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Xi Q, Zhao F, Hu J, Wang J, Liu X, Dang P, Luo Y, Li S. Expression and Variations in EPAS1 Associated with Oxygen Metabolism in Sheep. Genes (Basel) 2022; 13:genes13101871. [PMID: 36292756 PMCID: PMC9602176 DOI: 10.3390/genes13101871] [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: 09/26/2022] [Revised: 10/05/2022] [Accepted: 10/13/2022] [Indexed: 11/04/2022] Open
Abstract
Endothelial PAS domain protein 1 gene (EPAS1) is a member of the HIF gene family. This gene encodes a transcription factor subunit that is involved in the induction of oxygen-regulated genes. Several studies have demonstrated that a mutation in EPAS1 could affect oxygen sensing, polycythemia, and hemoglobin level. However, whether EPAS1 mutation affects sheep oxygen metabolism is still unknown. Therefore, we explored the relationship between the variation of EPAS1 and oxygen metabolism in sheep. In this study, variations in ovine EPAS1 exon 15 were investigated in 332 Tibetan sheep and 339 Hu sheep by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis. In addition, we studied the effect of these variations on blood gas in 176 Tibetan sheep and 231 Hu sheep. Finally, the mRNA expression of EPAS1 in six tissues of Hu sheep and Tibetan sheep living at different altitudes (2500 m, 3500 m, and 4500 m) was analyzed by real-time quantitative PCR (RT-qPCR). Four alleles (A, B, C, and D) were detected, and their distributions highly differed between Tibetan sheep and Hu sheep. In Tibetan sheep, B was the dominant allele, and C and D alleles were rare, whereas all four alleles were common in Hu sheep. Six single nucleotide polymorphisms (SNPs) were identified between the four alleles and one of them was non-synonymous (p.F606L). While studying the blood gas levels in Tibetan sheep and Hu sheep, one variant region was found to be associated with an elevated pO2 and sO2, which suggested that variations in EPAS1 are associated with oxygen metabolism in sheep. RT-qPCR results showed that EPAS1 was expressed in the six tissues of Hu sheep and Tibetan sheep at different altitudes. In addition, the expression of EPAS1 in four tissues (heart, liver, spleen, and longissimus dorsi muscle) of Hu sheep was lower than that in Tibetan sheep from three different altitudes, and the expression of EPAS1 was positively correlated with the altitude. These results indicate that the variations and expression of EPAS1 is closely related to oxygen metabolism.
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Affiliation(s)
- Qiming Xi
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- International Science and Technology Cooperation Base of Meat Sheep and Meat Cattle Genetic Improvement in Northwest of China, Gansu Agricultural University, Lanzhou 730070, China
| | - Fangfang Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- International Science and Technology Cooperation Base of Meat Sheep and Meat Cattle Genetic Improvement in Northwest of China, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- International Science and Technology Cooperation Base of Meat Sheep and Meat Cattle Genetic Improvement in Northwest of China, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- International Science and Technology Cooperation Base of Meat Sheep and Meat Cattle Genetic Improvement in Northwest of China, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- International Science and Technology Cooperation Base of Meat Sheep and Meat Cattle Genetic Improvement in Northwest of China, Gansu Agricultural University, Lanzhou 730070, China
| | - Pengju Dang
- International Science and Technology Cooperation Base of Meat Sheep and Meat Cattle Genetic Improvement in Northwest of China, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Agriculture Technology College, Lanzhou 730070, China
| | - Yuzhu Luo
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- International Science and Technology Cooperation Base of Meat Sheep and Meat Cattle Genetic Improvement in Northwest of China, Gansu Agricultural University, Lanzhou 730070, China
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- International Science and Technology Cooperation Base of Meat Sheep and Meat Cattle Genetic Improvement in Northwest of China, Gansu Agricultural University, Lanzhou 730070, China
- Correspondence:
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Crispo E, Tunna HR, Hussain N, Rodriguez SS, Pavey SA, Jackson LJ, Rogers SM. The evolution of the major histocompatibility complex in upstream versus downstream river populations of the longnose dace. Ecol Evol 2017; 7:3297-3311. [PMID: 28515867 PMCID: PMC5433983 DOI: 10.1002/ece3.2839] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/28/2017] [Indexed: 11/10/2022] Open
Abstract
Populations in upstream versus downstream river locations can be exposed to vastly different environmental and ecological conditions and can thus harbor different genetic resources due to selection and neutral processes. An interesting question is how upstream–downstream directionality in rivers affects the evolution of immune response genes. We used next‐generation amplicon sequencing to identify eight alleles of the major histocompatibility complex (MHC) class II β exon 2 in the cyprinid longnose dace (Rhinichthys cataractae) from three rivers in Alberta, upstream and downstream of municipal and agricultural areas along contaminant gradients. We used these data to test for directional and balancing selection on the MHC. We also genotyped microsatellite loci to examine neutral population processes in this system. We found evidence for balancing selection on the MHC in the form of increased nonsynonymous variation relative to neutral expectations, and selection occurred at more amino acid residues upstream than downstream in two rivers. We found this pattern despite no population structure or isolation by distance, based on microsatellite data, at these sites. Overall, our results suggest that MHC evolution is driven by upstream–downstream directionality in fish inhabiting this system.
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Affiliation(s)
- Erika Crispo
- Department of Biological Sciences University of Calgary Calgary AB Canada
| | - Haley R Tunna
- Department of Biological Sciences University of Calgary Calgary AB Canada
| | - Noreen Hussain
- Department of Biology Pace University New York NY USA.,Present address: Touro College of Pharmacy New York NY USA
| | - Silvia S Rodriguez
- Department of Biology Pace University New York NY USA.,Present address: Developmental Biology Sloan-Kettering Institute New York NY USA
| | - Scott A Pavey
- University of New Brunswick Saint John & Canadian Rivers Institute Saint John NB Canada
| | - Leland J Jackson
- Department of Biological Sciences University of Calgary Calgary AB Canada
| | - Sean M Rogers
- Department of Biological Sciences University of Calgary Calgary AB Canada
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Osborne MJ, Pilger TJ, Lusk JD, Turner TF. Spatio-temporal variation in parasite communities maintains diversity at the major histocompatibility complex class IIβ in the endangered Rio Grande silvery minnow. Mol Ecol 2016; 26:471-489. [PMID: 27864911 DOI: 10.1111/mec.13936] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 11/02/2016] [Accepted: 11/14/2016] [Indexed: 01/30/2023]
Abstract
Climate change will strongly impact aquatic ecosystems particularly in arid and semi-arid regions. Fish-parasite interactions will also be affected by predicted altered flow and temperature regimes, and other environmental stressors. Hence, identifying environmental and genetic factors associated with maintaining diversity at immune genes is critical for understanding species' adaptive capacity. Here, we combine genetic (MHC class IIβ and microsatellites), parasitological and ecological data to explore the relationship between these factors in the remnant wild Rio Grande silvery minnow (Hybognathus amarus) population, an endangered species found in the southwestern United States. Infections with multiple parasites on the gills were observed and there was spatio-temporal variation in parasite communities and patterns of infection among individuals. Despite its highly endangered status and chronically low genetic effective size, Rio Grande silvery minnow had high allelic diversity at MHC class IIβ with more alleles recognized at the presumptive DAB1 locus compared to the DAB3 locus. We identified significant associations between specific parasites and MHC alleles against a backdrop of generalist parasite prevalence. We also found that individuals with higher individual neutral heterozygosity and higher amino acid divergence between MHC alleles had lower parasite abundance and diversity. Taken together, these results suggest a role for fluctuating selection imposed by spatio-temporal variation in pathogen communities and divergent allele advantage in maintenance of high MHC polymorphism. Understanding the complex interaction of habitat, pathogens and immunity in protected species will require integrated experimental, genetic and field studies.
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Affiliation(s)
- Megan J Osborne
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, MSC 03-2020, Albuquerque, NM, 87131, USA
| | - Tyler J Pilger
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, MSC 03-2020, Albuquerque, NM, 87131, USA
| | - Joel D Lusk
- U.S. Fish and Wildlife Service, New Mexico Ecological Services, Albuquerque, NM, 87113, USA
| | - Thomas F Turner
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, MSC 03-2020, Albuquerque, NM, 87131, USA
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Ruskey JA, Taylor EB. Morphological and genetic analysis of sympatric dace within the Rhinichthys cataractaespecies complex: a case of isolation lost. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12657] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jennifer A. Ruskey
- Department of Zoology; Biodiversity Research Centre and Beaty Biodiversity Museum; University of British Columbia; #4200-6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Eric B. Taylor
- Department of Zoology; Biodiversity Research Centre and Beaty Biodiversity Museum; University of British Columbia; #4200-6270 University Blvd Vancouver BC V6T 1Z4 Canada
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Gonzalez-Quevedo C, Spurgin LG, Illera JC, Richardson DS. Drift, not selection, shapes toll-like receptor variation among oceanic island populations. Mol Ecol 2015; 24:5852-63. [PMID: 26509790 PMCID: PMC4737395 DOI: 10.1111/mec.13437] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 10/20/2015] [Accepted: 10/22/2015] [Indexed: 01/21/2023]
Abstract
Understanding the relative role of different evolutionary forces in shaping the level and distribution of functional genetic diversity among natural populations is a key issue in evolutionary and conservation biology. To do so accurately genetic data must be analysed in conjunction with an unambiguous understanding of the historical processes that have acted upon the populations. Here, we focused on diversity at toll‐like receptor (TLR) loci, which play a key role in the vertebrate innate immune system and, therefore, are expected to be under pathogen‐mediated selection. We assessed TLR variation within and among 13 island populations (grouped into three archipelagos) of Berthelot's pipit, Anthus berthelotii, for which detailed population history has previously been ascertained. We also compared the variation observed with that found in its widespread sister species, the tawny pipit, Anthus campestris. We found strong evidence for positive selection at specific codons in TLR1LA, TLR3 and TLR4. Despite this, we found that at the allele frequency level, demographic history has played the major role in shaping patterns of TLR variation in Berthelot's pipit. Levels of diversity and differentiation within and across archipelagos at all TLR loci corresponded very closely with neutral microsatellite variation and with the severity of the bottlenecks that occurred during colonization. Our study shows that despite the importance of TLRs in combating pathogens, demography can be the main driver of immune gene variation within and across populations, resulting in patterns of functional variation that can persist over evolutionary timescales.
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Affiliation(s)
- Catalina Gonzalez-Quevedo
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,Grupo Ecología y Evolución de Vertebrados, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Calle 70 No. 52-21, Medellin, Colombia
| | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Juan Carlos Illera
- Research Unit of Biodiversity (UO-CSIC-PA), Oviedo University, Campus of Mieres, Research Building, 5th Floor. C/Gonzalo Gutiérrez Quirós, s/n, 33600 Mieres, Asturias, Spain
| | - David S Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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Taylor EB, McPhail J, Ruskey J. Phylogeography of the longnose dace (Rhinichthys cataractae) species group in northwestern North America — the Nooksack dace problem. CAN J ZOOL 2015. [DOI: 10.1139/cjz-2015-0014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The longnose dace (Rhinichthys cataractae (Valenciennes, 1842); Cyprinidae) is one of the most widespread freshwater fishes in North America, and across its range there have been several divergent forms described that are of uncertain taxonomic status. One of these forms, the Nooksack dace, is found in southwestern British Columbia and adjacent portions of western Washington, and is distinguished from longnose dace by a lower number of lateral-line scales. We sequenced a total of approximately 1400 base pairs (bp) of mitochondrial DNA (mtDNA) and noted that the longnose dace found west of the Continental Divide and Nooksack dace constituted reciprocally monophyletic clades that differed from each other by between 2% and 3% sequence divergence. Sequence analysis at two nuclear loci (the S7 ribosomal protein intron 1 (S7) and recombination activation gene 1 (RAG1)), however, showed no consistent difference between longnose dace and Nooksack dace and several alleles were shared between them. By contrast, consistent differences at both mtDNA and nuclear DNA loci were resolved between R. cataractae samples from east and west of the Continental Divide. The Nooksack dace does not appear to warrant separate taxonomic status from the longnose dace, but the mtDNA differences support its recognition as an important component of the evolutionary and biogeographic legacy of R. cataractae.
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Affiliation(s)
- Eric B. Taylor
- Department of Zoology, Biodiversity Research Centre and Beaty Biodiversity Museum, The University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
- Department of Zoology, Biodiversity Research Centre and Beaty Biodiversity Museum, The University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - J.D. McPhail
- Department of Zoology, Biodiversity Research Centre and Beaty Biodiversity Museum, The University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
- Department of Zoology, Biodiversity Research Centre and Beaty Biodiversity Museum, The University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - J.A. Ruskey
- Department of Zoology, Biodiversity Research Centre and Beaty Biodiversity Museum, The University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
- Department of Zoology, Biodiversity Research Centre and Beaty Biodiversity Museum, The University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
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