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Direct and Indirect Effects of Maternal, Paternal, and Offspring Genotypes: Trio-GCTA. Behav Genet 2021; 51:154-161. [PMID: 33387132 DOI: 10.1007/s10519-020-10036-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 12/07/2020] [Indexed: 10/22/2022]
Abstract
Indirect genetic effects from relatives may result in misleading quantifications of heritability, but can also be of interest in their own right. In this paper we propose Trio-GCTA, a model for separating direct and indirect genetic effects when genome-wide single nucleotide polymorphism data have been collected from parent-offspring trios. The model is applicable to phenotypes obtained from any of the family members. We discuss appropriate parameter interpretations and apply the method to three exemplar phenotypes: offspring birth weight, maternal relationship satisfaction, and paternal body-mass index, using real data from the Norwegian Mother, Father and Child Cohort Study (MoBa).
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Gimenez MD, Vazquez DV, Trepat F, Cambiaso V, Rodríguez GR. Fruit quality and DNA methylation are affected by parental order in reciprocal crosses of tomato. PLANT CELL REPORTS 2021; 40:171-186. [PMID: 33079280 DOI: 10.1007/s00299-020-02624-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 10/03/2020] [Indexed: 06/11/2023]
Abstract
Reciprocal effects were found for tomato fruit quality and DNA methylation. The epigenetic identity of reciprocal hybrids indicates that DNA methylation might be one of the mechanisms involved in POEs. Crosses between different genotypes and even between different species are commonly used in plant breeding programs. Reciprocal hybrids are obtained by changing the cross direction (or the sexual role) of parental genotypes in a cross. Phenotypic differences between these hybrids constitute reciprocal effects (REs). The aim of this study was to evaluate phenotypic differences in tomato fruit traits and DNA methylation profiles in three inter- and intraspecific reciprocal crosses. REs were detected for 13 of the 16 fruit traits analyzed. The number of traits with REs was the lowest in the interspecific cross, whereas the highest was found in the cross between recombinant inbred lines (RILs) derived from the same interspecific cross. An extension of gene action analysis was proposed to incorporate parent-of-origin effects (POEs). Maternal and paternal dominance were found in four fruit traits. REs and paternal inheritance were found for epiloci located at coding and non-coding regions. The epigenetic identity displayed by the reciprocal hybrids accounts for the phenotypic differences among them, indicating that DNA methylation might be one of the mechanisms involved in POEs.
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Affiliation(s)
- Magalí Diana Gimenez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
- CIGEOBIO, (CONICET-UNSJ), Complejo Universitario "Islas Malvinas", FCEFN, Universidad de San Juan, Av. Ignacio de la Roza 590, J5402DCS, Rivadavia, San Juan, Argentina
| | - Dana Valeria Vazquez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Felipe Trepat
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Vladimir Cambiaso
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Gustavo Rubén Rodríguez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina.
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina.
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Announcement of the Fulker Award for a Paper Published in Behavior Genetics, Volume 48, 2018. Behav Genet 2019; 49:561. [PMID: 31608428 DOI: 10.1007/s10519-019-09974-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Introducing M-GCTA a Software Package to Estimate Maternal (or Paternal) Genetic Effects on Offspring Phenotypes. Behav Genet 2019; 50:51-66. [DOI: 10.1007/s10519-019-09969-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 12/11/2022]
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Mozaffari SV, DeCara JM, Shah SJ, Sidore C, Fiorillo E, Cucca F, Lang RM, Nicolae DL, Ober C. Parent-of-origin effects on quantitative phenotypes in a large Hutterite pedigree. Commun Biol 2019; 2:28. [PMID: 30675526 PMCID: PMC6338666 DOI: 10.1038/s42003-018-0267-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 12/14/2018] [Indexed: 12/22/2022] Open
Abstract
The impact of the parental origin of associated alleles in GWAS has been largely ignored. Yet sequence variants could affect traits differently depending on whether they are inherited from the mother or the father, as in imprinted regions, where identical inherited DNA sequences can have different effects based on the parental origin. To explore parent-of-origin effects (POEs), we studied 21 quantitative phenotypes in a large Hutterite pedigree to identify variants with single parent (maternal-only or paternal-only) effects, and then variants with opposite parental effects. Here we show that POEs, which can be opposite in direction, are relatively common in humans, have potentially important clinical effects, and will be missed in traditional GWAS. We identified POEs with 11 phenotypes, most of which are risk factors for cardiovascular disease. Many of the loci identified are characteristic of imprinted regions and are associated with the expression of nearby genes.
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Affiliation(s)
- Sahar V. Mozaffari
- Department of Human Genetics, University of Chicago, Chicago, IL 60637 USA
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL 60637 USA
| | - Jeanne M. DeCara
- Department of Medicine, University of Chicago, Chicago, IL 60637 USA
| | - Sanjiv J. Shah
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Carlo Sidore
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, 09042 Italy
| | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, 09042 Italy
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, 09042 Italy
- Dipartimento di Scienze Biomediche, Universita di Sassari, Sassari, 07100 Italy
| | - Roberto M. Lang
- Department of Medicine, University of Chicago, Chicago, IL 60637 USA
| | - Dan L. Nicolae
- Department of Human Genetics, University of Chicago, Chicago, IL 60637 USA
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL 60637 USA
- Department of Medicine, University of Chicago, Chicago, IL 60637 USA
- Department of Statistics, University of Chicago, Chicago, IL 60637 USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL 60637 USA
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL 60637 USA
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