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Bolton CM, Bekaert M, Eilertsen M, Helvik JV, Migaud H. Rhythmic Clock Gene Expression in Atlantic Salmon Parr Brain. Front Physiol 2021; 12:761109. [PMID: 34925060 PMCID: PMC8674837 DOI: 10.3389/fphys.2021.761109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/09/2021] [Indexed: 12/28/2022] Open
Abstract
To better understand the complexity of clock genes in salmonids, a taxon with an additional whole genome duplication, an analysis was performed to identify and classify gene family members (clock, arntl, period, cryptochrome, nr1d, ror, and csnk1). The majority of clock genes, in zebrafish and Northern pike, appeared to be duplicated. In comparison to the 29 clock genes described in zebrafish, 48 clock genes were discovered in salmonid species. There was also evidence of species-specific reciprocal gene losses conserved to the Oncorhynchus sister clade. From the six period genes identified three were highly significantly rhythmic, and circadian in their expression patterns (per1a.1, per1a.2, per1b) and two was significantly rhythmically expressed (per2a, per2b). The transcriptomic study of juvenile Atlantic salmon (parr) brain tissues confirmed gene identification and revealed that there were 2,864 rhythmically expressed genes (p < 0.001), including 1,215 genes with a circadian expression pattern, of which 11 were clock genes. The majority of circadian expressed genes peaked 2 h before and after daylight. These findings provide a foundation for further research into the function of clock genes circadian rhythmicity and the role of an enriched number of clock genes relating to seasonal driven life history in salmonids.
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Affiliation(s)
- Charlotte M Bolton
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Michaël Bekaert
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Mariann Eilertsen
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Jon Vidar Helvik
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Herve Migaud
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
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2
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Jaiswal S, Nandi S, Iquebal MA, Jasrotia RS, Patra S, Mishra G, Udit UK, Sahu DK, Angadi UB, Meher PK, Routray P, Sundaray JK, Verma DK, Das P, Jayasankar P, Rai A, Kumar D. Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing. BMC Genomics 2021; 22:685. [PMID: 34548034 PMCID: PMC8456608 DOI: 10.1186/s12864-021-08001-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 05/26/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Carp fish, rohu (Labeo rohita Ham.) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. There is no holistic study at transcriptome level revealing key candidate genes involved in such circannual rhythm regulated by biological clock genes (BCGs). Seasonality manifestation has two contrasting phases of reproduction, i.e., post-spawning resting and initiation of gonadal activity appropriate for revealing the associated candidate genes. It can be deciphered by RNA sequencing of tissues involved in BPGL (Brain-Pituitary-Gonad-Liver) axis controlling seasonality. How far such BCGs of this fish are evolutionarily conserved across different phyla is unknown. Such study can be of further use to enhance fish productivity as seasonality restricts seed production beyond monsoon season. RESULT A total of ~ 150 Gb of transcriptomic data of four tissues viz., BPGL were generated using Illumina TruSeq. De-novo assembled BPGL tissues revealed 75,554 differentially expressed transcripts, 115,534 SSRs, 65,584 SNPs, 514 pathways, 5379 transcription factors, 187 mature miRNA which regulates candidate genes represented by 1576 differentially expressed transcripts are available in the form of web-genomic resources. Findings were validated by qPCR. This is the first report in carp fish having 32 BCGs, found widely conserved in fish, amphibian, reptile, birds, prototheria, marsupials and placental mammals. This is due to universal mechanism of rhythmicity in response to environment and earth rotation having adaptive and reproductive significance. CONCLUSION This study elucidates evolutionary conserved mechanism of photo-periodism sensing, neuroendocrine secretion, metabolism and yolk synthesis in liver, gonadal maturation, muscular growth with sensory and auditory perception in this fish. Study reveals fish as a good model for research on biological clock besides its relevance in reproductive efficiency enhancement.
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Affiliation(s)
- Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Samiran Nandi
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Rahul Singh Jasrotia
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sunita Patra
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Gayatri Mishra
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Uday Kumar Udit
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Dinesh Kumar Sahu
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - U. B. Angadi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Prem Kumar Meher
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Padmanav Routray
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | | | | | - Paramananda Das
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | | | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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3
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Jackson T, Ishengoma E, Rhode C. Cross-species Exon Capture and Whole Exome Sequencing: Application, Utility and Challenges for Genomic Resource Development in Non-model Species. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:560-575. [PMID: 34241713 DOI: 10.1007/s10126-021-10046-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
Comprehending the genetic architecture of complex traits has many applications in evolution, ecology, conservation biology and plant and animal production systems. Underlying research questions in these fields are diverse species that often have limited genetic information available. In aquaculture, for example, genetic progress has been slow in many species due to a lack in such genetic information. In this study, zebrafish (as a well-studied model species) was used in cross-species transfer to develop genomic resources and identify candidate genes underling growth differentials in dusky kob. Dusky kob is a Sciaenid finfish and an emerging aquaculture species. The zebrafish All Exon Predesigned Probe-set capture protocol was used to enrich fractionated DNA samples from kob, classified as either large or small, before massive parallel sequencing on the Ion Torrent platform. Although vast quantities of sequence data were generated, only about 30% of contigs could be identified as zebrafish homologues. There were numerous species-specific sequences and inconsistent coverage of sequencing products across samples, likely due to non-specific binding of the probe-set as a result of the evolutionary divergence between zebrafish and kob. Nonetheless, more than 55,000 SNPs could be reliably identified and genotyped to the individual level. Using SNP genotypic divergence estimates, between large and small cohorts, a number of candidate genes associated with growth was also identified for future investigation. These findings contribute to the growing body of evidence demonstrating the utility of a cross-species capture approach in the development of important genomic resources for understanding traits of interest in species without reference genomes.
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Affiliation(s)
- T Jackson
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa
| | - E Ishengoma
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa
- Department of Biological Sciences, Mkwawa University College of Education, University of Dar Es Salaam, P.O. Box 2329, Dar es Salaam, Tanzania
| | - C Rhode
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa.
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4
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Wu C, Guo X, Li M, Shen J, Fu X, Xie Q, Hou Z, Zhai M, Qiu X, Cui Z, Xie H, Qin P, Weng X, Hu Z, Liang J. DeepHBV: a deep learning model to predict hepatitis B virus (HBV) integration sites. BMC Ecol Evol 2021; 21:138. [PMID: 34233610 PMCID: PMC8261932 DOI: 10.1186/s12862-021-01869-8] [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: 03/15/2021] [Accepted: 06/29/2021] [Indexed: 01/05/2023] Open
Abstract
Background The hepatitis B virus (HBV) is one of the main causes of viral hepatitis and liver cancer. HBV integration is one of the key steps in the virus-promoted malignant transformation. Results An attention-based deep learning model, DeepHBV, was developed to predict HBV integration sites. By learning local genomic features automatically, DeepHBV was trained and tested using HBV integration site data from the dsVIS database. Initially, DeepHBV showed an AUROC of 0.6363 and an AUPR of 0.5471 for the dataset. The integration of genomic features of repeat peaks and TCGA Pan-Cancer peaks significantly improved model performance, with AUROCs of 0.8378 and 0.9430 and AUPRs of 0.7535 and 0.9310, respectively. The transcription factor binding sites (TFBS) were significantly enriched near the genomic positions that were considered. The binding sites of the AR-halfsite, Arnt, Atf1, bHLHE40, bHLHE41, BMAL1, CLOCK, c-Myc, COUP-TFII, E2A, EBF1, Erra, and Foxo3 were highlighted by DeepHBV in both the dsVIS and VISDB datasets, revealing a novel integration preference for HBV. Conclusions DeepHBV is a useful tool for predicting HBV integration sites, revealing novel insights into HBV integration-related carcinogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01869-8.
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Affiliation(s)
- Canbiao Wu
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, Guangdong, China
| | - Xiaofang Guo
- Department of Medical Oncology of the Eastern Hospital, the First Affiliated Hospital, Sun Yat-Sen University, Guangdong, 510700, Guangzhou, China
| | - Mengyuan Li
- Department of Gynecological Oncology, the First Affiliated Hospital, Sun Yat-Sen University, Guangdong, 510080, Guangzhou, China
| | - Jingxian Shen
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, Guangdong, China
| | - Xiayu Fu
- Department of Thoracic Surgery, the First Affiliated Hospital, Sun Yat-Sen University, Guangdong, 510080, Guangzhou, China
| | - Qingyu Xie
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, Guangdong, China.,School of Computer Science, South China Normal University, Guangzhou, 510631, China
| | - Zeliang Hou
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, Guangdong, China
| | - Manman Zhai
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, Guangdong, China.,School of Psychology, South China Normal University, Guangzhou, 510080, Guangdong, China
| | - Xiaofan Qiu
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, Guangdong, China
| | - Zifeng Cui
- Department of Gynecological Oncology, the First Affiliated Hospital, Sun Yat-Sen University, Guangdong, 510080, Guangzhou, China
| | - Hongxian Xie
- Generulor Company Bio-X Lab, Guangzhou, 510006, Guangdong, China
| | - Pengmin Qin
- School of Psychology, South China Normal University, Guangzhou, 510080, Guangdong, China
| | - Xuchu Weng
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, Guangdong, China.,Key Laboratory of Brain, Cognition and Education Sciences (South China Normal University), Ministry of Education, Guangzhou, 510080, Guangdong, China
| | - Zheng Hu
- Department of Gynecological Oncology, the First Affiliated Hospital, Sun Yat-Sen University, Guangdong, 510080, Guangzhou, China. .,Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
| | - Jiuxing Liang
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, Guangdong, China. .,Key Laboratory of Brain, Cognition and Education Sciences (South China Normal University), Ministry of Education, Guangzhou, 510080, Guangdong, China.
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5
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Sbragaglia V, López-Olmeda JF, Frigato E, Bertolucci C, Arlinghaus R. Size-selective mortality induces evolutionary changes in group risk-taking behaviour and the circadian system in a fish. J Anim Ecol 2020; 90:387-403. [PMID: 33064849 DOI: 10.1111/1365-2656.13372] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 10/05/2020] [Indexed: 12/01/2022]
Abstract
Intensive and trait-selective mortality of fish and wildlife can cause evolutionary changes in a range of life-history and behavioural traits. These changes might in turn alter the circadian system due to co-evolutionary mechanisms or correlated selection responses both at behavioural and molecular levels, with knock-on effects on daily physiological processes and behavioural outputs. We examined the evolutionary impact of size-selective mortality on group risk-taking behaviour and the circadian system in a model fish species. We exposed zebrafish Danio rerio to either large or small size-selective harvesting relative to a control over five generations, followed by eight generations during which harvesting was halted to remove maternal effects. Size-selective mortality affected fine-scale timing of behaviours. In particular, small size-selective mortality, typical of specialized fisheries and gape-limited predators targeting smaller size classes, increased group risk-taking behaviuor during feeding and after simulated predator attacks. Moreover, small size-selective mortality increased early peaks of daily activity as well as extended self-feeding daily activity to the photophase compared to controls. By contrast large size-selective mortality, typical of most wild capture fisheries, only showed an almost significant effect of decreasing group risk-taking behaviour during the habituation phase and no clear changes in fine-scale timing of daily behavioural rhythms compared to controls. We also found changes in the molecular circadian core clockwork in response to both size-selective mortality treatments. These changes disappeared in the clock output pathway because both size-selected lines showed similar transcription profiles. This switch downstream to the molecular circadian core clockwork also resulted in similar overall behavioural rhythms (diurnal swimming and self-feeding in the last hours of darkness) independent of the underlying molecular clock. To conclude, our experimental harvest left an asymmetrical evolutionary legacy in group risk-taking behaviour and in fine-scale daily behavioural rhythms. Yet, the overall timing of activity showed evolutionary resistance probably maintained by a molecular switch. Our experimental findings suggest that size-selective mortality can have consequences for behaviour and physiological processes.
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Affiliation(s)
- Valerio Sbragaglia
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Department of Marine Renewable Resources, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | - Jose Fernando López-Olmeda
- Department of Physiology, Faculty of Biology, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, Murcia, Spain
| | - Elena Frigato
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Cristiano Bertolucci
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Robert Arlinghaus
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Division of Integrative Fisheries Management, Faculty of Life Sciences & Integrative Research Institute on Transformations of Human-Environment Systems (IRI THESys), Humboldt-Universität zu Berlin, Berlin, Germany
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6
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Sun Y, Liu C, Huang M, Huang J, Liu C, Zhang J, Postlethwait JH, Wang H. The Molecular Evolution of Circadian Clock Genes in Spotted Gar ( Lepisosteus oculatus). Genes (Basel) 2019; 10:genes10080622. [PMID: 31426485 PMCID: PMC6723592 DOI: 10.3390/genes10080622] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/09/2019] [Accepted: 08/14/2019] [Indexed: 12/22/2022] Open
Abstract
Circadian rhythms are biological rhythms with a period of approximately 24 h. While canonical circadian clock genes and their regulatory mechanisms appear highly conserved, the evolution of clock gene families is still unclear due to several rounds of whole genome duplication in vertebrates. The spotted gar (Lepisosteus oculatus), as a non-teleost ray-finned fish, represents a fish lineage that diverged before the teleost genome duplication (TGD), providing an outgroup for exploring the evolutionary mechanisms of circadian clocks after whole-genome duplication. In this study, we interrogated the spotted gar draft genome sequences and found that spotted gar contains 26 circadian clock genes from 11 families. Phylogenetic analysis showed that 9 of these 11 spotted gar circadian clock gene families have the same number of genes as humans, while the members of the nfil3 and cry families are different between spotted gar and humans. Using phylogenetic and syntenic analyses, we found that nfil3-1 is conserved in vertebrates, while nfil3-2 and nfil3-3 are maintained in spotted gar, teleost fish, amphibians, and reptiles, but not in mammals. Following the two-round vertebrate genome duplication (VGD), spotted gar retained cry1a, cry1b, and cry2, and cry3 is retained in spotted gar, teleost fish, turtles, and birds, but not in mammals. We hypothesize that duplication of core clock genes, such as (nfil3 and cry), likely facilitated diversification of circadian regulatory mechanisms in teleost fish. We also found that the transcription factor binding element (Ahr::Arnt) is retained only in one of the per1 or per2 duplicated paralogs derived from the TGD in the teleost fish, implicating possible subfuctionalization cases. Together, these findings help decipher the repertoires of the spotted gar’s circadian system and shed light on how the vertebrate circadian clock systems have evolved.
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Affiliation(s)
- Yi Sun
- School of Biology & Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China.
| | - Chao Liu
- School of Biology & Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China
- Center for Circadian Clocks, Soochow University, Suzhou 215123, China
| | - Moli Huang
- School of Biology & Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China
| | - Jian Huang
- School of Biology & Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China
| | - Changhong Liu
- School of Biology & Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China
| | - Jiguang Zhang
- School of Biology & Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China
- Center for Circadian Clocks, Soochow University, Suzhou 215123, China
| | | | - Han Wang
- School of Biology & Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China.
- Center for Circadian Clocks, Soochow University, Suzhou 215123, China.
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7
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Teleosts Genomics: Progress and Prospects in Disease Prevention and Control. Int J Mol Sci 2018; 19:ijms19041083. [PMID: 29617353 PMCID: PMC5979277 DOI: 10.3390/ijms19041083] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 03/11/2018] [Accepted: 03/29/2018] [Indexed: 12/26/2022] Open
Abstract
Genome wide studies based on conventional molecular tools and upcoming omics technologies are beginning to gain functional applications in the control and prevention of diseases in teleosts fish. Herein, we provide insights into current progress and prospects in the use genomics studies for the control and prevention of fish diseases. Metagenomics has emerged to be an important tool used to identify emerging infectious diseases for the timely design of rational disease control strategies, determining microbial compositions in different aquatic environments used for fish farming and the use of host microbiota to monitor the health status of fish. Expounding the use of antimicrobial peptides (AMPs) as therapeutic agents against different pathogens as well as elucidating their role in tissue regeneration is another vital aspect of genomics studies that had taken precedent in recent years. In vaccine development, prospects made include the identification of highly immunogenic proteins for use in recombinant vaccine designs as well as identifying gene signatures that correlate with protective immunity for use as benchmarks in optimizing vaccine efficacy. Progress in quantitative trait loci (QTL) mapping is beginning to yield considerable success in identifying resistant traits against some of the highly infectious diseases that have previously ravaged the aquaculture industry. Altogether, the synopsis put forth shows that genomics studies are beginning to yield positive contribution in the prevention and control of fish diseases in aquaculture.
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8
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Prokkola JM, Nikinmaa M, Lewis M, Anttila K, Kanerva M, Ikkala K, Seppänen E, Kolari I, Leder EH. Cold temperature represses daily rhythms in the liver transcriptome of a stenothermal teleost under decreasing day length. ACTA ACUST UNITED AC 2018; 221:jeb.170670. [PMID: 29361589 DOI: 10.1242/jeb.170670] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/15/2018] [Indexed: 12/19/2022]
Abstract
The climate-change-driven increase in temperature is occurring rapidly and decreasing the predictability of seasonal rhythms at high latitudes. It is therefore urgent to understand how a change in the relationship between photoperiod and temperature can affect ectotherms in these environments. We tested whether temperature affects daily rhythms of transcription in a cold-adapted salmonid using high-throughput RNA sequencing. Arctic char (Salvelinus alpinus) from a subarctic population were reared at a high and a low temperature (15 and 8°C) for 1 month under natural, decreasing day length during late summer. Liver transcriptomes were compared between samples collected in the middle and towards the end of the light period and in the middle of the dark period. Daily variation in transcription was lower in fish from the low temperature compared with strong daily variation in warm-acclimated fish, suggesting that cold temperatures dampen the cycling of transcriptional rhythms under a simultaneously decreasing day length. Different circadian clock genes had divergent expression patterns, responding either by decreased expression or by increased rhythmicity at 15°C compared with 8°C. The results point out mechanisms that can affect the ability of fish to adapt to increasing temperatures caused by climate change.
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Affiliation(s)
- Jenni M Prokkola
- Department of Biology, University of Turku, FI-20014 Turku, Finland .,Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
| | - Mikko Nikinmaa
- Department of Biology, University of Turku, FI-20014 Turku, Finland
| | - Mario Lewis
- Department of Biology, University of Turku, FI-20014 Turku, Finland
| | - Katja Anttila
- Department of Biology, University of Turku, FI-20014 Turku, Finland
| | - Mirella Kanerva
- Department of Biology, University of Turku, FI-20014 Turku, Finland
| | - Kaisa Ikkala
- Department of Biology, University of Turku, FI-20014 Turku, Finland
| | - Eila Seppänen
- Natural Resources Institute Finland (Luke), Laasalantie 9, FI-58175 Enonkoski, Finland
| | - Irma Kolari
- Natural Resources Institute Finland (Luke), Laasalantie 9, FI-58175 Enonkoski, Finland
| | - Erica H Leder
- Department of Biology, University of Turku, FI-20014 Turku, Finland.,Natural History Museum, University of Oslo, Oslo NO-0318, Norway
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9
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Otake S, Park MK. Expressional changes of AMH signaling system in the quail testis induced by photoperiod. Reproduction 2016; 152:575-589. [DOI: 10.1530/rep-16-0175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 08/31/2016] [Indexed: 12/29/2022]
Abstract
Gonadal sex differentiation proceeds by the interplay of various genes including the transcription factors and secretory factors in a complex network. The sex-differentiating genes are expressed not only during early sex differentiation but also throughout the gonadal development and even in the adult gonads. In addition, the evidence that they actually function in the adult gonads have been accumulated from the studies using the conditional knockout mice. However, many previous studies were focused on one single gene though those genes function in a network. In this study, the expressions of various sex-differentiating genes were analyzed simultaneously in the adult testis of the Japanese quail (Coturnix japonica), whose testicular functions are dramatically changed by altering the photoperiod, to elucidate the roles of them in the adult gonad. Anti-Müllerian hormone (AMH) was significantly upregulated in the regressed testis induced by the short-day condition. The expressions of the transcription factors that promoteAMHexpression in mammals (SF1,SOX9,WT1andGATA4) were also increased in the regressed testis. Moreover, AMH receptor (AMHR2) showed similar expression pattern to its ligand. We also analyzed the expressions of other transforming growth factor beta (TGFB) superfamily members and their receptors. The expressions of the ligands and receptors of TGFB family, and follistatin and betaglycan in addition to inhibin subunits were increased in the regressed testis. These results suggest that AMH is involved in the adult testicular functions of the Japanese quail together with other TGFB superfamily members.
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10
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Hadlow N, Brown SJ, Habib A, Wardrop R, Joseph J, Gillett M, Maguire R, Conradie J. Quantifying the intraindividual variation of antimüllerian hormone in the ovarian cycle. Fertil Steril 2016; 106:1230-1237. [PMID: 27351446 DOI: 10.1016/j.fertnstert.2016.06.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 05/19/2016] [Accepted: 06/03/2016] [Indexed: 10/21/2022]
Abstract
OBJECTIVE To quantify intraindividual variability of antimüllerian hormone (AMH) as analytical and biological coefficients of variation and assess the effects of variation on clinical classification. DESIGN Retrospective cohort study. SETTING Not applicable. PATIENT(S) Thirty-eight women referred by general practitioners. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Total intraindividual variability (CVW), analytical (CVA) and biological variability (CVI) for each woman and for AMH ranges: low (<5 pmol/L), reduced (5-10), moderate (>10-30) and high (>30 pmol/L), with calculation of proportion of women crossing clinical cutoffs and expected variability around each cutoff. RESULT(S) Cycling women (n = 38) contributed 238 blood samples (average 6 samples each). The average total intraindividual AMH variability was 20% (range: 2.1% to 73%). Biological variation was 19% (range: 0 to 71%) and at least twice the analytical variation of 6.9% (range: 4.5% to 16%). Reclassification rates were highest in women with low (33%) or reduced AMH (67%) levels. Expected variations around the 5, 10, and 30 pmol/L cutoffs were 3-7, 7-13, and 20-40 pmol/L, respectively. In a woman with mean AMH in the 10-30 pmol/L range, the span of results that could occur was 7-40 pmol/L. CONCLUSION(S) Total variation in AMH was 20%, and the majority of this was biological. Changes in AMH resulted in reclassification in 29% of women and occurred most frequently in those with low and reduced AMH. In cycling women, the variability in AMH should be considered by clinicians, especially if a result is close to a clinical cutoff.
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Affiliation(s)
- Narelle Hadlow
- Department of Biochemistry, PathWest Laboratory Medicine, Nedlands, Western Australia, Australia; School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, Western Australia, Australia; Western Diagnostic Pathology, Myaree, Western Australia, Australia.
| | - Suzanne J Brown
- Department of Endocrinology, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Afsana Habib
- Western Diagnostic Pathology, Myaree, Western Australia, Australia
| | - Robert Wardrop
- Department of Biochemistry, PathWest Laboratory Medicine, Nedlands, Western Australia, Australia
| | - John Joseph
- Department of Biochemistry, PathWest Laboratory Medicine, Nedlands, Western Australia, Australia
| | - Melissa Gillett
- Western Diagnostic Pathology, Myaree, Western Australia, Australia
| | - Rhonda Maguire
- Department of Biochemistry, PathWest Laboratory Medicine, Nedlands, Western Australia, Australia
| | - Johan Conradie
- Western Diagnostic Pathology, Myaree, Western Australia, Australia
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Portela-Bens S, Merlo MA, Rodríguez ME, Cross I, Manchado M, Kosyakova N, Liehr T, Rebordinos L. Integrated gene mapping and synteny studies give insights into the evolution of a sex proto-chromosome in Solea senegalensis. Chromosoma 2016; 126:261-277. [PMID: 27080536 DOI: 10.1007/s00412-016-0589-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 03/31/2016] [Accepted: 04/04/2016] [Indexed: 11/27/2022]
Abstract
The evolution of genes related to sex and reproduction in fish shows high plasticity and, to date, the sex determination system has only been identified in a few species. Solea senegalensis has 42 chromosomes and an XX/XY chromosome system for sex determination, while related species show the ZZ/ZW system. Next-generation sequencing (NGS), multi-color fluorescence in situ hybridization (mFISH) techniques, and bioinformatics analysis have been carried out, with the objective of revealing new information about sex determination and reproduction in S. senegalensis. To that end, several bacterial artificial chromosome (BAC) clones that contain candidate genes involved in such processes (dmrt1, dmrt2, dmrt3, dmrt4, sox3, sox6, sox8, sox9, lh, cyp19a1a, amh, vasa, aqp3, and nanos3) were analyzed and compared with the same region in other related species. Synteny studies showed that the co-localization of dmrt1-dmrt2-drmt3 in the largest metacentric chromosome of S. senegalensis is coincident with that found in the Z chromosome of Cynoglossus semilaevis, which would potentially make this a sex proto-chromosome. Phylogenetic studies show the close proximity of S. senegalensis to Oryzias latipes, a species with an XX/XY system and a sex master gene. Comparative mapping provides evidence of the preferential association of these candidate genes in particular chromosome pairs. By using the NGS and mFISH techniques, it has been possible to obtain an integrated genetic map, which shows that 15 out of 21 chromosome pairs of S. senegalensis have at least one BAC clone. This result is important for distinguishing those chromosome pairs of S. senegalensis that are similar in shape and size. The mFISH analysis shows the following co-localizations in the same chromosomes: dmrt1-dmrt2-dmrt3, dmrt4-sox9-thrb, aqp3-sox8, cyp19a1a-fshb, igsf9b-sox3, and lysg-sox6.
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Affiliation(s)
- Silvia Portela-Bens
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Manuel Alejandro Merlo
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - María Esther Rodríguez
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Ismael Cross
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Manuel Manchado
- Centro IFAPA "El Toruño", 11500, Puerto de Santa María, Cádiz, Spain
| | - Nadezda Kosyakova
- Institut für Humangenetik, Universitätsklinikum Jena, 07743, Jena, Germany
| | - Thomas Liehr
- Institut für Humangenetik, Universitätsklinikum Jena, 07743, Jena, Germany
| | - Laureana Rebordinos
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain.
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12
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Pfennig F, Standke A, Gutzeit HO. The role of Amh signaling in teleost fish--Multiple functions not restricted to the gonads. Gen Comp Endocrinol 2015; 223:87-107. [PMID: 26428616 DOI: 10.1016/j.ygcen.2015.09.025] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 09/24/2015] [Accepted: 09/25/2015] [Indexed: 12/16/2022]
Abstract
This review summarizes the important role of Anti-Müllerian hormone (Amh) during gonad development in fishes. This Tgfβ-domain bearing hormone was named after one of its known functions, the induction of the regression of Müllerian ducts in male mammalian embryos. Later in development it is involved in male and female gonad differentiation and extragonadal expression has been reported in mammals as well. Teleosts lack Müllerian ducts, but they have amh orthologous genes. amh expression is reported from 21 fish species and possible regulatory interactions with further factors like sex steroids and gonadotropic hormones are discussed. The gonadotropin Fsh inhibits amh expression in all fish species studied. Sex steroids show no consistent influence on amh expression. Amh is produced in male Sertoli cells and female granulosa cells and inhibits germ cell proliferation and differentiation as well as steroidogenesis in both sexes. Therefore, Amh might be a central player in gonad development and a target of gonadotropic Fsh. Furthermore, there is evidence that an Amh-type II receptor is involved in germ cell regulation. Amh and its corresponding type II receptor are also present in brain and pituitary, at least in some teleosts, indicating additional roles of Amh effects in the brain-pituitary-gonadal axis. Unraveling Amh signaling is important in stem cell research and for reproduction as well as for aquaculture and in environmental science.
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Affiliation(s)
- Frank Pfennig
- Institut für Zoologie, TU Dresden, D-01062 Dresden, Germany.
| | - Andrea Standke
- Institut für Zoologie, TU Dresden, D-01062 Dresden, Germany
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Genome-wide association study (GWAS) for growth rate and age at sexual maturation in Atlantic salmon (Salmo salar). PLoS One 2015; 10:e0119730. [PMID: 25757012 PMCID: PMC4355585 DOI: 10.1371/journal.pone.0119730] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 01/25/2015] [Indexed: 11/26/2022] Open
Abstract
Early sexual maturation is considered a serious drawback for Atlantic salmon aquaculture as it retards growth, increases production times and affects flesh quality. Although both growth and sexual maturation are thought to be complex processes controlled by several genetic and environmental factors, selection for these traits has been continuously accomplished since the beginning of Atlantic salmon selective breeding programs. In this genome-wide association study (GWAS) we used a 6.5K single-nucleotide polymorphism (SNP) array to genotype ∼480 individuals from the Cermaq Canada broodstock program and search for SNPs associated with growth and age at sexual maturation. Using a mixed model approach we identified markers showing a significant association with growth, grilsing (early sexual maturation) and late sexual maturation. The most significant associations were found for grilsing, with markers located in Ssa10, Ssa02, Ssa13, Ssa25 and Ssa12, and for late maturation with markers located in Ssa28, Ssa01 and Ssa21. A lower level of association was detected with growth on Ssa13. Candidate genes, which were linked to these genetic markers, were identified and some of them show a direct relationship with developmental processes, especially for those in association with sexual maturation. However, the relatively low power to detect genetic markers associated with growth (days to 5 kg) in this GWAS indicates the need to use a higher density SNP array in order to overcome the low levels of linkage disequilibrium observed in Atlantic salmon before the information can be incorporated into a selective breeding program.
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14
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Hecht BC, Valle ME, Thrower FP, Nichols KM. Divergence in expression of candidate genes for the smoltification process between juvenile resident rainbow and anadromous steelhead trout. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2014; 16:638-656. [PMID: 24952010 DOI: 10.1007/s10126-014-9579-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 06/03/2014] [Indexed: 06/03/2023]
Abstract
Rainbow and steelhead trout (Oncorhynchus mykiss), among other salmonid fishes, exhibit tremendous life history diversity, foremost of which is variation in migratory propensity. While some individuals possess the ability to undertake an anadromous marine migration, others remain resident in freshwater throughout their life cycle. Those that will migrate undergo tremendous physiological, morphological, and behavioral transformations in a process called smoltification which transitions freshwater-adapted parr to marine-adapted smolts. While the behavior, ecology, and physiology of smoltification are well described, our understanding of the proximate genetic mechanisms that trigger the process are not well known. Quantitative genetic analyses have identified several genomic regions associated with smoltification and migration-related traits within this species. Here we investigate the divergence in gene expression of 18 functional and positional candidate genes for the smoltification process in the brain, gill, and liver tissues of migratory smolts, resident parr, and precocious mature male trout at the developmental stage of out-migration. Our analysis reveals several genes differentially expressed between life history classes and validates the candidate nature of several genes in the parr-smolt transformation including Clock1α, FSHβ, GR, GH2, GHR1, GHR2, NDK7, p53, SC6a7, Taldo1, THRα, THRβ, and Vdac2.
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Affiliation(s)
- Benjamin C Hecht
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
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15
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Kim JH, White SL, Devlin RH. Interaction of growth hormone overexpression and nutritional status on pituitary gland clock gene expression in coho salmon,Oncorhynchus kisutch. Chronobiol Int 2014; 32:113-27. [DOI: 10.3109/07420528.2014.958160] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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16
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Allen MS, Ferguson MM, Danzmann RG. Molecular markers for variation in spawning date in a hatchery population of rainbow trout (Oncorhynchus mykiss). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2014; 16:289-298. [PMID: 24114565 DOI: 10.1007/s10126-013-9547-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 09/15/2013] [Indexed: 06/02/2023]
Abstract
We examined the distribution of alleles at 63 microsatellite loci distributed across 29 linkage groups in broodstock females from a commercial population of rainbow trout spawning on different dates throughout the season (August to January). A total of 368 females, 184 and 117 females from each of the tail-ends of the spawning distribution and a subsample of 67 females spawning in the middle, were used to detect marker-trait associations. Twenty-one loci in a subset of genomic regions (RT-5, 7, 8, 10, 12, 14, 15, 22, 23, 24, 25, 29, 30, and 31) were significantly associated with variation in spawning date. Many of these markers localize to regions with known spawning date quantitative trait loci based on previous studies. An individual assignment analysis was used to test how well the molecular data could be used to assign individuals to their correct spawning group, and markers were given a ranking reflecting their contribution to the accuracy of assignment. The top 15 ranked markers were successful at assigning the majority of females to the correct spawning group based on genotype with an average accuracy of 76 %. The most likely genes that could contribute to these differences in spawning date are discussed. Together, these data indicate that the loci could be incorporated into a selection index with phenotype data to increase the accuracy of selection for spawning date.
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Affiliation(s)
- M S Allen
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
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17
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Hale MC, Colletti JA, Gahr SA, Scardina J, Thrower FP, Harmon M, Carter M, Phillips RB, Thorgaard GH, Rexroad CE, Nichols KM. Mapping and Expression of Candidate Genes for Development Rate in Rainbow Trout (Oncorhynchus mykiss). J Hered 2014; 105:506-520. [PMID: 24744432 DOI: 10.1093/jhered/esu018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 02/13/2014] [Indexed: 01/21/2023] Open
Abstract
Development rate has important implications for individual fitness and physiology. In salmonid fishes, development rate correlates with many traits later in life, including life-history diversity, growth, and age and size at sexual maturation. In rainbow trout (Oncorhynchus mykiss), a quantitative trait locus for embryonic development rate has been detected on chromosome 5 across populations. However, few candidate genes have been identified within this region. In this study, we use gene mapping, gene expression, and quantitative genetic methods to further identify the genetic basis of embryonic developmental rate in O. mykiss Among the genes located in the region of the major development rate quantitative trait locus (GHR1, Clock1a, Myd118-1, and their paralogs), all were expressed early in embryonic development (fertilization through hatch), but none were differentially expressed between individuals with the fast- or slow-developing alleles for a major embryonic development rate quantitative trait locus. In a follow-up study of migratory and resident rainbow trout from natural populations in Alaska, we found significant additive variation in development rate and, moreover, found associations between development rate and allelic variation in all 3 candidate genes within the quantitative trait locus for embryonic development. The mapping of these genes to this region and associations in multiple populations provide positional candidates for further study of their roles in growth, development, and life-history diversity in this model salmonid.
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Affiliation(s)
- Matthew C Hale
- From the Department of Biological Sciences, Purdue University, West Lafayette, IN (Hale, Colletti, Scardina, Harmon, Carter, and Nichols); the Biology Department, St. Vincent College, Latrobe, PA (Gahr); Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK (Thrower); the Department of Biological Sciences, Washington State University, Vancouver, WA (Phillips); the Department of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA (Thorgaard); the United States Department of Agriculture, Agricultural Research Service, National Center for Cool and Coldwater Aquaculture, Leetown, WV (Rexroad); the Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN (Nichols); and the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division, 2725 Montlake Boulevard East, Seattle, WA 98112 (Nichols)
| | - John A Colletti
- From the Department of Biological Sciences, Purdue University, West Lafayette, IN (Hale, Colletti, Scardina, Harmon, Carter, and Nichols); the Biology Department, St. Vincent College, Latrobe, PA (Gahr); Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK (Thrower); the Department of Biological Sciences, Washington State University, Vancouver, WA (Phillips); the Department of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA (Thorgaard); the United States Department of Agriculture, Agricultural Research Service, National Center for Cool and Coldwater Aquaculture, Leetown, WV (Rexroad); the Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN (Nichols); and the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division, 2725 Montlake Boulevard East, Seattle, WA 98112 (Nichols)
| | - Scott A Gahr
- From the Department of Biological Sciences, Purdue University, West Lafayette, IN (Hale, Colletti, Scardina, Harmon, Carter, and Nichols); the Biology Department, St. Vincent College, Latrobe, PA (Gahr); Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK (Thrower); the Department of Biological Sciences, Washington State University, Vancouver, WA (Phillips); the Department of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA (Thorgaard); the United States Department of Agriculture, Agricultural Research Service, National Center for Cool and Coldwater Aquaculture, Leetown, WV (Rexroad); the Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN (Nichols); and the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division, 2725 Montlake Boulevard East, Seattle, WA 98112 (Nichols)
| | - Julie Scardina
- From the Department of Biological Sciences, Purdue University, West Lafayette, IN (Hale, Colletti, Scardina, Harmon, Carter, and Nichols); the Biology Department, St. Vincent College, Latrobe, PA (Gahr); Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK (Thrower); the Department of Biological Sciences, Washington State University, Vancouver, WA (Phillips); the Department of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA (Thorgaard); the United States Department of Agriculture, Agricultural Research Service, National Center for Cool and Coldwater Aquaculture, Leetown, WV (Rexroad); the Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN (Nichols); and the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division, 2725 Montlake Boulevard East, Seattle, WA 98112 (Nichols)
| | - Frank P Thrower
- From the Department of Biological Sciences, Purdue University, West Lafayette, IN (Hale, Colletti, Scardina, Harmon, Carter, and Nichols); the Biology Department, St. Vincent College, Latrobe, PA (Gahr); Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK (Thrower); the Department of Biological Sciences, Washington State University, Vancouver, WA (Phillips); the Department of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA (Thorgaard); the United States Department of Agriculture, Agricultural Research Service, National Center for Cool and Coldwater Aquaculture, Leetown, WV (Rexroad); the Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN (Nichols); and the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division, 2725 Montlake Boulevard East, Seattle, WA 98112 (Nichols)
| | - Matthew Harmon
- From the Department of Biological Sciences, Purdue University, West Lafayette, IN (Hale, Colletti, Scardina, Harmon, Carter, and Nichols); the Biology Department, St. Vincent College, Latrobe, PA (Gahr); Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK (Thrower); the Department of Biological Sciences, Washington State University, Vancouver, WA (Phillips); the Department of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA (Thorgaard); the United States Department of Agriculture, Agricultural Research Service, National Center for Cool and Coldwater Aquaculture, Leetown, WV (Rexroad); the Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN (Nichols); and the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division, 2725 Montlake Boulevard East, Seattle, WA 98112 (Nichols)
| | - Megan Carter
- From the Department of Biological Sciences, Purdue University, West Lafayette, IN (Hale, Colletti, Scardina, Harmon, Carter, and Nichols); the Biology Department, St. Vincent College, Latrobe, PA (Gahr); Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK (Thrower); the Department of Biological Sciences, Washington State University, Vancouver, WA (Phillips); the Department of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA (Thorgaard); the United States Department of Agriculture, Agricultural Research Service, National Center for Cool and Coldwater Aquaculture, Leetown, WV (Rexroad); the Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN (Nichols); and the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division, 2725 Montlake Boulevard East, Seattle, WA 98112 (Nichols)
| | - Ruth B Phillips
- From the Department of Biological Sciences, Purdue University, West Lafayette, IN (Hale, Colletti, Scardina, Harmon, Carter, and Nichols); the Biology Department, St. Vincent College, Latrobe, PA (Gahr); Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK (Thrower); the Department of Biological Sciences, Washington State University, Vancouver, WA (Phillips); the Department of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA (Thorgaard); the United States Department of Agriculture, Agricultural Research Service, National Center for Cool and Coldwater Aquaculture, Leetown, WV (Rexroad); the Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN (Nichols); and the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division, 2725 Montlake Boulevard East, Seattle, WA 98112 (Nichols)
| | - Gary H Thorgaard
- From the Department of Biological Sciences, Purdue University, West Lafayette, IN (Hale, Colletti, Scardina, Harmon, Carter, and Nichols); the Biology Department, St. Vincent College, Latrobe, PA (Gahr); Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK (Thrower); the Department of Biological Sciences, Washington State University, Vancouver, WA (Phillips); the Department of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA (Thorgaard); the United States Department of Agriculture, Agricultural Research Service, National Center for Cool and Coldwater Aquaculture, Leetown, WV (Rexroad); the Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN (Nichols); and the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division, 2725 Montlake Boulevard East, Seattle, WA 98112 (Nichols)
| | - Caird E Rexroad
- From the Department of Biological Sciences, Purdue University, West Lafayette, IN (Hale, Colletti, Scardina, Harmon, Carter, and Nichols); the Biology Department, St. Vincent College, Latrobe, PA (Gahr); Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK (Thrower); the Department of Biological Sciences, Washington State University, Vancouver, WA (Phillips); the Department of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA (Thorgaard); the United States Department of Agriculture, Agricultural Research Service, National Center for Cool and Coldwater Aquaculture, Leetown, WV (Rexroad); the Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN (Nichols); and the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division, 2725 Montlake Boulevard East, Seattle, WA 98112 (Nichols)
| | - Krista M Nichols
- From the Department of Biological Sciences, Purdue University, West Lafayette, IN (Hale, Colletti, Scardina, Harmon, Carter, and Nichols); the Biology Department, St. Vincent College, Latrobe, PA (Gahr); Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK (Thrower); the Department of Biological Sciences, Washington State University, Vancouver, WA (Phillips); the Department of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA (Thorgaard); the United States Department of Agriculture, Agricultural Research Service, National Center for Cool and Coldwater Aquaculture, Leetown, WV (Rexroad); the Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN (Nichols); and the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division, 2725 Montlake Boulevard East, Seattle, WA 98112 (Nichols).
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18
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Pearse DE, Miller MR, Abadía-Cardoso A, Garza JC. Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout. Proc Biol Sci 2014; 281:20140012. [PMID: 24671976 DOI: 10.1098/rspb.2014.0012] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. Such changes may be population-specific or, alternatively, may involve parallel evolution of the same genomic region in multiple populations, if that region contains genes or co-adapted gene complexes affecting the selected trait(s). Both quantitative and population genetic approaches have identified associations between specific genomic regions and the anadromous (steelhead) and resident (rainbow trout) life-history strategies of Oncorhynchus mykiss. Here, we use genotype data from 95 single nucleotide polymorphisms and show that the distribution of variation in a large region of one chromosome, Omy5, is strongly associated with life-history differentiation in multiple above-barrier populations of rainbow trout and their anadromous steelhead ancestors. The associated loci are in strong linkage disequilibrium, suggesting the presence of a chromosomal inversion or other rearrangement limiting recombination. These results provide the first evidence of a common genomic basis for life-history variation in O. mykiss in a geographically diverse set of populations and extend our knowledge of the heritable basis of rapid adaptation of complex traits in novel habitats.
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Affiliation(s)
- Devon E Pearse
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, , 110 Shaffer Road, Santa Cruz, CA 95060, USA, Institute of Marine Sciences, University of California, , Santa Cruz, CA 95060, USA, Institute of Molecular Biology, University of Oregon, , Eugene, OR 97403, USA, Department of Animal Science, University of California, , One Shields Avenue, Davis, CA 95616, USA
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19
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Hattori RS, Strüssmann CA, Fernandino JI, Somoza GM. Genotypic sex determination in teleosts: insights from the testis-determining amhy gene. Gen Comp Endocrinol 2013; 192:55-9. [PMID: 23602719 DOI: 10.1016/j.ygcen.2013.03.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/18/2013] [Accepted: 03/26/2013] [Indexed: 01/22/2023]
Abstract
The master sex-determining genes identified so far in fishes are clearly not conserved, as evidenced by several unrelated genes reported to play critical roles in sex determination. In this study, we reviewed the molecular process of sex determination in the Patagonian pejerrey Odontesthes hatcheri, an emerging model due to the recent discovery that a Y-chromosome linked, duplicated copy of the anti-Müllerian hormone gene, amhy plays a pivotal role in sex determination. A comparative analysis with other newly found sex-determining genes of teleost fish, DMY/dmrt1bY, sdY, amhr2, and gsdf(Y) is performed and alternative ideas are proposed to explain the mechanism involved in the rise of various types of non-homologous sex-determining genes.
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Affiliation(s)
- Ricardo Shohei Hattori
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan 4-5-7 Minato, Tokyo, Japan.
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20
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Daily patterns of mRNA expression of two core circadian regulatory proteins, Clock2 and Per1, and two appetite-regulating peptides, OX and NPY, in goldfish (Carassius auratus). Comp Biochem Physiol A Mol Integr Physiol 2012; 163:127-36. [DOI: 10.1016/j.cbpa.2012.05.197] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Revised: 05/20/2012] [Accepted: 05/21/2012] [Indexed: 11/24/2022]
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21
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A Y-linked anti-Müllerian hormone duplication takes over a critical role in sex determination. Proc Natl Acad Sci U S A 2012; 109:2955-9. [PMID: 22323585 DOI: 10.1073/pnas.1018392109] [Citation(s) in RCA: 310] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Gonadal sex determination in vertebrates generally follows a sequence of genetically programmed events. In what is seemingly becoming a pattern, all confirmed or current candidate "master" sex-determining genes reported in this group, e.g., SRY in eutherian mammals, DMY/dmrt1bY in medaka, DM-W in the African clawed frog, and DMRT1 in chicken encode transcription factors. In contrast, here we show that a male-specific, duplicated copy of the anti-Müllerian hormone (amh) is implicated in testicular development of the teleost fish Patagonian pejerrey (Odontesthes hatcheri). The gene, termed amhy because it is found in a single metacentric/submetacentric chromosome of XY individuals, is expressed much earlier than the autosomal amh (6 d after fertilization vs. 12 wk after fertilization) and is localized to presumptive Sertoli cells of XY males during testicular differentiation. Moreover, amhy knockdown in XY embryos resulted in the up-regulation of foxl2 and cyp19a1a mRNAs and the development of ovaries. These results are evidence of a functional amh duplication in vertebrates and suggest that amhy may be the master sex-determining gene in this species. If confirmed, this would be a unique instance of a hormone-related gene, a member of the TGF-β superfamily, in such a role.
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Küttner E, Moghadam HK, Skúlason S, Danzmann RG, Ferguson MM. Genetic architecture of body weight, condition factor and age of sexual maturation in Icelandic Arctic charr (Salvelinus alpinus). Mol Genet Genomics 2011; 286:67-79. [PMID: 21626198 DOI: 10.1007/s00438-011-0628-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 05/10/2011] [Indexed: 12/16/2022]
Abstract
The high commercial value from the aquaculture of salmonid fishes has prompted many studies into the genetic architecture of complex traits and the need to identify genomic regions that have repeatable associations with trait variation both within and among species. We searched for quantitative trait loci (QTL) for body weight (BW), condition factor (CF) and age of sexual maturation (MAT) in families of Arctic charr (Salvelinus alpinus) from an Icelandic breeding program. QTL with genome-wide significance were detected for each trait on multiple Arctic charr (AC) linkage groups (BW: AC-4, AC-20; CF: AC-7, AC-20, AC-23, AC-36; MAT: AC-13/34, AC-39). In addition to the genome-wide significant QTL for both BW and CF on AC-20, linkage groups AC-4, AC-7, AC-8, and AC-16 contain QTL for both BW and CF with chromosome-wide significance. These regions had effects (albeit weaker) on MAT with the exception of the region on AC-8. Comparisons with a North American cultured strain of Arctic charr, as well as North American populations of Atlantic salmon (Salmo salar), and rainbow trout (Oncorhynchus mykiss), reveal some conservation in QTL location and structure, particularly with respect to the joint associations of QTL influencing BW and CF. The detection of some differences in genetic architecture between the two aquaculture strains of Arctic charr may be reflective of the differential evolutionary histories experienced by these fishes, and illustrates the importance of including different strains to investigate genetic variation in a species where the intent is to use that variation in selective breeding programs.
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Affiliation(s)
- Eva Küttner
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
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