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Mondal D, Vanbelle S, Cassese A, Candel MJJM. Review of sample size determination methods for the intraclass correlation coefficient in the one-way analysis of variance model. Stat Methods Med Res 2024; 33:532-553. [PMID: 38320802 PMCID: PMC10981208 DOI: 10.1177/09622802231224657] [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] [Indexed: 03/28/2024]
Abstract
Reliability of measurement instruments providing quantitative outcomes is usually assessed by an intraclass correlation coefficient. When participants are repeatedly measured by a single rater or device, or, are each rated by a different group of raters, the intraclass correlation coefficient is based on a one-way analysis of variance model. When planning a reliability study, it is essential to determine the number of participants and measurements per participant (i.e. number of raters or number of repeated measurements). Three different sample size determination approaches under the one-way analysis of variance model were identified in the literature, all based on a confidence interval for the intraclass correlation coefficient. Although eight different confidence interval methods can be identified, Wald confidence interval with Fisher's large sample variance approximation remains most commonly used despite its well-known poor statistical properties. Therefore, a first objective of this work is comparing the statistical properties of all identified confidence interval methods-including those overlooked in previous studies. A second objective is developing a general procedure to determine the sample size using all approaches since a closed-form formula is not always available. This procedure is implemented in an R Shiny app. Finally, we provide advice for choosing an appropriate sample size determination method when planning a reliability study.
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Affiliation(s)
- Dipro Mondal
- Faculty of Health Medicine and Life Sciences, Department of Methodology and Statistics, Care and Public Health Research Institute (CAPHRI), Maastricht University, Limburg, The Netherlands
| | - Sophie Vanbelle
- Faculty of Health Medicine and Life Sciences, Department of Methodology and Statistics, Care and Public Health Research Institute (CAPHRI), Maastricht University, Limburg, The Netherlands
| | - Alberto Cassese
- Department of Statistics, Computer Science, Applications “Giuseppe Parenti”, The University of Florence, Italy
| | - Math JJM Candel
- Faculty of Health Medicine and Life Sciences, Department of Methodology and Statistics, Care and Public Health Research Institute (CAPHRI), Maastricht University, Limburg, The Netherlands
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2
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Moradi M, Warburton CL, Porto-Neto LR, Silva LFP. Estimating the heritability of nitrogen and carbon isotopes in the tail hair of beef cattle. Genet Sel Evol 2024; 56:3. [PMID: 38172694 PMCID: PMC10763070 DOI: 10.1186/s12711-023-00870-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND The natural abundance of nitrogen (δ15N) and carbon (δ13C) isotopes in animal tissues are used to estimate an animal's efficiency in nitrogen utilization, and their feed conversion efficiency, especially in tropical grazing systems with prolonged protein restriction. It is postulated that selection for improving these two characteristics (δ15N and δ13C) would assist the optimisation of the adaptation in ever-changing environments, particularly in response to climate change. The aim of this study was to determine the heritability of δ15N and δ13C in the tail hair of tropically adapted beef cattle to validate their inclusion in genetic breeding programs. METHODS In total, 492 steers from two breeds, Brahman (n = 268) and Droughtmaster (n = 224) were used in this study. These steers were managed in two mixed breed contemporary groups across two years (year of weaning): steers weaned in 2019 (n = 250) and 2020 (n = 242). Samples of tail switch hair representing hair segments grown during the dry season were collected and analysed for δ15N and δ13C with isotope-ratio mass spectrometry. Heritability and variance components were estimated in a univariate multibreed (and single breed) animal model in WOMBAT and ASReml using three generations of full pedigree. RESULTS The estimated heritability of both traits was significantly different from 0, i.e. 0.43 ± 0.14 and 0.41 ± 0.15 for δ15N and δ13C, respectively. These traits had favourable moderate to high genetic and phenotypic correlations (- 0.78 ± 0.16 and - 0.40 ± 0.04, respectively). The study also provides informative single-breed results in spite of the limited sample size, with estimated heritability values of 0.37 ± 0.19 and 0.19 ± 0.17 for δ15N and δ13C in Brahman, and 0.36 ± 0.21 and 0.46 ± 0.22 for δ15N and δ13C in Droughtmaster, respectively. CONCLUSIONS The findings of this study show, for the first time, that the natural abundances of both nitrogen and carbon isotopes in the tail hair in cattle may be moderately heritable. With further research and validation, tail hair isotopes can become a practical tool for the large-scale selection of more efficient cattle.
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Affiliation(s)
- Morteza Moradi
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Gatton, Qld, 4343, Australia
| | - Christie L Warburton
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Gatton, Qld, 4343, Australia
| | | | - Luis F P Silva
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Gatton, Qld, 4343, Australia.
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3
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Jahnel RE, Blunk I, Wittenburg D, Reinsch N. Relationship between milk urea content and important milk traits in Holstein cattle. Animal 2023; 17:100767. [PMID: 37141636 DOI: 10.1016/j.animal.2023.100767] [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: 06/08/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 05/06/2023] Open
Abstract
Breeding cattle with low nitrogen emissions has been proposed as a countermeasure against eutrophication due to dairy production. Milk urea content (MU) could potentially serve as a new readily measured indicator trait for nitrogen emissions by cows. Therefore, we estimated genetic parameters related to MU and its relationship with other milk traits. We analysed 4 178 735 milk samples collected between January 2008 and June 2019 from 261 866 German Holstein dairy cows during their first, second, and third lactations. Restricted maximum likelihood estimation was conducted using univariate and bivariate random regression sire models in WOMBAT. We obtained moderate average daily heritability estimates for the daily MU of 0.24 in first lactation cows, 0.23 in second lactation cows, and 0.21 in third lactation cows with average daily genetic SDs of 25.16 mg/kg, 24.93 mg/kg, and 23.75 mg/kg, respectively. Averaged over days in milk, the repeatability estimates were low at 0.41 in first, second, and third lactation cows. A strong positive genetic correlation was found between MU and milk urea yield (MUY; 0.72 on average). In addition, 305-day heritabilities were estimated as 0.50, 0.52, and 0.50 in first, second, and third lactation cows, respectively, with genetic correlations of 0.94 or higher for MU in different lactations. By contrast, the averaged estimates of the genetic correlations between MU and other milk traits were low (-0.07 to 0.15). Moderate heritability estimates clearly allow the possible selection for MU, and the near-zero estimates of genetic correlations indicate no risk of undesired correlated selection responses in other milk traits. However, a relationship still needs to be established between MU as an indicator trait and the target trait, defined as total individual nitrogen emissions.
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Affiliation(s)
- R E Jahnel
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - I Blunk
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - D Wittenburg
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - N Reinsch
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
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4
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Hardan A, Garnsworthy PC, Bell MJ. Variability in Enteric Methane Emissions among Dairy Cows during Lactation. Animals (Basel) 2022; 13:ani13010157. [PMID: 36611765 PMCID: PMC9817987 DOI: 10.3390/ani13010157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/04/2023] Open
Abstract
The aim of this study was to investigate variability in enteric CH4 emission rate and emissions per unit of milk across lactations among dairy cows on commercial farms in the UK. A total of 105,701 CH4 spot measurements were obtained from 2206 mostly Holstein-Friesian cows on 18 dairy farms using robotic milking stations. Eleven farms fed a partial mixed ration (PMR) and 7 farms fed a PMR with grazing. Methane concentrations (ppm) were measured using an infrared CH4 analyser at 1s intervals in breath samples taken during milking. Signal processing was used to detect CH4 eructation peaks, with maximum peak amplitude being used to derive CH4 emission rate (g/min) during each milking. A multiple-experiment meta-analysis model was used to assess effects of farm, week of lactation, parity, diet, and dry matter intake (DMI) on average CH4 emissions (expressed in g/min and g/kg milk) per individual cow. Estimated mean enteric CH4 emissions across the 18 farms was 0.38 (s.e. 0.01) g/min, ranging from 0.2 to 0.6 g/min, and 25.6 (s.e. 0.5) g/kg milk, ranging from 15 to 42 g/kg milk. Estimated dry matter intake was positively correlated with emission rate, which was higher in grazing cows, and negatively correlated with emissions per kg milk and was most significant in PMR-fed cows. Mean CH4 emission rate increased over the first 9 weeks of lactation and then was steady until week 70. Older cows were associated with lower emissions per minute and per kg milk. Rank correlation for CH4 emissions among weeks of lactation was generally high. We conclude that CH4 emissions appear to change across and within lactations, but ranking of a herd remains consistent, which is useful for obtaining CH4 spot measurements.
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Affiliation(s)
- Ali Hardan
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
- Correspondence:
| | - Philip C. Garnsworthy
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Matt J. Bell
- Animal and Agriculture Department, Hartpury University, Gloucester GL19 3BE, UK
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5
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Thunga P, Truong L, Rericha Y, Du JL, Morshead M, Tanguay RL, Reif DM. Utilizing a Population-Genetic Framework to Test for Gene-Environment Interactions between Zebrafish Behavior and Chemical Exposure. TOXICS 2022; 10:769. [PMID: 36548602 PMCID: PMC9781692 DOI: 10.3390/toxics10120769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/29/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Individuals within genetically diverse populations display broad susceptibility differences upon chemical exposures. Understanding the role of gene-environment interactions (GxE) in differential susceptibility to an expanding exposome is key to protecting public health. However, a chemical's potential to elicit GxE is often not considered during risk assessment. Previously, we've leveraged high-throughput zebrafish (Danio rerio) morphology screening data to reveal patterns of potential GxE effects. Here, using a population genetics framework, we apportioned variation in larval behavior and gene expression in three different PFHxA environments via mixed-effect modeling to assess significance of GxE term. We estimated the intraclass correlation (ICC) between full siblings from different families using one-way random-effects model. We found a significant GxE effect upon PFHxA exposure in larval behavior, and the ICC of behavioral responses in the PFHxA exposed population at the lower concentration was 43.7%, while that of the control population was 14.6%. Considering global gene expression data, a total of 3746 genes showed statistically significant GxE. By showing evidence that heritable genetics are directly affecting gene expression and behavioral susceptibility of individuals to PFHxA exposure, we demonstrate how standing genetic variation in a heterogeneous population such as ours can be leveraged to test for potential GxE.
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Affiliation(s)
- Preethi Thunga
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27607, USA
| | - Lisa Truong
- Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR 97331, USA
| | - Yvonne Rericha
- Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR 97331, USA
| | - Jane La Du
- Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR 97331, USA
| | - Mackenzie Morshead
- Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR 97331, USA
| | - Robyn L. Tanguay
- Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR 97331, USA
| | - David M. Reif
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27607, USA
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Confirmatory factor analysis and structural equation models to dissect the relationship between gait and morphology in Campolina horses. Livest Sci 2022. [DOI: 10.1016/j.livsci.2021.104779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Zhu X, Weng Q, Bush D, Zhou C, Zhao H, Wang P, Li F. High-density genetic linkage mapping reveals low stability of QTLs across environments for economic traits in Eucalyptus. FRONTIERS IN PLANT SCIENCE 2022; 13:1099705. [PMID: 37082511 PMCID: PMC10112524 DOI: 10.3389/fpls.2022.1099705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/28/2022] [Indexed: 05/03/2023]
Abstract
Introduction Eucalyptus urophylla, E. tereticornis and their hybrids are the most important commercial forest tree species in South China where they are grown for pulpwood and solid wood production. Construction of a fine-scale genetic linkage map and detecting quantitative trait loci (QTL) for economically important traits linked to these end-uses will facilitate identification of the main candidate genes and elucidate the regulatory mechanisms. Method A high-density consensus map (a total of 2754 SNPs with 1359.18 cM) was constructed using genotyping by sequencing (GBS) on clonal progenies of E. urophylla × tereticornis hybrids. QTL mapping of growth and wood property traits were conducted in three common garden experiments, resulting in a total of 108 QTLs. A total of 1052 candidate genes were screened by the efficient combination of QTL mapping and transcriptome analysis. Results Only ten QTLs were found to be stable across two environments, and only one (qSG10Stable mapped on chromosome 10, and associated with lignin syringyl-to-guaiacyl ratio) was stable across all three environments. Compared to other QTLs, qSG10Stable explained a very high level of phenotypic variation (18.4-23.6%), perhaps suggesting that QTLs with strong effects may be more stably inherited across multiple environments. Screened candidate genes were associated with some transcription factor families, such as TALE, which play an important role in the secondary growth of plant cell walls and the regulation of wood formation. Discussion While QTLs such as qSG10Stable, found to be stable across three sites, appear to be comparatively uncommon, their identification is likely to be a key to practical QTL-based breeding. Further research involving clonally-replicated populations, deployed across multiple target planting sites, will be required to further elucidate QTL-by-environment interactions.
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Affiliation(s)
- Xianliang Zhu
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Qijie Weng
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - David Bush
- Commonwealth Scientific and Industrial Research Organisation (CRISO) Australian Tree Seed Centre, Canberra, ACT, Australia
| | - Changpin Zhou
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Haiwen Zhao
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Ping Wang
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Fagen Li
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
- *Correspondence: Fagen Li,
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8
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Couvy-Duchesne B, Strike LT, Zhang F, Holtz Y, Zheng Z, Kemper KE, Yengo L, Colliot O, Wright MJ, Wray NR, Yang J, Visscher PM. A unified framework for association and prediction from vertex-wise grey-matter structure. Hum Brain Mapp 2020; 41:4062-4076. [PMID: 32687259 PMCID: PMC7469763 DOI: 10.1002/hbm.25109] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/11/2020] [Accepted: 06/14/2020] [Indexed: 01/29/2023] Open
Abstract
The recent availability of large‐scale neuroimaging cohorts facilitates deeper characterisation of the relationship between phenotypic and brain architecture variation in humans. Here, we investigate the association (previously coined morphometricity) of a phenotype with all 652,283 vertex‐wise measures of cortical and subcortical morphology in a large data set from the UK Biobank (UKB; N = 9,497 for discovery, N = 4,323 for replication) and the Human Connectome Project (N = 1,110). We used a linear mixed model with the brain measures of individuals fitted as random effects with covariance relationships estimated from the imaging data. We tested 167 behavioural, cognitive, psychiatric or lifestyle phenotypes and found significant morphometricity for 58 phenotypes (spanning substance use, blood assay results, education or income level, diet, depression, and cognition domains), 23 of which replicated in the UKB replication set or the HCP. We then extended the model for a bivariate analysis to estimate grey‐matter correlation between phenotypes, which revealed that body size (i.e., height, weight, BMI, waist and hip circumference, body fat percentage) could account for a substantial proportion of the morphometricity (confirmed using a conditional analysis), providing possible insight into previous MRI case–control results for psychiatric disorders where case status is associated with body mass index. Our LMM framework also allowed to predict some of the associated phenotypes from the vertex‐wise measures, in two independent samples. Finally, we demonstrated additional new applications of our approach (a) region of interest (ROI) analysis that retain the vertex‐wise complexity; (b) comparison of the information retained by different MRI processings.
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Affiliation(s)
- Baptiste Couvy-Duchesne
- Institute for Molecular Bioscience, the University of Queensland, St Lucia, Queensland, Australia
| | - Lachlan T Strike
- Queensland Brain Institute, the University of Queensland, St Lucia, Queensland, Australia
| | - Futao Zhang
- Institute for Molecular Bioscience, the University of Queensland, St Lucia, Queensland, Australia
| | - Yan Holtz
- Institute for Molecular Bioscience, the University of Queensland, St Lucia, Queensland, Australia.,Queensland Brain Institute, the University of Queensland, St Lucia, Queensland, Australia
| | - Zhili Zheng
- Institute for Molecular Bioscience, the University of Queensland, St Lucia, Queensland, Australia.,Institute for Advanced Research, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Kathryn E Kemper
- Institute for Molecular Bioscience, the University of Queensland, St Lucia, Queensland, Australia
| | - Loic Yengo
- Institute for Molecular Bioscience, the University of Queensland, St Lucia, Queensland, Australia
| | - Olivier Colliot
- ARAMIS, Inria, Paris, France.,ARAMIS, Paris Brain Institute, Paris, France.,ARAMIS, Inserm, Paris, France.,ARAMIS, CNRS, Paris, France.,ARAMIS, Sorbonne University, Paris, France
| | - Margaret J Wright
- Queensland Brain Institute, the University of Queensland, St Lucia, Queensland, Australia.,Centre for Advanced Imaging, the University of Queensland, St Lucia, Queensland, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, the University of Queensland, St Lucia, Queensland, Australia.,Queensland Brain Institute, the University of Queensland, St Lucia, Queensland, Australia
| | - Jian Yang
- Institute for Molecular Bioscience, the University of Queensland, St Lucia, Queensland, Australia.,Institute for Advanced Research, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Peter M Visscher
- Institute for Molecular Bioscience, the University of Queensland, St Lucia, Queensland, Australia.,Queensland Brain Institute, the University of Queensland, St Lucia, Queensland, Australia
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9
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Downie J, Silvertown J, Cavers S, Ennos R. Heritable genetic variation but no local adaptation in a pine-ectomycorrhizal interaction. MYCORRHIZA 2020; 30:185-195. [PMID: 32078050 PMCID: PMC7228896 DOI: 10.1007/s00572-020-00941-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 02/12/2020] [Indexed: 06/08/2023]
Abstract
Local adaptation of plants to mycorrhizal fungi helps determine the outcome of mycorrhizal interactions. However, there is comparatively little work exploring the potential for evolution in interactions with ectomycorrhizal fungi, and fewer studies have explored the heritability of mycorrhizal responsiveness, which is required for local adaptation to occur. We set up a reciprocal inoculation experiment using seedlings and soil from four populations of Scots pine (Pinus sylvestris) from Scotland, measuring seedling response to mycorrhizal inoculation after 4 months. We estimated heritability for the response traits and tested for genotype × environment interactions. While we found that ectomycorrhizal responsiveness was highly heritable, we found no evidence that pine populations were locally adapted to fungal communities. Instead, we found a complex suite of interactions between pine population and soil inoculum. Our results suggest that, while Scots pine has the potential to evolve in response to mycorrhizal fungi, evolution in Scotland has not resulted in local adaptation. Long generation times and potential for rapid shifts in fungal communities in response to environmental change may preclude the opportunity for such adaptation in this species, and selection for other factors such as resistance to fungal pathogens may explain the pattern of interactions found.
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Affiliation(s)
- Jim Downie
- Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, Scotland.
- Centre for Ecology and Hydrology, Bush Estate, Penicuik, Midlothian, Scotland.
| | - Jonathan Silvertown
- Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, Scotland
| | - Stephen Cavers
- Centre for Ecology and Hydrology, Bush Estate, Penicuik, Midlothian, Scotland
| | - Richard Ennos
- Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, Scotland
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10
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Calus MPL, Vandenplas J, Hulsegge I, Borg R, Henshall JM, Hawken R. Assessment of sire contribution and breed-of-origin of alleles in a three-way crossbred broiler dataset. Poult Sci 2020; 98:6270-6280. [PMID: 31393589 PMCID: PMC6870559 DOI: 10.3382/ps/pez458] [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: 02/13/2019] [Accepted: 07/28/2019] [Indexed: 11/30/2022] Open
Abstract
Broiler breeding programs rely on crossbreeding. With genomic selection, widespread use of crossbred performance in breeding programs comes within reach. Commercial crossbreds, however, may have unknown pedigrees and their genomes may include DNA from 2 to 4 different breeds. Our aim was, for a broiler dataset with a limited number of sires having both purebred and crossbred offspring generated using natural mating, to rapidly derive parentage, assess the distribution of the sire contribution to the offspring generation, and to assess breed-of-origin of alleles in crossbreds. The dataset contained genotypes for 56,075 SNPs for 5,882 purebred and 10,943 3-way crossbred offspring generated by natural mating of 164 purebred sires to 1,016 purebred and 1,386 F1 crossbred hens. Using our algorithm FindParents, joint parentage derivation for the offspring and parent generations required only 1 m 29 s to retrieve parentage for 20,253 animals considering 4,504 possible parents. FindParents was similarly accurate as a maximum likelihood based method, apart from situations where settings of FindParents did not match the genotyping error rate in the data. Numbers of offspring per sire had a very skewed distribution, ranging from 1 to 270 crossbreds and 1 to 154 purebreds. Derivation of breed-of-origin of alleles relied on phasing all genotypes, including 8,205, 372, and 720 animals from the 3 pure lines involved, and allocating haplotypes in the crossbreds to purebred lines based on observed frequencies in the purebred lines. Breed-of-origin could be derived for 96.94% of the alleles of the 1,386 F1 crossbred hens and for 91.88% of the alleles of the 10,943 3-way crossbred offspring, of which 49.49% to the sire line. The achieved percentage of assignment to the sire line was sufficient to proceed with subsequent analyses requiring only the breed-of-origin of the paternal alleles to be known. Although required number of animals may be population dependent, to increase the total percentage of assigned alleles, it seems advisable to use at least approx. 1,000 genotyped purebred animals for each of the lines involved.
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Affiliation(s)
- Mario P L Calus
- Wageningen University & Research Animal Breeding and Genomics, 6700 AH Wageningen, The Netherlands
| | - Jérémie Vandenplas
- Wageningen University & Research Animal Breeding and Genomics, 6700 AH Wageningen, The Netherlands
| | - Ina Hulsegge
- Wageningen University & Research Animal Breeding and Genomics, 6700 AH Wageningen, The Netherlands
| | - Randy Borg
- Cobb-Vantress Inc., Siloam Springs, AR 72761-1030
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Difford GF, Olijhoek DW, Hellwing ALF, Lund P, Bjerring MA, de Haas Y, Lassen J, Løvendahl P. Ranking cows’ methane emissions under commercial conditions with sniffers versus respiration chambers. ACTA AGR SCAND A-AN 2019. [DOI: 10.1080/09064702.2019.1572784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- G. F. Difford
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University Tjele, Denmark
- Animal Breeding and Genomics Centre, Wageningen University Wageningen, Netherlands
| | - D. W. Olijhoek
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University Tjele, Denmark
- Department of Animal Science, Aarhus University, AU-Foulum Tjele, Denmark
| | - A. L. F. Hellwing
- Department of Animal Science, Aarhus University, AU-Foulum Tjele, Denmark
| | - P. Lund
- Department of Animal Science, Aarhus University, AU-Foulum Tjele, Denmark
| | - M. A. Bjerring
- Department of Animal Science, Aarhus University, AU-Foulum Tjele, Denmark
| | - Y. de Haas
- Animal Breeding and Genomics Centre, Wageningen University Wageningen, Netherlands
| | - J. Lassen
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University Tjele, Denmark
| | - P. Løvendahl
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University Tjele, Denmark
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12
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Sharma MD, Wilson AJ, Hosken DJ. Fisher's sons' effect in sexual selection: absent, intermittent or just low experimental power? J Evol Biol 2016; 29:2464-2470. [PMID: 27575647 DOI: 10.1111/jeb.12973] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 08/28/2016] [Indexed: 11/27/2022]
Abstract
The Fisherian sexual selection paradigm has been called the null model of sexual selection. At its heart is the expectation of a genetic correlation (rG ) between female preference and male trait. However, recent meta-analysis has shown estimated correlations are often extremely weak and not statistically significant. We show here that systematic failure of studies to reject the null hypothesis that rG = 0 is almost certainly due to the low power of most experimental designs used. We provide an easy way to assess experimental power a priori and suggest that current data make it difficult to definitively test a key component of the Fisher effect.
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Affiliation(s)
- M D Sharma
- Center for Ecology and Conservation, The University of Exeter, Cornwall, UK
| | - A J Wilson
- Center for Ecology and Conservation, The University of Exeter, Cornwall, UK
| | - D J Hosken
- Center for Ecology and Conservation, The University of Exeter, Cornwall, UK
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Perry A, Brown AV, Cavers S, Cottrell JE, Ennos RA. Has Scots pine (Pinus sylvestris) co-evolved with Dothistroma septosporum in Scotland? Evidence for spatial heterogeneity in the susceptibility of native provenances. Evol Appl 2016; 9:982-93. [PMID: 27606006 PMCID: PMC4999528 DOI: 10.1111/eva.12395] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/14/2016] [Indexed: 11/29/2022] Open
Abstract
Spatial heterogeneity in pathogen pressure leads to genetic variation in, and evolution of, disease-related traits among host populations. In contrast, hosts are expected to be highly susceptible to exotic pathogens as there has been no evolution of defence responses. Host response to pathogens can therefore be an indicator of a novel or endemic pathosystem. Currently, the most significant threat to native British Scots pine (Pinus sylvestris) forests is Dothistroma needle blight (DNB) caused by the foliar pathogen Dothistroma septosporum which is presumed to be exotic. A progeny-provenance trial of 6-year-old Scots pine, comprising eight native provenances each with four families in six blocks, was translocated in April 2013 to a clear-fell site in Galloway adjacent to a DNB-infected forest. Susceptibility to D. septosporum, measured as DNB severity (estimated percentage nongreen current-year needles), was assessed visually over 2 years (2013-2014 and 2014-2015; two assessments per year). There were highly significant differences in susceptibility among provenances but not among families for each annual assessment. Provenance mean susceptibility to D. septosporum was negatively and significantly associated with water-related variables at site of origin, potentially due to the evolution of low susceptibility in the host in response to high historical pathogen pressure.
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Affiliation(s)
| | | | | | | | - Richard A. Ennos
- Institute of Evolutionary BiologyUniversity of EdinburghEdinburghUK
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14
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Perry A, Wachowiak W, Brown AV, Ennos RA, Cottrell JE, Cavers S. Substantial heritable variation for susceptibility to Dothistroma septosporum within populations of native British Scots pine ( Pinus sylvestris). PLANT PATHOLOGY 2016; 65:987-996. [PMID: 27587900 PMCID: PMC4984854 DOI: 10.1111/ppa.12528] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The threat from pests and pathogens to native and commercially planted forest trees is unprecedented and expected to increase under climate change. The degree to which forests respond to threats from pathogens depends on their adaptive capacity, which is determined largely by genetically controlled variation in susceptibility of the individual trees within them and the heritability and evolvability of this trait. The most significant current threat to the economically and ecologically important species Scots pine (Pinus sylvestris) is dothistroma needle blight (DNB), caused by the foliar pathogen Dothistroma septosporum. A progeny-population trial of 4-year-old Scots pine trees, comprising six populations from native Caledonian pinewoods each with three to five families in seven blocks, was artificially inoculated using a single isolate of D. septosporum. Susceptibility to D. septosporum, assessed as the percentage of non-green needles, was measured regularly over a period of 61 days following inoculation, during which plants were maintained in conditions ideal for DNB development (warm; high humidity; high leaf wetness). There were significant differences in susceptibility to D. septosporum among families indicating that variation in this trait is heritable, with high estimates of narrow-sense heritability (0.38-0.75) and evolvability (genetic coefficient of variation, 23.47). It is concluded that native Scots pine populations contain sufficient genetic diversity to evolve lower susceptibility to D. septosporum through natural selection in response to increased prevalence of this pathogen.
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Affiliation(s)
- A Perry
- Centre for Ecology and Hydrology Bush Estate Penicuik Midlothian EH26 0QB UK
| | - W Wachowiak
- Centre for Ecology and Hydrology Bush Estate Penicuik Midlothian EH26 0QB UK; Institute of Dendrology Polish Academy of Sciences Parkowa 562-035 Kórnik Poland
| | - A V Brown
- Forestry Commission 231 Corstorphine Road EH12 7AT UK
| | - R A Ennos
- Institute of Evolutionary Biology The University of Edinburgh Ashworth Building Charlotte Auerbach Road, King's Buildings Edinburgh EH9 3JF UK
| | - J E Cottrell
- Forest Research Northern Research Station Roslin Midlothian EH25 9SY UK
| | - S Cavers
- Centre for Ecology and Hydrology Bush Estate Penicuik Midlothian EH26 0QB UK
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Bijma P, Bastiaansen JWM. Standard error of the genetic correlation: how much data do we need to estimate a purebred-crossbred genetic correlation? Genet Sel Evol 2014; 46:79. [PMID: 25407726 PMCID: PMC4236448 DOI: 10.1186/s12711-014-0079-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 09/24/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The additive genetic correlation (rg) is a key parameter in livestock genetic improvement. The standard error (SE) of an estimate of rg, r^g, depends on whether both traits are recorded on the same individual or on distinct individuals. The genetic correlation between traits recorded on distinct individuals is relevant as a measure of, e.g., genotype-by-environment interaction and for traits expressed in purebreds vs. crossbreds. In crossbreeding schemes, rg between the purebred and crossbred trait is the key parameter that determines the need for crossbred information. This work presents a simple equation to predict the SE of r^g between traits recorded on distinct individuals for nested full-half sib schemes with common-litter effects, using the purebred-crossbred genetic correlation as an example. The resulting expression allows a priori optimization of designs that aim at estimating rg. An R-script that implements the expression is included. RESULTS The SE of r^g is determined by the true value of rg, the number of sire families (N), and the reliabilities of sire estimated breeding values (EBV):SEr^g≈1ρx2ρy2+1+0.5ρx4+0.5ρy4-2ρx2-2ρy2rg2+rg4N-1,where ρx2 and ρy2 are the reliabilities of the sire EBV for both traits. Results from stochastic simulation show that this equation is accurate since the average absolute error of the prediction across 320 alternative breeding schemes was 3.2%. Application to typical crossbreeding schemes shows that a large number of sire families is required, usually more than 100. Since SEr^g is a function of reliabilities of EBV, the result probably extends to other cases such as repeated records, but this was not validated by simulation. CONCLUSIONS This work provides an accurate tool to determine a priori the amount of data required to estimate a genetic correlation between traits measured on distinct individuals, such as the purebred-crossbred genetic correlation.
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Affiliation(s)
- Piter Bijma
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, 6700 AH, The Netherlands.
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16
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Kim MG. Case Deletion Diagnostics for Intraclass Correlation Model. COMMUNICATIONS FOR STATISTICAL APPLICATIONS AND METHODS 2014. [DOI: 10.5351/csam.2014.21.3.253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Visscher PM, Hemani G, Vinkhuyzen AAE, Chen GB, Lee SH, Wray NR, Goddard ME, Yang J. Statistical power to detect genetic (co)variance of complex traits using SNP data in unrelated samples. PLoS Genet 2014; 10:e1004269. [PMID: 24721987 PMCID: PMC3983037 DOI: 10.1371/journal.pgen.1004269] [Citation(s) in RCA: 230] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 02/03/2014] [Indexed: 12/29/2022] Open
Abstract
We have recently developed analysis methods (GREML) to estimate the genetic variance of a complex trait/disease and the genetic correlation between two complex traits/diseases using genome-wide single nucleotide polymorphism (SNP) data in unrelated individuals. Here we use analytical derivations and simulations to quantify the sampling variance of the estimate of the proportion of phenotypic variance captured by all SNPs for quantitative traits and case-control studies. We also derive the approximate sampling variance of the estimate of a genetic correlation in a bivariate analysis, when two complex traits are either measured on the same or different individuals. We show that the sampling variance is inversely proportional to the number of pairwise contrasts in the analysis and to the variance in SNP-derived genetic relationships. For bivariate analysis, the sampling variance of the genetic correlation additionally depends on the harmonic mean of the proportion of variance explained by the SNPs for the two traits and the genetic correlation between the traits, and depends on the phenotypic correlation when the traits are measured on the same individuals. We provide an online tool for calculating the power of detecting genetic (co)variation using genome-wide SNP data. The new theory and online tool will be helpful to plan experimental designs to estimate the missing heritability that has not yet been fully revealed through genome-wide association studies, and to estimate the genetic overlap between complex traits (diseases) in particular when the traits (diseases) are not measured on the same samples.
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Affiliation(s)
- Peter M. Visscher
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
- The University of Queensland Diamantina Institute, The Translational Research Institute, Brisbane, Queensland, Australia
- * E-mail: (PMV); (JY)
| | - Gibran Hemani
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
- The University of Queensland Diamantina Institute, The Translational Research Institute, Brisbane, Queensland, Australia
| | - Anna A. E. Vinkhuyzen
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Guo-Bo Chen
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Sang Hong Lee
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Naomi R. Wray
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Michael E. Goddard
- University of Melbourne, Department of Food and Agricultural Systems, Parkville, Victoria, Australia
- Biosciences Research Division, Department of Primary Industries, Bundoora, Victoria, Australia
| | - Jian Yang
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
- The University of Queensland Diamantina Institute, The Translational Research Institute, Brisbane, Queensland, Australia
- * E-mail: (PMV); (JY)
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Atenafu EG, Hamid JS, To T, Willan AR, Feldman BM, Beyene J. Bias-corrected estimator for intraclass correlation coefficient in the balanced one-way random effects model. BMC Med Res Methodol 2012; 12:126. [PMID: 22905752 PMCID: PMC3554464 DOI: 10.1186/1471-2288-12-126] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 07/18/2012] [Indexed: 11/10/2022] Open
Abstract
Background Intraclass correlation coefficients (ICCs) are used in a wide range of applications. However, most commonly used estimators for the ICC are known to be subject to bias. Methods Using second order Taylor series expansion, we propose a new bias-corrected estimator for one type of intraclass correlation coefficient, for the ICC that arises in the context of the balanced one-way random effects model. A simulation study is performed to assess the performance of the proposed estimator. Data have been generated under normal as well as non-normal scenarios. Results Our simulation results show that the new estimator has reduced bias compared to the least square estimator which is often referred to as the conventional or analytical estimator. The results also show marked bias reduction both in normal and non-normal data scenarios. In particular, our estimator outperforms the analytical estimator in a non-normal setting producing estimates that are very close to the true ICC values. Conclusions The proposed bias-corrected estimator for the ICC from a one-way random effects analysis of variance model appears to perform well in the scenarios we considered in this paper and can be used as a motivation to construct bias-corrected estimators for other types of ICCs that arise in more complex scenarios. It would also be interesting to investigate the bias-variance trade-off.
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Fabbrini F, Gaudet M, Bastien C, Zaina G, Harfouche A, Beritognolo I, Marron N, Morgante M, Scarascia-Mugnozza G, Sabatti M. Phenotypic plasticity, QTL mapping and genomic characterization of bud set in black poplar. BMC PLANT BIOLOGY 2012; 12:47. [PMID: 22471289 PMCID: PMC3378457 DOI: 10.1186/1471-2229-12-47] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 04/03/2012] [Indexed: 05/04/2023]
Abstract
BACKGROUND The genetic control of important adaptive traits, such as bud set, is still poorly understood in most forest trees species. Poplar is an ideal model tree to study bud set because of its indeterminate shoot growth. Thus, a full-sib family derived from an intraspecific cross of P. nigra with 162 clonally replicated progeny was used to assess the phenotypic plasticity and genetic variation of bud set in two sites of contrasting environmental conditions. RESULTS Six crucial phenological stages of bud set were scored. Night length appeared to be the most important signal triggering the onset of growth cessation. Nevertheless, the effect of other environmental factors, such as temperature, increased during the process. Moreover, a considerable role of genotype × environment (G × E) interaction was found in all phenological stages with the lowest temperature appearing to influence the sensitivity of the most plastic genotypes.Descriptors of growth cessation and bud onset explained the largest part of phenotypic variation of the entire process. Quantitative trait loci (QTL) for these traits were detected. For the four selected traits (the onset of growth cessation (date2.5), the transition from shoot to bud (date1.5), the duration of bud formation (subproc1) and bud maturation (subproc2)) eight and sixteen QTL were mapped on the maternal and paternal map, respectively. The identified QTL, each one characterized by small or modest effect, highlighted the complex nature of traits involved in bud set process. Comparison between map location of QTL and P. trichocarpa genome sequence allowed the identification of 13 gene models, 67 bud set-related expressional and six functional candidate genes (CGs). These CGs are functionally related to relevant biological processes, environmental sensing, signaling, and cell growth and development. Some strong QTL had no obvious CGs, and hold great promise to identify unknown genes that affect bud set. CONCLUSIONS This study provides a better understanding of the physiological and genetic dissection of bud set in poplar. The putative QTL identified will be tested for associations in P. nigra natural populations. The identified QTL and CGs will also serve as useful targets for poplar breeding.
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Affiliation(s)
- Francesco Fabbrini
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia, Via S. Camillo de Lellis, Viterbo 01100, Italy
| | - Muriel Gaudet
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia, Via S. Camillo de Lellis, Viterbo 01100, Italy
| | - Catherine Bastien
- INRA, UR 0588, National Institute for Agricultural Research, Orléans 2 F-45075, France
| | - Giusi Zaina
- Department of Agriculture and Environmental Sciences, University of Udine, Via delle Scienze, Udine 33100, Italy
| | - Antoine Harfouche
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia, Via S. Camillo de Lellis, Viterbo 01100, Italy
| | - Isacco Beritognolo
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia, Via S. Camillo de Lellis, Viterbo 01100, Italy
- Institute for Mediterranean Agriculture and Forest Systems, National Research Council, Via Madonna Alta, Perugia 06128, Italy
| | - Nicolas Marron
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia, Via S. Camillo de Lellis, Viterbo 01100, Italy
- INRA, UMR 1137, INRA-Nancy University, Champenoux F-54280, France
| | - Michele Morgante
- Department of Agriculture and Environmental Sciences, University of Udine, Via delle Scienze, Udine 33100, Italy
- Istituto di Genomica Applicata, Via J. Linussio 51, Udine 33100, Italy
| | - Giuseppe Scarascia-Mugnozza
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia, Via S. Camillo de Lellis, Viterbo 01100, Italy
- Department of Agronomy, Forestry and Land use, Agricultural Research Council, Via del Caravita, Roma 00186, Italy
| | - Maurizio Sabatti
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia, Via S. Camillo de Lellis, Viterbo 01100, Italy
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20
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de Miguel M, Sánchez-Gómez D, Cervera MT, Aranda I. Functional and genetic characterization of gas exchange and intrinsic water use efficiency in a full-sib family of Pinus pinaster Ait. in response to drought. TREE PHYSIOLOGY 2012; 32:94-103. [PMID: 22170437 DOI: 10.1093/treephys/tpr122] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Drought is an important environmental factor in Mediterranean ecosystems affecting seedling recruitment, productivity or susceptibility to fires and pathogens. Studying water use efficiency in these environments is crucial due to its adaptive value allowing trees to cope with low water availability. We studied the phenotypic variability and genetic control of intrinsic water use efficiency (WUE(i)) and related traits in a full-sib family of Pinus pinaster under drought imposition. We detected significant differences in WUE(i) between clones of the same family and moderate heritability estimates that indicate some degree of genetic control over this trait. Stomatal conductance to water vapor was the trait most affected by drought imposition and it showed the strongest influence in WUE(i). Stomatal conductance to water vapor and specific leaf area (SLA) were the traits with highest heritabilities and they showed a significant genetic correlation with WUE(i), suggesting that selection of needles with low SLA values will improve WUE(i) in this species by reducing water losses through stomatal control.
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Affiliation(s)
- Marina de Miguel
- Centro de Investigación Forestal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Carretera de La Coruña, Km. 7.5, 28040 Madrid, Spain
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22
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Fabbro T, Davison AC, Steinger T. Reliable confidence intervals in quantitative genetics: narrow-sense heritability. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 115:933-44. [PMID: 17874063 DOI: 10.1007/s00122-007-0619-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Accepted: 07/20/2007] [Indexed: 05/17/2023]
Abstract
Many quantitative genetic statistics are functions of variance components, for which a large number of replicates is needed for precise estimates and reliable measures of uncertainty, on which sound interpretation depends. Moreover, in large experiments the deaths of some individuals can occur, so methods for analysing such data need to be robust to missing values. We show how confidence intervals for narrow-sense heritability can be calculated in a nested full-sib/half-sib breeding design (males crossed with several females) in the presence of missing values. Simulations indicate that the method provides accurate results, and that estimator uncertainty is lowest for sampling designs with many males relative to the number of females per male, and with more females per male than progenies per female. Missing data generally had little influence on estimator accuracy, thus suggesting that the overall number of observations should be increased even if this results in unbalanced data. We also suggest the use of parametrically simulated data for prior investigation of the accuracy of planned experiments. Together with the proposed confidence intervals an informed decision on the optimal sampling design is possible, which allows efficient allocation of resources.
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Affiliation(s)
- Thomas Fabbro
- Department of Biology, University of Fribourg, 1700, Fribourg, Switzerland.
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23
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Bruun Brockhoff P. Sensory profile average data: combining mixed model ANOVA with measurement error methodology. Food Qual Prefer 2001. [DOI: 10.1016/s0950-3293(01)00032-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Friddle C, Koskela R, Ranade K, Hebert J, Cargill M, Clark CD, McInnis M, Simpson S, McMahon F, Stine OC, Meyers D, Xu J, MacKinnon D, Swift-Scanlan T, Jamison K, Folstein S, Daly M, Kruglyak L, Marr T, DePaulo JR, Botstein D. Full-genome scan for linkage in 50 families segregating the bipolar affective disease phenotype. Am J Hum Genet 2000; 66:205-15. [PMID: 10631152 PMCID: PMC1288327 DOI: 10.1086/302697] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/1999] [Accepted: 10/26/1999] [Indexed: 11/03/2022] Open
Abstract
A genome scan of approximately 12-cM initial resolution was done on 50 of a set of 51 carefully ascertained unilineal multiplex families segregating the bipolar affective disorder phenotype. In addition to standard multipoint linkage analysis methods, a simultaneous-search algorithm was applied in an attempt to surmount the problem of genetic heterogeneity. The results revealed no linkage across the genome. The results exclude monogenic models and make it unlikely that two genes account for the disease in this sample. These results support the conclusion that at least several hundred kindreds will be required in order to establish linkage of susceptibility loci to bipolar disorder in heterogeneous populations.
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Affiliation(s)
- Carl Friddle
- Department
of Genetics, Stanford University, Stanford, CA; Department of
Computational Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY; Department of Psychiatry, Johns Hopkins University School
of Medicine, Baltimore; Tufts University School of Medicine,
Boston; and Whitehead Institute for Biomedical Research,
Cambridge, MA
| | - Rebecca Koskela
- Department
of Genetics, Stanford University, Stanford, CA; Department of
Computational Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY; Department of Psychiatry, Johns Hopkins University School
of Medicine, Baltimore; Tufts University School of Medicine,
Boston; and Whitehead Institute for Biomedical Research,
Cambridge, MA
| | - Koustubh Ranade
- Department
of Genetics, Stanford University, Stanford, CA; Department of
Computational Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY; Department of Psychiatry, Johns Hopkins University School
of Medicine, Baltimore; Tufts University School of Medicine,
Boston; and Whitehead Institute for Biomedical Research,
Cambridge, MA
| | - Joan Hebert
- Department
of Genetics, Stanford University, Stanford, CA; Department of
Computational Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY; Department of Psychiatry, Johns Hopkins University School
of Medicine, Baltimore; Tufts University School of Medicine,
Boston; and Whitehead Institute for Biomedical Research,
Cambridge, MA
| | - Michele Cargill
- Department
of Genetics, Stanford University, Stanford, CA; Department of
Computational Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY; Department of Psychiatry, Johns Hopkins University School
of Medicine, Baltimore; Tufts University School of Medicine,
Boston; and Whitehead Institute for Biomedical Research,
Cambridge, MA
| | - Chris D. Clark
- Department
of Genetics, Stanford University, Stanford, CA; Department of
Computational Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY; Department of Psychiatry, Johns Hopkins University School
of Medicine, Baltimore; Tufts University School of Medicine,
Boston; and Whitehead Institute for Biomedical Research,
Cambridge, MA
| | - Melvin McInnis
- Department
of Genetics, Stanford University, Stanford, CA; Department of
Computational Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY; Department of Psychiatry, Johns Hopkins University School
of Medicine, Baltimore; Tufts University School of Medicine,
Boston; and Whitehead Institute for Biomedical Research,
Cambridge, MA
| | - Sylvia Simpson
- Department
of Genetics, Stanford University, Stanford, CA; Department of
Computational Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY; Department of Psychiatry, Johns Hopkins University School
of Medicine, Baltimore; Tufts University School of Medicine,
Boston; and Whitehead Institute for Biomedical Research,
Cambridge, MA
| | - Francis McMahon
- Department
of Genetics, Stanford University, Stanford, CA; Department of
Computational Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY; Department of Psychiatry, Johns Hopkins University School
of Medicine, Baltimore; Tufts University School of Medicine,
Boston; and Whitehead Institute for Biomedical Research,
Cambridge, MA
| | - O. Colin Stine
- Department
of Genetics, Stanford University, Stanford, CA; Department of
Computational Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY; Department of Psychiatry, Johns Hopkins University School
of Medicine, Baltimore; Tufts University School of Medicine,
Boston; and Whitehead Institute for Biomedical Research,
Cambridge, MA
| | - Deborah Meyers
- Department
of Genetics, Stanford University, Stanford, CA; Department of
Computational Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY; Department of Psychiatry, Johns Hopkins University School
of Medicine, Baltimore; Tufts University School of Medicine,
Boston; and Whitehead Institute for Biomedical Research,
Cambridge, MA
| | - Jianfeng Xu
- Department
of Genetics, Stanford University, Stanford, CA; Department of
Computational Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY; Department of Psychiatry, Johns Hopkins University School
of Medicine, Baltimore; Tufts University School of Medicine,
Boston; and Whitehead Institute for Biomedical Research,
Cambridge, MA
| | - Dean MacKinnon
- Department
of Genetics, Stanford University, Stanford, CA; Department of
Computational Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY; Department of Psychiatry, Johns Hopkins University School
of Medicine, Baltimore; Tufts University School of Medicine,
Boston; and Whitehead Institute for Biomedical Research,
Cambridge, MA
| | - Theresa Swift-Scanlan
- Department
of Genetics, Stanford University, Stanford, CA; Department of
Computational Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY; Department of Psychiatry, Johns Hopkins University School
of Medicine, Baltimore; Tufts University School of Medicine,
Boston; and Whitehead Institute for Biomedical Research,
Cambridge, MA
| | - Kay Jamison
- Department
of Genetics, Stanford University, Stanford, CA; Department of
Computational Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY; Department of Psychiatry, Johns Hopkins University School
of Medicine, Baltimore; Tufts University School of Medicine,
Boston; and Whitehead Institute for Biomedical Research,
Cambridge, MA
| | - Susan Folstein
- Department
of Genetics, Stanford University, Stanford, CA; Department of
Computational Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY; Department of Psychiatry, Johns Hopkins University School
of Medicine, Baltimore; Tufts University School of Medicine,
Boston; and Whitehead Institute for Biomedical Research,
Cambridge, MA
| | - Mark Daly
- Department
of Genetics, Stanford University, Stanford, CA; Department of
Computational Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY; Department of Psychiatry, Johns Hopkins University School
of Medicine, Baltimore; Tufts University School of Medicine,
Boston; and Whitehead Institute for Biomedical Research,
Cambridge, MA
| | - Leonid Kruglyak
- Department
of Genetics, Stanford University, Stanford, CA; Department of
Computational Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY; Department of Psychiatry, Johns Hopkins University School
of Medicine, Baltimore; Tufts University School of Medicine,
Boston; and Whitehead Institute for Biomedical Research,
Cambridge, MA
| | - Thomas Marr
- Department
of Genetics, Stanford University, Stanford, CA; Department of
Computational Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY; Department of Psychiatry, Johns Hopkins University School
of Medicine, Baltimore; Tufts University School of Medicine,
Boston; and Whitehead Institute for Biomedical Research,
Cambridge, MA
| | - J. Raymond DePaulo
- Department
of Genetics, Stanford University, Stanford, CA; Department of
Computational Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY; Department of Psychiatry, Johns Hopkins University School
of Medicine, Baltimore; Tufts University School of Medicine,
Boston; and Whitehead Institute for Biomedical Research,
Cambridge, MA
| | - David Botstein
- Department
of Genetics, Stanford University, Stanford, CA; Department of
Computational Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY; Department of Psychiatry, Johns Hopkins University School
of Medicine, Baltimore; Tufts University School of Medicine,
Boston; and Whitehead Institute for Biomedical Research,
Cambridge, MA
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