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Wehrenberg G, Tokarska M, Cocchiararo B, Nowak C. A reduced SNP panel optimised for non-invasive genetic assessment of a genetically impoverished conservation icon, the European bison. Sci Rep 2024; 14:1875. [PMID: 38253649 PMCID: PMC10803807 DOI: 10.1038/s41598-024-51495-9] [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: 04/18/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
The European bison was saved from the brink of extinction due to considerable conservation efforts since the early twentieth century. The current global population of > 9500 individuals is the result of successful ex situ breeding based on a stock of only 12 founders, resulting in an extremely low level of genetic variability. Due to the low allelic diversity, traditional molecular tools, such as microsatellites, fail to provide sufficient resolution for accurate genetic assessments in European bison, let alone from non-invasive samples. Here, we present a SNP panel for accurate high-resolution genotyping of European bison, which is suitable for a wide variety of sample types. The panel accommodates 96 markers allowing for individual and parental assignment, sex determination, breeding line discrimination, and cross-species detection. Two applications were shown to be utilisable in further Bos species with potential conservation significance. The new SNP panel will allow to tackle crucial tasks in European bison conservation, including the genetic monitoring of reintroduced populations, and a molecular assessment of pedigree data documented in the world's first studbook of a threatened species.
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Affiliation(s)
- Gerrit Wehrenberg
- Centre for Wildlife Genetics, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystraße 12, 63571, Gelnhausen, Germany.
- Department of Ecology and Evolution, Biologicum, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany.
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 8000, 90014, Oulu, Finland.
| | | | - Berardino Cocchiararo
- Centre for Wildlife Genetics, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystraße 12, 63571, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Carsten Nowak
- Centre for Wildlife Genetics, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystraße 12, 63571, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
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2
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Lewis MA, Schulte J, Matthews L, Vaden KI, Steves CJ, Williams FMK, Schulte BA, Dubno JR, Steel KP. Accurate phenotypic classification and exome sequencing allow identification of novel genes and variants associated with adult-onset hearing loss. PLoS Genet 2023; 19:e1011058. [PMID: 38011198 PMCID: PMC10718637 DOI: 10.1371/journal.pgen.1011058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 12/13/2023] [Accepted: 11/07/2023] [Indexed: 11/29/2023] Open
Abstract
Adult-onset progressive hearing loss is a common, complex disease with a strong genetic component. Although to date over 150 genes have been identified as contributing to human hearing loss, many more remain to be discovered, as does most of the underlying genetic diversity. Many different variants have been found to underlie adult-onset hearing loss, but they tend to be rare variants with a high impact upon the gene product. It is likely that combinations of more common, lower impact variants also play a role in the prevalence of the disease. Here we present our exome study of hearing loss in a cohort of 532 older adult volunteers with extensive phenotypic data, including 99 older adults with normal hearing, an important control set. Firstly, we carried out an outlier analysis to identify genes with a high variant load in older adults with hearing loss compared to those with normal hearing. Secondly, we used audiometric threshold data to identify individual variants which appear to contribute to different threshold values. We followed up these analyses in a second cohort. Using these approaches, we identified genes and variants linked to better hearing as well as those linked to worse hearing. These analyses identified some known deafness genes, demonstrating proof of principle of our approach. However, most of the candidate genes are novel associations with hearing loss. While the results support the suggestion that genes responsible for severe deafness may also be involved in milder hearing loss, they also suggest that there are many more genes involved in hearing which remain to be identified. Our candidate gene lists may provide useful starting points for improved diagnosis and drug development.
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Affiliation(s)
- Morag A. Lewis
- Wolfson Centre for Age-Related Diseases, King’s College London, United Kingdom
- The Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Jennifer Schulte
- The Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Lois Matthews
- The Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Kenneth I. Vaden
- The Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Claire J. Steves
- Department of Twin Research and Genetic Epidemiology, King’s College London, School of Life Course and Population Sciences, London, United Kingdom
| | - Frances M. K. Williams
- Department of Twin Research and Genetic Epidemiology, King’s College London, School of Life Course and Population Sciences, London, United Kingdom
| | - Bradley A. Schulte
- The Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Judy R. Dubno
- The Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Karen P. Steel
- Wolfson Centre for Age-Related Diseases, King’s College London, United Kingdom
- The Medical University of South Carolina, Charleston, South Carolina, United States of America
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3
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Rubio-Palis Y, Dzuris N, Sandi C, Vizcaino-Cabarrus RL, Corredor-Medina C, González JA, Lenhart AE. Insecticide resistance levels and associated mechanisms in three Aedes aegypti populations from Venezuela. Mem Inst Oswaldo Cruz 2023; 118:e220210. [PMID: 37377253 DOI: 10.1590/0074-02760220210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 05/18/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND The massive use of insecticides in public health has exerted selective pressure resulting in the development of resistance in Aedes aegypti to different insecticides in Venezuela. Between 2010 and 2020, the only insecticides available for vector control were the organophosphates (Ops) fenitrothion and temephos which were focally applied. OBJECTIVES To determine the state of insecticide resistance and to identify the possible biochemical and molecular mechanisms involved in three populations of Ae. aegypti from Venezuela. METHODS CDC bottle bioassays were conducted on Ae. aegypti collected between October 2019 and February 2020 in two hyperendemic localities for dengue in Aragua State and in a malaria endemic area in Bolívar State. Insecticide resistance mechanisms were studied using biochemical assays and polymerase chain reaction (PCR) to detect kdr mutations. FINDINGS Bioassays showed contrasting results among populations; Las Brisas was resistant to malathion, permethrin and deltamethrin, Urbanización 19 de Abril was resistant to permethrin and Nacupay to malathion. All populations showed significantly higher activity of mixed function oxidases and glutathione-S-transferases (GSTs) in comparison with the susceptible strain. The kdr mutations V410L, F1534C, and V1016I were detected in all populations, with F1534C at higher frequencies. MAIN CONCLUSION Insecticide resistance persists in three Ae. aegypti populations from Venezuela even in the relative absence of insecticide application.
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Affiliation(s)
- Yasmin Rubio-Palis
- Universidad de Carabobo, Instituto de Investigaciones Biomédicas, Maracay, Venezuela
| | - Nicole Dzuris
- US Centers for Disease Control and Prevention, Center for Global Health, Division of Parasitic Diseases and Malaria, Entomology Branch, Atlanta, GA, USA
| | - Christopher Sandi
- US Centers for Disease Control and Prevention, Center for Global Health, Division of Parasitic Diseases and Malaria, Entomology Branch, Atlanta, GA, USA
| | - Rita Lucrecia Vizcaino-Cabarrus
- US Centers for Disease Control and Prevention, Center for Global Health, Division of Parasitic Diseases and Malaria, Entomology Branch, Atlanta, GA, USA
| | - Claudia Corredor-Medina
- US Centers for Disease Control and Prevention, Center for Global Health, Division of Parasitic Diseases and Malaria, Entomology Branch, Atlanta, GA, USA
| | - Jesús Alberto González
- Ministerio del Poder Popular para la Salud, Dirección General de Salud Ambiental, Dirección de Control de Vectores, Maracay, Venezuela
| | - Audrey E Lenhart
- US Centers for Disease Control and Prevention, Center for Global Health, Division of Parasitic Diseases and Malaria, Entomology Branch, Atlanta, GA, USA
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4
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Atsawawaranunt K, Ewart KM, Major RE, Johnson RN, Santure AW, Whibley A. Tracing the introduction of the invasive common myna using population genomics. Heredity (Edinb) 2023:10.1038/s41437-023-00621-w. [PMID: 37193854 DOI: 10.1038/s41437-023-00621-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 04/30/2023] [Accepted: 04/30/2023] [Indexed: 05/18/2023] Open
Abstract
The common myna (Acridotheres tristis) is one of the most invasive bird species in the world, yet its colonisation history is only partly understood. We identified the introduction history and population structure, and quantified the genetic diversity of myna populations from the native range in India and introduced populations in New Zealand, Australia, Fiji, Hawaii, and South Africa, based on thousands of single nucleotide polymorphism markers in 814 individuals. We were able to identify the source population of mynas in several invasive locations: mynas from Fiji and Melbourne, Australia, were likely founded by individuals from a subpopulation in Maharashtra, India, while mynas in Hawaii and South Africa were likely independently founded by individuals from other localities in India. Our findings suggest that New Zealand mynas were founded by individuals from Melbourne, which, in turn, were founded by individuals from Maharashtra. We identified two genetic clusters among New Zealand mynas, divided by New Zealand's North Island's axial mountain ranges, confirming previous observations that mountains and thick forests may form barriers to myna dispersal. Our study provides a foundation for other population and invasion genomic studies and provides useful information for the management of this invasive species.
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Affiliation(s)
| | - Kyle M Ewart
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Richard E Major
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Rebecca N Johnson
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
- National Museum of Natural History, Smithsonian Institution, Washington D.C., DC, USA
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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5
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Lewis MA, Schulte J, Matthews L, Vaden KI, Steves CJ, Williams FMK, Schulte BA, Dubno JR, Steel KP. Accurate phenotypic classification and exome sequencing allow identification of novel genes and variants associated with adult-onset hearing loss. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.27.23289040. [PMID: 37163093 PMCID: PMC10168485 DOI: 10.1101/2023.04.27.23289040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Adult-onset progressive hearing loss is a common, complex disease with a strong genetic component. Although to date over 150 genes have been identified as contributing to human hearing loss, many more remain to be discovered, as does most of the underlying genetic diversity. Many different variants have been found to underlie adult-onset hearing loss, but they tend to be rare variants with a high impact upon the gene product. It is likely that combinations of more common, lower impact variants also play a role in the prevalence of the disease. Here we present our exome study of hearing loss in a cohort of 532 older adult volunteers with extensive phenotypic data, including 99 older adults with normal hearing, an important control set. Firstly, we carried out an outlier analysis to identify genes with a high variant load in older adults with hearing loss compared to those with normal hearing. Secondly, we used audiometric threshold data to identify individual variants which appear to contribute to different threshold values. We followed up these analyses in a second cohort. Using these approaches, we identified genes and variants linked to better hearing as well as those linked to worse hearing. These analyses identified some known deafness genes, demonstrating proof of principle of our approach. However, most of the candidate genes are novel associations with hearing loss. While the results support the suggestion that genes responsible for severe deafness may also be involved in milder hearing loss, they also suggest that there are many more genes involved in hearing which remain to be identified. Our candidate gene lists may provide useful starting points for improved diagnosis and drug development.
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Affiliation(s)
- Morag A Lewis
- Wolfson Centre for Age-Related Diseases, King's College London, SE1 1UL, UK
- The Medical University of South Carolina, SC, USA
| | | | | | | | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, School of Life Course and Population Sciences, London, UK
| | - Frances M K Williams
- Department of Twin Research and Genetic Epidemiology, King's College London, School of Life Course and Population Sciences, London, UK
| | | | - Judy R Dubno
- The Medical University of South Carolina, SC, USA
| | - Karen P Steel
- Wolfson Centre for Age-Related Diseases, King's College London, SE1 1UL, UK
- The Medical University of South Carolina, SC, USA
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6
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Sangbakembi-Ngounou C, Ngoagouni C, Akone-Ella O, Kengne P, Costantini C, Nakouné E, Ayala D. Temporal and biting dynamics of the chromosomal inversion 2La in the malaria vectors Anopheles gambiae and Anopheles coluzzii in Bangui, Central African Republic. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.986925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The chromosomal rearrangement 2La has been directly involved in the ecological and deadly epidemiological success of the malaria mosquitoes Anopheles gambiae and Anopheles coluzzii in sub-Saharan Africa. However, little is known about the biological and ecological factors that drive the local and temporal dynamics of this inversion in both species. Here, we performed a year-round longitudinal survey in Bangui, Central African Republic. We monthly sampled A. gambiae and A. coluzzii mosquitoes indoor and outdoor using human landing catches (HLC) for 48 h non-stop. We molecularly karyotyped all specimens to study the 2La inversion frequency variations, and monitored the mosquito spatial and temporal biting behavior throughout the year. In total, we successfully karyotyped 5121 A. gambiae and 986 A. coluzzii specimens. The 2La inversion frequency was higher in A. coluzzii than in A. gambiae across the year. In A. gambiae and A. coluzzii, the inversion frequency or karyotypes did not influence the biting behavior, either location or time. Moreover, the inversion frequency variation in both species was also independent of local climatic changes. Overall, our results revealed that in Bangui, the 2La inversion segregates at different frequency in each species, but this is not influenced by their trophic behavior. Studying the impact of urban settings and the population genetic structure of these two A. gambiae complex members could bring insights into the intrinsic relationship between 2La inversion and local conditions. More studies are needed to understand the polymorphic equilibrium of this inversion in Bangui.
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7
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Genomic basis of insularity and ecological divergence in barn owls (Tyto alba) of the Canary Islands. Heredity (Edinb) 2022; 129:281-294. [PMID: 36175501 PMCID: PMC9613907 DOI: 10.1038/s41437-022-00562-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 11/14/2022] Open
Abstract
Islands, and the particular organisms that populate them, have long fascinated biologists. Due to their isolation, islands offer unique opportunities to study the effect of neutral and adaptive mechanisms in determining genomic and phenotypical divergence. In the Canary Islands, an archipelago rich in endemics, the barn owl (Tyto alba), present in all the islands, is thought to have diverged into a subspecies (T. a. gracilirostris) on the eastern ones, Fuerteventura and Lanzarote. Taking advantage of 40 whole-genomes and modern population genomics tools, we provide the first look at the origin and genetic makeup of barn owls of this archipelago. We show that the Canaries hold diverse, long-standing and monophyletic populations with a neat distinction of gene pools from the different islands. Using a new method, less sensitive to structure than classical FST, to detect regions involved in local adaptation to insular environments, we identified a haplotype-like region likely under selection in all Canaries individuals and genes in this region suggest morphological adaptations to insularity. In the eastern islands, where the subspecies is present, genomic traces of selection pinpoint signs of adapted body proportions and blood pressure, consistent with the smaller size of this population living in a hot arid climate. In turn, genomic regions under selection in the western barn owls from Tenerife showed an enrichment in genes linked to hypoxia, a potential response to inhabiting a small island with a marked altitudinal gradient. Our results illustrate the interplay of neutral and adaptive forces in shaping divergence and early onset speciation.
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8
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Zarza-Rebollo JA, Molina E, López-Isac E, Pérez-Gutiérrez AM, Gutiérrez B, Cervilla JA, Rivera M. Interaction Effect between Physical Activity and the BDNF Val66Met Polymorphism on Depression in Women from the PISMA-ep Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19042068. [PMID: 35206257 PMCID: PMC8872527 DOI: 10.3390/ijerph19042068] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/03/2022] [Accepted: 02/09/2022] [Indexed: 02/05/2023]
Abstract
The relationship between depression and the Val66Met polymorphism at the brain-derived neurotrophic factor gene (BDNF), has been largely studied. It has also been related to physical activity, although the results remain inconclusive. The aim of this study is to investigate the relationship between this polymorphism, depression and physical activity in a thoroughly characterised sample of community-based individuals from the PISMA-ep study. A total of 3123 participants from the PISMA-ep study were genotyped for the BDNF Val66Met polymorphism, of which 209 had depression. Our results are in line with previous studies reporting a protective effect of physical activity on depression, specifically in light intensity. Interestingly, we report a gene-environment interaction effect in which Met allele carriers of the BDNF Val66Met polymorphism who reported more hours of physical activity showed a decreased prevalence of depression. This effect was observed in the total sample (OR = 0.95, 95%CI = 0.90–0.99, p = 0.027) and was strengthened in women (OR = 0.93, 95%CI = 0.87–0.98, p = 0.019). These results highlight the potential role of physical activity as a promising therapeutic strategy for preventing and adjuvant treatment of depression and suggest molecular and genetic particularities of depression between sexes.
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Affiliation(s)
- Juan Antonio Zarza-Rebollo
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (J.A.Z.-R.); (E.L.-I.); (A.M.P.-G.); (M.R.)
- Institute of Neurosciences, Biomedical Research Centre, University of Granada, 18016 Granada, Spain; (B.G.); (J.A.C.)
| | - Esther Molina
- Institute of Neurosciences, Biomedical Research Centre, University of Granada, 18016 Granada, Spain; (B.G.); (J.A.C.)
- Department of Nursing, Faculty of Health Sciences, University of Granada, 18071 Granada, Spain
- Correspondence:
| | - Elena López-Isac
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (J.A.Z.-R.); (E.L.-I.); (A.M.P.-G.); (M.R.)
- Institute of Neurosciences, Biomedical Research Centre, University of Granada, 18016 Granada, Spain; (B.G.); (J.A.C.)
| | - Ana M. Pérez-Gutiérrez
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (J.A.Z.-R.); (E.L.-I.); (A.M.P.-G.); (M.R.)
- Institute of Neurosciences, Biomedical Research Centre, University of Granada, 18016 Granada, Spain; (B.G.); (J.A.C.)
| | - Blanca Gutiérrez
- Institute of Neurosciences, Biomedical Research Centre, University of Granada, 18016 Granada, Spain; (B.G.); (J.A.C.)
- Department of Psychiatry, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Jorge A. Cervilla
- Institute of Neurosciences, Biomedical Research Centre, University of Granada, 18016 Granada, Spain; (B.G.); (J.A.C.)
- Department of Psychiatry, Faculty of Medicine, University of Granada, 18016 Granada, Spain
- Mental Health Service, University Hospital San Cecilio, 18016 Granada, Spain
| | - Margarita Rivera
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (J.A.Z.-R.); (E.L.-I.); (A.M.P.-G.); (M.R.)
- Institute of Neurosciences, Biomedical Research Centre, University of Granada, 18016 Granada, Spain; (B.G.); (J.A.C.)
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9
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Cumer T, Machado AP, Dumont G, Bontzorlos V, Ceccherelli R, Charter M, Dichmann K, Kassinis N, Lourenço R, Manzia F, Martens HD, Prévost L, Rakovic M, Roque I, Siverio F, Roulin A, Goudet J. Landscape and climatic variations shaped secondary contacts amid barn owls of the Western Palearctic. Mol Biol Evol 2021; 39:6454100. [PMID: 34893883 PMCID: PMC8789042 DOI: 10.1093/molbev/msab343] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The combined actions of climatic variations and landscape barriers shape the history of natural populations. When organisms follow their shifting niches, obstacles in the landscape can lead to the splitting of populations, on which evolution will then act independently. When two such populations are reunited, secondary contact occurs in a broad range of admixture patterns, from narrow hybrid zones to the complete dissolution of lineages. A previous study suggested that barn owls colonized the Western Palearctic after the last glaciation in a ring-like fashion around the Mediterranean Sea, and conjectured an admixture zone in the Balkans. Here, we take advantage of whole-genome sequences of 94 individuals across the Western Palearctic to reveal the complex history of the species in the region using observational and modeling approaches. Even though our results confirm that two distinct lineages colonized the region, one in Europe and one in the Levant, they suggest that it predates the last glaciation and identify a secondary contact zone between the two in Anatolia. We also show that barn owls recolonized Europe after the glaciation from two distinct glacial refugia: a previously identified western one in Iberia and a new eastern one in Italy. Both glacial lineages now communicate via eastern Europe, in a wide and permeable contact zone. This complex history of populations enlightens the taxonomy of Tyto alba in the region, highlights the key role played by mountain ranges and large water bodies as barriers and illustrates the power of population genomics in uncovering intricate demographic patterns.
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Affiliation(s)
- Tristan Cumer
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Ana Paula Machado
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Guillaume Dumont
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Vasileios Bontzorlos
- Green Fund, Kifisia, Athens, Greece.,"TYTO" - Organization for the Management and Conservation of Biodiversity in Agricultural Ecosystems, Larisa, Greece
| | | | - Motti Charter
- Shamir Research Institute, University of Haifa, Katzrin, Israel.,Department of Geography and Environmental Sciences, University of Haifa, Haifa, Israel
| | | | | | - Rui Lourenço
- MED Mediterranean Institute for Agriculture, Environment and Development, Laboratory of Ornithology, IIFA, University of Évora, Évora, Portugal
| | | | | | - Laure Prévost
- Association C.H.E.N.E, Centre d'Hébergement et d'Etude sur la Nature et l'Environnement, Allouville-Bellefosse, 76190, France
| | - Marko Rakovic
- Natural History Museum of Belgrade, Belgrade, Serbia
| | - Inês Roque
- MED Mediterranean Institute for Agriculture, Environment and Development, Laboratory of Ornithology, IIFA, University of Évora, Évora, Portugal
| | - Felipe Siverio
- Canary Islands' Ornithology and Natural History Group (GOHNIC), 38480 Buenavista del Norte, Tenerife, Canary Islands, Spain
| | - Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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10
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Alonso L, Piron A, Morán I, Guindo-Martínez M, Bonàs-Guarch S, Atla G, Miguel-Escalada I, Royo R, Puiggròs M, Garcia-Hurtado X, Suleiman M, Marselli L, Esguerra JLS, Turatsinze JV, Torres JM, Nylander V, Chen J, Eliasson L, Defrance M, Amela R, Mulder H, Gloyn AL, Groop L, Marchetti P, Eizirik DL, Ferrer J, Mercader JM, Cnop M, Torrents D. TIGER: The gene expression regulatory variation landscape of human pancreatic islets. Cell Rep 2021; 37:109807. [PMID: 34644572 PMCID: PMC8864863 DOI: 10.1016/j.celrep.2021.109807] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/23/2021] [Accepted: 09/16/2021] [Indexed: 12/30/2022] Open
Abstract
Genome-wide association studies (GWASs) identified hundreds of signals associated with type 2 diabetes (T2D). To gain insight into their underlying molecular mechanisms, we have created the translational human pancreatic islet genotype tissue-expression resource (TIGER), aggregating >500 human islet genomic datasets from five cohorts in the Horizon 2020 consortium T2DSystems. We impute genotypes using four reference panels and meta-analyze cohorts to improve the coverage of expression quantitative trait loci (eQTL) and develop a method to combine allele-specific expression across samples (cASE). We identify >1 million islet eQTLs, 53 of which colocalize with T2D signals. Among them, a low-frequency allele that reduces T2D risk by half increases CCND2 expression. We identify eight cASE colocalizations, among which we found a T2D-associated SLC30A8 variant. We make all data available through the TIGER portal (http://tiger.bsc.es), which represents a comprehensive human islet genomic data resource to elucidate how genetic variation affects islet function and translates into therapeutic insight and precision medicine for T2D.
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Affiliation(s)
- Lorena Alonso
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Anthony Piron
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels 1070, Belgium; Interuniversity Institute of Bioinformatics in Brussels (IB2), Brussels 1050, Belgium
| | - Ignasi Morán
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Marta Guindo-Martínez
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Sílvia Bonàs-Guarch
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM) Barcelona 08013, Spain
| | - Goutham Atla
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM) Barcelona 08013, Spain
| | - Irene Miguel-Escalada
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM) Barcelona 08013, Spain
| | - Romina Royo
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Montserrat Puiggròs
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Xavier Garcia-Hurtado
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM) Barcelona 08013, Spain
| | - Mara Suleiman
- Department of Clinical and Experimental Medicine and AOUP Cisanello University Hospital, University of Pisa, Pisa 56126, Italy
| | - Lorella Marselli
- Department of Clinical and Experimental Medicine and AOUP Cisanello University Hospital, University of Pisa, Pisa 56126, Italy
| | - Jonathan L S Esguerra
- Unit of Islet Cell Exocytosis, Lund University Diabetes Centre, Malmö 214 28, Sweden
| | | | - Jason M Torres
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | - Vibe Nylander
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7LE, UK
| | - Ji Chen
- Exeter Centre of Excellence for Diabetes Research (EXCEED), University of Exeter Medical School, Exeter EX4 4PY, UK
| | - Lena Eliasson
- Unit of Islet Cell Exocytosis, Lund University Diabetes Centre, Malmö 214 28, Sweden
| | - Matthieu Defrance
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels 1070, Belgium
| | - Ramon Amela
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Hindrik Mulder
- Unit of Molecular Metabolism, Lund University Diabetes Centre, Malmö 214 28, Sweden
| | - Anna L Gloyn
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK; Oxford Centre for Diabetes, Endocrinology, and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7LE, UK; Division of Endocrinology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA; NIHR Oxford Biomedical Research Centre, Churchill Hospital, Oxford OX3 7DQ, UK; Stanford Diabetes Research Centre, Stanford University, Stanford, CA 94305, USA
| | - Leif Groop
- Unit of Islet Cell Exocytosis, Lund University Diabetes Centre, Malmö 214 28, Sweden; Unit of Molecular Metabolism, Lund University Diabetes Centre, Malmö 214 28, Sweden; Finnish Institute of Molecular Medicine Finland (FIMM), Helsinki University, Helsinki 00014, Finland
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine and AOUP Cisanello University Hospital, University of Pisa, Pisa 56126, Italy
| | - Decio L Eizirik
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels 1070, Belgium; WELBIO, Université Libre de Bruxelles, Brussels 1050, Belgium
| | - Jorge Ferrer
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM) Barcelona 08013, Spain; Section of Epigenomics and Disease, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Josep M Mercader
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain; Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Miriam Cnop
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels 1070, Belgium; Division of Endocrinology, Erasmus Hospital, Université Libre de Bruxelles, Brussels 1070, Belgium.
| | - David Torrents
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain.
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11
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Lin KP, Chaw SM, Lo YH, Kinjo T, Tung CY, Cheng HC, Liu Q, Satta Y, Izawa M, Chen SF, Ko WY. Genetic Differentiation and Demographic Trajectory of the Insular Formosan and Orii's Flying Foxes. J Hered 2021; 112:192-203. [PMID: 33675222 PMCID: PMC8006818 DOI: 10.1093/jhered/esab007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/24/2021] [Indexed: 12/04/2022] Open
Abstract
Insular flying foxes are keystone species in island ecosystems due to their critical roles in plant pollination and seed dispersal. These species are vulnerable to population decline because of their small populations and low reproductive rates. The Formosan flying fox (Pteropus dasymallus formosus) is one of the 5 subspecies of the Ryukyu flying fox. Pteropus dasymallus formosus has suffered from a severe decline and is currently recognized as a critically endangered population in Taiwan. On the contrary, the Orii's flying fox (Pteropus dasymallus inopinatus) is a relatively stable population inhabiting Okinawa Island. Here, we applied a genomic approach called double digest restriction-site associated DNA sequencing to study these 2 subspecies for a total of 7 individuals. We detected significant genetic structure between the 2 populations. Despite their contrasting contemporary population sizes, both populations harbor very low degrees of genetic diversity. We further inferred their demographic history based on the joint folded site frequency spectrum and revealed that both P. d. formosus and P. d. inopinatus had maintained small population sizes for a long period of time after their divergence. Recently, these populations experienced distinct trajectories of demographic changes. While P. d. formosus suffered from a drastic ~10-fold population decline not long ago, P. d. inopinatus underwent a ~4.5-fold population expansion. Our results suggest separate conservation management for the 2 populations-population recovery is urgently needed for P. d. formosus while long-term monitoring for adverse genetic effects should be considered for P. d. inopinatus.
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Affiliation(s)
- Kung-Ping Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yun-Hwa Lo
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | | | - Chien-Yi Tung
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | | | - Quintin Liu
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Masako Izawa
- Kitakyushu Museum of Natural History and Human History, Fukuoka, Japan
| | - Shiang-Fan Chen
- Center for General Education, National Taipei University, New Taipei City, Taiwan
| | - Wen-Ya Ko
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
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12
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Black MH, Li S, LaDuca H, Lo M, Chen J, Hoiness R, Gutierrez S, Tippin‐Davis B, Lu H, Gielzak M, Wiley K, Shi Z, Wei J, Zheng SL, Helfand BT, Isaacs W, Xu J. Validation of a prostate cancer polygenic risk score. Prostate 2020; 80:1314-1321. [PMID: 33258481 PMCID: PMC7590110 DOI: 10.1002/pros.24058] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 07/31/2020] [Indexed: 12/25/2022]
Abstract
BACKGROUND Genome-wide association studies have identified over 100 single-nucleotide polymorphisms (SNPs) associated with prostate cancer (PrCa), and polygenic risk scores (PRS) based on their combined genotypes have been developed for risk stratification. We aimed to assess the contribution of PRS to PrCa risk in a large multisite study. METHODS The sample included 1972 PrCa cases and 1919 unaffected controls. Next-generation sequencing was used to assess pathogenic variants in 14 PrCa-susceptibility genes and 72 validated PrCa-associated SNPs. We constructed a population-standardized PRS and tested its association with PrCa using logistic regression adjusted for age and family history of PrCa. RESULTS The mean age of PrCa cases at diagnosis and age of controls at testing/last clinic visit was 59.5 ± 7.2 and 57.2 ± 13.0 years, respectively. Among 1740 cases with pathology data, 57.4% had Gleason score ≤ 6, while 42.6% had Gleason score ≥ 8. In addition, 39.6% cases and 20.1% controls had a family history of PrCa. The PRS was significantly higher in cases than controls (mean ± SD: 1.42 ± 1.11 vs 1.02 ± 0.76; P < .0001). Compared with men in the 1st quartile of age-adjusted PRS, those in the 2nd, 3rd, and 4th quartile were 1.58 (95% confidence interval [CI]: 1.31-1.90), 2.36 (95% CI: 1.96-2.84), and 3.98 (95% CI: 3.29-4.82) times as likely to have PrCa (all P < .0001). Adjustment for family history yielded similar results. PRS predictive performance was consistent with prior literature (area under the receiver operating curve = 0.64; 95% CI: 0.62-0.66). CONCLUSIONS These data suggest that a 72-SNP PRS is predictive of PrCa, supporting its potential use in clinical risk assessment.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Marta Gielzak
- Department of Urology, The James Buchanan Brady Urologic InstituteJohns Hopkins University School of MedicineBaltimoreMaryland
| | - Kathleen Wiley
- Department of Urology, The James Buchanan Brady Urologic InstituteJohns Hopkins University School of MedicineBaltimoreMaryland
| | - Zhuqing Shi
- Program for Personalized Cancer CareNorthShore University Health SystemEvanstonIllinois
| | - Jun Wei
- Program for Personalized Cancer CareNorthShore University Health SystemEvanstonIllinois
| | - Siqun Lilly Zheng
- Program for Personalized Cancer CareNorthShore University Health SystemEvanstonIllinois
| | - Brian T. Helfand
- Program for Personalized Cancer CareNorthShore University Health SystemEvanstonIllinois
| | - William Isaacs
- Department of Urology, The James Buchanan Brady Urologic InstituteJohns Hopkins University School of MedicineBaltimoreMaryland
| | - Jianfeng Xu
- Program for Personalized Cancer CareNorthShore University Health SystemEvanstonIllinois
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13
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Powell JH, Campbell MR. Contemporary genetic structure affects genetic stock identification of steelhead trout in the Snake River basin. Ecol Evol 2020; 10:10520-10531. [PMID: 33072277 PMCID: PMC7548200 DOI: 10.1002/ece3.6708] [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: 06/02/2020] [Revised: 07/28/2020] [Accepted: 07/30/2020] [Indexed: 11/09/2022] Open
Abstract
Genetic stock identification is a widely applied tool for the mixed‐stock management of salmonid species throughout the North Pacific Rim. The effectiveness of genetic stock identification is dependent on the level of differentiation among stocks which is often high due to the life history of these species that involves high homing fidelity to their natal streams. However, the utility of this tool can be reduced when natural genetic structuring has been altered by hatchery translocation and/or supplementation. We examined the genetic population structure of ESA‐listed steelhead in the Snake River basin of the United States. We analyzed 9,613 natural‐origin adult steelhead returning to Passive Integrated Transponder detection sites throughout the basin from 2010 through 2017. Individuals were genotyped at 180 single nucleotide polymorphic genetic markers and grouped into 20 populations based on their return location. While we expected to observe a common pattern of hierarchical genetic structuring due to isolation by distance, we observed low genetic differentiation between populations in the upper Salmon River basin compared to geographically distant populations in the lower Snake River basin. These results were consistent with lower genetic stock assignment probabilities observed for populations in this upper basin. We attribute these patterns of reduced genetic structure to the translocation of lower basin steelhead stocks and ongoing hatchery programs in the upper Salmon River basin. We discuss the implications of these findings on the utility of genetic stock identification in the basin and discuss opportunities for increasing assignment probabilities in the face of low genetic structure.
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14
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Chen L, Li D, Shao Y, Adni J, Wang H, Liu Y, Zhang Y. Comparative Analysis of Soil Microbiome Profiles in the Companion Planting of White Clover and Orchard Grass Using 16S rRNA Gene Sequencing Data. FRONTIERS IN PLANT SCIENCE 2020; 11:538311. [PMID: 33042174 PMCID: PMC7530175 DOI: 10.3389/fpls.2020.538311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
Companion planting is one of the most common and effective planting methods in modern agriculture. White clover (Trifolium repens L.) and orchard grass (Dactylis glomerata L.) are two typical pastures planted together to promote each other's growth. However, the detailed biological foundations of companion planting remain unclear. In this study, we screened typical microbiome profiles under separate and combination planting conditions using 16s RNA gene sequencing techniques. We identified the typical distinctive microorganism subtypes based on the microbiome profiles and recognized the enriched functions of top abundant microorganisms in soil using different planting strategies with the help of Kyoto Encyclopedia of Genes and Genomes and Clusters of Orthologous Groups annotation. This analysis confirmed that the optimal microorganisms and screened functional annotations are correlated with nitrogen fixation; thus, companion planting may improve the yield and efficacy of plants by improving the efficiency of nitrogen fixation.
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Affiliation(s)
- Lijuan Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Daojie Li
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Ye Shao
- School of Medicine, Huaqiao University, Quanzhou, China
| | - Jannati Adni
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Hui Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yuqing Liu
- School of Resources and Environment, Anhui Agricultural University, Hefei, China
| | - Yunhua Zhang
- School of Resources and Environment, Anhui Agricultural University, Hefei, China
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15
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Saito T, Shinozaki G, Koga M, Tanichi M, Takeshita S, Nakagawa R, Nagamine M, Cho HR, Morimoto Y, Kobayashi Y, Yoshino A, Toda H. Effect of interaction between a specific subtype of child abuse and the FKBP5 rs1360780 SNP on DNA methylation among patients with bipolar disorder. J Affect Disord 2020; 272:417-422. [PMID: 32553385 DOI: 10.1016/j.jad.2020.03.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/05/2020] [Accepted: 03/29/2020] [Indexed: 01/10/2023]
Abstract
BACKGROUND Child abuse is a risk factor for mood disorders, and linked to decreased DNA methylation (DNAm) of FKBP5 intron 7 through interactions with the single nucleotide polymorphism (SNP) rs1360780. However, no study has investigated which specific subtypes of child abuse are related to decreased DNAm of FKBP5 intron 7 in mood disorders. We therefore aimed to examine the relationship among various subtypes of child abuse, rs1360780, and the DNAm level of FKBP5 intron 7. METHODS A total of 190 subjects (87 patients with major depressive disorder [MDD], 61 patients with bipolar disorder [BD], and 42 healthy controls) participated. The Child Abuse and Trauma Scale (CATS) was used to evaluate child abuse. Whole blood was processed for genotyping, and pyrosequencing was conducted to assess the DNAm level of FKBP5 intron 7. A multiple regression analysis was used to analyze the DNAm level as a dependent variable, and the CATS subtypes and rs1360780 were used as independent variables. RESULTS Emotional abuse/neglect, one of the specific subtypes of child abuse, was related to lower DNAm of FKBP5 intron 7 interacting with rs1360780 in the BD patients. There were no significant results in the MDD patients or the controls. LIMITATIONS Since the study was limited to Japanese individuals, particularly those with MDD and BD, the findings are not generalizable. Furthermore, as child abuse was measured retrospectively, there may be recall bias. CONCLUSIONS This finding indicates that a specific subtype of child abuse may play an important role in the development of BD.
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Affiliation(s)
- Taku Saito
- Department of Psychiatry, School of Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan; Department of Psychiatry, University of Iowa, Iowa City, Iowa, USA
| | - Gen Shinozaki
- Department of Psychiatry, University of Iowa, Iowa City, Iowa, USA; Department of Neurosurgery, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA; Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, USA; Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, Iowa, USA
| | - Minori Koga
- Department of Psychiatry, School of Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan
| | - Masaaki Tanichi
- Department of Psychiatry, School of Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan
| | - Shogo Takeshita
- Department of Psychiatry, School of Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan
| | - Ryuichi Nakagawa
- Department of Psychiatry, School of Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan
| | - Masanori Nagamine
- Division of Behavioral Science, National Defense Medical College Research Institute, Tokorozawa, Saitama, Japan
| | - Hyunkeun R Cho
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, Iowa, USA
| | - Yuji Morimoto
- Department of Physiology, School of Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan
| | - Yasushi Kobayashi
- Department of Anatomy and Neurobiology, School of Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan
| | - Aihide Yoshino
- Department of Psychiatry, School of Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan
| | - Hiroyuki Toda
- Department of Psychiatry, School of Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan.
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16
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Hague MTJ, Stokes AN, Feldman CR, Brodie ED, Brodie ED. The geographic mosaic of arms race coevolution is closely matched to prey population structure. Evol Lett 2020; 4:317-332. [PMID: 32774881 PMCID: PMC7403720 DOI: 10.1002/evl3.184] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 05/11/2020] [Accepted: 05/22/2020] [Indexed: 01/09/2023] Open
Abstract
Reciprocal adaptation is the hallmark of arms race coevolution. Local coadaptation between natural enemies should generate a geographic mosaic pattern where both species have roughly matched abilities across their shared range. However, mosaic variation in ecologically relevant traits can also arise from processes unrelated to reciprocal selection, such as population structure or local environmental conditions. We tested whether these alternative processes can account for trait variation in the geographic mosaic of arms race coevolution between resistant garter snakes (Thamnophis sirtalis) and toxic newts (Taricha granulosa). We found that predator resistance and prey toxin levels are functionally matched in co-occurring populations, suggesting that mosaic variation in the armaments of both species results from the local pressures of reciprocal selection. By the same token, phenotypic and genetic variation in snake resistance deviates from neutral expectations of population genetic differentiation, showing a clear signature of adaptation to local toxin levels in newts. Contrastingly, newt toxin levels are best predicted by genetic differentiation among newt populations, and to a lesser extent, by the local environment and snake resistance. Exaggerated armaments suggest that coevolution occurs in certain hotspots, but prey population structure seems to be of particular influence on local phenotypic variation in both species throughout the geographic mosaic. Our results imply that processes other than reciprocal selection, like historical biogeography and environmental pressures, represent an important source of variation in the geographic mosaic of coevolution. Such a pattern supports the role of "trait remixing" in the geographic mosaic theory, the process by which non-adaptive forces dictate spatial variation in the interactions among species.
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Affiliation(s)
- Michael T J Hague
- Division of Biological Sciences University of Montana Missoula Montana 59812.,Department of Biology University of Virginia Charlottesville Virginia 22904
| | - Amber N Stokes
- Department of Biology California State University Bakersfield California 93311
| | - Chris R Feldman
- Department of Biology University of Nevada Reno Nevada 89557
| | - Edmund D Brodie
- Department of Biology Utah State University Logan Utah 84322
| | - Edmund D Brodie
- Department of Biology University of Virginia Charlottesville Virginia 22904
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17
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Santos FAB, Lemes RB, Otto PA. HW_TEST, a program for comprehensive HARDY-WEINBERG equilibrium testing. Genet Mol Biol 2020; 43:e20190380. [PMID: 32422648 PMCID: PMC7323896 DOI: 10.1590/1678-4685-gmb-2019-0380] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/16/2020] [Indexed: 11/23/2022] Open
Abstract
This article deals with a Windows (© Microsoft Inc.) executable, user-friendly
program that tests the hypothesis of Hardy-Weinberg (HW) proportions from
autosomal multiallelic data using different methods that include parametric,
nonparametric and exact bootstrap tests, the latter obtained through computer
simulations. The program can be obtained free of charge directly from the
internet repository https://github.com/Lemes-RenanB/HardyWeinbergTesting.
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Affiliation(s)
- Fernando Azenha Bautzer Santos
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, Laboratório de Genética Humana, São Paulo, SP, Brazil
| | - Renan Barbosa Lemes
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, Laboratório de Genética Humana, São Paulo, SP, Brazil
| | - Paulo Alberto Otto
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, Laboratório de Genética Humana, São Paulo, SP, Brazil
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18
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Sex linkage of the skeletal muscle sodium channel gene (SCN4A) explains apparent deviations from Hardy-Weinberg equilibrium of tetrodotoxin-resistance alleles in garter snakes (Thamnophis sirtalis). Heredity (Edinb) 2020; 124:647-657. [PMID: 32111979 DOI: 10.1038/s41437-020-0300-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/13/2020] [Accepted: 02/13/2020] [Indexed: 01/01/2023] Open
Abstract
The arms race between tetrodotoxin-bearing Pacific newts (Taricha) and their garter snake predators (Thamnophis) in western North America has become a classic example of coevolution, shedding light on predator-prey dynamics, the molecular basis of adaptation, and patterns of convergent evolution. Newts are defended by tetrodotoxin (TTX), a neurotoxin that binds to voltage-gated sodium channels (Nav proteins), arresting electrical activity in nerves and muscles and paralyzing would-be predators. However, populations of the common garter snake (T. sirtalis) have overcome this defense, largely through polymorphism at the locus SCN4A, which renders the encoded protein (Nav1.4) less vulnerable to TTX. Previous work suggests that SCN4A commonly shows extreme deviations from Hardy-Weinberg equilibrium (HWE) in these populations, which has been interpreted as the result of intense selection imposed by newts. Here we show that much of this apparent deviation can be attributed to sex linkage of SCN4A. Using genomic data and quantitative PCR, we show that SCN4A is on the Z chromosome in Thamnophis and other advanced snakes. Taking Z-linkage into account, we find that most apparent deviations from HWE can be explained by female hemizygosity rather than low heterozygosity. Sex linkage can affect mutation rates, selection, and drift, and our results suggest that Z-linkage of SCN4A may make significant contributions to the overall dynamics of the coevolutionary arms race between newts and snakes.
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19
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Gaudillo J, Rodriguez JJR, Nazareno A, Baltazar LR, Vilela J, Bulalacao R, Domingo M, Albia J. Machine learning approach to single nucleotide polymorphism-based asthma prediction. PLoS One 2019; 14:e0225574. [PMID: 31800601 PMCID: PMC6892549 DOI: 10.1371/journal.pone.0225574] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 11/07/2019] [Indexed: 12/31/2022] Open
Abstract
Machine learning (ML) is poised as a transformational approach uniquely positioned to discover the hidden biological interactions for better prediction and diagnosis of complex diseases. In this work, we integrated ML-based models for feature selection and classification to quantify the risk of individual susceptibility to asthma using single nucleotide polymorphism (SNP). Random forest (RF) and recursive feature elimination (RFE) algorithm were implemented to identify the SNPs with high implication to asthma. K-nearest neighbor (kNN) and support vector machine (SVM) algorithms were trained to classify the identified SNPs whether associated with non-asthmatic or asthmatic samples. Feature selection step showed that RF outperformed RFE and the feature importance score derived from RF was consistently high for a subset of SNPs, indicating the robustness of RF in selecting relevant features associated with asthma. Model comparison showed that the integration of RF-SVM obtained the highest model performance with an accuracy, precision, and sensitivity of 62.5%, 65.3%, and 69%, respectively, when compared to the baseline, RF-kNN, and an external MeanDiff-kNN models. Furthermore, results show that the occurrence of asthma can be predicted with an Area under the Curve (AUC) of 0.62 and 0.64 for RF-SVM and RF-kNN models, respectively. This study demonstrates the integration of ML models to augment traditional methods in predicting genetic predisposition to multifactorial diseases such as asthma.
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Affiliation(s)
- Joverlyn Gaudillo
- Institute of Mathematical Sciences and Physics, University of the Philippines Los Baños, Philippines
- Computational Interdisciplinary Research Laboratories (CINTERLabs), University of the Philippines Los Baños, Philippines
| | - Jae Joseph Russell Rodriguez
- Genetics and Molecular Biology Division, Institute of Biological Sciences, University of the Philippines Los Baños, Philippines
| | - Allen Nazareno
- Institute of Mathematical Sciences and Physics, University of the Philippines Los Baños, Philippines
| | - Lei Rigi Baltazar
- Institute of Mathematical Sciences and Physics, University of the Philippines Los Baños, Philippines
- Computational Interdisciplinary Research Laboratories (CINTERLabs), University of the Philippines Los Baños, Philippines
| | - Julianne Vilela
- Philippine Genome Center Program for Agriculture, Office of the Vice Chancellor for Research and Extension, University of the Philippines Los Baños, Philippines
| | - Rommel Bulalacao
- Domingo Artificial Intelligence Research Center, Los Baños, Philippines
| | - Mario Domingo
- Domingo Artificial Intelligence Research Center, Los Baños, Philippines
| | - Jason Albia
- Institute of Mathematical Sciences and Physics, University of the Philippines Los Baños, Philippines
- Computational Interdisciplinary Research Laboratories (CINTERLabs), University of the Philippines Los Baños, Philippines
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20
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Abdel-Kahaar E, Winter S, Tremmel R, Schaeffeler E, Olbricht CJ, Wieland E, Schwab M, Shipkova M, Jaeger SU. The Impact of CYP3A4*22 on Tacrolimus Pharmacokinetics and Outcome in Clinical Practice at a Single Kidney Transplant Center. Front Genet 2019; 10:871. [PMID: 31616470 PMCID: PMC6775237 DOI: 10.3389/fgene.2019.00871] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/20/2019] [Indexed: 12/16/2022] Open
Abstract
Background: Although there is evidence that the CYP3A4*22 variant should be considered in tacrolimus dosing in renal transplantation, its impact beyond tacrolimus dose requirements remains controversial. Methods: In a cohort of 121 kidney transplant recipients, we analyzed the CYP3A4*1B, CYP3A4*22, and CYP3A5*3 alleles and the ABCB1 variants 1236C>T, 2677G>T/A, and 3435C>T for their impact on exposure and dose requirement. Relevant clinical outcome measures such as acute rejection within the first year after transplantation, delayed graft function, and renal function at discharge (estimated glomerular filtration rate) were evaluated. Results: Extensive metabolizer (n = 17, CYP3A4*1/*1 carriers with at least one CYP3A5*1 allele) showed significantly higher tacrolimus dose requirement (P = 0.004) compared with both intermediate metabolizer (IM, n = 93, CYP3A5*3/*3 plus CYP3A4*1/*1 or CYP3A4*22 carriers plus one CYP3A5*1 allele), and poor metabolizer (n = 11, CYP3A4*22 allele in combination with CYP3A5*3/*3) after onset of therapy. Significantly higher dose requirement was observed in CYP3A5 expressers (P = 0.046) compared with non-expressers again at onset of therapy. Using the log additive genetic model, the area under the curve for the total observation period up to 16 days was significantly associated with the CYP3A5*3 genotype (P = 3.34 × 10-4) as well as with the IM or extensive metabolizer phenotype (P = 1.54 × 10-4), even after adjustment for multiple testing. Heterozygous carriers for CYP3A4*22 showed significantly higher areas under the curve than the CYP3A4*1/*1 genotype in the second week post-transplantation (adjusted P = 0.016). Regarding clinical outcomes, acute rejection was significantly associated with human leukocyte antigen mismatch (≥3 alleles; OR = 12.14, 95% CI 1.76, 525.21, P = 0.019 after correction for multiple testing). Graft recipients from deceased donors showed higher incidende of delayed graft function (OR 7.15, 95% CI 2.23, 30.46, adjusted P = 0.0008) and a lower estimated glomerular filtration rate at discharge (P = 0.0001). Tested CYP3A4 or CYP3A5 variants did not show any effects on clinical outcome parameters. ABCB1 variants did neither impact on pharmacokinetics nor on clinical endpoints. Conclusion: At our transplantation center, both CYP3A5*3 and, to a lesser extent, CYP3A4*22 affect tacrolimus pharmacokinetics early after onset of therapy with consequences for steady-state treatment in routine clinical practice.
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Affiliation(s)
- Emaad Abdel-Kahaar
- Institute of Pharmacology of Natural Products and Clinical Pharmacology, University of Ulm, Ulm, Germany
- Department of Pharmacology, Qena Faculty of Medicine, South Valley University, Qena, Egypt
| | - Stefan Winter
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Roman Tremmel
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | | | - Eberhard Wieland
- Central Institute for Clinical Chemistry and Laboratory Medicine, Klinikum Stuttgart, Stuttgart, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- Departments of Clinical Pharmacology, Pharmacy and Biochemistry, University of Tübingen, Tübingen, Germany
| | - Maria Shipkova
- Central Institute for Clinical Chemistry and Laboratory Medicine, Klinikum Stuttgart, Stuttgart, Germany
| | - Simon U. Jaeger
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
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21
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Dribnokhodova OP, Korchagin VI, Mironov KO, Dunaeva EA, Titkov AV, Akselrod EV, Raskurazhev AA, Tanashyan MM, Illarioshkin SN, Platonov AE, Shipulin GA. [A comparative analysis of allele frequencies of rs1801133 and rs1801131 of MTHFR in patients with stroke and healthy people from the Moscow region]. Zh Nevrol Psikhiatr Im S S Korsakova 2019; 119:18-23. [PMID: 31184621 DOI: 10.17116/jnevro201911903218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
AIM To study genetic characteristics of the population of the Moscow region and analyze the association of rs1801133 and rs1801131 of MTHFR with the risk of ischemic stroke (IS). MATERIAL AND METHODS A sample of 170 and 115 patients with atherothrombotic and cardioembolic subtypes of IS and 360 residents of the Moscow region without IS were examined. MTHFR alleles were determined by a multiplex real-time polymerase chain reaction. RESULTS AND CONCLUSION No association between the frequencies of MTHFR alleles and the risk of ischemic stroke was found. The comparison of allele frequencies with those in Caucasian populations published in the dbSNP (NCBI) and 1000 Genomes Project databases revealed significant differences for rs1801133 from the EUR 1000 Genomes Project. The allele frequency data for MTHFR could increase the accuracy and reliability of the individual risk calculation for multifactorial diseases in the Russian population.
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Affiliation(s)
| | - V I Korchagin
- Central Research Institute of Epidemiology, Moscow, Russia
| | - K O Mironov
- Central Research Institute of Epidemiology, Moscow, Russia
| | - E A Dunaeva
- Central Research Institute of Epidemiology, Moscow, Russia
| | - A V Titkov
- Central Research Institute of Epidemiology, Moscow, Russia
| | - E V Akselrod
- Central Research Institute of Epidemiology, Moscow, Russia
| | | | | | | | - A E Platonov
- Central Research Institute of Epidemiology, Moscow, Russia
| | - G A Shipulin
- Central Research Institute of Epidemiology, Moscow, Russia
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22
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Puig X, Ginebra J, Graffelman J. Bayesian model selection for the study of Hardy-Weinberg proportions and homogeneity of gender allele frequencies. Heredity (Edinb) 2019; 123:549-564. [PMID: 31142813 DOI: 10.1038/s41437-019-0232-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/15/2019] [Accepted: 05/02/2019] [Indexed: 12/24/2022] Open
Abstract
Standard statistical tests for Hardy-Weinberg equilibrium assume the equality of allele frequencies in the sexes, whereas tests for the equality of allele frequencies in the sexes assume Hardy-Weinberg equilibrium. This produces a circularity in the testing of genetic variants, which has recently been resolved with new frequentist likelihood and exact procedures. In this paper, we tackle the same problem by posing it as a Bayesian model comparison problem. We formulate an exhaustive set of ten alternative scenarios for biallelic genetic variants. Using Dirichlet and Beta priors for genotype and allele frequencies, we derive marginal likelihoods for all scenarios, and select the most likely scenario using the posterior probabilities that each of these scenarios is the one in place. Different from the usual frequentist testing approach, the Bayesian approach allows one to compare any number of models, and not just two at a time, and the models compared do not have to be nested. We illustrate our Bayesian approach with genetic data from the 1,000 genomes project and through a simulation study.
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Affiliation(s)
- Xavier Puig
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Josep Ginebra
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Jan Graffelman
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Spain. .,Department of Biostatistics, University of Washington, Seattle, WA, USA.
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23
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Meléndez-Rosa J, Bi K, Lacey EA. Genomic analysis of MHC-based mate choice in the monogamous California mouse. Behav Ecol 2018; 29:1167-1180. [PMID: 30214134 PMCID: PMC6129947 DOI: 10.1093/beheco/ary096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 06/13/2018] [Accepted: 06/22/2018] [Indexed: 01/06/2023] Open
Abstract
Variation at Major Histocompatibility Complex (MHC) genes is thought to be an important mechanism underlying mate choice in vertebrates, with individuals typically predicted to prefer MHC-dissimilar reproductive partners. However, analyses based on individual MHC loci have generated contradictory results regarding the role of these genes in mate-choice decisions. To provide a more comprehensive assessment of relationships between MHC variation and mating behavior, we used an exome capture strategy to characterize variability at 13 MHC loci, 312 innate immune system genes, and 1044 nonimmune genes in 25 obligate monogamous pairs of California mice (Peromyscus californicus) from 2 free-living populations of this species in Monterey County, California. Pairwise genotypic comparisons and analyses of SNP-based allelic differences failed to detect disassortative mating based on MHC variability; reproductive partners were not more dissimilar than randomly generated male-female pairs at MHC, innate or nonimmune loci. Within populations, individuals tended to be more closely related at MHC genes than at innate or nonimmune genes. Consistent with the functional role of immunogenes, the 2 study populations were highly differentiated at MHC and innate genes but not at nonimmune loci. Collectively, our results suggest that MHC genetic variation in California mice reflects local differences in pathogen exposure rather than disassortative mating based on variability at MHC Class I and II genes.
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Affiliation(s)
- Jesyka Meléndez-Rosa
- Department of Integrative Biology, University of California, Berkeley, CA
- Museum of Vertebrate Zoology, University of California, Berkeley Valley Life Sciences Bldg., Berkeley, CA
| | - Ke Bi
- Museum of Vertebrate Zoology, University of California, Berkeley Valley Life Sciences Bldg., Berkeley, CA
- Computational Genomics Resource, MC University of California, Berkeley, CA
| | - Eileen A Lacey
- Department of Integrative Biology, University of California, Berkeley, CA
- Museum of Vertebrate Zoology, University of California, Berkeley Valley Life Sciences Bldg., Berkeley, CA
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24
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Chen B, Chen J, Du Q, Zhou D, Wang L, Xie J, Li Y, Zhang D. Genetic variants in microRNA biogenesis genes as novel indicators for secondary growth in Populus. THE NEW PHYTOLOGIST 2018; 219:1263-1282. [PMID: 29916214 DOI: 10.1111/nph.15262] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/06/2018] [Indexed: 05/21/2023]
Abstract
MicroRNAs (miRNAs) function as key regulators of complex traits, but how genetic alterations in miRNA biogenesis genes (miRBGs) affect quantitative variation has not been elucidated. We conducted transcript analyses and association genetics to investigate how miRBGs, miRNA genes (MIRNAs) and their respective targets contribute to secondary growth in a natural population of 435 Populus tomentosa individuals. This analysis identified 29 843 common single-nucleotide polymorphisms (SNPs; frequency > 0.10) within 682 genes (80 miRBGs, 152 MIRNAs, and 457 miRNA targets). Single-SNP association analysis found SNPs in 234 candidate genes exhibited significant additive/dominant effects on phenotypes. Among these, specific candidates that associated with the same traits produced 791 miRBG-MIRNA-target combinations, suggesting possible genetic miRBG-MIRNA and MIRNA-target interactions, providing an important clue for the regulatory mechanisms of miRBGs. Multi-SNP association found 4672 epistatic pairs involving 578 genes that showed significant associations with traits and identified 106 miRBG-MIRNA-target combinations. Two multi-hierarchical networks were constructed based on correlations of miRBG-miRNA and miRNA-target expression to further probe the mechanisms of trait diversity underlying changes in miRBGs. Our study opens avenues for the investigation of miRNA function in perennial plants and underscored miRBGs as potentially modulating quantitative variation in traits.
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Affiliation(s)
- Beibei Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Jinhui Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Qingzhang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Daling Zhou
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Longxin Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Jianbo Xie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Ying Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Deqiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
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25
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Common marmoset (Callithrix jacchus) personality, subjective well-being, hair cortisol level and AVPR1a, OPRM1, and DAT genotypes. Sci Rep 2018; 8:10255. [PMID: 29980755 PMCID: PMC6035208 DOI: 10.1038/s41598-018-28112-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 06/04/2018] [Indexed: 11/08/2022] Open
Abstract
We studied personality, subjective well-being, and hair cortisol level, in common marmosets Callithrix jacchus, a small, cooperatively breeding New World monkey, by examining their associations with one another and genotypes. Subjects were 68 males and 9 females that lived in the RIKEN Center for Life Science Technologies. Personality and subjective well-being were assessed by keeper ratings on two questionnaires, hair samples were obtained to assay cortisol level and buccal swabs were used to assess AVPR1a, OPRM1 and DAT genotypes. Three personality domains-Dominance, Sociability, and Neuroticism-were identified. Consistent with findings in other species, Sociability and Neuroticism were related to higher and lower subjective well-being, respectively. Sociability was also associated with higher hair cortisol levels. The personality domains and hair cortisol levels were heritable and associated with genotypes: the short form of AVPR1a was associated with lower Neuroticism and the AA genotype of the A111T SNP of OPRM1 was related to lower Dominance, lower Neuroticism, and higher hair cortisol level. Some genetic associations were not in directions that one would expect given findings in other species. These findings provide insights into the proximate and ultimate bases of personality in common marmosets, other primates and humans.
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26
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Snahnicanova Z, Mendelova A, Grendar M, Holubekova V, Kostkova M, Pozorciakova K, Jancinová M, Kasubova I, Vojtkova J, Durdik P, Lasabova Z, Ciljakova M, Banovcin P. Association of Polymorphisms in CYBA, SOD1, and CAT Genes with Type 1 Diabetes and Diabetic Peripheral Neuropathy in Children and Adolescents. Genet Test Mol Biomarkers 2018; 22:413-419. [PMID: 29924645 DOI: 10.1089/gtmb.2018.0018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AIMS The aim of our study was to investigate possible associations between three SNPs: rs4673 in the CYBA gene; rs1041740 in the SOD1 gene; and rs1001179 in the CAT gene, and type 1 diabetes (T1D) or diabetic peripheral neuropathy (DPN) in T1D patients. MATERIALS AND METHODS Allelic variants of the selected SNPs were determined by allelic discrimination assays in 114 T1D patients enrolled in the study group and in 90 healthy individuals from a control group. Associations between each of the three SNPs were tested in subgroups of T1D patients divided according to the presence of DPN. RESULTS The TT genotype of rs4673 in the CYBA gene was associated with DPN in T1D patients (OR 4.997, 95% CI 1.403-19.083, p = 0.016). Weak significance was observed for a protective effect of the TT genotype of rs1041740 in the SOD1 gene relative to T1D development (OR 0.318, 95% CI 0.092-0.959, p = 0.056). There was no significant association between the CAT gene SNP rs1001179 and T1D or DPN. CONCLUSION We showed a strong association of the CYBA polymorphism rs4673 with DPN in Slovak children and adolescents with T1D. Further studies are necessary to assess the relationship between rs1041740 and T1D or DPN.
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Affiliation(s)
- Zuzana Snahnicanova
- 1 Pediatric Department, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava , Martin, Slovakia .,2 Division of Oncology, Biomedical Center Martin JFM CU, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava , Martin, Slovakia
| | - Andrea Mendelova
- 3 Division of Molecular Medicine, Biomedical Center Martin JFM CU, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava , Martin, Slovakia
| | - Marian Grendar
- 4 Bioinformatic Unit, Biomedical Center Martin JFM CU, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava , Martin, Slovakia
| | - Veronika Holubekova
- 2 Division of Oncology, Biomedical Center Martin JFM CU, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava , Martin, Slovakia
| | - Martina Kostkova
- 1 Pediatric Department, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava , Martin, Slovakia
| | - Katarina Pozorciakova
- 1 Pediatric Department, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava , Martin, Slovakia
| | - Maria Jancinová
- 1 Pediatric Department, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava , Martin, Slovakia
| | - Ivana Kasubova
- 2 Division of Oncology, Biomedical Center Martin JFM CU, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava , Martin, Slovakia
| | - Jarmila Vojtkova
- 1 Pediatric Department, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava , Martin, Slovakia
| | - Peter Durdik
- 1 Pediatric Department, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava , Martin, Slovakia
| | - Zora Lasabova
- 2 Division of Oncology, Biomedical Center Martin JFM CU, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava , Martin, Slovakia
| | - Miriam Ciljakova
- 1 Pediatric Department, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava , Martin, Slovakia
| | - Peter Banovcin
- 1 Pediatric Department, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava , Martin, Slovakia
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27
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Opi DH, Swann O, Macharia A, Uyoga S, Band G, Ndila CM, Harrison EM, Thera MA, Kone AK, Diallo DA, Doumbo OK, Lyke KE, Plowe CV, Moulds JM, Shebbe M, Mturi N, Peshu N, Maitland K, Raza A, Kwiatkowski DP, Rockett KA, Williams TN, Rowe JA. Two complement receptor one alleles have opposing associations with cerebral malaria and interact with α +thalassaemia. eLife 2018; 7:e31579. [PMID: 29690995 PMCID: PMC5953541 DOI: 10.7554/elife.31579] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 04/01/2018] [Indexed: 12/13/2022] Open
Abstract
Malaria has been a major driving force in the evolution of the human genome. In sub-Saharan African populations, two neighbouring polymorphisms in the Complement Receptor One (CR1) gene, named Sl2 and McCb, occur at high frequencies, consistent with selection by malaria. Previous studies have been inconclusive. Using a large case-control study of severe malaria in Kenyan children and statistical models adjusted for confounders, we estimate the relationship between Sl2 and McCb and malaria phenotypes, and find they have opposing associations. The Sl2 polymorphism is associated with markedly reduced odds of cerebral malaria and death, while the McCb polymorphism is associated with increased odds of cerebral malaria. We also identify an apparent interaction between Sl2 and α+thalassaemia, with the protective association of Sl2 greatest in children with normal α-globin. The complex relationship between these three mutations may explain previous conflicting findings, highlighting the importance of considering genetic interactions in disease-association studies.
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Affiliation(s)
- D Herbert Opi
- Kenya Medical Research Institute-Wellcome Trust Research ProgrammeKilifiKenya
- Centre for Immunity, Infection and Evolution, Institute of Immunology and Infection Research, School of Biological SciencesUniversity of EdinburghEdinburghUnited Kingdom
| | - Olivia Swann
- Centre for Immunity, Infection and Evolution, Institute of Immunology and Infection Research, School of Biological SciencesUniversity of EdinburghEdinburghUnited Kingdom
| | - Alexander Macharia
- Kenya Medical Research Institute-Wellcome Trust Research ProgrammeKilifiKenya
| | - Sophie Uyoga
- Kenya Medical Research Institute-Wellcome Trust Research ProgrammeKilifiKenya
| | - Gavin Band
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - Carolyne M Ndila
- Kenya Medical Research Institute-Wellcome Trust Research ProgrammeKilifiKenya
| | - Ewen M Harrison
- Centre for Medical InfomaticsUsher Insitute of Population Health Sciences and Informatics, University of EdinburghEdinburghUnited Kingdom
| | - Mahamadou A Thera
- Malaria Research and Training Centre, Faculty of Medicine, Pharmacy, and DentistryUniversity of BamakoBamakoMali
| | - Abdoulaye K Kone
- Malaria Research and Training Centre, Faculty of Medicine, Pharmacy, and DentistryUniversity of BamakoBamakoMali
| | - Dapa A Diallo
- Malaria Research and Training Centre, Faculty of Medicine, Pharmacy, and DentistryUniversity of BamakoBamakoMali
| | - Ogobara K Doumbo
- Malaria Research and Training Centre, Faculty of Medicine, Pharmacy, and DentistryUniversity of BamakoBamakoMali
| | - Kirsten E Lyke
- Division of Malaria Research, Institute for Global HealthUniversity of Maryland School of MedicineBaltimoreUnited States
| | - Christopher V Plowe
- Division of Malaria Research, Institute for Global HealthUniversity of Maryland School of MedicineBaltimoreUnited States
| | | | - Mohammed Shebbe
- Kenya Medical Research Institute-Wellcome Trust Research ProgrammeKilifiKenya
| | - Neema Mturi
- Kenya Medical Research Institute-Wellcome Trust Research ProgrammeKilifiKenya
| | - Norbert Peshu
- Kenya Medical Research Institute-Wellcome Trust Research ProgrammeKilifiKenya
| | - Kathryn Maitland
- Kenya Medical Research Institute-Wellcome Trust Research ProgrammeKilifiKenya
- Department of MedicineImperial CollegeLondonUnited Kingdom
| | - Ahmed Raza
- Centre for Immunity, Infection and Evolution, Institute of Immunology and Infection Research, School of Biological SciencesUniversity of EdinburghEdinburghUnited Kingdom
| | - Dominic P Kwiatkowski
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
- Wellcome Trust Sanger InstituteCambridgeUnited Kingdom
| | - Kirk A Rockett
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - Thomas N Williams
- Kenya Medical Research Institute-Wellcome Trust Research ProgrammeKilifiKenya
- Department of MedicineImperial CollegeLondonUnited Kingdom
| | - J Alexandra Rowe
- Centre for Immunity, Infection and Evolution, Institute of Immunology and Infection Research, School of Biological SciencesUniversity of EdinburghEdinburghUnited Kingdom
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28
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Martorell-Marugan J, Toro-Dominguez D, Alarcon-Riquelme ME, Carmona-Saez P. MetaGenyo: a web tool for meta-analysis of genetic association studies. BMC Bioinformatics 2017; 18:563. [PMID: 29246109 PMCID: PMC5732412 DOI: 10.1186/s12859-017-1990-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/06/2017] [Indexed: 11/26/2022] Open
Abstract
Background Genetic association studies (GAS) aims to evaluate the association between genetic variants and phenotypes. In the last few years, the number of this type of study has increased exponentially, but the results are not always reproducible due to experimental designs, low sample sizes and other methodological errors. In this field, meta-analysis techniques are becoming very popular tools to combine results across studies to increase statistical power and to resolve discrepancies in genetic association studies. A meta-analysis summarizes research findings, increases statistical power and enables the identification of genuine associations between genotypes and phenotypes. Meta-analysis techniques are increasingly used in GAS, but it is also increasing the amount of published meta-analysis containing different errors. Although there are several software packages that implement meta-analysis, none of them are specifically designed for genetic association studies and in most cases their use requires advanced programming or scripting expertise. Results We have developed MetaGenyo, a web tool for meta-analysis in GAS. MetaGenyo implements a complete and comprehensive workflow that can be executed in an easy-to-use environment without programming knowledge. MetaGenyo has been developed to guide users through the main steps of a GAS meta-analysis, covering Hardy-Weinberg test, statistical association for different genetic models, analysis of heterogeneity, testing for publication bias, subgroup analysis and robustness testing of the results. Conclusions MetaGenyo is a useful tool to conduct comprehensive genetic association meta-analysis. The application is freely available at http://bioinfo.genyo.es/metagenyo/. Electronic supplementary material The online version of this article (10.1186/s12859-017-1990-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Daniel Toro-Dominguez
- Bioinformatics Unit, Centre for Genomics and Oncological Research (GENYO), Granada, Spain.,Medical Genomics, Centre for Genomics and Oncological Research (GENYO), Granada, Spain
| | - Marta E Alarcon-Riquelme
- Medical Genomics, Centre for Genomics and Oncological Research (GENYO), Granada, Spain.,Institute for Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Pedro Carmona-Saez
- Bioinformatics Unit, Centre for Genomics and Oncological Research (GENYO), Granada, Spain.
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Graffelman J, Weir BS. On the testing of Hardy-Weinberg proportions and equality of allele frequencies in males and females at biallelic genetic markers. Genet Epidemiol 2017; 42:34-48. [PMID: 29071737 PMCID: PMC5813254 DOI: 10.1002/gepi.22079] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 05/22/2017] [Accepted: 08/17/2017] [Indexed: 01/21/2023]
Abstract
Standard statistical tests for equality of allele frequencies in males and females and tests for Hardy‐Weinberg equilibrium are tightly linked by their assumptions. Tests for equality of allele frequencies assume Hardy‐Weinberg equilibrium, whereas the usual chi‐square or exact test for Hardy‐Weinberg equilibrium assume equality of allele frequencies in the sexes. In this paper, we propose ways to break this interdependence in assumptions of the two tests by proposing an omnibus exact test that can test both hypotheses jointly, as well as a likelihood ratio approach that permits these phenomena to be tested both jointly and separately. The tests are illustrated with data from the 1000 Genomes project.
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Affiliation(s)
- Jan Graffelman
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Spain.,Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Bruce S Weir
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
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Genome-Wide SNP Discovery and Analysis of Genetic Diversity in Farmed Sika Deer ( Cervus nippon) in Northeast China Using Double-Digest Restriction Site-Associated DNA Sequencing. G3-GENES GENOMES GENETICS 2017; 7:3169-3176. [PMID: 28751500 PMCID: PMC5592941 DOI: 10.1534/g3.117.300082] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Sika deer are an economically valuable species owing to their use in traditional Chinese medicine, particularly their velvet antlers. Sika deer in northeast China are mostly farmed in enclosure. Therefore, genetic management of farmed sika deer would benefit from detailed knowledge of their genetic diversity. In this study, we generated over 1.45 billion high-quality paired-end reads (288 Gbp) across 42 unrelated individuals using double-digest restriction site-associated DNA sequencing (ddRAD-seq). A total of 96,188 (29.63%) putative biallelic SNP loci were identified with an average sequencing depth of 23×. Based on the analysis, we found that the majority of the loci had a deficit of heterozygotes (FIS >0) and low values of Hobs, which could be due to inbreeding and Wahlund effects. We also developed a collection of high-quality SNP probes that will likely be useful in a variety of applications in genotyping for cervid species in the future.
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Pellegrini S, Palumbo S, Iofrida C, Melissari E, Rota G, Mariotti V, Anastasio T, Manfrinati A, Rumiati R, Lotto L, Sarlo M, Pietrini P. Genetically-Driven Enhancement of Dopaminergic Transmission Affects Moral Acceptability in Females but Not in Males: A Pilot Study. Front Behav Neurosci 2017; 11:156. [PMID: 28900390 PMCID: PMC5581873 DOI: 10.3389/fnbeh.2017.00156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/08/2017] [Indexed: 11/13/2022] Open
Abstract
Moral behavior has been a key topic of debate for philosophy and psychology for a long time. In recent years, thanks to the development of novel methodologies in cognitive sciences, the question of how we make moral choices has expanded to the study of neurobiological correlates that subtend the mental processes involved in moral behavior. For instance, in vivo brain imaging studies have shown that distinct patterns of brain neural activity, associated with emotional response and cognitive processes, are involved in moral judgment. Moreover, while it is well-known that responses to the same moral dilemmas differ across individuals, to what extent this variability may be rooted in genetics still remains to be understood. As dopamine is a key modulator of neural processes underlying executive functions, we questioned whether genetic polymorphisms associated with decision-making and dopaminergic neurotransmission modulation would contribute to the observed variability in moral judgment. To this aim, we genotyped five genetic variants of the dopaminergic pathway [rs1800955 in the dopamine receptor D4 (DRD4) gene, DRD4 48 bp variable number of tandem repeat (VNTR), solute carrier family 6 member 3 (SLC6A3) 40 bp VNTR, rs4680 in the catechol-O-methyl transferase (COMT) gene, and rs1800497 in the ankyrin repeat and kinase domain containing 1 (ANKK1) gene] in 200 subjects, who were requested to answer 56 moral dilemmas. As these variants are all located in genes belonging to the dopaminergic pathway, they were combined in multilocus genetic profiles for the association analysis. While no individual variant showed any significant effects on moral dilemma responses, the multilocus genetic profile analysis revealed a significant gender-specific influence on human moral acceptability. Specifically, those genotype combinations that improve dopaminergic signaling selectively increased moral acceptability in females, by making their responses to moral dilemmas more similar to those provided by males. As females usually give more emotionally-based answers and engage the "emotional brain" more than males, our results, though preliminary and therefore in need of replication in independent samples, suggest that this increase in dopamine availability enhances the cognitive and reduces the emotional components of moral decision-making in females, thus favoring a more rationally-driven decision process.
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Affiliation(s)
- Silvia Pellegrini
- Department of Experimental and Clinical Medicine, University of PisaPisa, Italy
| | - Sara Palumbo
- Department of Surgical, Medical, Molecular Pathology and Critical Care, University of PisaPisa, Italy
| | | | - Erika Melissari
- Department of Surgical, Medical, Molecular Pathology and Critical Care, University of PisaPisa, Italy
| | - Giuseppina Rota
- Clinical Psychology Branch, Azienda Ospedaliero-Universitaria PisanaPisa, Italy
| | - Veronica Mariotti
- Department of Experimental and Clinical Medicine, University of PisaPisa, Italy
| | - Teresa Anastasio
- Department of Experimental and Clinical Medicine, University of PisaPisa, Italy
| | - Andrea Manfrinati
- Applied Research Division for Cognitive and Psychological Science, European Institute of OncologyMilan, Italy
| | - Rino Rumiati
- Department of Developmental Psychology and Socialization and Center for Cognitive Neuroscience, University of PadovaPadova, Italy
| | - Lorella Lotto
- Department of Developmental Psychology and Socialization and Center for Cognitive Neuroscience, University of PadovaPadova, Italy
| | - Michela Sarlo
- Department of General Psychology and Center for Cognitive Neuroscience, University of PadovaPadova, Italy
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Lefebvre FA, Cody NA, Bouvrette LPB, Bergalet J, Wang X, Lécuyer E. CeFra-seq: Systematic mapping of RNA subcellular distribution properties through cell fractionation coupled to deep-sequencing. Methods 2017; 126:138-148. [DOI: 10.1016/j.ymeth.2017.05.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 05/18/2017] [Accepted: 05/21/2017] [Indexed: 12/18/2022] Open
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Abstract
The Hardy-Weinberg principle, one of the most important principles in population genetics, was originally developed for the study of allele frequency changes in a population over generations. It is now, however, widely used in studies of human diseases to detect inbreeding, population stratification, and genotyping errors. For assessment of deviation from Hardy-Weinberg proportions in data, the most popular approaches include the asymptotic Pearson's chi-squared goodness-of-fit test and the exact test. Pearson's chi-squared goodness-of-fit test is simple and straightforward, but is very sensitive to a small sample size or rare allele frequency. The exact test of Hardy-Weinberg proportions is preferable in these situations. The exact test can be performed through complete enumeration of heterozygote genotypes or on the basis of the Markov chain Monte Carlo procedure. In this chapter, we describe the Hardy-Weinberg principle and the commonly used Hardy-Weinberg proportion tests and their applications, and we demonstrate how the chi-squared test and exact test of Hardy-Weinberg proportions can be performed step-by-step using the popular software programs SAS, R, and PLINK, which have been widely used in genetic association studies, along with numerical examples. We also discuss approaches for testing Hardy-Weinberg proportions in case-control study designs that are better than traditional approaches for testing Hardy-Weinberg proportions in controls only. Finally, we note that deviation from the Hardy-Weinberg proportions in affected individuals can provide evidence for an association between genetic variants and diseases.
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Affiliation(s)
- Jian Wang
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sanjay Shete
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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Wilson VAD, Weiss A, Humle T, Morimura N, Udono T, Idani G, Matsuzawa T, Hirata S, Inoue-Murayama M. Chimpanzee Personality and the Arginine Vasopressin Receptor 1A Genotype. Behav Genet 2016; 47:215-226. [PMID: 27804047 PMCID: PMC5306277 DOI: 10.1007/s10519-016-9822-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 09/29/2016] [Indexed: 12/05/2022]
Abstract
Polymorphisms of the arginine vasopressin receptor 1a (AVPR1a) gene have been linked to various measures related to human social behavior, including sibling conflict and agreeableness. In chimpanzees, AVPR1a polymorphisms have been associated with traits important for social interactions, including sociability, joint attention, dominance, conscientiousness, and hierarchical personality dimensions named low alpha/stability, disinhibition, and negative emotionality/low dominance. We examined associations between AVPR1a and six personality domains and hierarchical personality dimensions in 129 chimpanzees (Pan troglodytes) living in Japan or in a sanctuary in Guinea. We fit three linear and three animal models. The first model included genotype, the second included sex and genotype, and the third included genotype, sex, and sex × genotype. All personality phenotypes were heritable. Chimpanzees possessing the long form of the allele were higher in conscientiousness, but only in models that did not include the other predictors; however, additional analyses suggested that this may have been a consequence of study design. In animal models that included sex and sex × genotype, chimpanzees homozygous for the short form of the allele were higher in extraversion. Taken with the findings of previous studies of chimpanzees and humans, the findings related to conscientiousness suggest that AVPR1a may be related to lower levels of impulsive aggression. The direction of the association between AVPR1a genotype and extraversion ran counter to what one would expect if AVPR1a was related to social behaviors. These results help us further understand the genetic basis of personality in chimpanzees.
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Affiliation(s)
- V A D Wilson
- Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK.,Cognitive Ethology, German Primate Center, Georg-August-University Goettingen, Leibniz-ScienceCampus, Göttingen, Germany
| | - A Weiss
- Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK.
| | - T Humle
- Durrell Institute of Conservation and Ecology (DICE), School of Anthropology and Conservation, University of Kent, Canterbury, UK
| | - N Morimura
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - T Udono
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - G Idani
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - T Matsuzawa
- Institute for Advanced Study, Kyoto University, Kyoto, Japan.,Primate Research Institute, Kyoto University, Inuyama, Japan.,Japan Monkey Centre, Inuyama, Japan
| | - S Hirata
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - M Inoue-Murayama
- Wildlife Research Center, Kyoto University, Kyoto, Japan.,National Institute for Environmental Studies, Tsukuba, Japan
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Reichel K, Masson JP, Malrieu F, Arnaud-Haond S, Stoeckel S. Rare sex or out of reach equilibrium? The dynamics of F IS in partially clonal organisms. BMC Genet 2016; 17:76. [PMID: 27286682 PMCID: PMC4902967 DOI: 10.1186/s12863-016-0388-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 06/01/2016] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Partially clonal organisms are very common in nature, yet the influence of partial asexuality on the temporal dynamics of genetic diversity remains poorly understood. Mathematical models accounting for clonality predict deviations only for extremely rare sex and only towards mean inbreeding coefficient [Formula: see text]. Yet in partially clonal species, both F IS < 0 and F IS > 0 are frequently observed also in populations where there is evidence for a significant amount of sexual reproduction. Here, we studied the joint effects of partial clonality, mutation and genetic drift with a state-and-time discrete Markov chain model to describe the dynamics of F IS over time under increasing rates of clonality. RESULTS Results of the mathematical model and simulations show that partial clonality slows down the asymptotic convergence to F IS = 0. Thus, although clonality alone does not lead to departures from Hardy-Weinberg expectations once reached the final equilibrium state, both negative and positive F IS values can arise transiently even at intermediate rates of clonality. More importantly, such "transient" departures from Hardy Weinberg proportions may last long as clonality tunes up the temporal variation of F IS and reduces its rate of change over time, leading to a hyperbolic increase of the maximal time needed to reach the final mean [Formula: see text] value expected at equilibrium. CONCLUSION Our results argue for a dynamical interpretation of F IS in clonal populations. Negative values cannot be interpreted as unequivocal evidence for extremely scarce sex but also as intermediate rates of clonality in finite populations. Complementary observations (e.g. frequency distribution of multiloci genotypes, population history) or time series data may help to discriminate between different possible conclusions on the extent of clonality when mean [Formula: see text] values deviating from zero and/or a large variation of F IS over loci are observed.
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Affiliation(s)
- Katja Reichel
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, 35650, Le Rheu, France
| | - Jean-Pierre Masson
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, 35650, Le Rheu, France
| | - Florent Malrieu
- Université de Tours, CNRS-UMR7350 LMPT, F-37200, Tours, France
| | | | - Solenn Stoeckel
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, 35650, Le Rheu, France.
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Graffelman J, Weir BS. Testing for Hardy-Weinberg equilibrium at biallelic genetic markers on the X chromosome. Heredity (Edinb) 2016; 116:558-68. [PMID: 27071844 PMCID: PMC4868269 DOI: 10.1038/hdy.2016.20] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 01/25/2016] [Accepted: 01/26/2016] [Indexed: 11/22/2022] Open
Abstract
Testing genetic markers for Hardy–Weinberg equilibrium (HWE) is an important tool for detecting genotyping errors in large-scale genotyping studies. For markers at the X chromosome, typically the χ2 or exact test is applied to the females only, and the hemizygous males are considered to be uninformative. In this paper we show that the males are relevant, because a difference in allele frequency between males and females may indicate HWE not to hold. The testing of markers on the X chromosome has received little attention, and in this paper we lay down the foundation for testing biallelic X-chromosomal markers for HWE. We develop four frequentist statistical test procedures for X-linked markers that take both males and females into account: the χ2 test, likelihood ratio test, exact test and permutation test. Exact tests that include males are shown to have a better Type I error rate. Empirical data from the GENEVA project on venous thromboembolism is used to illustrate the proposed tests. Results obtained with the new tests differ substantially from tests that are based on female genotype counts only. The new tests detect differences in allele frequencies and seem able to uncover additional genotyping error that would have gone unnoticed in HWE tests based on females only.
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Affiliation(s)
- J Graffelman
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - B S Weir
- Department of Biostatistics, University of Washington, Seattle, WA, USA
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Allwright MR, Payne A, Emiliani G, Milner S, Viger M, Rouse F, Keurentjes JJB, Bérard A, Wildhagen H, Faivre-Rampant P, Polle A, Morgante M, Taylor G. Biomass traits and candidate genes for bioenergy revealed through association genetics in coppiced European Populus nigra (L.). BIOTECHNOLOGY FOR BIOFUELS 2016; 9:195. [PMID: 27617034 PMCID: PMC5017058 DOI: 10.1186/s13068-016-0603-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/22/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Second generation (2G) bioenergy from lignocellulosic feedstocks has the potential to develop as a sustainable source of renewable energy; however, significant hurdles still remain for large-scale commercialisation. Populus is considered as a promising 2G feedstock and understanding the genetic basis of biomass yield and feedstock quality are a research priority in this model tree species. RESULTS We report the first coppiced biomass study for 714 members of a wide population of European black poplar (Populus nigra L.), a native European tree, selected from 20 river populations ranging in latitude and longitude between 40.5 and 52.1°N and 1.0 and 16.4°E, respectively. When grown at a single site in southern UK, significant Site of Origin (SO) effects were seen for 14 of the 15 directly measured or derived traits including biomass yield, leaf area and stomatal index. There was significant correlation (p < 0.001) between biomass yield traits over 3 years of harvest which identified leaf size and cell production as strong predictors of biomass yield. A 12 K Illumina genotyping array (constructed from 10,331 SNPs in 14 QTL regions and 4648 genes) highlighted significant population genetic structure with pairwise FST showing strong differentiation (p < 0.001) between the Spanish and Italian subpopulations. Robust associations reaching genome-wide significance are reported for main stem height and cell number per leaf; two traits tightly linked to biomass yield. These genotyping and phenotypic data were also used to show the presence of significant isolation by distance (IBD) and isolation by adaption (IBA) within this population. CONCLUSIONS The three associations identified reaching genome-wide significance at p < 0.05 include a transcription factor; a putative stress response gene and a gene of unknown function. None of them have been previously linked to bioenergy yield; were shown to be differentially expressed in a panel of three selected genotypes from the collection and represent exciting, novel candidates for further study in a bioenergy tree native to Europe and Euro-Asia. A further 26 markers (22 genes) were found to reach putative significance and are also of interest for biomass yield, leaf area, epidermal cell expansion and stomatal patterning. This research on European P. nigra provides an important foundation for the development of commercial native trees for bioenergy and for advanced, molecular breeding in these species.
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Affiliation(s)
- Mike Robert Allwright
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
| | - Adrienne Payne
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
| | - Giovanni Emiliani
- CNR-IVALSA, Sesto Fiorentino, via Madonna del Piano, 10, 50019 Sesto Fiorentino, FI Italy
| | - Suzanne Milner
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
| | - Maud Viger
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
| | - Franchesca Rouse
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
| | - Joost J. B. Keurentjes
- Laboratory of Genetics, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | | | | | | | - Andrea Polle
- Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Michele Morgante
- Dipartimento di Scienze agroalimentari, ambientali e animali, Università di Udine, Via delle Scienze 206, 33100 Udine, Italy
- Istituto di Genomica Applicata (IGA), via J. Linussio 51, 33100 Udine, Italy
| | - Gail Taylor
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
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Edwards HA, Hajduk GK, Durieux G, Burke T, Dugdale HL. No Association between Personality and Candidate Gene Polymorphisms in a Wild Bird Population. PLoS One 2015; 10:e0138439. [PMID: 26473495 PMCID: PMC4608812 DOI: 10.1371/journal.pone.0138439] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 08/31/2015] [Indexed: 02/06/2023] Open
Abstract
Consistency of between-individual differences in behaviour or personality is a phenomenon in populations that can have ecological consequences and evolutionary potential. One way that behaviour can evolve is to have a genetic basis. Identifying the molecular genetic basis of personality could therefore provide insight into how and why such variation is maintained, particularly in natural populations. Previously identified candidate genes for personality in birds include the dopamine receptor D4 (DRD4), and serotonin transporter (SERT). Studies of wild bird populations have shown that exploratory and bold behaviours are associated with polymorphisms in both DRD4 and SERT. Here we tested for polymorphisms in DRD4 and SERT in the Seychelles warbler (Acrocephalus sechellensis) population on Cousin Island, Seychelles, and then investigated correlations between personality and polymorphisms in these genes. We found no genetic variation in DRD4, but identified four polymorphisms in SERT that clustered into five haplotypes. There was no correlation between bold or exploratory behaviours and SERT polymorphisms/haplotypes. The null result was not due to lack of power, and indicates that there was no association between these behaviours and variation in the candidate genes tested in this population. These null findings provide important data to facilitate representative future meta-analyses on candidate personality genes.
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Affiliation(s)
- Hannah A. Edwards
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- * E-mail:
| | - Gabriela K. Hajduk
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Gillian Durieux
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Terry Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Hannah L. Dugdale
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
- Nature Seychelles, Mahe, Republic of Seychelles
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FTO Is Associated with Aortic Valve Stenosis in a Gender Specific Manner of Heterozygote Advantage: A Population-Based Case-Control Study. PLoS One 2015; 10:e0139419. [PMID: 26431034 PMCID: PMC4592246 DOI: 10.1371/journal.pone.0139419] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 09/14/2015] [Indexed: 12/18/2022] Open
Abstract
Background Single nucleotide polymorphisms (SNPs) within the Fat mass and obesity associated (FTO) gene have been linked with increased body weight. However, the data on an association of FTO with cardiovascular diseases remains conflicting. Therefore, we ascertained whether FTO is associated with aortic valve stenosis (AVS), one of the most frequent cardiovascular diseases in the Western world. Methods and Findings In this population-based case-control study the FTO SNP rs9939609 was analyzed in 300 German patients with AVS and 429 German controls of the KORA survey S4, representing a random population. Blood samples were collected prior to aortic valve replacement in AVS cases and FTO rs9939609 was genotyped via ARMS-PCR. Genotype frequencies differed significantly between AVS cases and KORA controls (p = 0.004). Separate gender-analyses uncovered an association of FTO with AVS exclusively in males; homozygote carriers for the risk-allele (A) had a higher risk to develop AVS (p = 0.017, odds ratio (OR) 1.727; 95% confidence interval (CI) 1.087–2.747, recessive model), whereas heterozygote carriers for the risk-allele showed a lower risk (p = 0.002, OR 0.565, 95% CI 0.384–0.828, overdominant model). After adjustment for multiple co-variables, the odds ratios of heterozygotes remained significant for an association with AVS (p = 0.008, OR 0.565, 95% CI 0.369–0.861). Conclusions This study revealed an association of FTO rs9939609 with AVS. Furthermore, this association was restricted to men, with heterozygotes having a significantly lower chance to develop AVS. Lastly, the association between FTO and AVS was independent of BMI and other variables such as diabetes mellitus.
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40
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Moons T, De Hert M, Kenis G, Viechtbauer W, van Os J, Gohlke H, Claes S, van Winkel R. No association between genetic or epigenetic variation in insulin growth factors and antipsychotic-induced metabolic disturbances in a cross-sectional sample. Pharmacogenomics 2015; 15:951-62. [PMID: 24956249 DOI: 10.2217/pgs.14.46] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
AIM Second-generation antipsychotics (SGA) are known to induce metabolic disturbances. Genetic pathways, such as the IGF pathway could be associated with increased metabolic syndrome (MetS). Additionally, IGF2 methylation varies as a function of environmental influences and is associated with schizophrenia and MetS. The current study aims to evaluate whether genetic and epigenetic variation in genes of the IGF pathway are associated with metabolic disturbances in patients under treatment with SGAs. METHODS Cross-sectional metabolic data from 438 patients with schizophrenia spectrum disorder was analyzed. Using the Sequenom MassARRAY iPLEX(TM) platform, 27 SNPs of the IGF1 and IGF2 genes and the IGF receptors IGF1R and IGF2R were genotyped. Methylation status of seven IGF2 CpG dinucleotides was evaluated using a Sequenom MALDI-TOF spectrometer. RESULTS & CONCLUSION There was a significant association between IGF2 methylation and genotype, but no significant association between genetic or epigenetic variability and metabolic parameters in the present study.
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Affiliation(s)
- Tim Moons
- GRASP Research Unit, University Psychiatric Centre Catholic University Leuven, Herestraat 49, 3000 Leuven, Belgium
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McKown AD, Klápště J, Guy RD, Geraldes A, Porth I, Hannemann J, Friedmann M, Muchero W, Tuskan GA, Ehlting J, Cronk QCB, El-Kassaby YA, Mansfield SD, Douglas CJ. Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa. THE NEW PHYTOLOGIST 2014; 203:535-553. [PMID: 24750093 DOI: 10.1111/nph.12815] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 03/14/2014] [Indexed: 05/02/2023]
Abstract
In order to uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa) from much of its range in western North America. Extensive data from large-scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34 K Populus single nucleotide polymorphism (SNP) array) of all accessions were used for gene discovery in a genome-wide association study (GWAS). We performed GWAS with 40 biomass, ecophysiology and phenology traits and 29,355 filtered SNPs representing 3518 genes. The association analyses were carried out using a Unified Mixed Model accounting for population structure effects among accessions. We uncovered 410 significant SNPs using a Bonferroni-corrected threshold (P<1.7×10(-6)). Markers were found across 19 chromosomes, explained 1-13% of trait variation, and implicated 275 unique genes in trait associations. Phenology had the largest number of associated genes (240 genes), followed by biomass (53 genes) and ecophysiology traits (25 genes). The GWAS results propose numerous loci for further investigation. Many traits had significant associations with multiple genes, underscoring their genetic complexity. Genes were also identified with multiple trait associations within and/or across trait categories. In some cases, traits were genetically correlated while in others they were not.
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Affiliation(s)
- Athena D McKown
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jaroslav Klápště
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Dendrology and Forest Tree Breeding, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, 165 21, Czech Republic
| | - Robert D Guy
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Armando Geraldes
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Ilga Porth
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jan Hannemann
- Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - Michael Friedmann
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Wellington Muchero
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Gerald A Tuskan
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jürgen Ehlting
- Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - Quentin C B Cronk
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Carl J Douglas
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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McKown AD, Guy RD, Klápště J, Geraldes A, Friedmann M, Cronk QCB, El-Kassaby YA, Mansfield SD, Douglas CJ. Geographical and environmental gradients shape phenotypic trait variation and genetic structure in Populus trichocarpa. THE NEW PHYTOLOGIST 2014; 201:1263-1276. [PMID: 24491114 DOI: 10.1111/nph.12601] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 10/09/2013] [Indexed: 05/18/2023]
Abstract
• Populus trichocarpa is widespread across western North America spanning extensive variation in photoperiod, growing season and climate. We investigated trait variation in P. trichocarpa using over 2000 trees from a common garden at Vancouver, Canada, representing replicate plantings of 461 genotypes originating from 136 provenance localities. • We measured 40 traits encompassing phenological events, biomass accumulation, growth rates, and leaf, isotope and gas exchange-based ecophysiology traits. With replicated plantings and 29,354 single nucleotide polymorphisms (SNPs) from 3518 genes, we estimated both broad-sense trait heritability (H(2)) and overall population genetic structure from principal component analysis. • Populus trichocarpa had high phenotypic variation and moderate/high H(2) for many traits. H(2) ranged from 0.3 to 0.9 in phenology, 0.3 to 0.8 in biomass and 0.1 to 0.8 in ecophysiology traits. Most traits correlated strongly with latitude, maximum daylength and temperature of tree origin, but not necessarily with elevation, precipitation or heat : moisture indices. Trait H(2) values reflected trait correlation strength with geoclimate variables. The population genetic structure had one significant principal component (PC1) which correlated with daylength and showed enrichment for genes relating to circadian rhythm and photoperiod. • Robust relationships between traits, population structure and geoclimate in P. trichocarpa reflect patterns which suggest that range-wide geographical and environment gradients have shaped its genotypic and phenotypic variability.
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Affiliation(s)
- Athena D McKown
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Robert D Guy
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jaroslav Klápště
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Dendrology and Forest Tree Breeding, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, 165 21, Czech Republic
| | - Armando Geraldes
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Michael Friedmann
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Quentin C B Cronk
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Carl J Douglas
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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Graffelman J, Sánchez M, Cook S, Moreno V. Statistical inference for Hardy-Weinberg proportions in the presence of missing genotype information. PLoS One 2013; 8:e83316. [PMID: 24391752 PMCID: PMC3877411 DOI: 10.1371/journal.pone.0083316] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 11/04/2013] [Indexed: 11/18/2022] Open
Abstract
In genetic association studies, tests for Hardy-Weinberg proportions are often employed as a quality control checking procedure. Missing genotypes are typically discarded prior to testing. In this paper we show that inference for Hardy-Weinberg proportions can be biased when missing values are discarded. We propose to use multiple imputation of missing values in order to improve inference for Hardy-Weinberg proportions. For imputation we employ a multinomial logit model that uses information from allele intensities and/or neighbouring markers. Analysis of an empirical data set of single nucleotide polymorphisms possibly related to colon cancer reveals that missing genotypes are not missing completely at random. Deviation from Hardy-Weinberg proportions is mostly due to a lack of heterozygotes. Inbreeding coefficients estimated by multiple imputation of the missings are typically lowered with respect to inbreeding coefficients estimated by discarding the missings. Accounting for missings by multiple imputation qualitatively changed the results of 10 to 17% of the statistical tests performed. Estimates of inbreeding coefficients obtained by multiple imputation showed high correlation with estimates obtained by single imputation using an external reference panel. Our conclusion is that imputation of missing data leads to improved statistical inference for Hardy-Weinberg proportions.
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Affiliation(s)
- Jan Graffelman
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Spain
- * E-mail:
| | - Milagros Sánchez
- Biomedical Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain
| | | | - Victor Moreno
- Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Biomedical Research Institute of Bellvitge (IDIBELL), Consorcio de Investigación Biomédica de Epidemiología y Salud Pública (CIBERESP), and School of Medicine, University of Barcelona (UB), Barcelona, Spain
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Sun Y, Abbott RJ, Li L, Li L, Zou J, Liu J. Evolutionary history of Purple cone spruce (Picea purpurea) in the Qinghai-Tibet Plateau: homoploid hybrid origin and Pleistocene expansion. Mol Ecol 2013; 23:343-59. [PMID: 26010556 DOI: 10.1111/mec.12599] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 11/20/2013] [Accepted: 11/20/2013] [Indexed: 01/29/2023]
Abstract
Hybridization and introgression can play an important role in speciation. Here, we examine their roles in the origin and evolution of Picea purpurea, a diploid spruce species occurring on the Qinghai-Tibet Plateau (QTP). Phylogenetic relationships and ecological differences between this species and its relatives, P. schrenkiana, P. likiangensis and P. wilsonii, are unclear. To clarify them, we surveyed sequence variation within and between them for 11 nuclear loci, three chloroplast (cp) and two mitochondrial (mt) DNA fragments, and examined their ecological requirements using ecological niche modelling. Initial analyses based on 11 nuclear loci rejected a close relationship between P. schrenkiana and P. purpurea. BP&P tests and ecological niche modelling indicated substantial divergence between the remaining three species and supported the species status of P. purpurea, which contained many private alleles as expected for a well-established species. Sequence variation for cpDNA and mtDNA suggested a close relationship between P. purpurea and P. wilsonii, while variation at the nuclear se1364 gene suggested P. purpurea was more closely related to P. likiangensis. Analyses of genetic divergence, Bayesian clustering and model comparison using approximate Bayesian computation (ABC) of nuclear (nr) DNA variation all supported the hypothesis that P. purpurea originated by homoploid hybrid speciation from P. wilsonii and P. likiangensis. The ABC analysis dated the origin of P. purpurea at the Pleistocene, and the estimated hybrid parameter indicated that 69% of its nuclear composition was contributed by P. likiangensis and 31% by P. wilsonii. Our results further suggested that during or immediately following its formation, P. purpurea was subject to organelle DNA introgression from P. wilsonii such that it came to possess both mtDNA and cpDNA of P. wilsonii. The estimated parameters indicated that following its origin, P. purpurea underwent an expansion during/after the largest Pleistocene glaciation recorded for the QTP.
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Affiliation(s)
- Yongshuai Sun
- State Key Laboratory of Grassland Agro-ecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China.,Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Richard J Abbott
- School of Biology, University of St Andrews, Mitchell Building, St Andrews, Fife, KY16 9TH, UK
| | - Lili Li
- State Key Laboratory of Grassland Agro-ecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Long Li
- State Key Laboratory of Grassland Agro-ecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Jiabin Zou
- State Key Laboratory of Grassland Agro-ecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-ecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
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La Mantia J, Klápště J, El-Kassaby YA, Azam S, Guy RD, Douglas CJ, Mansfield SD, Hamelin R. Association analysis identifies Melampsora ×columbiana poplar leaf rust resistance SNPs. PLoS One 2013; 8:e78423. [PMID: 24236018 PMCID: PMC3827267 DOI: 10.1371/journal.pone.0078423] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 09/19/2013] [Indexed: 12/14/2022] Open
Abstract
Populus species are currently being domesticated through intensive time- and resource-dependent programs for utilization in phytoremediation, wood and paper products, and conversion to biofuels. Poplar leaf rust disease can greatly reduce wood volume. Genetic resistance is effective in reducing economic losses but major resistance loci have been race-specific and can be readily defeated by the pathogen. Developing durable disease resistance requires the identification of non-race-specific loci. In the presented study, area under the disease progress curve was calculated from natural infection of Melampsora ×columbiana in three consecutive years. Association analysis was performed using 412 P. trichocarpa clones genotyped with 29,355 SNPs covering 3,543 genes. We found 40 SNPs within 26 unique genes significantly associated (permutated P<0.05) with poplar rust severity. Moreover, two SNPs were repeated in all three years suggesting non-race-specificity and three additional SNPs were differentially expressed in other poplar rust interactions. These five SNPs were found in genes that have orthologs in Arabidopsis with functionality in pathogen induced transcriptome reprogramming, Ca²⁺/calmodulin and salicylic acid signaling, and tolerance to reactive oxygen species. The additive effect of non-R gene functional variants may constitute high levels of durable poplar leaf rust resistance. Therefore, these findings are of significance for speeding the genetic improvement of this long-lived, economically important organism.
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Affiliation(s)
- Jonathan La Mantia
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jaroslav Klápště
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Dendrology and Forest Tree Breeding, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká, Czech Republic
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shofiul Azam
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert D. Guy
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carl J. Douglas
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shawn D. Mansfield
- Department of Wood Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Richard Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Natural Resources Canada, Laurentian Forestry Center, Québec, Canada
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Nicotinic receptor gene variants interact with attention deficient hyperactive disorder symptoms to predict smoking trajectories from early adolescence to adulthood. Addict Behav 2013; 38:2683-9. [PMID: 23899432 DOI: 10.1016/j.addbeh.2013.06.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 05/30/2013] [Accepted: 06/17/2013] [Indexed: 12/25/2022]
Abstract
OBJECTIVE To examine the association of single nucleotide polymorphisms (SNPs) of the CHRNB3 (rs13280604) and CHRNA6 (rs892413) nicotinic acetylcholine receptor (nAChR) genes and symptoms of attention deficit hyperactivity disorder (ADHD) in predicting smoking patterns from early adolescence to adulthood. METHOD A longitudinal cohort of 1137 unrelated youths from the National Longitudinal Study of Adolescent Health provided responses to four surveys from Waves I to IV, and a genetic sample in Wave III. Growth mixture modeling was used to identify smoking patterns and to assess the effects of the two SNPs and ADHD symptoms on cigarette use over time. RESULTS There were significant main effects of ADHD symptoms and CHRNA6 variants in predicting the number of cigarettes smoked and the pattern of use over time, respectively. There were no main effects of the CHRNB3 variants. However, a significant CHRNB3 variant×ADHD symptom interaction was observed, such that individuals with elevated ADHD symptoms and a particular CHRNB3 variant were at increased risk of cigarette use over time. CONCLUSIONS These findings demonstrate that a SNP in a nicotinic receptor gene may interact with ADHD symptoms to link with increased cigarette use across adolescence and young adulthood. Unique associations between specific variants and patterns of ADHD symptoms were identified which may be useful for targeting prevention efforts to individuals at greatest risk for cigarette smoking.
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Tveitevåg Svingen GF, Ueland PM, Pedersen EKR, Schartum-Hansen H, Seifert R, Ebbing M, Løland KH, Tell GS, Nygård O. Plasma Dimethylglycine and Risk of Incident Acute Myocardial Infarction in Patients With Stable Angina Pectoris. Arterioscler Thromb Vasc Biol 2013; 33:2041-8. [DOI: 10.1161/atvbaha.113.301714] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Objective—
Dimethylglycine is linked to lipid metabolism, and increased plasma levels may be associated with adverse prognosis in patients with coronary artery disease. We evaluated the relationship between plasma dimethylglycine and risk of incident acute myocardial infarction in a large prospective cohort of patients with stable angina pectoris, of whom approximately two thirds were participants in a B-vitamin intervention trial. Model discrimination and reclassification when adding plasma dimethylglycine to established risk factors were obtained. We also explored temporal changes and the test–retest reliability of plasma dimethylglycine.
Approach and Results—
Four thousand one hundred fifty patients (72% men; median age 62 years) were included. Plasma dimethylglycine was associated with several traditional coronary artery disease risk factors. During a median follow-up of 4.6 years, 343 (8.3%) patients experienced an acute myocardial infarction. The hazard ratio (95% confidence interval) for acute myocardial infarction was 1.95 (1.42–2.68;
P
<0.001) when comparing plasma dimethylglycine quartile 4 to 1 in a Cox regression model adjusted for age, sex, and fasting status. Adjusting for traditional coronary artery disease risk factors only slightly modified the estimates, which were particularly strong among nonsmokers and among patients with serum triglyceride or apolipoprotein B100 levels ≤median (
P
for interaction=0.004, 0.004, and 0.03, respectively). Plasma dimethylglycine improved discrimination and reclassification and had high test–retest reliability.
Conclusions—
Plasma dimethylglycine is independently related to incident acute myocardial infarction and enhances risk prediction in patients with stable angina pectoris. Our results motivate further studies on the relationship between 1-carbon metabolism and atherothrombosis. A potential interplay with lipid and energy metabolism merits particular attention.
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Affiliation(s)
- Gard Frodahl Tveitevåg Svingen
- From the Department of Clinical Science (G.F.T.S., E.K.R.P., P.M.U., K.H.L., O.N.), Department of Global Public Health and Primary Care (G.S.T.), University of Bergen, Bergen, Norway; Department of Heart Disease, Haukeland University Hospital, Bergen, Norway (H.S.H., R.S., O.N.); and Norwegian Cardiovascular Disease Registry, Norwegian Institute of Public Health, Oslo, Norway (M.E.)
| | - Per Magne Ueland
- From the Department of Clinical Science (G.F.T.S., E.K.R.P., P.M.U., K.H.L., O.N.), Department of Global Public Health and Primary Care (G.S.T.), University of Bergen, Bergen, Norway; Department of Heart Disease, Haukeland University Hospital, Bergen, Norway (H.S.H., R.S., O.N.); and Norwegian Cardiovascular Disease Registry, Norwegian Institute of Public Health, Oslo, Norway (M.E.)
| | - Eva Kristine Ringdal Pedersen
- From the Department of Clinical Science (G.F.T.S., E.K.R.P., P.M.U., K.H.L., O.N.), Department of Global Public Health and Primary Care (G.S.T.), University of Bergen, Bergen, Norway; Department of Heart Disease, Haukeland University Hospital, Bergen, Norway (H.S.H., R.S., O.N.); and Norwegian Cardiovascular Disease Registry, Norwegian Institute of Public Health, Oslo, Norway (M.E.)
| | - Hall Schartum-Hansen
- From the Department of Clinical Science (G.F.T.S., E.K.R.P., P.M.U., K.H.L., O.N.), Department of Global Public Health and Primary Care (G.S.T.), University of Bergen, Bergen, Norway; Department of Heart Disease, Haukeland University Hospital, Bergen, Norway (H.S.H., R.S., O.N.); and Norwegian Cardiovascular Disease Registry, Norwegian Institute of Public Health, Oslo, Norway (M.E.)
| | - Reinhard Seifert
- From the Department of Clinical Science (G.F.T.S., E.K.R.P., P.M.U., K.H.L., O.N.), Department of Global Public Health and Primary Care (G.S.T.), University of Bergen, Bergen, Norway; Department of Heart Disease, Haukeland University Hospital, Bergen, Norway (H.S.H., R.S., O.N.); and Norwegian Cardiovascular Disease Registry, Norwegian Institute of Public Health, Oslo, Norway (M.E.)
| | - Marta Ebbing
- From the Department of Clinical Science (G.F.T.S., E.K.R.P., P.M.U., K.H.L., O.N.), Department of Global Public Health and Primary Care (G.S.T.), University of Bergen, Bergen, Norway; Department of Heart Disease, Haukeland University Hospital, Bergen, Norway (H.S.H., R.S., O.N.); and Norwegian Cardiovascular Disease Registry, Norwegian Institute of Public Health, Oslo, Norway (M.E.)
| | - Kjetil Halvorsen Løland
- From the Department of Clinical Science (G.F.T.S., E.K.R.P., P.M.U., K.H.L., O.N.), Department of Global Public Health and Primary Care (G.S.T.), University of Bergen, Bergen, Norway; Department of Heart Disease, Haukeland University Hospital, Bergen, Norway (H.S.H., R.S., O.N.); and Norwegian Cardiovascular Disease Registry, Norwegian Institute of Public Health, Oslo, Norway (M.E.)
| | - Grethe S. Tell
- From the Department of Clinical Science (G.F.T.S., E.K.R.P., P.M.U., K.H.L., O.N.), Department of Global Public Health and Primary Care (G.S.T.), University of Bergen, Bergen, Norway; Department of Heart Disease, Haukeland University Hospital, Bergen, Norway (H.S.H., R.S., O.N.); and Norwegian Cardiovascular Disease Registry, Norwegian Institute of Public Health, Oslo, Norway (M.E.)
| | - Ottar Nygård
- From the Department of Clinical Science (G.F.T.S., E.K.R.P., P.M.U., K.H.L., O.N.), Department of Global Public Health and Primary Care (G.S.T.), University of Bergen, Bergen, Norway; Department of Heart Disease, Haukeland University Hospital, Bergen, Norway (H.S.H., R.S., O.N.); and Norwegian Cardiovascular Disease Registry, Norwegian Institute of Public Health, Oslo, Norway (M.E.)
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Lin WY, Liu N. Reducing bias of allele frequency estimates by modeling SNP genotype data with informative missingness. Front Genet 2012; 3:107. [PMID: 22719749 PMCID: PMC3376470 DOI: 10.3389/fgene.2012.00107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 05/25/2012] [Indexed: 01/30/2023] Open
Abstract
The presence of missing single-nucleotide polymorphism (SNP) genotypes is common in genetic studies. For studies with low-density SNPs, the most commonly used approach to dealing with genotype missingness is to simply remove the observations with missing genotypes from the analyses. This naïve method is straightforward but is valid only when the missingness is random. However, a given assay often has a different capability in genotyping heterozygotes and homozygotes, causing the phenomenon of "differential dropout" in the sense that the missing rates of heterozygotes and homozygotes are different. In practice, differential dropout among genotypes exists in even carefully designed studies, such as the data from the HapMap project and the Wellcome Trust Case Control Consortium. Under the assumption of Hardy-Weinberg equilibrium and no genotyping error, we here propose a statistical method to model the differential dropout among different genotypes. Compared with the naïve method, our method provides more accurate allele frequency estimates when the differential dropout is present. To demonstrate its practical use, we further apply our method to the HapMap data and a scleroderma data set.
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Affiliation(s)
- Wan-Yu Lin
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University Taipei, Taiwan
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Abstract
The Hardy-Weinberg principle, one of the most important principles in population genetics, was originally developed for the study of allele frequency changes in a population over generations. It is now, however, widely used in studies of human diseases to detect inbreeding, populations stratification, and genotyping errors. For assessment of deviation from the Hardy-Weinberg proportions in data, the most popular approaches include the asymptotic Pearson's chi-square goodness-of-fit test and the exact test. The Pearson's chi-square goodness-of-fit test is simple and straightforward, but it is very sensitive to small sample size or rare allele frequency. The exact test of Hardy-Weinberg proportions is preferable in these situations. The exact test can be performed through complete enumeration of heterozygote genotypes or on the basis of the Markov chain Monte Carlo procedure. In this chapter, we describe the Hardy-Weinberg principle and the commonly used Hardy-Weinberg proportions tests and their applications, and we demonstrate how the chi-square test and exact test of Hardy-Weinberg proportions can be performed step-by-step using the popular software programs SAS, R, and PLINK, which have been widely used in genetic association studies, along with numerical examples. We also discuss recent approaches for testing Hardy-Weinberg proportions in case-control study designs that are better than traditional approaches for testing Hardy-Weinberg proportions in controls only. Finally, we note that deviation from the Hardy-Weinberg proportions in affected individuals can provide evidence for an association between genetic variants and diseases.
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Affiliation(s)
- Jian Wang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Maróti-Agóts A, Bodó I, Jávorka L, Gyurmán A, Solymosi N, Zenke P, Skogseth M, Zöldág L. Possible genetic sign of heat stress adaptation in Hungarian Grey Bos taurus breed. ACTA BIOLOGICA HUNGARICA 2011; 62:65-72. [PMID: 21388920 DOI: 10.1556/abiol.61.2011.1.6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The synthesis of Heat Shock Protein 70.2 mRNA is also regulated by the Upper Promoter elements of the gene. This promoter region is polymorphic in cattle. These polymorphisms have a major effect on the activity of the mRNA transcription. In a comparison of quantity of transcribed mRNA from the wild type and AP2 mutant allele the wild type can produce 2-3-fold more transcripts.The Hungarian Grey Cattle (HG) and Norwegian Red (NFR) as control breed were genotyped with PCR-RFLP method. Our results showed that the frequencies of alleles in breeds (p(wt)HG = 0.859419, p(wt)NFR = 0.5) are different. The effective response to heat stress in the Norwegian Red seems to be less important than in the Hungarian Grey breed. The extensive keeping in hot and arid region during centuries could have been proved as selection pressure for the heat tolerance.Our results combined with the global climate forecasts emphasize the role of autochthonous, well adopted, heat tolerant breeds in the near future.
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Affiliation(s)
- A Maróti-Agóts
- Department of Animal Breeding, Nutrition and Laboratory Animal Science, Faculty of Veterinary Science, Szent István University, István u. 2 H-1078, Budapest, Hungary.
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