1
|
Andrade F, Howell L, Percival CJ, Richtsmeier JT, Marcucio RS, Hallgrímsson B, Cheverud JM. Genetic architecture of trait variance in craniofacial morphology. Genetics 2024; 226:iyae028. [PMID: 38386896 PMCID: PMC11090463 DOI: 10.1093/genetics/iyae028] [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: 12/19/2023] [Revised: 12/19/2023] [Accepted: 01/26/2024] [Indexed: 02/24/2024] Open
Abstract
The genetic architecture of trait variance has long been of interest in genetics and evolution. One of the earliest attempts to understand this architecture was presented in Lerner's Genetic Homeostasis (1954). Lerner proposed that heterozygotes should be better able to tolerate environmental perturbations because of functional differences between the alleles at a given locus, with each allele optimal for slightly different environments. This greater robustness to environmental variance, he argued, would result in smaller trait variance for heterozygotes. The evidence for Lerner's hypothesis has been inconclusive. To address this question using modern genomic methods, we mapped loci associated with differences in trait variance (vQTL) on 1,101 individuals from the F34 of an advanced intercross between LG/J and SM/J mice. We also mapped epistatic interactions for these vQTL in order to understand the influence of epistasis for the architecture of trait variance. We did not find evidence supporting Lerner's hypothesis, that heterozygotes tend to have smaller trait variances than homozygotes. We further show that the effects of most mapped loci on trait variance are produced by epistasis affecting trait means and that those epistatic effects account for about a half of the differences in genotypic-specific trait variances. Finally, we propose a model where the different interactions between the additive and dominance effects of the vQTL and their epistatic partners can explain Lerner's original observations but can also be extended to include other conditions where heterozygotes are not the least variable genotype.
Collapse
Affiliation(s)
- Fernando Andrade
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
| | - Lisa Howell
- Department of Anthropology, Penn State University, University Park, PA 16802, USA
| | | | - Joan T Richtsmeier
- Department of Anthropology, Penn State University, University Park, PA 16802, USA
| | - Ralph S Marcucio
- Department of Orthopedic Surgery, School of Medicine, University of California San Francisco, San Francisco, CA 94110, USA
| | - Benedikt Hallgrímsson
- Department of Cell Biology and Anatomy, Cumming School of Medicine, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - James M Cheverud
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
| |
Collapse
|
2
|
Liu H, Cao M, Jin Y, Jia B, Wang L, Dong M, Han L, Abankwah J, Liu J, Zhou T, Chen B, Wang Y, Bian Y. Network pharmacology and experimental validation to elucidate the pharmacological mechanisms of Bushen Huashi decoction against kidney stones. Front Endocrinol (Lausanne) 2023; 14:1031895. [PMID: 36864834 PMCID: PMC9971497 DOI: 10.3389/fendo.2023.1031895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/30/2023] [Indexed: 02/16/2023] Open
Abstract
INTRODUCTION Kidney stone disease (KS) is a complicated disease with an increasing global incidence. It was shown that Bushen Huashi decoction (BSHS) is a classic Chinese medicine formula that has therapeutic benefits for patients with KS. However, its pharmacological profile and mechanism of action are yet to be elucidated. METHODS The present study used a network pharmacology approach to characterize the mechanism by which BSHS affects KS. Compounds were retrieved from corresponding databases, and active compounds were selected based on their oral bioavailability (≥30) and drug-likeness index (≥0.18). BSHS potential proteins were obtained from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database, whereas KS potential genes were obtained from GeneCards and OMIM, TTD, and DisGeNET. Gene ontology and pathway enrichment analysis were used to determine potential pathways associated with genes. The ingredients of BSHS extract were identified by the ultra-high-performance liquid chromatography coupled with quadrupole orbitrap mass spectrometry (UHPLC-Q/Orbitrap MS). The network pharmacology analyses predicted the potential underlying action mechanisms of BSHS on KS, which were further validated experimentally in the rat model of calcium oxalate kidney stones. RESULTS Our study found that BSHS reduced renal crystal deposition and improved renal function in ethylene glycol(EG)+ammonium chloride(AC)-induced rats, and also reversed oxidative stress levels and inhibited renal tubular epithelial cell apoptosis in rats. BSHS upregulated protein and mRNA expression of E2, ESR1, ESR2, BCL2, NRF2, and HO-1 in EG+AC-induced rat kidney while downregulating BAX protein and mRNA expression, consistent with the network pharmacology results. DISCUSSION This study provides evidence that BSHS plays a critical role in anti-KS via regulation of E2/ESR1/2, NRF2/HO-1, and BCL2/BAX signaling pathways, indicating that BSHS is a candidate herbal drug for further investigation in treating KS.
Collapse
Affiliation(s)
- Haizhao Liu
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Min Cao
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yutong Jin
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Beitian Jia
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Liming Wang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Mengxue Dong
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lu Han
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Joseph Abankwah
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Jianwei Liu
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Tao Zhou
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Baogui Chen
- Wuqing Hospital of Traditional Chinese Medicine Affiliated with Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yiyang Wang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- *Correspondence: Yiyang Wang, ; Yuhong Bian,
| | - Yuhong Bian
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- *Correspondence: Yiyang Wang, ; Yuhong Bian,
| |
Collapse
|
3
|
Sell-Kubiak E, Knol EF, Lopes M. Evaluation of the phenotypic and genomic background of variability based on litter size of Large White pigs. Genet Sel Evol 2022; 54:1. [PMID: 34979897 PMCID: PMC8722267 DOI: 10.1186/s12711-021-00692-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genetic background of trait variability has captured the interest of ecologists and animal breeders because the genes that control it could be involved in buffering various environmental effects. Phenotypic variability of a given trait can be assessed by studying the heterogeneity of the residual variance, and the quantitative trait loci (QTL) that are involved in the control of this variability are described as variance QTL (vQTL). This study focuses on litter size (total number born, TNB) and its variability in a Large White pig population. The variability of TNB was evaluated either using a simple method, i.e. analysis of the log-transformed variance of residuals (LnVar), or the more complex double hierarchical generalized linear model (DHGLM). We also performed a single-SNP (single nucleotide polymorphism) genome-wide association study (GWAS). To our knowledge, this is only the second study that reports vQTL for litter size in pigs and the first one that shows GWAS results when using two methods to evaluate variability of TNB: LnVar and DHGLM. RESULTS Based on LnVar, three candidate vQTL regions were detected, on Sus scrofa chromosomes (SSC) 1, 7, and 18, which comprised 18 SNPs. Based on the DHGLM, three candidate vQTL regions were detected, i.e. two on SSC7 and one on SSC11, which comprised 32 SNPs. Only one candidate vQTL region overlapped between the two methods, on SSC7, which also contained the most significant SNP. Within this vQTL region, two candidate genes were identified, ADGRF1, which is involved in neurodevelopment of the brain, and ADGRF5, which is involved in the function of the respiratory system and in vascularization. The correlation between estimated breeding values based on the two methods was 0.86. Three-fold cross-validation indicated that DHGLM yielded EBV that were much more accurate and had better prediction of missing observations than LnVar. CONCLUSIONS The results indicated that the LnVar and DHGLM methods resulted in genetically different traits. Based on their validation, we recommend the use of DHGLM over the simpler method of log-transformed variance of residuals. These conclusions can be useful for future studies on the evaluation of the variability of any trait in any species.
Collapse
Affiliation(s)
- Ewa Sell-Kubiak
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Poznań, Poland.
| | - Egbert F Knol
- Topigs Norsvin Research Centre, Beuningen, The Netherlands
| | - Marcos Lopes
- Topigs Norsvin Research Centre, Beuningen, The Netherlands.,Topigs Norsvin, Curitiba, Brazil
| |
Collapse
|
4
|
Hussain W, Campbell MT, Jarquin D, Walia H, Morota G. Variance heterogeneity genome-wide mapping for cadmium in bread wheat reveals novel genomic loci and epistatic interactions. THE PLANT GENOME 2020; 13:e20011. [PMID: 33016629 DOI: 10.1002/tpg2.20011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/22/2020] [Indexed: 06/11/2023]
Abstract
Genome-wide association mapping identifies quantitative trait loci (QTL) that influence the mean differences between the marker genotypes for a given trait. While most loci influence the mean value of a trait, certain loci, known as variance heterogeneity QTL (vQTL) determine the variability of the trait instead of the mean trait value (mQTL). In the present study, we performed a variance heterogeneity genome-wide association study (vGWAS) for grain cadmium (Cd) concentration in bread wheat. We used double generalized linear model and hierarchical generalized linear model to identify vQTL associated with grain Cd. We identified novel vQTL regions on chromosomes 2A and 2B that contribute to the Cd variation and loci that affect both mean and variance heterogeneity (mvQTL) on chromosome 5A. In addition, our results demonstrated the presence of epistatic interactions between vQTL and mvQTL, which could explain variance heterogeneity. Overall, we provide novel insights into the genetic architecture of grain Cd concentration and report the first application of vGWAS in wheat. Moreover, our findings indicated that epistasis is an important mechanism underlying natural variation for grain Cd concentration.
Collapse
Affiliation(s)
- Waseem Hussain
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Malachy T Campbell
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Diego Jarquin
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Gota Morota
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| |
Collapse
|
5
|
Bruijning M, Metcalf CJE, Jongejans E, Ayroles JF. The Evolution of Variance Control. Trends Ecol Evol 2020; 35:22-33. [PMID: 31519463 PMCID: PMC7482585 DOI: 10.1016/j.tree.2019.08.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 08/08/2019] [Accepted: 08/12/2019] [Indexed: 12/12/2022]
Abstract
Genetically identical individuals can be phenotypically variable, even in constant environmental conditions. The ubiquity of this phenomenon, known as 'intra-genotypic variability', is increasingly evident and the relevant mechanistic underpinnings are beginning to be understood. In parallel, theory has delineated a number of formal expectations for contexts in which such a feature would be adaptive. Here, we review empirical evidence across biological systems and theoretical expectations, including nonlinear averaging and bet hedging. We synthesize existing results to illustrate the dependence of selection outcomes both on trait characteristics, features of environmental variability, and species' demographic context. We conclude by discussing ways to bridge the gap between empirical evidence of intra-genotypic variability, studies demonstrating its genetic component, and evidence that it is adaptive.
Collapse
Affiliation(s)
- Marjolein Bruijning
- Department of Animal Ecology and Physiology, Radboud University, 6500, GL, Nijmegen, The Netherlands; Department of Ecology and Evolutionary Biology, Princeton University, 08540 Princeton, NJ, USA
| | - C Jessica E Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, 08540 Princeton, NJ, USA
| | - Eelke Jongejans
- Department of Animal Ecology and Physiology, Radboud University, 6500, GL, Nijmegen, The Netherlands
| | - Julien F Ayroles
- Department of Ecology and Evolutionary Biology, Princeton University, 08540 Princeton, NJ, USA.
| |
Collapse
|
6
|
Perry GML. 'Fat's chances': Loci for phenotypic dispersion in plasma leptin in mouse models of diabetes mellitus. PLoS One 2019; 14:e0222654. [PMID: 31661517 PMCID: PMC6818960 DOI: 10.1371/journal.pone.0222654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 09/04/2019] [Indexed: 01/29/2023] Open
Abstract
Background Leptin, a critical mediator of feeding, metabolism and diabetes, is expressed on an incidental basis according to satiety. The genetic regulation of leptin should similarly be episodic. Methodology Data from three mouse cohorts hosted by the Jackson Laboratory– 402 (174F, 228M) F2 Dilute Brown non-Agouti (DBA/2)×DU6i intercrosses, 142 Non Obese Diabetic (NOD/ShiLtJ×(NOD/ShiLtJ×129S1/SvImJ.H2g7) N2 backcross females, and 204 male Nonobese Nondiabetic (NON)×New Zealand Obese (NZO/HlLtJ) reciprocal backcrosses–were used to test for loci associated with absolute residuals in plasma leptin and arcsin-transformed percent fat (‘phenotypic dispersion’; PDpLep and PDAFP). Individual data from 1,780 mice from 43 inbred strains was also used to estimate genetic variances and covariances for dispersion in each trait. Principal findings Several loci for PDpLep were detected, including possibly syntenic Chr 17 loci, but there was only a single position on Chr 6 for PDAFP. Coding SNP in genes linked to the consensus Chr 17 PDpLep locus occurred in immunological and cancer genes, genes linked to diabetes and energy regulation, post-transcriptional processors and vomeronasal variants. There was evidence of intersexual differences in the genetic architecture of PDpLep. PDpLep had moderate heritability (hs2=0.29) and PDAFP low heritability (hs2=0.12); dispersion in these traits was highly genetically correlated r = 0.8). Conclusions Greater genetic variance for dispersion in plasma leptin, a physiological trait, may reflect its more ephemeral nature compared to body fat, an accrued progressive character. Genetic effects on incidental phenotypes such as leptin might be effectively characterized with randomization-detection methodologies in addition to classical approaches, helping identify incipient or borderline cases or providing new therapeutic targets.
Collapse
Affiliation(s)
- Guy M. L. Perry
- Department of Biology, University of Prince Edward Island, Charlottetown, PEI, Canada
- * E-mail:
| |
Collapse
|
7
|
Genetic Effects on Dispersion in Urinary Albumin and Creatinine in Three House Mouse ( Mus musculus) Cohorts. G3-GENES GENOMES GENETICS 2019; 9:699-708. [PMID: 30606755 PMCID: PMC6404620 DOI: 10.1534/g3.118.200940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Conventionally, quantitative genetics concerns the heredity of trait means, but there is growing evidence for the existence of architectures in which certain alleles cause random variance in phenotype, termed ‘phenotypic dispersion’ (PD) or ‘variance QTL’ (vQTL), including in physiological traits like disease signs. However, the structure of this phenomenon is still poorly known. PD for urinary albumin (PDUAlb) and creatinine (PDUCrea) was mapped using curated data from two nearly genetically identical F2 mouse (Mus musculus) cohorts (383 male F2 C57BL/6J×A/J (97 SNP) and 207 male F2 C57BL/6J×A/J ApoE knockout mice (144 SNP)) and a related mapping cohort (340 male F2 DBA/2J×C57BL/6J (83 SNP, 8 microsatellites)). PDUAlb was associated with markers in regions of Chr 1 (5-64 megabases (MB); 141-158 MB), 3 (∼113 MB), 8 (37-68 MB), 14 (92-117 MB) and 17 (14-24 MB) with several positions and quantitative architectures in common between the two C57BL/6J×A/J cohorts, most of which had a negative dominant construction. One locus for PDUCrea was detected on Chr 19 (57 MB) in the C57BL/6J×A/J ApoE−/− cohort. The large number of negative dominant loci for albuminuria dispersion relative to conventional quantitative trait loci suggests that the development of albuminuria may be largely genetically dynamic and that randomization in this development is detrimental.
Collapse
|
8
|
Conley D, Johnson R, Domingue B, Dawes C, Boardman J, Siegal M. A sibling method for identifying vQTLs. PLoS One 2018; 13:e0194541. [PMID: 29617452 PMCID: PMC5884517 DOI: 10.1371/journal.pone.0194541] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 03/05/2018] [Indexed: 12/11/2022] Open
Abstract
The propensity of a trait to vary within a population may have evolutionary, ecological, or clinical significance. In the present study we deploy sibling models to offer a novel and unbiased way to ascertain loci associated with the extent to which phenotypes vary (variance-controlling quantitative trait loci, or vQTLs). Previous methods for vQTL-mapping either exclude genetically related individuals or treat genetic relatedness among individuals as a complicating factor addressed by adjusting estimates for non-independence in phenotypes. The present method uses genetic relatedness as a tool to obtain unbiased estimates of variance effects rather than as a nuisance. The family-based approach, which utilizes random variation between siblings in minor allele counts at a locus, also allows controls for parental genotype, mean effects, and non-linear (dominance) effects that may spuriously appear to generate variation. Simulations show that the approach performs equally well as two existing methods (squared Z-score and DGLM) in controlling type I error rates when there is no unobserved confounding, and performs significantly better than these methods in the presence of small degrees of confounding. Using height and BMI as empirical applications, we investigate SNPs that alter within-family variation in height and BMI, as well as pathways that appear to be enriched. One significant SNP for BMI variability, in the MAST4 gene, replicated. Pathway analysis revealed one gene set, encoding members of several signaling pathways related to gap junction function, which appears significantly enriched for associations with within-family height variation in both datasets (while not enriched in analysis of mean levels). We recommend approximating laboratory random assignment of genotype using family data and more careful attention to the possible conflation of mean and variance effects.
Collapse
Affiliation(s)
- Dalton Conley
- Department of Sociology, Princeton University, Princeton, NJ, United States of America
| | - Rebecca Johnson
- Department of Sociology, Princeton University, Princeton, NJ, United States of America
| | - Ben Domingue
- Graduate School of Education, Stanford University, Stanford, CA, United States of America
| | - Christopher Dawes
- Wilff Family Department of Politics, New York University, New York City, NY, United States of America
| | - Jason Boardman
- Institute for Behavioral Sciences, University of Colorado, Boulder, Boulder, CO, United States of America
| | - Mark Siegal
- Center for Genomics and Systems Biology, New York University, New York University, New York City, NY, United States of America
| |
Collapse
|
9
|
Ivarsdottir EV, Steinthorsdottir V, Daneshpour MS, Thorleifsson G, Sulem P, Holm H, Sigurdsson S, Hreidarsson AB, Sigurdsson G, Bjarnason R, Thorsson AV, Benediktsson R, Eyjolfsson G, Sigurdardottir O, Olafsson I, Zeinali S, Azizi F, Thorsteinsdottir U, Gudbjartsson DF, Stefansson K. Effect of sequence variants on variance in glucose levels predicts type 2 diabetes risk and accounts for heritability. Nat Genet 2017; 49:1398-1402. [DOI: 10.1038/ng.3928] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/11/2017] [Indexed: 12/18/2022]
|
10
|
Sell-Kubiak E, Duijvesteijn N, Lopes MS, Janss LLG, Knol EF, Bijma P, Mulder HA. Genome-wide association study reveals novel loci for litter size and its variability in a Large White pig population. BMC Genomics 2015; 16:1049. [PMID: 26652161 PMCID: PMC4674943 DOI: 10.1186/s12864-015-2273-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 12/03/2015] [Indexed: 01/11/2023] Open
Abstract
Background In many traits, not only individual trait levels are under genetic control, but also the variation around that level. In other words, genotypes do not only differ in mean, but also in (residual) variation around the genotypic mean. New statistical methods facilitate gaining knowledge on the genetic architecture of complex traits such as phenotypic variability. Here we study litter size (total number born) and its variation in a Large White pig population using a Double Hierarchical Generalized Linear model, and perform a genome-wide association study using a Bayesian method. Results In total, 10 significant single nucleotide polymorphisms (SNPs) were detected for total number born (TNB) and 9 SNPs for variability of TNB (varTNB). Those SNPs explained 0.83 % of genetic variance in TNB and 1.44 % in varTNB. The most significant SNP for TNB was detected on Sus scrofa chromosome (SSC) 11. A possible candidate gene for TNB is ENOX1, which is involved in cell growth and survival. On SSC7, two possible candidate genes for varTNB are located. The first gene is coding a swine heat shock protein 90 (HSPCB = Hsp90), which is a well-studied gene stabilizing morphological traits in Drosophila and Arabidopsis. The second gene is VEGFA, which is activated in angiogenesis and vasculogenesis in the fetus. Furthermore, the genetic correlation between additive genetic effects on TNB and on its variation was 0.49. This indicates that the current selection to increase TNB will also increase the varTNB. Conclusions To the best of our knowledge, this is the first study reporting SNPs associated with variation of a trait in pigs. Detected genomic regions associated with varTNB can be used in genomic selection to decrease varTNB, which is highly desirable to avoid very small or very large litters in pigs. However, the percentage of variance explained by those regions was small. The SNPs detected in this study can be used as indication for regions in the Sus scrofa genome involved in maintaining low variability of litter size, but further studies are needed to identify the causative loci.
Collapse
Affiliation(s)
- E Sell-Kubiak
- Animal Breeding and Genomics Center, Wageningen University, P.O. Box 338, 6700, Wageningen, AH, The Netherlands.
| | - N Duijvesteijn
- Topigs Norsvin Research Center B.V, P.O. Box 43, 6640, Beuningen, AA, The Netherlands.
| | - M S Lopes
- Topigs Norsvin Research Center B.V, P.O. Box 43, 6640, Beuningen, AA, The Netherlands.
| | - L L G Janss
- Department of Molecular Biology and Genetics, Aarhus University, P.O. Box 50, 8830, Tjele, Denmark.
| | - E F Knol
- Topigs Norsvin Research Center B.V, P.O. Box 43, 6640, Beuningen, AA, The Netherlands.
| | - P Bijma
- Animal Breeding and Genomics Center, Wageningen University, P.O. Box 338, 6700, Wageningen, AH, The Netherlands.
| | - H A Mulder
- Animal Breeding and Genomics Center, Wageningen University, P.O. Box 338, 6700, Wageningen, AH, The Netherlands.
| |
Collapse
|
11
|
Gilks WP, Abbott JK, Morrow EH. Sex differences in disease genetics: evidence, evolution, and detection. Trends Genet 2014; 30:453-63. [DOI: 10.1016/j.tig.2014.08.006] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 08/27/2014] [Accepted: 08/27/2014] [Indexed: 12/13/2022]
|
12
|
Lee CR, Anderson JT, Mitchell-Olds T. Unifying genetic canalization, genetic constraint, and genotype-by-environment interaction: QTL by genomic background by environment interaction of flowering time in Boechera stricta. PLoS Genet 2014; 10:e1004727. [PMID: 25340779 PMCID: PMC4207664 DOI: 10.1371/journal.pgen.1004727] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 09/02/2014] [Indexed: 01/01/2023] Open
Abstract
Natural populations exhibit substantial variation in quantitative traits. A quantitative trait is typically defined by its mean and variance, and to date most genetic mapping studies focus on loci altering trait means but not (co)variances. For single traits, the control of trait variance across genetic backgrounds is referred to as genetic canalization. With multiple traits, the genetic covariance among different traits in the same environment indicates the magnitude of potential genetic constraint, while genotype-by-environment interaction (GxE) concerns the same trait across different environments. While some have suggested that these three attributes of quantitative traits are different views of similar concepts, it is not yet clear, however, whether they have the same underlying genetic mechanism. Here, we detect quantitative trait loci (QTL) influencing the (co)variance of phenological traits in six distinct environments in Boechera stricta, a close relative of Arabidopsis. We identified nFT as the QTL altering the magnitude of phenological trait canalization, genetic constraint, and GxE. Both the magnitude and direction of nFT's canalization effects depend on the environment, and to our knowledge, this reversibility of canalization across environments has not been reported previously. nFT's effects on trait covariance structure (genetic constraint and GxE) likely result from the variable and reversible canalization effects across different traits and environments, which can be explained by the interaction among nFT, genomic backgrounds, and environmental stimuli. This view is supported by experiments demonstrating significant nFT by genomic background epistatic interactions affecting phenological traits and expression of the candidate gene, FT. In contrast to the well-known canalization gene Hsp90, the case of nFT may exemplify an alternative mechanism: Our results suggest that (at least in traits with major signal integrators such as flowering time) genetic canalization, genetic constraint, and GxE may have related genetic mechanisms resulting from interactions among major QTL, genomic backgrounds, and environments.
Collapse
Affiliation(s)
- Cheng-Ruei Lee
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Jill T. Anderson
- Department of Biological Sciences, Environment and Sustainability Program, University of South Carolina, Columbia, South Carolina, United States of America
| | - Thomas Mitchell-Olds
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
| |
Collapse
|
13
|
Ng AH, Frick KK, Krieger NS, Asplin JR, Cohen-McFarlane M, Culbertson CD, Kyker-Snowman K, Grynpas MD, Bushinsky DA. 1,25(OH)₂D₃ induces a mineralization defect and loss of bone mineral density in genetic hypercalciuric stone-forming rats. Calcif Tissue Int 2014; 94:531-43. [PMID: 24481706 PMCID: PMC4276134 DOI: 10.1007/s00223-014-9838-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 01/07/2014] [Indexed: 11/29/2022]
Abstract
Genetic hypercalciuric stone-forming (GHS) rats, bred to maximize urine (u) calcium (Ca) excretion, demonstrate increased intestinal Ca absorption, increased bone Ca resorption, and reduced renal Ca reabsorption, all leading to elevated uCa compared to the parental Sprague-Dawley (SD) rats. GHS rats have increased numbers of vitamin D receptors (VDRs) at each site, with normal levels of 1,25(OH)₂D₃ (1,25D), suggesting their VDR is undersaturated with 1,25D. We have shown that 1,25D induces a greater increase in uCa in GHS than SD rats. To examine the effect of the increased VDR on the osseous response to 1,25D, we fed GHS and SD rats an ample Ca diet and injected either 1,25D [low dose (LD) 12.5 or high dose (HD) 25 ng/100 g body weight/day] or vehicle (veh) daily for 16 days. Femoral areal bone mineral density (aBMD, by DEXA) was decreased in GHS+LD and GHS+HD relative to GHS+veh, while there was no effect on SD. Vertebral aBMD was lower in GHS compared to SD and further decreased in GHS+HD. Both femoral and L6 vertebral volumetric BMD (by μCT) were lower in GHS and further reduced by HD. Histomorphometry indicated a decreased osteoclast number in GHS+HD compared to GHS+veh or SD+HD. In tibiae, GHS+HD trabecular thickness and number increased, with a 12-fold increase in osteoid volume but only a threefold increase in bone volume. Bone formation rate was decreased in GHS+HD relative to GHS+veh, confirming the mineralization defect. The loss of BMD and the mineralization defect in GHS rats contribute to increased hypercalciuria; if these effects persist, they would result in decreased bone strength, making these bones more fracture-prone. The enhanced effect of 1,25D in GHS rats indicates that the increased VDRs are biologically active.
Collapse
Affiliation(s)
- Adeline H. Ng
- Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada
| | - Kevin K. Frick
- Division of Nephrology, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Nancy S. Krieger
- Division of Nephrology, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | | | | | - Christopher D. Culbertson
- Division of Nephrology, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Kelly Kyker-Snowman
- Division of Nephrology, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Marc D. Grynpas
- Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada
| | - David A. Bushinsky
- Division of Nephrology, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| |
Collapse
|
14
|
Frick KK, Asplin JR, Culbertson CD, Granja I, Krieger NS, Bushinsky DA. Persistence of 1,25D-induced hypercalciuria in alendronate-treated genetic hypercalciuric stone-forming rats fed a low-calcium diet. Am J Physiol Renal Physiol 2014; 306:F1081-7. [PMID: 24573387 DOI: 10.1152/ajprenal.00680.2013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Genetic hypercalciuric stone-forming (GHS) rats demonstrate increased intestinal Ca absorption, increased bone resorption, and reduced renal tubular Ca reabsorption leading to hypercalciuria and all form kidney stones. GHS have increased vitamin D receptors (VDR) at these sites of Ca transport. Injection of 1,25(OH)2D3 (1,25D) leads to a greater increase in urine (u)Ca in GHS than in control Sprague-Dawley (SD), possibly due to the additional VDR. In GHS the increased uCa persists on a low-Ca diet (LCD) suggesting enhanced bone resorption. We tested the hypothesis that LCD, coupled to inhibition of bone resorption by alendronate (alen), would eliminate the enhanced 1,25D-induced hypercalciuria in GHS. SD and GHS were fed LCD and half were injected daily with 1,25D. After 8 days all were also given alen until euthanasia at day 16. At 8 days, 1,25D increased uCa in SD and to a greater extent in GHS. At 16 days, alen eliminated the 1,25D-induced increase in uCa in SD. However, in GHS alen decreased, but did not eliminate, the 1,25D-induced hypercalciuria, suggesting maximal alen cannot completely prevent the 1,25D-induced bone resorption in GHS, perhaps due to increased VDR. There was no consistent effect on mRNA expression of renal transcellular or paracellular Ca transporters. Urine CaP and CaOx supersaturation (SS) increased with 1,25D alone in both SD and GHS. Alen eliminated the increase in CaP SS in SD but not in GHS. If these results are confirmed in humans with IH, the use of bisphosphonates, such as alen, may not prevent the decreased bone density observed in these patients.
Collapse
Affiliation(s)
- Kevin K Frick
- Research Assistant Professor of Medicine, Univ. of Rochester School of Medicine and Dentistry, Division of Nephrology, Dept. of Medicine, 601 Elmwood Ave., Box 675, Rochester, NY 14642.
| | | | | | | | | | | |
Collapse
|
15
|
Additive, epistatic, and environmental effects through the lens of expression variability QTL in a twin cohort. Genetics 2013; 196:413-25. [PMID: 24298061 DOI: 10.1534/genetics.113.157503] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The expression of a gene can vary across individuals in the general population, as well as between monozygotic twins. This variable expression is assumed to be due to the influence of both genetic and nongenetic factors. Yet little evidence supporting this assumption has been obtained from empirical data. In this study, we used expression data from a large twin cohort to investigate the influences of genetic and nongenetic factors on variable gene expression. We focused on a set of expression variability QTL (evQTL)--i.e., genetic loci associated with the variance, as opposed to the mean, of gene expression. We identified evQTL for 99, 56, and 79 genes in lymphoblastoid cell lines, skin, and fat, respectively. The differences in gene expression, measured by the relative mean difference (RMD), tended to be larger between pairs of dizygotic (DZ) twins than between pairs of monozygotic (MZ) twins, showing that genetic background influenced the expression variability. Furthermore, a more profound RMD was observed between pairs of MZ twins whose genotypes were associated with greater expression variability than the RMD found between pairs of MZ twins whose genotypes were associated with smaller expression variability. This suggests that nongenetic (e.g., environmental) factors contribute to the variable expression. Lastly, we demonstrated that the formation of evQTL is likely due to partial linkages between eQTL SNPs that are additively associated with the mean of gene expression; in most cases, no epistatic effect is involved. Our findings have implications for understanding divergent sources of gene expression variability.
Collapse
|
16
|
Frick KK, Asplin JR, Krieger NS, Culbertson CD, Asplin DM, Bushinsky DA. 1,25(OH)₂D₃-enhanced hypercalciuria in genetic hypercalciuric stone-forming rats fed a low-calcium diet. Am J Physiol Renal Physiol 2013; 305:F1132-8. [PMID: 23926184 DOI: 10.1152/ajprenal.00296.2013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The inbred genetic hypercalciuric stone-forming (GHS) rats exhibit many features of human idiopathic hypercalciuria and have elevated levels of vitamin D receptors (VDR) in calcium (Ca)-transporting organs. On a normal-Ca diet, 1,25(OH)2D3 (1,25D) increases urine (U) Ca to a greater extent in GHS than in controls [Sprague-Dawley (SD)]. The additional UCa may result from an increase in intestinal Ca absorption and/or bone resorption. To determine the source, we asked whether 1,25D would increase UCa in GHS fed a low-Ca (0.02%) diet (LCD). With 1,25D, UCa in SD increased from 1.2 ± 0.1 to 9.3 ± 0.9 mg/day and increased more in GHS from 4.7 ± 0.3 to 21.5 ± 0.9 mg/day (P < 0.001). In GHS rats on LCD with or without 1,25D, UCa far exceeded daily Ca intake (2.6 mg/day). While the greater excess in UCa in GHS rats must be derived from bone mineral, there may also be a 1,25D-mediated decrease in renal tubular Ca reabsorption. RNA expression of the components of renal Ca transport indicated that 1,25D administration results in a suppression of klotho, an activator of the renal Ca reabsorption channel TRPV5, in both SD and GHS rats. This fall in klotho would decrease tubular reabsorption of the 1,25D-induced bone Ca release. Thus, the greater increase in UCa with 1,25D in GHS fed LCD strongly suggests that the additional UCa results from an increase in bone resorption, likely due to the increased number of VDR in the GHS rat bone cells, with a possible component of decreased renal tubular calcium reabsorption.
Collapse
Affiliation(s)
- Kevin K Frick
- Univ. of Rochester School of Medicine and Dentistry, Div. of Nephrology, Dept. of Medicine, 601 Elmwood Ave., Box 675, Rochester, NY 14642.
| | | | | | | | | | | |
Collapse
|
17
|
Perry GML, Scheinman SJ, Asplin JR. Effects of Sex on Intra-Individual Variance in Urinary Solutes in Stone-Formers Collected from a Single Clinical Laboratory. PLoS One 2013; 8:e53637. [PMID: 23840293 PMCID: PMC3686766 DOI: 10.1371/journal.pone.0053637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 12/03/2012] [Indexed: 11/18/2022] Open
Abstract
Background/Aims Our work in a rodent model of urinary calcium suggests genetic and gender effects on increased residual variability in urine chemistries. Based on these findings, we hypothesized that sex would similarly be associated with residual variation in human urine solutes. Sex-related effects on residuals might affect the establishment of physiological baselines and error in medical assays. Methods We tested the effects of sex on residual variation in urine chemistry by estimating coefficients of variation (CV) for urinary solutes in paired sequential 24-h urines (≤72 hour interval) in 6,758 females and 9,024 males aged 16–80 submitted to a clinical laboratory. Results Females had higher CVs than males for urinary phosphorus overall at the False Discovery Rate (P<0.01). There was no effect of sex on CV for calcium (P>0.3). Males had higher CVs for citrate (P<0.01) from ages 16–45 and females higher CVs for citrate (P<0.01) from ages 56–80, suggesting effects of an extant oestral cycle on residual variance. Conclusions Our findings indicate the effects of sex on residual variance of the excretion of urinary solutes including phosphorus and citrate; differences in CV by sex might reflect dietary lability, differences in the fidelity of reporting or genetic differentiation in renal solute consistency. Such an effect could complicate medical analysis by the addition of random error to phenotypic assays. Renal analysis might require explicit incorporation of heterogeneity among factorial effects, and for sex in particular.
Collapse
Affiliation(s)
- Guy M. L. Perry
- Department of Medicine, SUNY Upstate Medical University, Syracuse, New York, United States of America
- * E-mail:
| | - Steven J. Scheinman
- Department of Medicine, SUNY Upstate Medical University, Syracuse, New York, United States of America
| | - John R. Asplin
- Litholink Corporation, Chicago, Illinois United States of America
| |
Collapse
|
18
|
Perry GML, Scheinman SJ, Asplin JR. Weight, age and coefficients of variation in renal solute excretion. Nephron Clin Pract 2013; 122:13-8. [PMID: 23595094 DOI: 10.1159/000346148] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 11/27/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Homoscedasticity (constant variance over axes or among statistical factors) is an integral assumption of most statistical analyses. However, a number of empirical studies in model organisms and humans demonstrate significant differences in residual variance (that component of phenotype unexplained by known factors) or intra-individual variation among genotypes. Our work suggests that renal traits may be particularly susceptible to randomization by genetic and non-genetic factors, including endogenous variables like age and weight. METHODS We tested associations between age, weight and intra-individual variation in urinary calcium, citrate, chloride, creatinine, potassium, magnesium, sodium, ammonium, oxalate, phosphorus, sulfate, uric acid and urea nitrogen in 9,024 male and 6,758 female kidney stone patients. Coefficients of variation (CVs) were calculated for each individual for each solute from paired 24-hour urines. Analysis of CVs was corrected for inter-measurement collection variance in creatinine and urine volume. CVs for sodium and urea nitrogen were included to correct for dietary salt and protein. RESULTS Age was positively associated with individual CVs for calcium and negatively associated with CVs for potassium, ammonium and phosphorus (p(FDR) < 0.01). Weight was associated with CVs for creatinine, magnesium and uric acid, and negatively associated with CVs for calcium, potassium and oxalate (p(FDR) < 0.05). CONCLUSION Intra-individual variation changes over age and weight axes for numerous urinary solutes. Changing residual variance over age and weight could cause bias in the detection or estimation of genetic or environmental effects. New methodologies may need to account for such residual unpredictability, especially in diverse collections.
Collapse
Affiliation(s)
- Guy M L Perry
- Department of Medicine, SUNY Upstate Medical University, Syracuse, NY 13210, USA.
| | | | | |
Collapse
|
19
|
Frick KK, Asplin JR, Favus MJ, Culbertson C, Krieger NS, Bushinsky DA. Increased biological response to 1,25(OH)(2)D(3) in genetic hypercalciuric stone-forming rats. Am J Physiol Renal Physiol 2013; 304:F718-26. [PMID: 23344574 DOI: 10.1152/ajprenal.00645.2012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genetic hypercalciuric stone-forming (GHS) rats, bred to maximize urine (U) calcium (Ca) excretion, have increased intestinal Ca absorption and bone Ca resorption and reduced renal Ca reabsorption, leading to increased UCa compared with the Sprague-Dawley (SD) rats. GHS rats have increased vitamin D receptors (VDR) at each of these sites, with normal levels of 1,25(OH)(2)D(3) (1,25D), indicating that their VDR is undersaturated with 1,25D. We tested the hypothesis that 1,25D would induce a greater increase in UCa in GHS rats by feeding both strains ample Ca and injecting 1,25D (25 ng · 100 g body wt(-1) · day(-1)) or vehicle for 16 days. With 1,25D, UCa in SD increased from 1.7 ± 0.3 mg/day to 24.4 ± 1.2 (Δ = 22.4 ± 1.5) and increased more in GHS from 10.5 ± 0.7 to 41.9 ± 0.7 (Δ = 29.8 ± 1.8; P = 0.003). To determine the mechanism of the greater increase in UCa in GHS rats, we measured kidney RNA expression of components of renal Ca transport. Expression of transient receptor potential vanilloid (TRPV)5 and calbindin D(28K) were increased similarly in SD + 1,25D and GHS + 1,25D. The Na(+)/Ca(2+) exchanger (NCX1) was increased in GHS + 1,25D. Klotho was decreased in SD + 1,25D and GHS + 1,25D. TRPV6 was increased in SD + 1,25D and increased further in GHS + 1,25D. Claudin 14, 16, and 19, Na/K/2Cl transporter (NKCC2), and secretory K channel (ROMK) did not differ between SD + 1,25D and GHS + 1,25D. Increased UCa with 1,25D in GHS exceeded that of SD, indicating that the increased VDR in GHS induces a greater biological response. This increase in UCa, which must come from the intestine and/or bone, must exceed any effect of 1,25D on TRPV6 or NCX1-mediated renal Ca reabsorption.
Collapse
Affiliation(s)
- Kevin K Frick
- Division of Nephrology, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA.
| | | | | | | | | | | |
Collapse
|
20
|
Rönnegård L, Valdar W. Recent developments in statistical methods for detecting genetic loci affecting phenotypic variability. BMC Genet 2012; 13:63. [PMID: 22827487 PMCID: PMC3493319 DOI: 10.1186/1471-2156-13-63] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Accepted: 07/24/2012] [Indexed: 12/15/2022] Open
Abstract
A number of recent works have introduced statistical methods for detecting genetic loci that affect phenotypic variability, which we refer to as variability-controlling quantitative trait loci (vQTL). These are genetic variants whose allelic state predicts how much phenotype values will vary about their expected means. Such loci are of great potential interest in both human and non-human genetic studies, one reason being that a detected vQTL could represent a previously undetected interaction with other genes or environmental factors. The simultaneous publication of these new methods in different journals has in many cases precluded opportunity for comparison. We survey some of these methods, the respective trade-offs they imply, and the connections between them. The methods fall into three main groups: classical non-parametric, fully parametric, and semi-parametric two-stage approximations. Choosing between alternatives involves balancing the need for robustness, flexibility, and speed. For each method, we identify important assumptions and limitations, including those of practical importance, such as their scope for including covariates and random effects. We show in simulations that both parametric methods and their semi-parametric approximations can give elevated false positive rates when they ignore mean-variance relationships intrinsic to the data generation process. We conclude that choice of method depends on the trait distribution, the need to include non-genetic covariates, and the population size and structure, coupled with a critical evaluation of how these fit with the assumptions of the statistical model.
Collapse
Affiliation(s)
- Lars Rönnegård
- Statistics Unit, Dalarna University, SE-781 70 Borlänge, Sweden.
| | | |
Collapse
|