). Genome-wide significant quantitative trait locus (QTL)-controlling red blotches were mapped onto two chromosomes (chrLG5 and chrLG15) explaining 9.7% and 8.2% of phenotypic variances by a genome-wide association study (GWAS) and linkage-based QTL mapping. Six SNPs from the chromosome chrLG5 (four), chrLG15 (one), and unplaced supercontig GL831288-1 (one) were significantly associated to the red blotch trait in GWAS analysis. We developed nine microsatellite markers and validated significant correlations between genotypes and blotch data (p < 0.05). Our study laid a foundation for exploring a genetic mechanism of body colors and carrying out genetic improvement for color quality in tilapia.
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Affiliation(s)
- Bi Jun Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Zong Xian Zhu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Xiao Hui Gu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Hao Ran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Jun Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China.
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22
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Wang L, Xie N, Shen Y, Ye B, Yue GH, Feng X. Constructing High-Density Genetic Maps and Developing Sexing Markers in Northern Snakehead (Channa argus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:348-358. [PMID: 30888532 DOI: 10.1007/s10126-019-09884-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
High-density genetic maps are essential for mapping QTL, improving genome assembly, comparative genomics, and studying sex chromosome evolution. The northern snakehead (Channa argus) is an economically important foodfish species with significant sexual dimorphism, where the males grow much faster and bigger than the females. However, to date, the sex determination pattern is still not clear, limiting identification of sex chromosomes, even sex determination genes and development of monosex populations that are valuable for both sex evolution of vertebrates and aquaculture practices. Here, a sex-averaged map and two sex-specific genetic maps were constructed with 2974, 2323, and 2338 SNPs, respectively. Little difference was observed in the pattern of sex-specific recombination between female- and male-specific genetic maps. Genome scan identified a major locus for sex determination at LG16. Females and males are, respectively, homogametic and heterogametic, suggesting an XY sex determination system for this species. By resequencing genomes, InDels in the sex-associated QTL region were discovered and used for developing sex-specific PCR assays for fast sexing of snakehead. These high-density genetic maps provide useful resources for future genomic studies in snakehead and its related species. The PCR assays for sexing are of importance in developing all male populations for aquaculture.
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Affiliation(s)
- Le Wang
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore
| | - Nan Xie
- Institute of Fishery Science, Hangzhou Academy of Agriculture Sciences, 228 East Yuanpu Road, Hangzhou, 310024, China
| | - Yubang Shen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Baoqing Ye
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore
| | - Gen Hua Yue
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore.
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Republic of Singapore.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
| | - Xiaoyu Feng
- Institute of Fishery Science, Hangzhou Academy of Agriculture Sciences, 228 East Yuanpu Road, Hangzhou, 310024, China.
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23
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Zhang B, Zhao N, Jia L, Peng K, Che J, Li K, He X, Sun J, Bao B. Seminal Plasma Exosomes: Promising Biomarkers for Identification of Male and Pseudo-Males in Cynoglossus semilaevis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:310-319. [PMID: 30863906 DOI: 10.1007/s10126-019-09881-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/30/2019] [Indexed: 06/09/2023]
Abstract
In mammals, small RNAs enclosed in exosomes have been identified as appropriate signatures for disease diagnosis. However, there is limited information on exosomes derived from seminal plasma, and few studies have reported analyzed the composition of exosomes and enclosed small RNAs in fish. The half-smooth tongue sole (Cynoglossus semilaevis) is an economically important fish for aquaculture, and it exhibits sexual dimorphism: the female gender show higher growth rates and larger body sizes than males. Standard karyotype analysis and artificial gynogenesis tests have revealed that this species uses heterogametic sex determination (ZW/ZZ), and so-called sex-reversed pseudo-males exist. In this study, we successfully identified exosomes in the seminal plasma of C. semilaevis; to the best of our knowledge, this is the first report of exosomes in fish seminal plasma. Analysis of the nucleotide composition showed that miRNAs were dominant in the exosomes, and the miRNAs were sequenced and compared to identify signature miRNAs as sexual biomarkers. Moreover, target genes of the signature miRNAs were predicted by sequence matching and annotation. Finally, four miRNAs (dre-miR-141-3P, dre-miR-10d-5p, ssa-miR-27b-3p, and ssa-miR-23a-3p) with significant differential expression in the males and pseudo-males were selected from the signature candidate miRNAs as markers for sex identification, and their expression profiles were verified using real-time quantitative PCR. Our findings could provide an effective detection method for sex differentiation in fish.
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Affiliation(s)
- Bo Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University, Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
- Tianjin Bohai Sea Fisheries Research Institute, Tianjin, China
| | - Na Zhao
- Tianjin Sheng Fa Biotechnology Co, Ltd, Tianjin, China
| | - Lei Jia
- Tianjin Bohai Sea Fisheries Research Institute, Tianjin, China
| | - Kang Peng
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University, Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Jinyuan Che
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University, Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Kunming Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University, Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Xiaoxu He
- Tianjin Bohai Sea Fisheries Research Institute, Tianjin, China
| | - Jinsheng Sun
- Tianjin Bohai Sea Fisheries Research Institute, Tianjin, China
| | - Baolong Bao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University, Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.
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24
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Wang Q, Yu Y, Zhang Q, Zhang X, Yuan J, Huang H, Xiang J, Li F. A Novel Candidate Gene Associated With Body Weight in the Pacific White Shrimp Litopenaeus vannamei. Front Genet 2019; 10:520. [PMID: 31214248 PMCID: PMC6555256 DOI: 10.3389/fgene.2019.00520] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 05/13/2019] [Indexed: 11/13/2022] Open
Abstract
Improvements of growth traits are always the focus in selective breeding programs for the Pacific white shrimp Litopenaeus vannamei (L. vannamei). Identification of growth-related genes or markers can contribute to the application of modern breeding technologies, and thus accelerate the genetic improvement of growth traits. The aim of this study was to identify the genes and molecular markers associated with the growth traits of L. vannamei. A population of 200 individuals was genotyped using 2b-RAD techniques for genome-wide linkage disequilibrium (LD) analysis and genome-wide association study (GWAS). The results showed that the LD decayed fast in the studied population, which suggest that it is feasible to fine map the growth-related genes with GWAS in L. vannamei. One gene designated as LvSRC, encoding the class C scavenger receptor (SRC), was identified as a growth-related candidate gene by GWAS. Further targeted sequencing of the candidate gene in another population of 322 shrimps revealed that several non-synonymous mutations within LvSRC were significantly associated with the body weight (P < 0.01), and the most significant marker (SRC_24) located in the candidate gene could explain 13% of phenotypic variance. The current results provide not only molecular markers for genetic improvement in L. vannamei, but also new insights for understanding the growth regulation mechanism in penaeid shrimp.
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Affiliation(s)
- Quanchao Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Yang Yu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qian Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojun Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jianbo Yuan
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hao Huang
- Hainan Grand Suntop Ocean Breeding Co., Ltd., Wenchang, China
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Fuhua Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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25
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Galindo-Torres P, Ventura-López C, Llera-Herrera R, Ibarra AM. A natural antisense transcript of the fem-1 gene was found expressed in female gonads during the characterization, expression profile, and cellular localization of the fem-1 gene in Pacific white shrimp Penaeus vannamei. Gene 2019; 706:19-31. [PMID: 31028869 DOI: 10.1016/j.gene.2019.04.066] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 03/29/2019] [Accepted: 04/23/2019] [Indexed: 12/19/2022]
Abstract
The fem-1 gene in Caenorhabditis elegans is involved in sex differentiation; it is specifically required for all aspects of male development. In this study, the full-length cDNA of the fem-1 (Pvfem-1) gene was isolated from the Pacific whiteleg shrimp Penaeus vannamei. The Pvfem-1 transcript is 3778 nt long and encodes a putative protein (PvFEM-1) of 638 amino acids that presented eight ankyrin repeats. The translated protein showed a significant (P < 0.05) structural similitude by superposition with C. elegans FEM-1 protein. Pvfem-1 expression was evaluated by qPCR and in situ hybridization (ISH) during embryogenesis, larval development, and gonads of both genders in subadult and adult life stages. Pvfem-1 was found expressed in brain, intestine, hepatopancreas, and in the gonads of both genders in subadults and adults when quantified by RT-qPCR. A significant finding was the discovery of a natural antisense transcript (NAT) of Pvfem-1 by ISH. It was present in the oocyte nucleus of subadult female shrimp gonads but was not seen within oocytes from adult females, although it was detected in follicular cells, suggesting a possible post-transcriptional regulation of Pvfem-1 in female gonad. Conversely, in males, no NAT was observed, and Pvfem-1 was found expressed in spermatogonia of both, subadult and adult shrimps indicating a function in male sexual differentiation and gametes generation. This study represents the first step for future functional analysis that is expected to contribute to clarifying the role of Pvfem-1 in sex differentiation and determination.
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Affiliation(s)
- Pavel Galindo-Torres
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Aquaculture Genetics and Breeding Laboratory, Ave. Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita, 23096 La Paz, Baja California Sur, Mexico.
| | - Claudia Ventura-López
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Aquaculture Genetics and Breeding Laboratory, Ave. Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita, 23096 La Paz, Baja California Sur, Mexico
| | - Raúl Llera-Herrera
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Aquaculture Genetics and Breeding Laboratory, Ave. Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita, 23096 La Paz, Baja California Sur, Mexico
| | - Ana M Ibarra
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Aquaculture Genetics and Breeding Laboratory, Ave. Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita, 23096 La Paz, Baja California Sur, Mexico.
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26
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Kong S, Ke Q, Chen L, Zhou Z, Pu F, Zhao J, Bai H, Peng W, Xu P. Constructing a High-Density Genetic Linkage Map for Large Yellow Croaker (Larimichthys crocea) and Mapping Resistance Trait Against Ciliate Parasite Cryptocaryon irritans. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:262-275. [PMID: 30783862 DOI: 10.1007/s10126-019-09878-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 01/18/2019] [Indexed: 06/09/2023]
Abstract
The large yellow croaker (Larimichthys crocea) is the most economically important marine cage-farming fish in China in the past decade. However, the sustainable development of large yellow croaker aquaculture has been severely hampered by several diseases, of which, the white spot disease caused by ciliate protozoan parasite Cryptocaryon irritans ranks the most damaging disease in large yellow croaker cage farms. To better understand the genetic basis of parasite infection and disease resistance to C. irritans, it is vital to map the traits and localize the underlying candidate genes in L. crocea genome. Here, we constructed a high-density genetic linkage map using double-digest restriction-site associated DNA (ddRAD)-based high-throughput SNP genotyping data of a F1 mapping family, which had been challenged with C. irritans for resistant trait measure. A total of 5261 SNPs was grouped and oriented into 24 linkage groups (LGs), representing 24 chromosomes of L. crocea. The total genetic map length was 1885.67 cM with an average inter-locus distance of 0.36 cM. Quantitative trait loci (QTL) mapping identified seven significant QTLs in four LGs linked to C. irritans disease resistance. Candidate genes underlying disease resistance were identified from the reference genome, including ifnar1, ifngr2, ikbke, and CD112. Comparative genomic analysis between large yellow croaker and the four closely related species revealed high evolutionary conservation of chromosomes, though inter-chromosomal rearrangements do exist. Especially, the croaker genome structure was closer to the medaka genome than stickleback, indicating that the croaker genome might retain the teleost ancestral genome structure. The high-density genetic linkage map provides an important tool and resource for fine mapping, comparative genome analysis, and molecular selective breeding of large yellow croaker.
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Affiliation(s)
- Shengnan Kong
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Qiaozhen Ke
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Lin Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Zhixiong Zhou
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Fei Pu
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China
| | - Ji Zhao
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China
| | - Huaqiang Bai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Wenzhu Peng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Peng Xu
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China.
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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27
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Perez-Enriquez R, Robledo D, Houston RD, Llera-Herrera R. SNP markers for the genetic characterization of Mexican shrimp broodstocks. Genomics 2018; 110:423-429. [PMID: 30308223 DOI: 10.1016/j.ygeno.2018.10.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/20/2018] [Accepted: 10/03/2018] [Indexed: 12/21/2022]
Abstract
Selective breeding of shrimp has major potential to enhance production traits, including growth and disease resistance. Genetic characterization of broodstock populations is a key element of breeding programs, as it enables decisions on inbreeding restrictions, family structure, and the potential use of genomic selection. Single Nucleotide Polymorphisms (SNPs) are suitable genetic markers for this purpose. A set of SNPs was developed to characterize commercial breeding stocks in Mexico. Individuals from local and imported lines were selected for sequencing using the nextRAD technique, resulting in the identification of 2619 SNPs. Genetic structure analysis showed three to five genetic groups of Ecuadorian and Mexican origins. A subset of 1231 SNPs has potential for stock identification and management. Further, three SNPs were identified as candidate sex-linked markers. The role of SNPs possibly associated with genes related to traits of importance to shrimp farming, such as growth and immune response, should be further investigated.
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Affiliation(s)
- Ricardo Perez-Enriquez
- Aquaculture Genetics & Breeding Lab, Centro de Investigaciones Biológicas del Noroeste, S.C., La Paz, Baja California Sur 23096, Mexico.
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian EH25 9RG, UK
| | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian EH25 9RG, UK
| | - Raúl Llera-Herrera
- CONACyT - Centro de Investigaciones en Alimentación y Desarrollo A.C. Sábalo-Cerritos s.n. Mazatlán, Sinaloa 82112, Mexico; Unidad Académica Mazatlán, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, PO Box 811, CP 82040 Mazatlán, Sinaloa, Mexico.
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28
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Lv J, Sun D, Huan P, Song L, Liu P, Li J. QTL Mapping and Marker Identification for Sex-Determining: Indicating XY Sex Determination System in the Swimming Crab ( Portunus trituberculatus). Front Genet 2018; 9:337. [PMID: 30210528 PMCID: PMC6119780 DOI: 10.3389/fgene.2018.00337] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/07/2018] [Indexed: 12/23/2022] Open
Abstract
Sex determination is an important area of research, which has always had an intriguing aspect in evolutionary and developmental biology. Quantitative trait locus (QTL) mapping for sex will be helpful in clarifying the sex determination system. In this study, the sex QTL mapping of the swimming crab (Portunus trituberculatus) was performed based on a high-density linkage map, and a highly significant QTL specifically mapped on a single linkage group (LG) was firstly identified (LG24, LOD > 14). Twenty markers in the QTL region showed significant associations with sex by association analysis, of which heterogametic genotypes in males supported the XY sex determination mechanism. Two sex-specific markers at the family level were identified via segregation distortion analysis, which were known to be the most closely linked to the sex of P. trituberculatus. Based on sex marker sequences (Marker3840, Marker20320, and Marker10494), three potential sex-related genes were identified, and the quantitative real-time PCR results suggested that these genes were important in spermatogenesis or sex characteristics in males. Our results will contribute to the fine-mapping of sex-determining genes and clarify the sex determination mechanism of P. trituberculatus.
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Affiliation(s)
- Jianjian Lv
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Dongfang Sun
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Pengpeng Huan
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Liu Song
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Ping Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jian Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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29
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López-Cuadros I, García-Gasca A, Gomez-Anduro G, Escobedo-Fregoso C, Llera-Herrera RA, Ibarra AM. Isolation of the sex-determining gene Sex-lethal (Sxl) in Penaeus (Litopenaeus) vannamei (Boone, 1931) and characterization of its embryogenic, gametogenic, and tissue-specific expression. Gene 2018; 668:33-47. [PMID: 29758296 DOI: 10.1016/j.gene.2018.05.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/03/2018] [Accepted: 05/07/2018] [Indexed: 12/11/2022]
Abstract
The Pacific white shrimp Penaeus vannamei is the most cultured shrimp species around the world. Because females grow larger than males, the culture of 'only females' is of great interest, but knowledge on sex determination and differentiation is required for producing only females. In an effort to obtain information associated with reproduction in P. vannamei, transcriptomic data from female gonads was generated, and partial sequences of a transcript were identified as Sex-lethal (Sxl). Its characterization indicated that, differently from other penaeids in which this gene has been isolated, there are six isoforms of the Sxl transcript in P. vannamei (PvanSxl 1-6). These isoforms result from alternative splicing at three splice sites (SS1, SS2, SS3). The first splice-site is unique to P. vannamei, as it has not been reported for other Arthropod species; the second splice-site (SS2) is common among crustaceans, and the third splice-site (SS3) is also unique to P. vannamei and when spliced-out, it is always together with SS2. All isoforms are expressed during embryogenesis as well as gametogenesis of both genders. The two shorter isoforms, PvanSxl-5 and PvanSxl-6, which result from the splicing of SS2 and SS3, were found mostly expressed in adult testis, but PvanSxl-6 was also expressed in oocytes during gametogenesis. During oogenesis, the second largest isoform, PvanSxl-2, which splices-out only SS1, and PvanSxl-4 that splices-out SS1 and SS2 were highly expressed. These two isoforms were also highly expressed during embryonic development. In situ hybridization allowed pinpointing more specifically the cells where the PvanSxl transcripts were expressed. During embryogenesis, hybridization was observed from the one-cell stage embryo to late gastrula. In the female gonad in previtellogenesis, hybridization occurred in the nucleus of oocytes, whereas in secondary vitellogenesis the transcript also hybridized cytoplasmic granules and cortical crypts. Finally, in situ hybridization corroborated the expression of PvanSxl also in the male gonad during spermatogenesis, mostly occurring in the cytoplasm from spermatogonia and spermatocytes.
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Affiliation(s)
- Itzia López-Cuadros
- Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR). Programa de Acuacultura, Av. Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur C.P. 23096, Mexico
| | - Alejandra García-Gasca
- Centro de Investigación en Alimentación y Desarrollo A.C., (CIAD) Unidad Mazatlán, Av. Sábalo-Cerritos S/N. Col. Estero del Yugo, C.P. 82000 Mazatlán, Sinaloa, Mexico
| | - Gracia Gomez-Anduro
- Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR). Programa de Acuacultura, Av. Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur C.P. 23096, Mexico
| | - Cristina Escobedo-Fregoso
- Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR). Programa de Acuacultura, Av. Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur C.P. 23096, Mexico; CONACYT, Consejo Nacional de Ciencia y Tecnología, Av. Insurgentes Sur 1582, Ciudad de México 03940, Mexico
| | - Raúl A Llera-Herrera
- Centro de Investigación en Alimentación y Desarrollo A.C., (CIAD) Unidad Mazatlán, Av. Sábalo-Cerritos S/N. Col. Estero del Yugo, C.P. 82000 Mazatlán, Sinaloa, Mexico; CONACYT, Consejo Nacional de Ciencia y Tecnología, Av. Insurgentes Sur 1582, Ciudad de México 03940, Mexico
| | - Ana M Ibarra
- Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR). Programa de Acuacultura, Av. Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur C.P. 23096, Mexico.
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Lin G, Wang L, Ngoh ST, Ji L, Orbán L, Yue GH. Mapping QTL for Omega-3 Content in Hybrid Saline Tilapia. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:10-19. [PMID: 29204906 DOI: 10.1007/s10126-017-9783-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/07/2017] [Indexed: 06/07/2023]
Abstract
Tilapia is one of most important foodfish species. The low omega-3 to omega-6 fatty acid ratio in freshwater tilapia meat is disadvantageous for human health. Increasing omega-3 content is an important task in breeding to increase the nutritional value of tilapia. However, conventional breeding to increase omega-3 content is difficult and slow. To accelerate the increase of omega-3 through marker-assisted selection (MAS), we conducted QTL mapping for fatty acid contents and profiles in a F2 family of saline tilapia generated by crossing red tilapia and Mozambique tilapia. The total omega-3 content in F2 hybrid tilapia was 2.5 ± 1.0 mg/g, higher than that (2.00 mg/g) in freshwater tilapia. Genotyping by sequencing (GBS) technology was used to discover and genotype SNP markers, and microsatellites were also genotyped. We constructed a linkage map with 784 markers (151 microsatellites and 633 SNPs). The linkage map was 2076.7 cM long and consisted of 22 linkage groups. Significant and suggestive QTL for total lipid content were mapped on six linkage groups (LG3, -4, -6, -8, -13, and -15) and explained 5.8-8.3% of the phenotypic variance. QTL for omega-3 fatty acids were located on four LGs (LG11, -18, -19, and -20) and explained 5.0 to 7.5% of the phenotypic variance. Our data suggest that the total lipid and omega-3 fatty acid content were determined by multiple genes in tilapia. The markers flanking the QTL for omega-3 fatty acids can be used in MAS to accelerate the genetic improvements of these traits in salt-tolerant tilapia.
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Affiliation(s)
- Grace Lin
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Le Wang
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Si Te Ngoh
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Lianghui Ji
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Laszlo Orbán
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
- Department of Animal Sciences and Animal Husbandry, Georgikon Faculty, University of Pannonia, Keszthely, H-8360, Hungary.
- Centre for Comparative Genomics, Murdoch University, Murdoch, WA 6150, Australia.
| | - Gen Hua Yue
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.
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