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Luigi-Sierra MG, Martínez A, Macri M, Delgado JV, Castelló A, Alvarez JF, Such X, Jordana J, Amills M. Single and longitudinal genome-wide association studies for dairy traits available in goats with three recorded lactations. Anim Genet 2024; 55:257-264. [PMID: 38131417 DOI: 10.1111/age.13391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]
Abstract
Milk yield and composition phenotypes are systematically recorded across several lactations in goats, but the majority of genome-wide association studies (GWAS) performed so far have rather ignored the longitudinal nature of such data. Here, we have used two different GWAS approaches to analyse data from three lactations recorded in Murciano-Granadina goats. In Analysis 1, independent GWAS have been carried out for each trait and lactation, while a single longitudinal GWAS, jointly considering all data, has been performed in Analysis 2. In both analyses, genome-wide significant QTL for lactose percentage on chromosome 2 (129.77-131.01 Mb) and for milk protein percentage on the chromosome 6 (74.8-94.6 Mb) casein gene cluster region were detected. In Analysis 1, several QTL were not replicated in all three lactations, possibly due to the existence of lactation-specific genetic determinants. In Analysis 2, we identified several genome-wide significant QTL related to milk yield and protein content that were not uncovered in Analysis 1. The increased number of QTL identified in Analysis 2 suggests that the longitudinal GWAS is particularly well suited for the genetic analysis of dairy traits. Moreover, our data confirm that variability within or close to the casein complex is the main genetic determinant of milk protein percentage in Murciano-Granadina goats.
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Affiliation(s)
- Maria Gracia Luigi-Sierra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Amparo Martínez
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | - Martina Macri
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | | | - Anna Castelló
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Javier Fernández Alvarez
- Asociación Nacional de Criadores de Caprino de Raza Murciano-Granadina (CAPRIGRAN), Granada, Spain
| | - Xavier Such
- Group of Research in Ruminants (G2R), Department of Animal and Food Science, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Jordi Jordana
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Spain
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Reyer H, Abou-Soliman I, Schulze M, Henne H, Reinsch N, Schoen J, Wimmers K. Genome-Wide Association Analysis of Semen Characteristics in Piétrain Boars. Genes (Basel) 2024; 15:382. [PMID: 38540441 PMCID: PMC10969825 DOI: 10.3390/genes15030382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 06/14/2024] Open
Abstract
Since artificial insemination is common practice in pig breeding, the quality and persistence of the semen are decisive for the usability of individual boars. In the current study, genome-wide association analyses were performed to investigate the genetic variability underlying phenotypic variations in semen characteristics. These traits comprise sperm morphology and sperm motility under different temporal and thermal storage conditions, in addition to standard semen quality parameters. Two consecutive samples of the fourth and fifth ejaculates from the same boar were comprehensively analyzed in a genotyped Piétrain boar population. A total of 13 genomic regions on different chromosomes were identified that contain single-nucleotide polymorphisms significantly associated with these traits. Subsequent analysis of the genomic regions revealed candidate genes described to be involved in spermatogenesis, such as FOXL3, GPER1, PDGFA, PRKAR1B, SNRK, SUN1, and TSPO, and sperm motility, including ARRDC4, CEP78, DNAAF5, and GPER1. Some of these genes were also associated with male fertility or infertility in mammals (e.g., CEP78, GPER1). The analyses based on these laboriously determined and valuable phenotypes contribute to a better understanding of the genetic background of male fertility traits in pigs and could prospectively contribute to the improvement of sperm quality through breeding approaches.
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Affiliation(s)
- Henry Reyer
- Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (I.A.-S.); (N.R.); (K.W.)
| | - Ibrahim Abou-Soliman
- Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (I.A.-S.); (N.R.); (K.W.)
- Department of Animal and Poultry Breeding, Desert Research Center, Cairo 11753, Egypt
| | - Martin Schulze
- Institute for Reproduction of Farm Animals Schönow, 16321 Bernau, Germany;
| | | | - Norbert Reinsch
- Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (I.A.-S.); (N.R.); (K.W.)
| | - Jennifer Schoen
- Leibniz Institute for Zoo and Wildlife Research (IZW), 10315 Berlin, Germany;
- Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany
| | - Klaus Wimmers
- Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (I.A.-S.); (N.R.); (K.W.)
- Faculty of Agricultural and Environmental Sciences, University of Rostock, 18059 Rostock, Germany
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Hodge MJ, de Las Heras-Saldana S, Rindfleish SJ, Stephen CP, Pant SD. QTLs and Candidate Genes Associated with Semen Traits in Merino Sheep. Animals (Basel) 2023; 13:2286. [PMID: 37508063 PMCID: PMC10376747 DOI: 10.3390/ani13142286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Ram semen traits play a significant role in conception outcomes, which in turn may influence reproductive efficiency and the overall productivity and profitability of sheep enterprises. Since hundreds of ewes may be inseminated from a single ejaculate, it is important to evaluate semen quality prior to use in sheep breeding programs. Given that semen traits have been found to be heritable, genetic variation likely contributes to the variability observed in these traits. Identifying such genetic variants could provide novel insights into the molecular mechanisms underlying variability in semen traits. Therefore, this study aimed to identify quantitative trait loci (QTLs) associated with semen traits in Merino sheep. A genome-wide association study (GWAS) was undertaken using 4506 semen collection records from 246 Merino rams collected between January 2002 and May 2021. The R package RepeatABEL was used to perform a GWAS for semen volume, gross motility, concentration, and percent post-thaw motility. A total of 35 QTLs, located on 16 Ovis aries autosomes (OARs), were significantly associated with either of the four semen traits in this study. A total of 89, 95, 33, and 73 candidate genes were identified, via modified Bonferroni, within the QTLs significantly associated with volume, gross motility, concentration, and percent post-thaw motility, respectively. Among the candidate genes identified, SORD, SH2B1, and NT5E have been previously described to significantly influence spermatogenesis, spermatozoal motility, and high percent post-thaw motility, respectively. Several candidate genes identified could potentially influence ram semen traits based on existing evidence in the literature. As such, validation of these putative candidates may offer the potential to develop future strategies to improve sheep reproductive efficiency. Furthermore, Merino ram semen traits are lowly heritable (0.071-0.139), and thus may be improved by selective breeding.
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Affiliation(s)
- Marnie J Hodge
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- Apiam Animal Health, Apiam Genetic Services, Dubbo, NSW 2830, Australia
| | - Sara de Las Heras-Saldana
- Animal Genetics and Breeding Unit, a Joint Venture of NSW Department of Primary Industries and University of New England, Armidale, NSW 2351, Australia
| | | | - Cyril P Stephen
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- Gulbali Institute, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW 2678, Australia
| | - Sameer D Pant
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- Gulbali Institute, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW 2678, Australia
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Gauzere J, Pemberton JM, Slate J, Morris A, Morris S, Walling CA, Johnston SE. A polygenic basis for birth weight in a wild population of red deer (Cervus elaphus). G3 (BETHESDA, MD.) 2023; 13:jkad018. [PMID: 36652410 PMCID: PMC10085764 DOI: 10.1093/g3journal/jkad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/09/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023]
Abstract
The genetic architecture of traits under selection has important consequences for the response to selection and potentially for population viability. Early QTL mapping studies in wild populations have reported loci with large effect on trait variation. However, these results are contradicted by more recent genome-wide association analyses, which strongly support the idea that most quantitative traits have a polygenic basis. This study aims to re-evaluate the genetic architecture of a key morphological trait, birth weight, in a wild population of red deer (Cervus elaphus), using genomic approaches. A previous study using 93 microsatellite and allozyme markers and linkage mapping on a kindred of 364 deer detected a pronounced QTL on chromosome 21 explaining 29% of the variance in birth weight, suggesting that this trait is partly controlled by genes with large effects. Here, we used data for more than 2,300 calves genotyped at >39,000 SNP markers and two approaches to characterise the genetic architecture of birth weight. First, we performed a genome-wide association (GWA) analysis, using a genomic relatedness matrix to account for population structure. We found no SNPs significantly associated with birth weight. Second, we used genomic prediction to estimate the proportion of variance explained by each SNP and chromosome. This analysis confirmed that most genetic variance in birth weight was explained by loci with very small effect sizes. Third, we found that the proportion of variance explained by each chromosome was slightly positively correlated with its size. These three findings highlight a highly polygenic architecture for birth weight, which contradicts the previous QTL study. These results are probably explained by the differences in how associations are modelled between QTL mapping and GWA. Our study suggests that models of polygenic adaptation are the most appropriate to study the evolutionary trajectory of this trait.
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Affiliation(s)
- Julie Gauzere
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
- AGAP, Université Montpellier, CIRAD, INRAE, Institut Agro, 34090 Montpellier, France
| | | | - Jon Slate
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Alison Morris
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sean Morris
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Craig A Walling
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Susan E Johnston
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
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Johnsson M, Wall H, Lopes Pinto FA, Fleming RH, McCormack HA, Benavides-Reyes C, Dominguez-Gasca N, Sanchez-Rodriguez E, Dunn IC, Rodriguez-Navarro AB, Kindmark A, de Koning DJ. Genetics of tibia bone properties of crossbred commercial laying hens in different housing systems. G3 (BETHESDA, MD.) 2022; 13:6855652. [PMID: 36453438 PMCID: PMC9911068 DOI: 10.1093/g3journal/jkac302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/02/2021] [Accepted: 11/07/2022] [Indexed: 12/05/2022]
Abstract
Osteoporosis and bone fractures are a severe problem for the welfare of laying hens, with genetics and environment, such as housing system, each making substantial contributions to bone strength. In this work, we performed genetic analyses of bone strength, bone mineral density, and bone composition, as well as body weight, in 860 commercial crossbred laying hens from 2 different companies, kept in either furnished cages or floor pens. We compared bone traits between housing systems and crossbreds and performed a genome-wide association study of bone properties and body weight. As expected, the 2 housing systems produced a large difference in bone strength, with layers housed in floor pens having stronger bones. These differences were accompanied by differences in bone geometry, mineralization, and chemical composition. Genome scans either combining or independently analyzing the 2 housing systems revealed no genome-wide significant loci for bone breaking strength. We detected 3 loci for body weight that were shared between the housing systems on chromosomes 4, 6, and 27 (either genome-wide significant or suggestive) and these coincide with associations for bone length. In summary, we found substantial differences in bone strength, content, and composition between hens kept in floor pens and furnished cages that could be attributed to greater physical activity in pen housing. We found little evidence for large-effect loci for bone strength in commercial crossbred hens, consistent with a highly polygenic architecture for bone strength in the production environment. The lack of consistent genetic associations between housing systems in combination with the differences in bone phenotypes could be due to gene-by-environment interactions with housing system or a lack of power to detect shared associations for bone strength.
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Affiliation(s)
- Martin Johnsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 756 51 Uppsala, Sweden
| | - Helena Wall
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Fernando A Lopes Pinto
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 756 51 Uppsala, Sweden
| | - Robert H Fleming
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | | | | | | | | | - Ian C Dunn
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | | | - Andreas Kindmark
- Department of Medical Sciences, Uppsala University, Akademiska sjukhuset, 751 85 Uppsala, Sweden
| | - Dirk-Jan de Koning
- Corresponding author. Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07 Uppsala, Sweden.
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Pepke ML, Kvalnes T, Lundregan S, Boner W, Monaghan P, Saether BE, Jensen H, Ringsby TH. Genetic architecture and heritability of early-life telomere length in a wild passerine. Mol Ecol 2022; 31:6360-6381. [PMID: 34825754 DOI: 10.1111/mec.16288] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 10/01/2021] [Accepted: 11/09/2021] [Indexed: 01/31/2023]
Abstract
Early-life telomere length (TL) is associated with fitness in a range of organisms. Little is known about the genetic basis of variation in TL in wild animal populations, but to understand the evolutionary and ecological significance of TL it is important to quantify the relative importance of genetic and environmental variation in TL. In this study, we measured TL in 2746 house sparrow nestlings sampled across 20 years and used an animal model to show that there is a small heritable component of early-life TL (h2 = 0.04). Variation in TL among individuals was mainly driven by environmental (annual) variance, but also brood and parental effects. Parent-offspring regressions showed a large maternal inheritance component in TL ( h maternal 2 = 0.44), but no paternal inheritance. We did not find evidence for a negative genetic correlation underlying the observed negative phenotypic correlation between TL and structural body size. Thus, TL may evolve independently of body size and the negative phenotypic correlation is likely to be caused by nongenetic environmental effects. We further used genome-wide association analysis to identify genomic regions associated with TL variation. We identified several putative genes underlying TL variation; these have been inferred to be involved in oxidative stress, cellular growth, skeletal development, cell differentiation and tumorigenesis in other species. Together, our results show that TL has a low heritability and is a polygenic trait strongly affected by environmental conditions in a free-living bird.
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Affiliation(s)
- Michael Le Pepke
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Thomas Kvalnes
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Sarah Lundregan
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Winnie Boner
- Institute of Biodiversity, Animal Health and Comparative Medicine (IBAHCM), University of Glasgow, Glasgow, UK
| | - Pat Monaghan
- Institute of Biodiversity, Animal Health and Comparative Medicine (IBAHCM), University of Glasgow, Glasgow, UK
| | - Bernt-Erik Saether
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Henrik Jensen
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Thor Harald Ringsby
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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Barraud A, Barascou L, Lefebvre V, Sene D, Le Conte Y, Alaux C, Grillenzoni FV, Corvucci F, Serra G, Costa C, Vanderplanck M, Michez D. Variations in Nutritional Requirements Across Bee Species. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.824750] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
With 2,000 species currently recorded in Europe, bees are a highly diversified and efficient group of pollinating insects. They obtain their nutrients from nectar and pollen of flowers. However, the chemical composition of these resources, especially of pollen (e.g., protein, lipid, amino acids, fatty acids, or sterol content), is highly variable among plant species. While it is well-known that bees show interspecific variation in their floral choices, there is a lack of information on the nutritional requirements of different bee species. We therefore developed original experiments in laboratory conditions to evaluate the interspecific variations in bee nutritional requirements. We analyzed the chemical content of eight pollen blends, different in terms of protein, lipid, amino acids, and sterols total concentration and profiles. Each pollen blend was provided to four different bee model species: honey bees (Apis mellifera), bumblebees (Bombus terrestris), mason bees (Osmia bicornis and Osmia cornuta). For each species, specific protocols were used to monitor their development (e.g., weight, timing, survival) and resource collection. Overall, we found that the nutritional requirements across those species are different, and that a low-quality diet for one species is not necessarily low-quality for another one. While honey bees are negatively impacted by diets with a high protein content (~40%), bumblebees and mason bees develop normally on these diets but struggle on diets with a low total amino acid and sterol content, specifically with low concentrations of 24-methylenecholesterol and β-sitosterol. Overall, our study supports the need of conserving and/or introducing plant diversity into managed ecosystems to meet the natural nutritional preferences of bees at species and community level.
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Genomic Selection and Genome-Wide Association Analysis for Stress Response, Disease Resistance and Body Weight in European Seabass. Animals (Basel) 2022; 12:ani12030277. [PMID: 35158601 PMCID: PMC8833606 DOI: 10.3390/ani12030277] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary In the present study, the genetic architecture of the stress response, body weight, and disease resistance in European seabass were studied, providing fruitful results for further research. Initially, the above traits were recorded and genotyping on a large scale was performed in those fish. The recorded data and genotypes were combined and analyzed to find genomic areas affecting them as well as to estimate the heritability of those traits. Stress response traits and body weight were medium heritable, while genomic regions affecting them were detected. However, no genomic areas related to disease resistance were revealed. These findings improve our knowledge of the genetic structure of those traits and can be utilized in a breeding program for the genetic improvement of aquaculture broodstocks. Abstract The majority of the genetic studies in aquaculture breeding programs focus on commercial traits such as body weight, morphology, and resistance against diseases. However, studying stress response in European seabass may contribute to the understanding of the genetic component of stress and its future use to select broodstock whose offspring may potentially be less affected by handling. A total of 865 European seabass offspring were used to measure body weight and stress response. Moreover, a disease challenge experiment with Vibrio anguillarum was conducted in a subset (332) of the above fish to study disease resistance. Fish were genotyped with a 57k SNP array, and a Genome-Wide Association study (GWAS) was performed. Five SNPs were found to be statistically significant, three of which affect stress indicators and body weight (in a subgroup of the population), and a putative SNP affects growth performance, while no SNP associated with resistance to Vibrio was found. A moderate to high genomic heritability regarding stress indicators and body weight was estimated using the Restricted Maximum Likelihood (REML) process. Finally, the accuracy, along with the correlation between Estimated Breeding Values (EBVs) and Genomic Estimated Breeding Values (GEBVs), were calculated for all the traits.
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Peters L, Huisman J, Kruuk LEB, Pemberton JM, Johnston SE. Genomic analysis reveals a polygenic architecture of antler morphology in wild red deer (Cervus elaphus). Mol Ecol 2021; 31:1281-1298. [PMID: 34878674 DOI: 10.1111/mec.16314] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 11/28/2022]
Abstract
Sexually selected traits show large variation and rapid evolution across the animal kingdom, yet genetic variation often persists within populations despite apparent directional selection. A key step in solving this long-standing paradox is to determine the genetic architecture of sexually selected traits to understand evolutionary drivers and constraints at the genomic level. Antlers are a form of sexual weaponry in male red deer (Cervus elaphus). On the island of Rum, Scotland, males with larger antlers have increased breeding success, yet there has been no evidence of any response to selection at the genetic level. To try and understand the mechanisms underlying this observation, we investigate the genetic architecture of ten antler traits and their principal components using genomic data from >38,000 SNPs. We estimate the heritabilities and genetic correlations of the antler traits using a genomic relatedness approach. We then use genome-wide association and haplotype-based regional heritability to identify regions of the genome underlying antler morphology, and an empirical Bayes approach to estimate the underlying distributions of allele effect sizes. We show that antler morphology is highly repeatable over an individual's lifetime, heritable and has a polygenic architecture and that almost all antler traits are positively genetically correlated with some loci identified as having pleiotropic effects. Our findings suggest that a large mutational target and genetic covariances among antler traits, in part maintained by pleiotropy, are likely to contribute to the maintenance of genetic variation in antler morphology in this population.
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Affiliation(s)
- Lucy Peters
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Jisca Huisman
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Loeske E B Kruuk
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Susan E Johnston
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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10
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Esmaeili-Fard SM, Gholizadeh M, Hafezian SH, Abdollahi-Arpanahi R. Genes and Pathways Affecting Sheep Productivity Traits: Genetic Parameters, Genome-Wide Association Mapping, and Pathway Enrichment Analysis. Front Genet 2021; 12:710613. [PMID: 34394196 PMCID: PMC8355708 DOI: 10.3389/fgene.2021.710613] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 07/02/2021] [Indexed: 11/13/2022] Open
Abstract
Ewe productivity is a composite and maternal trait that is considered the most important economic trait in sheep meat production. The objective of this study was the application of alternative genome-wide association study (GWAS) approaches followed by gene set enrichment analysis (GSEA) on the ewes’ genome to identify genes affecting pregnancy outcomes and lamb growth after parturition in Iranian Baluchi sheep. Three maternal composite traits at birth and weaning were considered. The traits were progeny birth weight, litter mean weight at birth, total litter weight at birth, progeny weaning weight, litter mean weight at weaning, and total litter weight at weaning. GWASs were performed on original phenotypes as well as on estimated breeding values. The significant SNPs associated with composite traits at birth were located within or near genes RDX, FDX1, ARHGAP20, ZC3H12C, THBS1, and EPG5. Identified genes and pathways have functions related to pregnancy, such as autophagy in the placenta, progesterone production by the placenta, placental formation, calcium ion transport, and maternal immune response. For composite traits at weaning, genes (NR2C1, VEZT, HSD17B4, RSU1, CUBN, VIM, PRLR, and FTH1) and pathways affecting feed intake and food conservation, development of mammary glands cytoskeleton structure, and production of milk components like fatty acids, proteins, and vitamin B-12, were identified. The results show that calcium ion transport during pregnancy and feeding lambs by milk after parturition can have the greatest impact on weight gain as compared to other effects of maternal origin.
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Affiliation(s)
- Seyed Mehdi Esmaeili-Fard
- Department of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran
| | - Mohsen Gholizadeh
- Department of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran
| | - Seyed Hasan Hafezian
- Department of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran
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11
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Johnsson M, Whalen A, Ros-Freixedes R, Gorjanc G, Chen CY, Herring WO, de Koning DJ, Hickey JM. Genetic variation in recombination rate in the pig. Genet Sel Evol 2021; 53:54. [PMID: 34171988 PMCID: PMC8235837 DOI: 10.1186/s12711-021-00643-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/02/2021] [Indexed: 11/10/2022] Open
Abstract
Background Meiotic recombination results in the exchange of genetic material between homologous chromosomes. Recombination rate varies between different parts of the genome, between individuals, and is influenced by genetics. In this paper, we assessed the genetic variation in recombination rate along the genome and between individuals in the pig using multilocus iterative peeling on 150,000 individuals across nine genotyped pedigrees. We used these data to estimate the heritability of recombination and perform a genome-wide association study of recombination in the pig. Results Our results confirmed known features of the recombination landscape of the pig genome, including differences in genetic length of chromosomes and marked sex differences. The recombination landscape was repeatable between lines, but at the same time, there were differences in average autosome-wide recombination rate between lines. The heritability of autosome-wide recombination rate was low but not zero (on average 0.07 for females and 0.05 for males). We found six genomic regions that are associated with recombination rate, among which five harbour known candidate genes involved in recombination: RNF212, SHOC1, SYCP2, MSH4 and HFM1. Conclusions Our results on the variation in recombination rate in the pig genome agree with those reported for other vertebrates, with a low but nonzero heritability, and the identification of a major quantitative trait locus for recombination rate that is homologous to that detected in several other species. This work also highlights the utility of using large-scale livestock data to understand biological processes. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00643-0.
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Affiliation(s)
- Martin Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK. .,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 750 07, Uppsala, Sweden.
| | - Andrew Whalen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK
| | - Roger Ros-Freixedes
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK.,Departament de Ciència Animal, Universitat de Lleida-Agrotecnio-CERCA Center, Lleida, Spain
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK
| | - Ching-Yi Chen
- Pig Improvement Company, Genus plc, 100 Bluegrass Commons Blvd., Ste2200, Hendersonville, TN, 37075, USA
| | - William O Herring
- Pig Improvement Company, Genus plc, 100 Bluegrass Commons Blvd., Ste2200, Hendersonville, TN, 37075, USA
| | - Dirk-Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 750 07, Uppsala, Sweden
| | - John M Hickey
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK
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12
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Blanc F, Maroilley T, Revilla M, Lemonnier G, Leplat JJ, Billon Y, Ravon L, Bouchez O, Bidanel JP, Bed'Hom B, Pinard-van der Laan MH, Estellé J, Rogel-Gaillard C. Influence of genetics and the pre-vaccination blood transcriptome on the variability of antibody levels after vaccination against Mycoplasma hyopneumoniae in pigs. Genet Sel Evol 2021; 53:24. [PMID: 33731010 PMCID: PMC7972226 DOI: 10.1186/s12711-021-00614-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 02/16/2021] [Indexed: 12/13/2022] Open
Abstract
Background The impact of individual genetic and genomic variations on immune responses is an emerging lever investigated in vaccination strategies. In our study, we used genetic and pre-vaccination blood transcriptomic data to study vaccine effectiveness in pigs. Results A cohort of 182 Large White pigs was vaccinated against Mycoplasma hyopneumoniae (M. hyo) at weaning (28 days of age), with a booster 21 days later. Vaccine response was assessed by measuring seric M. hyo antibodies (Ab) at 0 (vaccination day), 21 (booster day), 28, 35, and 118 days post-vaccination (dpv). Inter-individual variability of M. hyo Ab levels was observed at all time points and the corresponding heritabilities ranged from 0.46 to 0.57. Ab persistence was higher in females than in males. Genome-wide association studies with a 658 K SNP panel revealed two genomic regions associated with variations of M. hyo Ab levels at 21 dpv at positions where immunity-related genes have been mapped, DAB2IP on chromosome 1, and ASAP1, CYRIB and GSDMC on chromosome 4. We studied covariations of Ab responses with the pre-vaccination blood transcriptome obtained by RNA-Seq for a subset of 82 pigs. Weighted gene correlation network and differential expression analyses between pigs that differed in Ab responses highlighted biological functions that were enriched in heme biosynthesis and platelet activation for low response at 21 dpv, innate antiviral immunity and dendritic cells for high response at 28 and 35 dpv, and cell adhesion and extracellular matrix for high response at 118 dpv. Sparse partial least squares discriminant analysis identified 101 genes that efficiently predicted divergent responders at all time points. We found weak negative correlations of M. hyo Ab levels with body weight traits, which revealed a trade-off that needs to be further explored. Conclusions We confirmed the influence of the host genetics on vaccine effectiveness to M. hyo and provided evidence that the pre-vaccination blood transcriptome co-varies with the Ab response. Our results highlight that both genetic markers and blood biomarkers could be used as potential predictors of vaccine response levels and more studies are required to assess whether they can be exploited in breeding programs.
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Affiliation(s)
- Fany Blanc
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
| | - Tatiana Maroilley
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Manuel Revilla
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Gaëtan Lemonnier
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Jean-Jacques Leplat
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | | | | | | | - Jean-Pierre Bidanel
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Bertrand Bed'Hom
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | | | - Jordi Estellé
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
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13
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Ravindran SP, Tams V, Cordellier M. Transcriptome‐wide genotype–phenotype associations in
Daphnia
in a predation risk environment. J Evol Biol 2020; 34:879-892. [DOI: 10.1111/jeb.13699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 08/03/2020] [Accepted: 08/29/2020] [Indexed: 12/30/2022]
Affiliation(s)
- Suda Parimala Ravindran
- Department of Marine Sciences Tjärnö Marine Laboratory University of Gothenburg Strömstad Sweden
| | - Verena Tams
- Institute of Marine Ecosystem and Fishery Science Universität Hamburg Hamburg Germany
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14
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Duntsch L, Tomotani BM, de Villemereuil P, Brekke P, Lee KD, Ewen JG, Santure AW. Polygenic basis for adaptive morphological variation in a threatened Aotearoa | New Zealand bird, the hihi ( Notiomystis cincta). Proc Biol Sci 2020; 287:20200948. [PMID: 32842928 PMCID: PMC7482260 DOI: 10.1098/rspb.2020.0948] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 07/30/2020] [Indexed: 12/26/2022] Open
Abstract
To predict if a threatened species can adapt to changing selective pressures, it is crucial to understand the genetic basis of adaptive traits, especially in species historically affected by severe bottlenecks. We estimated the heritability of three hihi (Notiomystis cincta) morphological traits known to be under selection (nestling tarsus length, body mass and head-bill length) using 523 individuals and 39 699 single nucleotide polymorphisms (SNPs) from a 50 K Affymetrix SNP chip. We then examined the genetic architecture of the traits via chromosome partitioning analyses and genome-wide association scans (GWAS). Heritabilities estimated using pedigree relatedness or genomic relatedness were low. For tarsus length, the proportion of genetic variance explained by each chromosome was positively correlated with its size, and more than one chromosome explained significant variation for body mass and head-bill length. Finally, GWAS analyses suggested many loci of small effect contributing to trait variation for all three traits, although one locus (an SNP within an intron of the transcription factor HEY2) was tentatively associated with tarsus length. Our findings suggest a polygenic nature for the morphological traits, with many small effect size loci contributing to the majority of the variation, similar to results from many other wild populations. However, the small effective population size, polygenic architecture and already low heritabilities suggest that both the total response and rate of response to selection are likely to be limited in hihi.
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Affiliation(s)
- Laura Duntsch
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Pierre de Villemereuil
- Institut de Systématique, Évolution, Biodiversité (ISYEB), École Pratique des Hautes Études PSL, MNHN, CNRS, Sorbonne Université, Université des Antilles, Paris, France
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - Kate D. Lee
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - John G. Ewen
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - Anna W. Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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15
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Lundregan SL, Niskanen AK, Muff S, Holand H, Kvalnes T, Ringsby T, Husby A, Jensen H. Resistance to gapeworm parasite has both additive and dominant genetic components in house sparrows, with evolutionary consequences for ability to respond to parasite challenge. Mol Ecol 2020; 29:3812-3829. [DOI: 10.1111/mec.15491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 05/12/2020] [Accepted: 05/21/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Sarah L. Lundregan
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
| | - Alina K. Niskanen
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
- Ecology and Genetics Research Unit University of Oulu Oulu Finland
| | - Stefanie Muff
- Centre for Biodiversity Dynamics Department of Mathematical Sciences Norwegian University of Science and Technology Trondheim Norway
| | - Håkon Holand
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
| | - Thomas Kvalnes
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
| | - Thor‐Harald Ringsby
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
| | - Arild Husby
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
- Evolutionary Biology Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Henrik Jensen
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
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16
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Shafquat A, Crystal RG, Mezey JG. Identifying novel associations in GWAS by hierarchical Bayesian latent variable detection of differentially misclassified phenotypes. BMC Bioinformatics 2020; 21:178. [PMID: 32381021 PMCID: PMC7204256 DOI: 10.1186/s12859-020-3387-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 01/24/2020] [Indexed: 12/22/2022] Open
Abstract
Background Heterogeneity in the definition and measurement of complex diseases in Genome-Wide Association Studies (GWAS) may lead to misdiagnoses and misclassification errors that can significantly impact discovery of disease loci. While well appreciated, almost all analyses of GWAS data consider reported disease phenotype values as is without accounting for potential misclassification. Results Here, we introduce Phenotype Latent variable Extraction of disease misdiagnosis (PheLEx), a GWAS analysis framework that learns and corrects misclassified phenotypes using structured genotype associations within a dataset. PheLEx consists of a hierarchical Bayesian latent variable model, where inference of differential misclassification is accomplished using filtered genotypes while implementing a full mixed model to account for population structure and genetic relatedness in study populations. Through simulations, we show that the PheLEx framework dramatically improves recovery of the correct disease state when considering realistic allele effect sizes compared to existing methodologies designed for Bayesian recovery of disease phenotypes. We also demonstrate the potential of PheLEx for extracting new potential loci from existing GWAS data by analyzing bipolar disorder and epilepsy phenotypes available from the UK Biobank. From the PheLEx analysis of these data, we identified new candidate disease loci not previously reported for these datasets that have value for supplemental hypothesis generation. Conclusion PheLEx shows promise in reanalyzing GWAS datasets to provide supplemental candidate loci that are ignored by traditional GWAS analysis methodologies.
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Affiliation(s)
- Afrah Shafquat
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA.,Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jason G Mezey
- Department of Computational Biology, Cornell University, Ithaca, NY, USA. .,Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA.
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17
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Gervais L, Hewison AJM, Morellet N, Bernard M, Merlet J, Cargnelutti B, Chaval Y, Pujol B, Quéméré E. Pedigree-free quantitative genetic approach provides evidence for heritability of movement tactics in wild roe deer. J Evol Biol 2020; 33:595-607. [PMID: 31985133 DOI: 10.1111/jeb.13594] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 01/07/2020] [Accepted: 01/13/2020] [Indexed: 11/30/2022]
Abstract
Assessing the evolutionary potential of animal populations in the wild is crucial to understanding how they may respond to selection mediated by rapid environmental change (e.g. habitat loss and fragmentation). A growing number of studies have investigated the adaptive role of behaviour, but assessments of its genetic basis in a natural setting remain scarce. We combined intensive biologging technology with genome-wide data and a pedigree-free quantitative genetic approach to quantify repeatability, heritability and evolvability for a suite of behaviours related to the risk avoidance-resource acquisition trade-off in a wild roe deer (Capreolus capreolus) population inhabiting a heterogeneous, human-dominated landscape. These traits, linked to the stress response, movement and space-use behaviour, were all moderately to highly repeatable. Furthermore, the repeatable among-individual component of variation in these traits was partly due to additive genetic variance, with heritability estimates ranging from 0.21 ± 0.08 to 0.70 ± 0.11 and evolvability ranging from 1.1% to 4.3%. Changes in the trait mean can therefore occur under hypothetical directional selection over just a few generations. To the best of our knowledge, this is the first empirical demonstration of additive genetic variation in space-use behaviour in a free-ranging population based on genomic relatedness data. We conclude that wild animal populations may have the potential to adjust their spatial behaviour to human-driven environmental modifications through microevolutionary change.
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Affiliation(s)
- Laura Gervais
- CEFS, INRAE, Université de Toulouse, Castanet-Tolosan, France.,LTSER ZA PYRénées GARonne, Auzeville-Tolosane, France.,Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), CNRS, IRD, UPS, Université Fédérale de Toulouse Midi-Pyrénées, Toulouse, France
| | - Aidan J M Hewison
- CEFS, INRAE, Université de Toulouse, Castanet-Tolosan, France.,LTSER ZA PYRénées GARonne, Auzeville-Tolosane, France
| | - Nicolas Morellet
- CEFS, INRAE, Université de Toulouse, Castanet-Tolosan, France.,LTSER ZA PYRénées GARonne, Auzeville-Tolosane, France
| | - Maria Bernard
- INRAE, GABI, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,INRAE, SIGENAE, Jouy-en-Josas, France
| | - Joël Merlet
- CEFS, INRAE, Université de Toulouse, Castanet-Tolosan, France.,LTSER ZA PYRénées GARonne, Auzeville-Tolosane, France
| | - Bruno Cargnelutti
- CEFS, INRAE, Université de Toulouse, Castanet-Tolosan, France.,LTSER ZA PYRénées GARonne, Auzeville-Tolosane, France
| | - Yannick Chaval
- CEFS, INRAE, Université de Toulouse, Castanet-Tolosan, France.,LTSER ZA PYRénées GARonne, Auzeville-Tolosane, France
| | - Benoit Pujol
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), CNRS, IRD, UPS, Université Fédérale de Toulouse Midi-Pyrénées, Toulouse, France.,USR 3278 CRIOBE, PSL Université Paris: EPHE-UPVD-CNRS, Université de Perpignan, Perpignan Cedex, France
| | - Erwan Quéméré
- CEFS, INRAE, Université de Toulouse, Castanet-Tolosan, France.,LTSER ZA PYRénées GARonne, Auzeville-Tolosane, France.,ESE, Ecology and Ecosystems Health, Ouest, INRAE, Rennes, France
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18
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Sim Z, Coltman DW. Heritability of Horn Size in Thinhorn Sheep. Front Genet 2019; 10:959. [PMID: 31681413 PMCID: PMC6797622 DOI: 10.3389/fgene.2019.00959] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 09/09/2019] [Indexed: 12/31/2022] Open
Abstract
Understanding the genetic basis of fitness-related trait variation has long been of great interest to evolutionary biologists. Secondary sexual characteristics, such as horns in bovids, are particularly intriguing since they can be potentially affected by both natural and sexual selection. Until recently, however, the study of fitness-related quantitative trait variation in wild species has been hampered by a lack of genomic resources, pedigree, and/or phenotype data. Recent innovations in genomic technologies have enabled wildlife researchers to perform marker-based relatedness estimation and acquire adequate loci density, enabling both the “top-down” approach of quantitative genetics and the “bottom-up” approach of association studies to describe the genetic basis of fitness-related traits. Here we combine a cross species application of the OvineHD BeadChip and horn measurements (horn length, base circumference, and volume) from harvested thinhorn sheep to examine the heritability and to perform a genome-wide single-nucleotide polymorphism association study of horn size in the species. Thinhorn sheep are mountain ungulates that reside in the mountainous regions of northwestern North America. Thinhorn sheep males grow massive horns that determine the social rank and mating success. We found horn length, base circumference, and volume to be moderately heritable and two loci to be suggestively associated with horn length.
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Affiliation(s)
- Zijian Sim
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.,Fish and Wildlife Forensic Unit, Alberta Fish and Wildlife Enforcement Branch, Government of Alberta, Edmonton, AB, Canada
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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19
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Sutera AM, Riggio V, Mastrangelo S, Di Gerlando R, Sardina MT, Pong-Wong R, Tolone M, Portolano B. Genome-wide association studies for milk production traits in Valle del Belice sheep using repeated measures. Anim Genet 2019; 50:311-314. [PMID: 30983012 DOI: 10.1111/age.12789] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2019] [Indexed: 12/17/2022]
Abstract
Genome-wide association studies (GWASes) have become a powerful tool for identifying genomic regions associated with important traits in livestock. Milk production traits in dairy sheep are measured at different time points during their life span. Using phenotypic data generated from longitudinal traits could improve the power of association studies but until now have received less attention in GWASes as a methodology and has not been implemented. The aim of this study was to carry out a GWAS for milk production traits in Valle del Belice sheep using repeated measures. After quality control, 469 ewes and 37 228 SNPs were retained for the analysis, and phenotypic data included 5586 test-day records for five milk production traits (milk yield, MY; fat yield and percentage, FY and F%; protein yield and percentage, PY and P%). Nine SNPs located within or close to known genes were found to be associated with milk production traits. In particular, rs398340969, associated with both milk yield and protein yield, is located within the DCPS gene. In addition, rs425417915 and rs417079368, both associated with both fat percentage and protein percentage, are located within the TTC7B gene and at 0.37 Mb within the SUCNR1 gene respectively. In summary, the use of repeated records was beneficial for mapping genomic regions affecting milk production traits in the Valle del Belice sheep.
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Affiliation(s)
- A M Sutera
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - V Riggio
- The Roslin Institute and R(D)SVS, Easter Bush, Roslin, EH25 9RG, UK
| | - S Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - R Di Gerlando
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - M T Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - R Pong-Wong
- The Roslin Institute and R(D)SVS, Easter Bush, Roslin, EH25 9RG, UK
| | - M Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - B Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
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20
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Kardos M, Shafer AB. The Peril of Gene-Targeted Conservation. Trends Ecol Evol 2018; 33:827-839. [DOI: 10.1016/j.tree.2018.08.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 08/27/2018] [Accepted: 08/28/2018] [Indexed: 01/01/2023]
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21
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Santure AW, Garant D. Wild GWAS-association mapping in natural populations. Mol Ecol Resour 2018; 18:729-738. [PMID: 29782705 DOI: 10.1111/1755-0998.12901] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 12/27/2022]
Abstract
The increasing affordability of sequencing and genotyping technologies has transformed the field of molecular ecology in recent decades. By correlating marker variants with trait variation using association analysis, large-scale genotyping and phenotyping of individuals from wild populations has enabled the identification of genomic regions that contribute to phenotypic differences among individuals. Such "gene mapping" studies are enabling us to better predict evolutionary potential and the ability of populations to adapt to challenges, such as changing environment. These studies are also allowing us to gain insight into the evolutionary processes maintaining variation in natural populations, to better understand genotype-by-environment and epistatic interactions and to track the dynamics of allele frequency change at loci contributing to traits under selection. Gene mapping in the wild using genomewide association scans (GWAS) do, however, come with a number of methodological challenges, not least the population structure in space and time inherent to natural populations. We here provide an overview of these challenges, summarize the exciting methodological advances and applications of association mapping in natural populations reported in this special issue and provide some guidelines for future "wild GWAS" research.
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Affiliation(s)
- Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Dany Garant
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
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22
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Kosch TA, Silva CNS, Brannelly LA, Roberts AA, Lau Q, Marantelli G, Berger L, Skerratt LF. Genetic potential for disease resistance in critically endangered amphibians decimated by chytridiomycosis. Anim Conserv 2018. [DOI: 10.1111/acv.12459] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- T. A. Kosch
- One Health Research Group College of Public Health, Medical and Veterinary Sciences James Cook University Townsville Qld Australia
| | - C. N. S. Silva
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville Qld Australia
| | - L. A. Brannelly
- One Health Research Group College of Public Health, Medical and Veterinary Sciences James Cook University Townsville Qld Australia
- Department of Biological Sciences University of Pittsburgh Pittsburgh PA USA
| | - A. A. Roberts
- One Health Research Group College of Public Health, Medical and Veterinary Sciences James Cook University Townsville Qld Australia
| | - Q. Lau
- Department of Evolutionary Studies of Biosystems Sokendai (The Graduate University for Advanced Studies) Hayama Japan
| | | | - L. Berger
- One Health Research Group College of Public Health, Medical and Veterinary Sciences James Cook University Townsville Qld Australia
| | - L. F. Skerratt
- One Health Research Group College of Public Health, Medical and Veterinary Sciences James Cook University Townsville Qld Australia
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23
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Hendricks S, Anderson EC, Antao T, Bernatchez L, Forester BR, Garner B, Hand BK, Hohenlohe PA, Kardos M, Koop B, Sethuraman A, Waples RS, Luikart G. Recent advances in conservation and population genomics data analysis. Evol Appl 2018. [PMCID: PMC6099823 DOI: 10.1111/eva.12659] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
New computational methods and next‐generation sequencing (NGS) approaches have enabled the use of thousands or hundreds of thousands of genetic markers to address previously intractable questions. The methods and massive marker sets present both new data analysis challenges and opportunities to visualize, understand, and apply population and conservation genomic data in novel ways. The large scale and complexity of NGS data also increases the expertise and effort required to thoroughly and thoughtfully analyze and interpret data. To aid in this endeavor, a recent workshop entitled “Population Genomic Data Analysis,” also known as “ConGen 2017,” was held at the University of Montana. The ConGen workshop brought 15 instructors together with knowledge in a wide range of topics including NGS data filtering, genome assembly, genomic monitoring of effective population size, migration modeling, detecting adaptive genomic variation, genomewide association analysis, inbreeding depression, and landscape genomics. Here, we summarize the major themes of the workshop and the important take‐home points that were offered to students throughout. We emphasize increasing participation by women in population and conservation genomics as a vital step for the advancement of science. Some important themes that emerged during the workshop included the need for data visualization and its importance in finding problematic data, the effects of data filtering choices on downstream population genomic analyses, the increasing availability of whole‐genome sequencing, and the new challenges it presents. Our goal here is to help motivate and educate a worldwide audience to improve population genomic data analysis and interpretation, and thereby advance the contribution of genomics to molecular ecology, evolutionary biology, and especially to the conservation of biodiversity.
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Affiliation(s)
- Sarah Hendricks
- Institute for Bioinformatics and Evolutionary Studies University of Idaho Moscow Idaho
| | - Eric C. Anderson
- Fisheries Ecology Division Southwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration Santa Cruz California
- University of California Santa Cruz California
| | - Tiago Antao
- Division of Biological Sciences University of Montana Missoula Montana
| | - Louis Bernatchez
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | | | - Brittany Garner
- Flathead Lake Biological Station Montana Conservation Genomics Laboratory Division of Biological Science University of Montana Missoula Montana
- Wildlife Program Fish and Wildlife Genomics Group College of Forestry and Conservation University of Montana Missoula Montana
| | - Brian K. Hand
- Flathead Lake Biological Station Montana Conservation Genomics Laboratory Division of Biological Science University of Montana Missoula Montana
| | - Paul A. Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies University of Idaho Moscow Idaho
| | - Martin Kardos
- Flathead Lake Biological Station Montana Conservation Genomics Laboratory Division of Biological Science University of Montana Missoula Montana
| | - Ben Koop
- Department of Biology Centre for Biomedical Research University of Victoria Victoria British Columbia Canada
| | - Arun Sethuraman
- Department of Biological Sciences California State University San Marcos San Marcos California
| | - Robin S. Waples
- NOAA Fisheries Northwest Fisheries Science Center Seattle Washington
| | - Gordon Luikart
- Flathead Lake Biological Station Montana Conservation Genomics Laboratory Division of Biological Science University of Montana Missoula Montana
- Wildlife Program Fish and Wildlife Genomics Group College of Forestry and Conservation University of Montana Missoula Montana
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24
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Lundregan SL, Hagen IJ, Gohli J, Niskanen AK, Kemppainen P, Ringsby TH, Kvalnes T, Pärn H, Rønning B, Holand H, Ranke PS, Båtnes AS, Selvik LK, Lien S, Saether BE, Husby A, Jensen H. Inferences of genetic architecture of bill morphology in house sparrow using a high-density SNP array point to a polygenic basis. Mol Ecol 2018; 27:3498-3514. [DOI: 10.1111/mec.14811] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/15/2018] [Accepted: 06/28/2018] [Indexed: 01/15/2023]
Affiliation(s)
- Sarah L. Lundregan
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Ingerid J. Hagen
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
- Norwegian Institute for Nature Research; Trondheim Norway
| | - Jostein Gohli
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
- Organismal and Evolutionary Biology Research Programme; University of Helsinki; Helsinki Finland
| | - Alina K. Niskanen
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
- Department of Ecology and Genetics; University of Oulu; Oulu Finland
| | - Petri Kemppainen
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
- Organismal and Evolutionary Biology Research Programme; University of Helsinki; Helsinki Finland
| | - Thor Harald Ringsby
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Thomas Kvalnes
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Henrik Pärn
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Bernt Rønning
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Håkon Holand
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Peter S. Ranke
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Anna S. Båtnes
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Linn-Karina Selvik
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics; Department of Animal and Aquacultural Sciences; Faculty of Life Sciences; Norwegian University of Life Sciences; Ås Norway
| | - Bernt-Erik Saether
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Arild Husby
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
- Organismal and Evolutionary Biology Research Programme; University of Helsinki; Helsinki Finland
- Department of Ecology and Genetics; EBC; Uppsala University; Uppsala Sweden
| | - Henrik Jensen
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
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25
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Wessinger CA, Kelly JK, Jiang P, Rausher MD, Hileman LC. SNP-skimming: A fast approach to map loci generating quantitative variation in natural populations. Mol Ecol Resour 2018; 18:1402-1414. [PMID: 30033616 DOI: 10.1111/1755-0998.12930] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 06/13/2018] [Accepted: 06/20/2018] [Indexed: 01/20/2023]
Abstract
Genome-wide association mapping (GWAS) is a method to estimate the contribution of segregating genetic loci to trait variation. A major challenge for applying GWAS to nonmodel species has been generating dense genome-wide markers that satisfy the key requirement that marker data are error-free. Here, we present an approach to map loci within natural populations using inexpensive shallow genome sequencing. This "SNP-skimming" approach involves two steps: an initial genome-wide scan to identify putative targets followed by deep sequencing for confirmation of targeted loci. We apply our method to a test data set of floral dimension variation in the plant Penstemon virgatus, a member of a genus that has experienced dynamic floral adaptation that reflects repeated transitions in primary pollinator. The ability to detect SNPs that generate phenotypic variation depends on population genetic factors such as population allele frequency, effect size and epistasis, as well as sampling effects contingent on missing data and genotype uncertainty. However, both simulations and the Penstemon data suggest that the most significant tests from the initial SNP skim are likely to be true positives-loci with subtle but significant quantitative effects on phenotype. We discuss the promise and limitations of this method and consider optimal experimental design for a given sequencing effort. Simulations demonstrate that sampling a larger number of individual at the expense of average read depth per individual maximizes the power to detect loci.
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Affiliation(s)
- Carolyn A Wessinger
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas
| | - John K Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas
| | - Peng Jiang
- Department of Biology, Duke University, Durham, North Carolina
| | - Mark D Rausher
- Department of Biology, Duke University, Durham, North Carolina
| | - Lena C Hileman
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas
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26
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Brinker T, Bijma P, Vereijken A, Ellen ED. The genetic architecture of socially-affected traits: a GWAS for direct and indirect genetic effects on survival time in laying hens showing cannibalism. Genet Sel Evol 2018; 50:38. [PMID: 30037326 PMCID: PMC6057005 DOI: 10.1186/s12711-018-0409-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/06/2018] [Indexed: 12/01/2022] Open
Abstract
Background Cannibalism is an important welfare problem in the layer industry. Cannibalism is a social behavior where individual survival is affected by direct genetic effects (DGE) and indirect genetic effects (IGE). Previous studies analysed repeated binomial survival, instead of survival time, which improved accuracies of breeding value predictions. Our study aimed at identifying SNPs associated with DGE and IGE for survival time, and comparing results from models that analyse survival time and repeated binomial survival. Methods Survival data of three layer crosses (W1 * WA, W1 * WB, and W1 * WC) were used. Each individual had one survival time record and 13 monthly survival (0/1) records. Approximately 30,000 single nucleotide polymorphisms (SNPs) were included in the genome-wide association study (GWAS), using a linear mixed model for survival time, a linear mixed model and a generalized linear mixed model for repeated binomial survival (0/1). Backwards elimination was used to determine phenotypic and genetic variance explained by SNPs. Results The same quantitative trait loci were identified with all models. A SNP associated with DGE was found in cross W1 * WA, with an allele substitution effect of 22 days. This SNP explained 3% of the phenotypic variance, and 36% of the total genetic variance. Four SNPs associated with DGE were found in cross W1 * WB, with effects ranging from 16 to 35 days. These SNPs explained 1 to 6% of the phenotypic variance and 9 to 44% of the total genetic variance. Our results suggest a link of DGE and IGE for survival time in layers with the gamma-aminobutyric acid (GABA) system, since a SNP located near a gene for a GABA receptor was associated with DGE and with IGE (not significant). Conclusions This is one of the first large studies investigating the genetic architecture of a socially-affected trait. The power to detect SNP associations was relatively low and thus we expect that many effects on DGE and IGE remained undetected. Yet, GWAS results revealed SNPs with large DGE and a link of DGE and IGE for survival time in layers with the GABAergic system, which supports existing evidence for the involvement of GABA in the development of abnormal behaviors. Electronic supplementary material The online version of this article (10.1186/s12711-018-0409-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tessa Brinker
- Animal Breeding and Genomics, Wageningen University and Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Piter Bijma
- Animal Breeding and Genomics, Wageningen University and Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Addie Vereijken
- Research and Technology Centre, Hendrix Genetics, P.O. Box 114, 5830 AC, Boxmeer, The Netherlands
| | - Esther D Ellen
- Animal Breeding and Genomics, Wageningen University and Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands.
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27
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Johnston SE, Huisman J, Pemberton JM. A Genomic Region Containing REC8 and RNF212B Is Associated with Individual Recombination Rate Variation in a Wild Population of Red Deer ( Cervus elaphus). G3 (BETHESDA, MD.) 2018; 8:2265-2276. [PMID: 29764960 PMCID: PMC6027875 DOI: 10.1534/g3.118.200063] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Recombination is a fundamental feature of sexual reproduction, ensuring proper disjunction, preventing mutation accumulation and generating new allelic combinations upon which selection can act. However it is also mutagenic, and breaks up favorable allelic combinations previously built up by selection. Identifying the genetic drivers of recombination rate variation is a key step in understanding the causes and consequences of this variation, how loci associated with recombination are evolving and how they affect the potential of a population to respond to selection. However, to date, few studies have examined the genetic architecture of recombination rate variation in natural populations. Here, we use pedigree data from ∼ 2,600 individuals genotyped at ∼ 38,000 SNPs to investigate the genetic architecture of individual autosomal recombination rate in a wild population of red deer (Cervus elaphus). Female red deer exhibited a higher mean and phenotypic variance in autosomal crossover counts (ACC). Animal models fitting genomic relatedness matrices showed that ACC was heritable in females ([Formula: see text] = 0.12) but not in males. A regional heritability mapping approach showed that almost all heritable variation in female ACC was explained by a genomic region on deer linkage group 12 containing the candidate loci REC8 and RNF212B, with an additional region on linkage group 32 containing TOP2B approaching genome-wide significance. The REC8/RNF212B region and its paralogue RNF212 have been associated with recombination in cattle, mice, humans and sheep. Our findings suggest that mammalian recombination rates have a relatively conserved genetic architecture in both domesticated and wild systems, and provide a foundation for understanding the association between recombination loci and individual fitness within this population.
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Affiliation(s)
- Susan E Johnston
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, United Kingdom
| | - Jisca Huisman
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, United Kingdom
| | - Josephine M Pemberton
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, United Kingdom
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28
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Malenfant RM, Davis CS, Richardson ES, Lunn NJ, Coltman DW. Heritability of body size in the polar bears of Western Hudson Bay. Mol Ecol Resour 2018; 18:854-866. [DOI: 10.1111/1755-0998.12889] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 03/23/2018] [Accepted: 03/29/2018] [Indexed: 12/16/2022]
Affiliation(s)
- René M. Malenfant
- Department of Biology University of New Brunswick Fredericton NB Canada
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
| | - Corey S. Davis
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
| | - Evan S. Richardson
- Wildlife Research Division Science and Technology Branch Environment and Climate Change Canada Winnipeg MB Canada
| | - Nicholas J. Lunn
- Wildlife Research Division Science and Technology Branch Environment and Climate Change Canada University of Alberta Edmonton AB Canada
| | - David W. Coltman
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
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29
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Hansson B, Sigeman H, Stervander M, Tarka M, Ponnikas S, Strandh M, Westerdahl H, Hasselquist D. Contrasting results from GWAS and QTL mapping on wing length in great reed warblers. Mol Ecol Resour 2018; 18:867-876. [DOI: 10.1111/1755-0998.12785] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 03/26/2018] [Accepted: 03/29/2018] [Indexed: 01/08/2023]
Affiliation(s)
| | | | - Martin Stervander
- Department of Biology Lund University Lund Sweden
- Institute of Ecology and Evolution University of Oregon Eugene Oregon
| | - Maja Tarka
- Department of Biology Lund University Lund Sweden
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30
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Brieuc MSO, Waters CD, Drinan DP, Naish KA. A practical introduction to Random Forest for genetic association studies in ecology and evolution. Mol Ecol Resour 2018; 18:755-766. [PMID: 29504715 DOI: 10.1111/1755-0998.12773] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 02/08/2018] [Accepted: 02/17/2018] [Indexed: 12/25/2022]
Abstract
Large genomic studies are becoming increasingly common with advances in sequencing technology, and our ability to understand how genomic variation influences phenotypic variation between individuals has never been greater. The exploration of such relationships first requires the identification of associations between molecular markers and phenotypes. Here, we explore the use of Random Forest (RF), a powerful machine-learning algorithm, in genomic studies to discern loci underlying both discrete and quantitative traits, particularly when studying wild or nonmodel organisms. RF is becoming increasingly used in ecological and population genetics because, unlike traditional methods, it can efficiently analyse thousands of loci simultaneously and account for nonadditive interactions. However, understanding both the power and limitations of Random Forest is important for its proper implementation and the interpretation of results. We therefore provide a practical introduction to the algorithm and its use for identifying associations between molecular markers and phenotypes, discussing such topics as data limitations, algorithm initiation and optimization, as well as interpretation. We also provide short R tutorials as examples, with the aim of providing a guide to the implementation of the algorithm. Topics discussed here are intended to serve as an entry point for molecular ecologists interested in employing Random Forest to identify trait associations in genomic data sets.
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Affiliation(s)
- Marine S O Brieuc
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA.,Center for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Charles D Waters
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Daniel P Drinan
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
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31
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Miller JM, Festa-Bianchet M, Coltman DW. Genomic analysis of morphometric traits in bighorn sheep using the Ovine Infinium ® HD SNP BeadChip. PeerJ 2018; 6:e4364. [PMID: 29473002 PMCID: PMC5817937 DOI: 10.7717/peerj.4364] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/23/2018] [Indexed: 11/20/2022] Open
Abstract
Elucidating the genetic basis of fitness-related traits is a major goal of molecular ecology. Traits subject to sexual selection are particularly interesting, as non-random mate choice should deplete genetic variation and thereby their evolutionary benefits. We examined the genetic basis of three sexually selected morphometric traits in bighorn sheep (Ovis canadensis): horn length, horn base circumference, and body mass. These traits are of specific concern in bighorn sheep as artificial selection through trophy hunting opposes sexual selection. Specifically, horn size determines trophy status and, in most North American jurisdictions, if an individual can be legally harvested. Using between 7,994–9,552 phenotypic measures from the long-term individual-based study at Ram Mountain (Alberta, Canada), we first showed that all three traits are heritable (h2 = 0.15–0.23). We then conducted a genome-wide association study (GWAS) utilizing a set of 3,777 SNPs typed in 76 individuals using the Ovine Infinium® HD SNP BeadChip. We found suggestive association for body mass at a single locus (OAR9_91647990). The absence of strong associations with SNPs suggests that the traits are likely polygenic. These results represent a step forward for characterizing the genetic architecture of fitness related traits in sexually dimorphic ungulates.
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Affiliation(s)
- Joshua M Miller
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.,Current affiliation: Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | | | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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32
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A sex-linked supergene controls sperm morphology and swimming speed in a songbird. Nat Ecol Evol 2017; 1:1168-1176. [DOI: 10.1038/s41559-017-0235-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 06/06/2017] [Indexed: 01/08/2023]
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33
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Silva CNS, McFarlane SE, Hagen IJ, Rönnegård L, Billing AM, Kvalnes T, Kemppainen P, Rønning B, Ringsby TH, Sæther BE, Qvarnström A, Ellegren H, Jensen H, Husby A. Insights into the genetic architecture of morphological traits in two passerine bird species. Heredity (Edinb) 2017; 119:197-205. [PMID: 28613280 DOI: 10.1038/hdy.2017.29] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 04/08/2017] [Accepted: 05/04/2017] [Indexed: 01/15/2023] Open
Abstract
Knowledge about the underlying genetic architecture of phenotypic traits is needed to understand and predict evolutionary dynamics. The number of causal loci, magnitude of the effects and location in the genome are, however, still largely unknown. Here, we use genome-wide single-nucleotide polymorphism (SNP) data from two large-scale data sets on house sparrows and collared flycatchers to examine the genetic architecture of different morphological traits (tarsus length, wing length, body mass, bill depth, bill length, total and visible badge size and white wing patches). Genomic heritabilities were estimated using relatedness calculated from SNPs. The proportion of variance captured by the SNPs (SNP-based heritability) was lower in house sparrows compared with collared flycatchers, as expected given marker density (6348 SNPs in house sparrows versus 38 689 SNPs in collared flycatchers). Indeed, after downsampling to similar SNP density and sample size, this estimate was no longer markedly different between species. Chromosome-partitioning analyses demonstrated that the proportion of variance explained by each chromosome was significantly positively related to the chromosome size for some traits and, generally, that larger chromosomes tended to explain proportionally more variation than smaller chromosomes. Finally, we found two genome-wide significant associations with very small-effect sizes. One SNP on chromosome 20 was associated with bill length in house sparrows and explained 1.2% of phenotypic variation (VP), and one SNP on chromosome 4 was associated with tarsus length in collared flycatchers (3% of VP). Although we cannot exclude the possibility of undetected large-effect loci, our results indicate a polygenic basis for morphological traits.
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Affiliation(s)
- C N S Silva
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, Helsinki, Finland
| | - S E McFarlane
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - I J Hagen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - L Rönnegård
- School of Technology and Business Studies, Dalarna University, Falun, Sweden.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - A M Billing
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - T Kvalnes
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - P Kemppainen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - B Rønning
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - T H Ringsby
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - B-E Sæther
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - A Qvarnström
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - H Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - H Jensen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - A Husby
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, Helsinki, Finland.,Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
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34
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Han Y, Peñagaricano F. Unravelling the genomic architecture of bull fertility in Holstein cattle. BMC Genet 2016; 17:143. [PMID: 27842509 PMCID: PMC5109745 DOI: 10.1186/s12863-016-0454-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 11/04/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fertility is considered an important economic trait in dairy cattle. Most studies have investigated cow fertility while bull fertility has received much less consideration. The main objective of this study was to perform a comprehensive genomic analysis in order to unravel the genomic architecture underlying sire fertility in Holstein dairy cattle. The analysis included the application of alternative genome-wide association mapping approaches and the subsequent use of diverse gene set enrichment tools. RESULTS The association analyses identified at least eight genomic regions strongly associated with bull fertility. Most of these regions harbor genes, such as KAT8, CKB, TDRD9 and IGF1R, with functions related to sperm biology, including sperm development, motility and sperm-egg interaction. Moreover, the gene set analyses revealed many significant functional terms, including fertilization, sperm motility, calcium channel regulation, and SNARE proteins. Most of these terms are directly implicated in sperm physiology and male fertility. CONCLUSIONS This study contributes to the identification of genetic variants and biological processes underlying sire fertility. These findings can provide opportunities for improving bull fertility via marker-assisted selection.
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Affiliation(s)
- Yi Han
- Department of Animal Sciences, University of Florida, 2250 Shealy Drive, Gainesville, FL, 32611, USA.,University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Francisco Peñagaricano
- Department of Animal Sciences, University of Florida, 2250 Shealy Drive, Gainesville, FL, 32611, USA. .,University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32610, USA.
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35
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Abstract
Development of free/libre open source software is usually done by a community of people with an interest in the tool. For scientific software, however, this is less often the case. Most scientific software is written by only a few authors, often a student working on a thesis. Once the paper describing the tool has been published, the tool is no longer developed further and is left to its own device. Here we describe the broad, multidisciplinary community we formed around a set of tools for statistical genomics. The GenABEL project for statistical omics actively promotes open interdisciplinary development of statistical methodology and its implementation in efficient and user-friendly software under an open source licence. The software tools developed withing the project collectively make up the GenABEL suite, which currently consists of eleven tools. The open framework of the project actively encourages involvement of the community in all stages, from formulation of methodological ideas to application of software to specific data sets. A web forum is used to channel user questions and discussions, further promoting the use of the GenABEL suite. Developer discussions take place on a dedicated mailing list, and development is further supported by robust development practices including use of public version control, code review and continuous integration. Use of this open science model attracts contributions from users and developers outside the “core team”, facilitating agile statistical omics methodology development and fast dissemination.
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Affiliation(s)
- Lennart C Karssen
- PolyOmica, Groningen, 9722 HC, Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, 3000 CA, Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, 3000 CA, Netherlands
| | - Yurii S Aulchenko
- PolyOmica, Groningen, 9722 HC, Netherlands; Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, 630090, Russian Federation; Novosibirsk State University, Novosibirsk, 630090, Russian Federation; Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
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