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Alektiar JM, Shan M, Radyk MD, Zhang L, Halbrook CJ, Lin L, Espinoza C, Mier IF, Lavoie BL, Salvatore L, Pasca di Magliano M, Cantley LC, Mueller JL, Lyssiotis CA. Malic enzyme 1 knockout has no deleterious phenotype and is favored in the male germline under standard laboratory conditions. PLoS One 2024; 19:e0303577. [PMID: 38843233 PMCID: PMC11156412 DOI: 10.1371/journal.pone.0303577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 04/26/2024] [Indexed: 06/09/2024] Open
Abstract
Malic Enzyme 1 (ME1) plays an integral role in fatty acid synthesis and cellular energetics through its production of NADPH and pyruvate. As such, it has been identified as a gene of interest in obesity, type 2 diabetes, and an array of epithelial cancers, with most work being performed in vitro. The current standard model for ME1 loss in vivo is the spontaneous Mod-1 null allele, which produces a canonically inactive form of ME1. Herein, we describe two new genetically engineered mouse models exhibiting ME1 loss at dynamic timepoints. Using murine embryonic stem cells and Flp/FRT and Cre/loxP class switch recombination, we established a germline Me1 knockout model (Me1 KO) and an inducible conditional knockout model (Me1 cKO), activated upon tamoxifen treatment in adulthood. Collectively, neither the Me1 KO nor Me1 cKO models exhibited deleterious phenotype under standard laboratory conditions. Knockout of ME1 was validated by immunohistochemistry and genotype confirmed by PCR. Transmission patterns favor Me1 loss in Me1 KO mice when maternally transmitted to male progeny. Hematological examination of these models through complete blood count and serum chemistry panels revealed no discrepancy with their wild-type counterparts. Orthotopic pancreatic tumors in Me1 cKO mice grow similarly to Me1 expressing mice. Similarly, no behavioral phenotype was observed in Me1 cKO mice when aged for 52 weeks. Histological analysis of several tissues revealed no pathological phenotype. These models provide a more modern approach to ME1 knockout in vivo while opening the door for further study into the role of ME1 loss under more biologically relevant, stressful conditions.
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Affiliation(s)
- Jonathan M. Alektiar
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Mengrou Shan
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Megan D. Radyk
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Li Zhang
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Christopher J. Halbrook
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lin Lin
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Carlos Espinoza
- Department of Surgery, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ivan F. Mier
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Brooke L. Lavoie
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lucie Salvatore
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Marina Pasca di Magliano
- Department of Surgery, University of Michigan, Ann Arbor, Michigan, United States of America
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lewis C. Cantley
- Department of Cancer Biology, Dana Farber Cancer Center, Boston, Massachusetts, United States of America
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jacob L. Mueller
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Costas A. Lyssiotis
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, United States of America
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, United States of America
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
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Machhua S, Kumar Jindal A, Basu S, Jangra I, Barman P, Tyagi R, Sil A, Tyagi R, Kaur A, Chawla S, Kumaran SM, Dogra S, Dhaliwal M, Sharma S, Rawat A, Singh S. Transmission patterns of C1-INH deficiency hereditary angioedema favors a wild-type male offspring: Our experience at Chandigarh, India. Immunobiology 2024; 229:152790. [PMID: 38340462 DOI: 10.1016/j.imbio.2024.152790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/19/2023] [Accepted: 01/24/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND Deficiency of C1-inhibitor (C1-INH) protein, caused by pathogenic variants in the Serpin family G member 1 (SERPING1) gene, is the commonest pathophysiological abnormality (in ∼95 % cases) in patients with hereditary angioedema (HAE). C1-INH protein provides negative control over kallikrein-kinin system (KKS). Although the inheritance of the HAE-C1-INH is autosomal dominant, female predominance has often been observed in patients with HAE. OBJECTIVE To analyze the risk of transmission of SERPING1 gene variant from father or mother to their offspring. METHODS Pedigree charts of 42 families with a confirmed diagnosis of HAE-C1-INH and a pathogenic variant in the SERPING1 gene were analysed. Patients with HAE who had had at least one child were included for analyses to assess the risk of transmission from the father or mother to their offspring. RESULTS Overall, 49 % (189/385) of all offspring inherited the genetic defect. In the subgroup analyses, 54.8 % (90/164) female offspring and 44.8 % (99/221; p < 0.02) male offspring inherited the genetic defect. Inheritance of the genetic defect was significantly lower in male offspring. Fathers with SERPING1 gene variant had a statistically significant skewed transmission of the wild type to the male offspring as compared to the variant (57.8 % wild type vs. 42.1 % variant; p < 0.02), whereas no statistically significant difference was found when a father transmitted the variant to a female offspring. Mothers with SERPING1 gene variant had no statistically significant difference in variant transmission to male or female offsprings. CONCLUSION Results of the study suggest that the transmission pattern of SERPING1 gene variant favours the transmission of wild-type alleles in males, especially when the father is the carrier; hence, overall, fewer males and more female offspring inherited the variant. This could be because of a selection of wild-type male sperms during spermatogenesis, as the KLK system has been reported to play a crucial role in the regulation of spermatogenesis. Although, a similar pattern was observed in the maternal transmission of the SERPING1 gene variant; the difference was not statistically significant, likely because of a small sample size.
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Affiliation(s)
- Sanghamitra Machhua
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Ankur Kumar Jindal
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
| | - Suprit Basu
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Isheeta Jangra
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Prabal Barman
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Rahul Tyagi
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Archan Sil
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Reva Tyagi
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Anit Kaur
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Sanchi Chawla
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Sendhil M Kumaran
- Department of Dermatology, Venereology and Leprology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Sunil Dogra
- Department of Dermatology, Venereology and Leprology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Manpreet Dhaliwal
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Saniya Sharma
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Amit Rawat
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Surjit Singh
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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Perdomo-González DI, Id-Lahoucine S, Molina A, Cánovas A, Laseca N, Azor PJ, Valera M. Transmission ratio distortion detection by neutral genetic markers in the Pura Raza Española horse breed. Animal 2023; 17:101012. [PMID: 37950978 DOI: 10.1016/j.animal.2023.101012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 11/13/2023] Open
Abstract
Transmission Ratio Distortion (TRD) is a genetic phenomenon widely demonstrated in several livestock species, but barely in equine species. The TRD occurs when certain genotypes are over- or under-represented in the offspring of a particular mating and can be caused by a variety of factors during gamete formation or during embryonic development. For this study, 126 394 trios consisting of a stallion, mare, and offspring were genotyped using a panel of 17 neutral microsatellite markers recommended by the International Society for Animal Genetics for paternity tests and individual identification. The number of alleles available for each marker ranges from 13 to 18, been 268 the total number of alleles investigated. The TRDscan v.2.0 software was used with the biallelic procedure to identify regions with distorted segregation ratios. After completing the analysis, a total of 12 alleles (out of 11 microsatellites) were identified with decisive evidence for genotypic TRD; 3 and 9 with additive and heterosis patterns, respectively. In addition, 19 alleles (out of 10 microsatellites) were identified displaying allelic TRD. Among them, 14 and 5 were parent-unspecific and stallion-mare-specific TRD. Out of the TRD regions, 24 genes were identified and annotated, predominantly associated with cholesterol metabolism and homeostasis. These genes are often linked to non-specific symptoms like impaired fertility, stunted growth, and compromised overall health. The results suggest a significant impact on the inheritance of certain genetic traits in horses. Further analysis and validation are needed to better understand the TRD impact before the potential implementation in the horse breeding programme strategies.
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Affiliation(s)
| | - S Id-Lahoucine
- Department of Animal and Veterinary Science, Scotland's Rural College, Easter Bush, Edinburgh EH25 9RG, United Kingdom
| | - A Molina
- Departamento de Genética, Universidad de Córdoba, Córdoba 14014, Spain
| | - A Cánovas
- Center of Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - N Laseca
- Departamento de Genética, Universidad de Córdoba, Córdoba 14014, Spain
| | - P J Azor
- Real Asociación Nacional de Criadores de Caballos de Pura Raza Española (ANCCE), Sevilla 41014, Spain
| | - M Valera
- Departamento de Agronomía, ETSIA, Universidad de Sevilla, Sevilla 41005, Spain
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Id-Lahoucine S, Casellas J, Lu D, Sargolzaei M, Miller S, Cánovas A. Distortion of Mendelian segregation across the Angus cattle genome uncovering regions affecting reproduction. Sci Rep 2023; 13:13393. [PMID: 37591956 PMCID: PMC10435455 DOI: 10.1038/s41598-023-37710-z] [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: 12/11/2022] [Accepted: 06/26/2023] [Indexed: 08/19/2023] Open
Abstract
Nowadays, the availability of genotyped trios (sire-dam-offspring) in the livestock industry enables the implementation of the transmission ratio distortion (TRD) approach to discover deleterious alleles in the genome. Various biological mechanisms at different stages of the reproductive cycle such as gametogenesis, embryo development and postnatal viability can induce signals of TRD (i.e., deviation from Mendelian inheritance expectations). In this study, TRD was evaluated using both SNP-by-SNP and sliding windows of 2-, 4-, 7-, 10- and 20-SNP across 92,942 autosomal SNPs for 258,140 genotyped Angus cattle including 7,486 sires, 72,688 dams and 205,966 offspring. Transmission ratio distortion was characterized using allelic (specific- and unspecific-parent TRD) and genotypic parameterizations (additive- and dominance-TRD). Across the Angus autosomal chromosomes, 851 regions were clearly found with decisive evidence for TRD. Among these findings, 19 haplotypes with recessive patterns (potential lethality for homozygote individuals) and 52 regions with allelic patterns exhibiting complete or quasi-complete absence for homozygous individuals in addition to under-representation (potentially reduced viability) of the carrier (heterozygous) offspring were found. In addition, 64 (12) and 20 (4) regions showed significant influence on the trait heifer pregnancy at p-value < 0.05 (after chromosome-wise false discovery rate) and 0.01, respectively, reducing the pregnancy rate up to 15%, thus, supporting the biological importance of TRD phenomenon in reproduction.
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Affiliation(s)
- S Id-Lahoucine
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - J Casellas
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - D Lu
- Angus Genetics Inc., St. Joseph, MO, 64506, USA
| | - M Sargolzaei
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Department of Pathobiology, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Select Sires, Inc., Plain City, OH, 43064, USA
| | - S Miller
- AGBU, a joint venture of NSW Department of Primary Industries and University of New England, Armidale, 2351, Australia
| | - A Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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Laseca N, Cánovas Á, Valera M, Id-Lahoucine S, Perdomo-González DI, Fonseca PAS, Demyda-Peyrás S, Molina A. Genomic screening of allelic and genotypic transmission ratio distortion in horse. PLoS One 2023; 18:e0289066. [PMID: 37556504 PMCID: PMC10411798 DOI: 10.1371/journal.pone.0289066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 07/11/2023] [Indexed: 08/11/2023] Open
Abstract
The phenomenon in which the expected Mendelian inheritance is altered is known as transmission ratio distortion (TRD). The TRD analysis relies on the study of the transmission of one of the two alleles from a heterozygous parent to the offspring. These distortions are due to biological mechanisms affecting gametogenesis, embryo development and/or postnatal viability, among others. In this study, TRD phenomenon was characterized in horses using SNP-by-SNP model by TRDscan v.2.0 software. A total of 1,041 Pura Raza Español breed horses were genotyped with 554,634 SNPs. Among them, 277 horses genotyped in trios (stallion-mare-offspring) were used to perform the TRD analysis. Our results revealed 140 and 42 SNPs with allelic and genotypic patterns, respectively. Among them, 63 displayed stallion-TRD and 41 exhibited mare-TRD, while 36 SNPs showed overall TRD. In addition, 42 SNPs exhibited heterosis pattern. Functional analyses revealed that the annotated genes located within the TRD regions identified were associated with biological processes and molecular functions related to spermatogenesis, oocyte division, embryonic development, and hormonal activity. A total of 10 functional candidate genes related to fertility were found. To our knowledge, this is the most extensive study performed to evaluate the presence of alleles and functional candidate genes with transmission ratio distortion affecting reproductive performance in the domestic horse.
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Affiliation(s)
- Nora Laseca
- Department of Genetics, University of Cordoba, Córdoba, Spain
| | - Ángela Cánovas
- Center of Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
| | - Mercedes Valera
- Department of Agronomy, School of Agronomy Engineering, University of Seville, Seville, Spain
| | - Samir Id-Lahoucine
- Department of Animal and Veterinary Science, Scotland’s Rural College, Aberdeen, Scotland, United Kingdom
| | | | | | | | - Antonio Molina
- Department of Genetics, University of Cordoba, Córdoba, Spain
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Id-Lahoucine S, Casellas J, Suárez-Vega A, Fonseca PAS, Schenkel FS, Sargolzaei M, Cánovas A. Unravelling transmission ratio distortion across the bovine genome: identification of candidate regions for reproduction defects. BMC Genomics 2023; 24:383. [PMID: 37422635 DOI: 10.1186/s12864-023-09455-6] [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: 04/12/2023] [Accepted: 06/15/2023] [Indexed: 07/10/2023] Open
Abstract
BACKGROUND Biological mechanisms affecting gametogenesis, embryo development and postnatal viability have the potential to alter Mendelian inheritance expectations resulting in observable transmission ratio distortion (TRD). Although the discovery of TRD cases have been around for a long time, the current widespread and growing use of DNA technologies in the livestock industry provides a valuable resource of large genomic data with parent-offspring genotyped trios, enabling the implementation of TRD approach. In this research, the objective is to investigate TRD using SNP-by-SNP and sliding windows approaches on 441,802 genotyped Holstein cattle and 132,991 (or 47,910 phased) autosomal SNPs. RESULTS The TRD was characterized using allelic and genotypic parameterizations. Across the whole genome a total of 604 chromosomal regions showed strong significant TRD. Most (85%) of the regions presented an allelic TRD pattern with an under-representation (reduced viability) of carrier (heterozygous) offspring or with the complete or quasi-complete absence (lethality) for homozygous individuals. On the other hand, the remaining regions with genotypic TRD patterns exhibited the classical recessive inheritance or either an excess or deficiency of heterozygote offspring. Among them, the number of most relevant novel regions with strong allelic and recessive TRD patterns were 10 and 5, respectively. In addition, functional analyses revealed candidate genes regulating key biological processes associated with embryonic development and survival, DNA repair and meiotic processes, among others, providing additional biological evidence of TRD findings. CONCLUSIONS Our results revealed the importance of implementing different TRD parameterizations to capture all types of distortions and to determine the corresponding inheritance pattern. Novel candidate genomic regions containing lethal alleles and genes with functional and biological consequences on fertility and pre- and post-natal viability were also identified, providing opportunities for improving breeding success in cattle.
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Affiliation(s)
- Samir Id-Lahoucine
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Joaquim Casellas
- Departament de Ciència Animal I Dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Aroa Suárez-Vega
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Pablo A S Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Mehdi Sargolzaei
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Department of Pathobiology, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Select Sires, Inc, Plain City, OH, 43064, USA
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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Aubert-Mucca M, Huber C, Baujat G, Michot C, Zarhrate M, Bras M, Boutaud L, Malan V, Attie-Bitach T, Cormier-Daire V. Ellis-Van Creveld Syndrome: Clinical and Molecular Analysis of 50 Individuals. J Med Genet 2023; 60:337-345. [PMID: 35927022 DOI: 10.1136/jmg-2022-108435] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 07/09/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND Ellis-Van Creveld (EVC) syndrome is one of the entities belonging to the skeletal ciliopathies short rib-polydactyly subgroup. Major signs are ectodermal dysplasia, chondrodysplasia, polydactyly and congenital cardiopathy, with a high degree of variability in phenotypes ranging from lethal to mild clinical presentations. The EVC and EVC2 genes are the major genes causative of EVC syndrome. However, an increased number of genes involved in the ciliopathy complex have been identified in EVC syndrome, leading to a better understanding of its physiopathology, namely, WDR35, GLI1, DYNC2LI1, PRKACA, PRKACB and SMO. They all code for proteins located in the primary cilia, playing a key role in signal transduction of the Hedgehog pathways. METHODS The aim of this study was the analysis of 50 clinically identified EVC cases from 45 families to further define the phenotype and molecular bases of EVC. RESULTS Our detection rate in the cohort of 45 families was of 91.11%, with variants identified in EVC/EVC2 (77.8%), DYNC2H1 (6.7%), DYNC2LI1 (2.2%), SMO (2.2%) or PRKACB (2.2%). No distinctive feature was remarkable of a specific genotype-phenotype correlation. Interestingly, we identified a high proportion of heterozygous deletions in EVC/EVC2 of variable sizes (26.92%), mostly inherited from the mother, and probably resulting from recombinations involving Alu sequences. CONCLUSION We confirmed that EVC and EVC2 are the major genes involved in the EVC phenotype and highlighted the high prevalence of previously unreported CNVs (Copy Number Variation).
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Affiliation(s)
- Marion Aubert-Mucca
- Centre de Référence des Maladies Osseuses Constitutionnelles, Service de Médecine Génomique des Maladies Rares, Hôpital Universitaire Necker-Enfants Malades, Paris, France
| | - Céline Huber
- Université Paris Cité, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Genevieve Baujat
- Centre de Référence des Maladies Osseuses Constitutionnelles, Service de Médecine Génomique des Maladies Rares, Hôpital Universitaire Necker-Enfants Malades, Paris, France
- Université Paris Cité, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Caroline Michot
- Centre de Référence des Maladies Osseuses Constitutionnelles, Service de Médecine Génomique des Maladies Rares, Hôpital Universitaire Necker-Enfants Malades, Paris, France
- Université Paris Cité, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Mohammed Zarhrate
- Genomics Core Facility, Institut Imagine-Structure Fédérative de Recherche Necker, INSERM U1163 et INSERM US24/CNRS UMS3633, Imagine Institute, Paris, France
| | - Marc Bras
- Bioinformatics Platform, Imagine Institute, Paris, France
| | - Lucile Boutaud
- Université Paris Cité, INSERM UMR 1163, Imagine Institute, Paris, France
- Service de Médecine Génomique des Maladies Rares, Hopital Universitaire Necker-Enfants Malades, Paris, France
| | - Valérie Malan
- Université Paris Cité, INSERM UMR 1163, Imagine Institute, Paris, France
- Service de Médecine Génomique des Maladies Rares, Hopital Universitaire Necker-Enfants Malades, Paris, France
| | - Tania Attie-Bitach
- Université Paris Cité, INSERM UMR 1163, Imagine Institute, Paris, France
- Service de Médecine Génomique des Maladies Rares, Hopital Universitaire Necker-Enfants Malades, Paris, France
| | | | - Valerie Cormier-Daire
- Centre de Référence des Maladies Osseuses Constitutionnelles, Service de Médecine Génomique des Maladies Rares, Hôpital Universitaire Necker-Enfants Malades, Paris, France
- Université Paris Cité, INSERM UMR 1163, Imagine Institute, Paris, France
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Unravelling the genetics of non-random fertilization associated with gametic incompatibility. Sci Rep 2022; 12:22314. [PMID: 36566278 PMCID: PMC9789956 DOI: 10.1038/s41598-022-26910-8] [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: 07/22/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022] Open
Abstract
In the dairy industry, mate allocation is dependent on the producer's breeding goals and the parents' breeding values. The probability of pregnancy differs among sire-dam combinations, and the compatibility of a pair may vary due to the combination of gametic haplotypes. Under the hypothesis that incomplete incompatibility would reduce the odds of fertilization, and complete incompatibility would lead to a non-fertilizing or lethal combination, deviation from Mendelian inheritance expectations would be observed for incompatible pairs. By adding an interaction to a transmission ratio distortion (TRD) model, which detects departure from the Mendelian expectations, genomic regions linked to gametic incompatibility can be identified. This study aimed to determine the genetic background of gametic incompatibility in Holstein cattle. A total of 283,817 genotyped Holstein trios were used in a TRD analysis, resulting in 422 significant regions, which contained 2075 positional genes further investigated for network, overrepresentation, and guilt-by-association analyses. The identified biological pathways were associated with immunology and cellular communication and a total of 16 functional candidate genes were identified. Further investigation of gametic incompatibility will provide opportunities to improve mate allocation for the dairy cattle industry.
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Id-Lahoucine S, Casellas J, Fonseca PAS, Suárez-Vega A, Schenkel FS, Cánovas A. Deviations from Mendelian Inheritance on Bovine X-Chromosome Revealing Recombination, Sex-of-Offspring Effects and Fertility-Related Candidate Genes. Genes (Basel) 2022; 13:genes13122322. [PMID: 36553588 PMCID: PMC9778079 DOI: 10.3390/genes13122322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Transmission ratio distortion (TRD), or significant deviations from Mendelian inheritance, is a well-studied phenomenon on autosomal chromosomes, but has not yet received attention on sex chromosomes. TRD was analyzed on 3832 heterosomal single nucleotide polymorphisms (SNPs) and 400 pseudoautosomal SNPs spanning the length of the X-chromosome using 436,651 genotyped Holstein cattle. On the pseudoautosomal region, an opposite sire-TRD pattern between male and female offspring was identified for 149 SNPs. This finding revealed unique SNPs linked to a specific-sex (Y- or X-) chromosome and describes the accumulation of recombination events across the pseudoautosomal region. On the heterosomal region, 13 SNPs and 69 haplotype windows were identified with dam-TRD. Functional analyses for TRD regions highlighted relevant biological functions responsible to regulate spermatogenesis, development of Sertoli cells, homeostasis of endometrium tissue and embryonic development. This study uncovered the prevalence of different TRD patterns across both heterosomal and pseudoautosomal regions of the X-chromosome and revealed functional candidate genes for bovine reproduction.
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Affiliation(s)
- Samir Id-Lahoucine
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Joaquim Casellas
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Pablo A. S. Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Aroa Suárez-Vega
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Flavio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
- Correspondence:
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10
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Transmission ratio distortion of mutations in the master regulator of centriole biogenesis PLK4. Hum Genet 2022; 141:1785-1794. [PMID: 35536377 PMCID: PMC9556372 DOI: 10.1007/s00439-022-02461-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/26/2022] [Indexed: 11/04/2022]
Abstract
The evolutionary conserved Polo-like kinase 4 (PLK4) is essential for centriole duplication, spindle assembly, and de novo centriole formation. In man, homozygous mutations in PLK4 lead to primary microcephaly, altered PLK4 expression is associated with aneuploidy in human embryos. Here, we report on a consanguineous four-generation family with 8 affected individuals compound heterozygous for a novel missense variant, c.881 T > G, and a deletion of the PLK4 gene. The clinical phenotype of the adult patients is mild compared to individuals with previously described PLK4 mutations. One individual was homozygous for the variant c.881G and phenotypically unaffected. The deletion was inherited by 14 of 16 offspring and thus exhibits transmission ratio distortion (TRD). Moreover, based on the already published families with PLK4 mutations, it could be shown that due to the preferential transmission of the mutant alleles, the number of affected offspring is significantly increased. It is assumed that reduced expression of PLK4 decreases the intrinsically high error rate of the first cell divisions after fertilization, increases the number of viable embryos and thus leads to preferential transmission of the deleted/mutated alleles.
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11
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Zhang C, Wang J, Xiao X, Wang D, Yuan Z, Zhang X, Sun W, Yu S. Fine Mapping of Two Interacting Loci for Transmission Ratio Distortion in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:866276. [PMID: 35422832 PMCID: PMC9002327 DOI: 10.3389/fpls.2022.866276] [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: 01/31/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Transmission ratio distortion (TRD) denotes the observed allelic or genotypic frequency deviation from the expected Mendelian segregation ratios in the offspring of a heterozygote. TRD can severely hamper gene flow between and within rice species. Here, we report the fine mapping and characterization of two loci (TRD4.1 and TRD4.2) for TRD using large F2 segregating populations, which are derived from rice chromosome segment substitution lines, each containing a particular genomic segment introduced from the japonica cultivar Nipponbare (NIP) into the indica cultivar Zhenshan (ZS97). The two loci exhibited a preferential transmission of ZS97 alleles in the derived progeny. Reciprocal crossing experiments using near-isogenic lines harboring three different alleles at TRD4.1 suggest that the gene causes male gametic selection. Moreover, the transmission bias of TRD4.2 was diminished in heterozygotes when they carried homozygous TRD4.1 ZS97. This indicates an epistatic interaction between these two loci. TRD4.2 was mapped into a 35-kb region encompassing one candidate gene that is specifically expressed in the reproductive organs in rice. These findings broaden the understanding of the genetic mechanisms of TRD and offer an approach to overcome the barrier of gene flow between the subspecies in rice, thus facilitating rice improvement by introgression breeding.
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Affiliation(s)
- Chaopu Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jilin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiongfeng Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Dianwen Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhiyang Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaodan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wenqiang Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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12
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Kinosian SP, Rowe CA, Wolf PG. Why Do Heterosporous Plants Have So Few Chromosomes? FRONTIERS IN PLANT SCIENCE 2022; 13:807302. [PMID: 35251082 PMCID: PMC8888854 DOI: 10.3389/fpls.2022.807302] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
The mechanisms controlling chromosome number, size, and shape, and the relationship of these traits to genome size, remain some of the least understood aspects of genome evolution. Across vascular plants, there is a striking disparity in chromosome number between homosporous and heterosporous lineages. Homosporous plants (comprising most ferns and some lycophytes) have high chromosome numbers compared to heterosporous lineages (some ferns and lycophytes and all seed plants). Many studies have investigated why homosporous plants have so many chromosomes. However, homospory is the ancestral condition from which heterospory has been derived several times. Following this phylogenetic perspective, a more appropriate question to ask is why heterosporous plants have so few chromosomes. Here, we review life history differences between heterosporous and homosporous plants, previous work on chromosome number and genome size in each lineage, known mechanisms of genome downsizing and chromosomal rearrangements, and conclude with future prospects for comparative research.
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Affiliation(s)
- Sylvia P. Kinosian
- Negaunee Institute for Plant Conservation Science, Chicago Botanic Garden, Glencoe, IL, United States
| | - Carol A. Rowe
- Earth System Science Center, The University of Alabama in Huntsville, Huntsville, AL, United States
| | - Paul G. Wolf
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, United States
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13
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Arends D, Kärst S, Heise S, Korkuc P, Hesse D, Brockmann GA. Transmission distortion and genetic incompatibilities between alleles in a multigenerational mouse advanced intercross line. Genetics 2022; 220:iyab192. [PMID: 34791189 PMCID: PMC8733443 DOI: 10.1093/genetics/iyab192] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/15/2021] [Indexed: 11/23/2022] Open
Abstract
While direct additive and dominance effects on complex traits have been mapped repeatedly, additional genetic factors contributing to the heterogeneity of complex traits have been scarcely investigated. To assess genetic background effects, we investigated transmission ratio distortions (TRDs) of alleles from parent to offspring using an advanced intercross line (AIL) of an initial cross between the mouse inbred strains C57BL/6NCrl (B6N) and BFMI860-12 [Berlin Fat Mouse Inbred (BFMI)]. A total of 341 males of generation 28 and their respective 61 parents and 66 grandparents were genotyped using Mega Mouse Universal Genotyping Arrays. TRDs were investigated using allele transmission asymmetry tests, and pathway overrepresentation analysis was performed. Sequencing data were used to test for overrepresentation of nonsynonymous SNPs (nsSNPs) in TRD regions. Genetic incompatibilities were tested using the Bateson-Dobzhansky-Muller two-locus model. A total of 62 TRD regions were detected, many in close proximity to the telocentric centromere. TRD regions contained 44.5% more nsSNPs than randomly selected regions (182 vs 125.9 ± 17.0, P < 1 × 10-4). Testing for genetic incompatibilities between TRD regions identified 29 genome-wide significant incompatibilities between TRD regions [P(BF) < 0.05]. Pathway overrepresentation analysis of genes in TRD regions showed that DNA methylation, epigenetic regulation of RNA, and meiotic/meiosis regulation pathways were affected independent of the parental origin of the TRD. Paternal BFMI TRD regions showed overrepresentation in the small interfering RNA biogenesis and in the metabolism of lipids and lipoproteins. Maternal B6N TRD regions harbored genes involved in meiotic recombination, cell death, and apoptosis pathways. The analysis of genes in TRD regions suggests the potential distortion of protein-protein interactions influencing obesity and diabetic retinopathy as a result of disadvantageous combinations of allelic variants in Aass, Pgx6, and Nme8. Using an AIL significantly improves the resolution at which we can investigate TRD. Our analysis implicates distortion of protein-protein interactions as well as meiotic drive as the underlying mechanisms leading to the observed TRD in our AIL. Furthermore, genes with large amounts of nsSNPs located in TRD regions are more likely to be involved in pathways that are related to the phenotypic differences between the parental strains. Genes in these TRD regions provide new targets for investigating genetic adaptation, protein-protein interactions, and determinants of complex traits such as obesity.
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Affiliation(s)
- Danny Arends
- Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Humboldt University Berlin, Berlin D-10115, Germany
| | - Stefan Kärst
- Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Humboldt University Berlin, Berlin D-10115, Germany
| | - Sebastian Heise
- Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Humboldt University Berlin, Berlin D-10115, Germany
| | - Paula Korkuc
- Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Humboldt University Berlin, Berlin D-10115, Germany
| | - Deike Hesse
- Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Humboldt University Berlin, Berlin D-10115, Germany
| | - Gudrun A Brockmann
- Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Humboldt University Berlin, Berlin D-10115, Germany
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14
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Gòdia M, Casellas J, Ruiz-Herrera A, Rodríguez-Gil JE, Castelló A, Sánchez A, Clop A. Whole genome sequencing identifies allelic ratio distortion in sperm involving genes related to spermatogenesis in a swine model. DNA Res 2021; 27:5906030. [PMID: 32931559 PMCID: PMC7750926 DOI: 10.1093/dnares/dsaa019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 09/02/2020] [Indexed: 12/28/2022] Open
Abstract
Transmission Ratio Distortion (TRD), the uneven transmission of an allele from a parent to its offspring, can be caused by allelic differences affecting gametogenesis, fertilization or embryogenesis. However, TRD remains vaguely studied at a genomic scale. We sequenced the diploid and haploid genomes of three boars from leukocytes and spermatozoa at 50x to shed light into the genetic basis of spermatogenesis-caused Allelic Ratio Distortion (ARD). We first developed a Binomial model to identify ARD by simultaneously analysing all three males. This led to the identification of 55 ARD SNPs, most of which were animal-specific. We then evaluated ARD individually within each pig by a Fisher’s exact test and identified two shared genes (TOP3A and UNC5B) and four shared genomic regions harbouring distinct ARD SNPs in the three boars. The shared genomic regions contained candidate genes with functions related to spermatogenesis including AK7, ARID4B, BDKRB2, GSK3B, NID1, NSMCE1, PALB2, VRK1 and ZC3H13. Using the Fisher’s test, we also identified 378 genes containing variants with protein damaging potential in at least one boar, a high proportion of which, including FAM120B, TDRD15, JAM2 or AOX4 among others, are associated to spermatogenesis. Overall, our results show that sperm is subjected to ARD with variants associated to a wide variety of genes involved in different stages of spermatogenesis.
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Affiliation(s)
- Marta Gòdia
- Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Cerdanyola del Vallès, Catalonia 08193, Spain
| | - Joaquim Casellas
- Department of Animal and Food Sciences, Autonomous University of Barcelona, Cerdanyola del Vallès, Catalonia 08193, Spain
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cel.lular, Fisiologia i Immunologia, Autonomous University of Barcelona, Cerdanyola del Vallès, Catalonia 08193, Spain.,Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Autonomous University of Barcelona, Cerdanyola del Vallès, Catalonia 08193, Spain
| | - Joan E Rodríguez-Gil
- Unit of Animal Reproduction, Department of Animal Medicine and Surgery, Autonomous University of Barcelona, Cerdanyola del Vallès, Catalonia 08193, Spain
| | - Anna Castelló
- Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Cerdanyola del Vallès, Catalonia 08193, Spain.,Department of Animal and Food Sciences, Autonomous University of Barcelona, Cerdanyola del Vallès, Catalonia 08193, Spain
| | - Armand Sánchez
- Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Cerdanyola del Vallès, Catalonia 08193, Spain.,Department of Animal and Food Sciences, Autonomous University of Barcelona, Cerdanyola del Vallès, Catalonia 08193, Spain
| | - Alex Clop
- Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Cerdanyola del Vallès, Catalonia 08193, Spain.,Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Catalonia 08003, Spain
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15
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Auboeuf D. The Physics-Biology continuum challenges darwinism: Evolution is directed by the homeostasis-dependent bidirectional relation between genome and phenotype. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 167:121-139. [PMID: 34097984 DOI: 10.1016/j.pbiomolbio.2021.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/19/2021] [Accepted: 05/31/2021] [Indexed: 10/21/2022]
Abstract
The physics-biology continuum relies on the fact that life emerged from prebiotic molecules. Here, I argue that life emerged from the coupling between nucleic acid and protein synthesis during which proteins (or proto-phenotypes) maintained the physicochemical parameter equilibria (or proto-homeostasis) in the proximity of their encoding nucleic acids (or proto-genomes). This protected the proto-genome physicochemical integrity (i.e., atomic composition) from environmental physicochemical constraints, and therefore increased the probability of reproducing the proto-genome without variation. From there, genomes evolved depending on the biological activities they generated in response to environmental fluctuations. Thus, a genome maintaining homeostasis (i.e., internal physicochemical parameter equilibria), despite and in response to environmental fluctuations, maintains its physicochemical integrity and has therefore a higher probability to be reproduced without variation. Consequently, descendants have a higher probability to share the same phenotype than their parents. Otherwise, the genome is modified during replication as a consequence of the imbalance of the internal physicochemical parameters it generates, until new mutation-deriving biological activities maintain homeostasis in offspring. In summary, evolution depends on feedforward and feedback loops between genome and phenotype, as the internal physicochemical conditions that a genome generates ─ through its derived phenotype in response to environmental fluctuations ─ in turn either guarantee its stability or direct its variation. Evolution may not be explained by the Darwinism-derived, unidirectional principle (random mutations-phenotypes-natural selection) but rather by the bidirectional relationship between genome and phenotype, in which the phenotype in interaction with the environment directs the evolution of the genome it derives from.
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Affiliation(s)
- Didier Auboeuf
- ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée D'Italie, Site Jacques Monod, F-69007, Lyon, France.
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16
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Ren P, Deng F, Chen S, Ran J, Li J, Yin L, Wang Y, Yin H, Zhu Q, Liu Y. Whole-genome resequencing reveals loci with allelic transmission ratio distortion in F 1 chicken population. Mol Genet Genomics 2021; 296:331-339. [PMID: 33404883 DOI: 10.1007/s00438-020-01744-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/30/2020] [Indexed: 11/28/2022]
Abstract
Allelic transmission ratio distortion (TRD) is the significant deviation from the expected ratio under Mendelian inheritance theory, which may be resulted from multiple disrupted biological processes, including germline selection, meiotic drive, gametic competition, imprint error, and embryo lethality. However, it is less known that whether or what extent the allelic TRD is present in farm animals. In this study, whole-genome resequencing technology was applied to reveal TRD loci in chicken by constructing a full-sib F1 hybrid population. Through the whole-genome resequencing data of two parents (30 ×) and 38 offspring (5 ×), we detected a total of 2850 TRD SNPs (p-adj < 0.05) located within 400 genes showing TRD, and all of them were unevenly distributed on macrochromosomes and microchromosomes. Our findings suggested that TRD in the chicken chromosome 16 might play an important role in chicken immunity and disease resistance and the MYH1F with significant TRD and allele-specific expression could play a key role in the fast muscle development. In addition, functional enrichment analyses revealed that many genes (e.g., TGFBR2, TGFBR3, NOTCH1, and NCOA1) with TRD were found in the significantly enriched biological process and InterPro terms in relation to embryonic lethality and germline selection. Our results suggested that TRD is considerably prevalent in the chicken genome and has functional implications.
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Affiliation(s)
- Peng Ren
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Feilong Deng
- Special Key Laboratory of Microbial Resources and Drug Development, Zunyi Medical University, Zunyi, 563000, China
| | - Shiyi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Jinshan Ran
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Jingjing Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Lingqian Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Yan Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Huadong Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Qing Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Yiping Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China. .,Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, 211 Huiming Road, Wenjiang, Sichuan, 611130, China.
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17
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Abdalla EA, Id‐Lahoucine S, Cánovas A, Casellas J, Schenkel FS, Wood BJ, Baes CF. Discovering lethal alleles across the turkey genome using a transmission ratio distortion approach. Anim Genet 2020; 51:876-889. [PMID: 33006154 PMCID: PMC7702127 DOI: 10.1111/age.13003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2020] [Indexed: 12/23/2022]
Abstract
Deviation from Mendelian inheritance expectations (transmission ratio distortion, TRD) has been observed in several species, including the mouse and humans. In this study, TRD was characterized in the turkey genome using both allelic (specific- and unspecific-parent TRD) and genotypic (additive- and dominance-TRD) parameterizations within a Bayesian framework. In this study, we evaluated TRD for 23 243 genotyped Turkeys across 56 393 autosomal SNPs. The analyses included 500 sires, 2013 dams and 11 047 offspring (trios). Three different haplotype sliding windows of 4, 10 and 20 SNPs were used across the autosomal chromosomes. Based on the genotypic parameterizations, 14 haplotypes showed additive and dominance TRD effects highlighting regions with a recessive TRD pattern. In contrast, the allelic model uncovered 12 haplotype alleles with the allelic TRD pattern which showed an underrepresentation of heterozygous offspring in addition to the absence of homozygous animals. For regions with the allelic pattern, only one particular region showed a parent-specific TRD where the penetrance was high via the dam, but low via the sire. The gene set analysis uncovered several gene ontology functional terms, Reactome pathways and several Medical Subject Headings that showed significant enrichment of genes associated with TRD. Many of these gene ontology functional terms (e.g. mitotic spindle assembly checkpoint, DRM complex and Aneuploidy), Reactome pathways (e.g. Mismatch repair) and Medical Subject Headings (e.g. Adenosine monophosphate) are known to be related to fertility, embryo development and lethality. The results of this study revealed potential novel candidate lethal haplotypes, functional terms and pathways that may enhance breeding programs in Turkeys through reducing mortality and improving reproduction rate.
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Affiliation(s)
- E. A. Abdalla
- Centre for Genetic Improvement of Livestock, Department of Animal BiosciencesUniversity of GuelphGuelphONN1G 2W1Canada
| | - S. Id‐Lahoucine
- Centre for Genetic Improvement of Livestock, Department of Animal BiosciencesUniversity of GuelphGuelphONN1G 2W1Canada
| | - A. Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal BiosciencesUniversity of GuelphGuelphONN1G 2W1Canada
| | - J. Casellas
- Departament de Ciència Animal i dels AlimentsUniversitat Autònoma de BarcelonaBellaterra08193Spain
| | - F. S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal BiosciencesUniversity of GuelphGuelphONN1G 2W1Canada
| | - B. J. Wood
- Centre for Genetic Improvement of Livestock, Department of Animal BiosciencesUniversity of GuelphGuelphONN1G 2W1Canada
- Hybrid TurkeysC‐650 Riverbend Drive, Suite CKitchenerONN2K 3S2Canada
- School of Veterinary ScienceUniversity of QueenslandGattonQld4343Australia
| | - C. F. Baes
- Centre for Genetic Improvement of Livestock, Department of Animal BiosciencesUniversity of GuelphGuelphONN1G 2W1Canada
- Institute of Genetics, Vetsuisse FacultyUniversity of BernBern3001Switzerland
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18
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Clinical Implications and Gender Differences of KCNQ1 p.Gly168Arg Pathogenic Variant in Long QT Syndrome. J Clin Med 2020; 9:jcm9123846. [PMID: 33256261 PMCID: PMC7760054 DOI: 10.3390/jcm9123846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/19/2020] [Accepted: 11/24/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Long QT syndrome (LQTS) is an inheritable arrhythmogenic disorder associated with life-threatening arrhythmic events (LAEs). In general, patients with LQTS2 (KCNH2) and LQTS3 (SCN5A) are considered to be a greater risk of LAEs than LQTS1 (KCNQ1) patients. Gender differences are also important. Series analyzing families with the same pathogenic variants may help in the progress of elaborating strong specific genotype-phenotype management strategies. In this manuscript, we describe the phenotype of seven unrelated families, carriers of the KCNQ1 G168R pathogenic variant. METHODS we identified all consecutive index cases referred for genetic testing with LQTS diagnosis carriers of KCNQ1 G168R variant. Genetic and clinical screening for all available relatives was performed. RESULTS we evaluated seven unrelated families, with a total 34 KCNQ1 G168R carriers (two obligated carriers died without available EKGs to evaluate the phenotype). All index cases but one were women and three of them presented with aborted sudden cardiac death (SCD) or syncope. The presence of sudden death in these families is notable, with a total of nine unexplained sudden deaths and four aborted SCD. Phenotype penetrance was 100% in women and 37.5% in men. CONCLUSIONS KCNQ1 G168R is a pathogenic variant, with a high penetrance among women and mild penetrance among men. Risk for LAEs in this variant seems not negligible, especially among woman, and risk stratification should always be carefully evaluated.
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19
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Stabile M, Colavito D, Del Giudice E, Rispoli AF, Ingenito MC, Naumova AK. A novel exomal ATRX mutation with preferential transmission to offspring: A case report and review of the literature for transmission ratio distortion in ATRX families. Mol Med Rep 2020; 22:4561-4566. [PMID: 33173999 PMCID: PMC7646821 DOI: 10.3892/mmr.2020.11574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/21/2020] [Indexed: 12/19/2022] Open
Abstract
The present case report describes an Italian family with three affected probands, who exhibited serious mental disability, which has not been associated with other anomalies, except with slight facial dysmorphism. Molecular multigenic analysis for intellectual disability identified a previously unreported variant, p.Ile1765Met (c.5295C>G) in the SNF domain of the ATRX protein (in exon 24). The identified mutation was found in a hemizygous state in all three affected probands and in a heterozygous state in the asymptomatic mother and the female sibling. With respect to the phenotypic similarities found in the patients with those described in previous studies, the consistency in the mode of inheritance and segregation of the mutation, the variant reported in the present case report may be considered as ‘likely pathogenic’. To investigate the hypothesis that the preferential transmission of the ATRX mutation observed in this family reflected a general trend, a meta-analysis into the segregation of ATRX mutations from published pedigrees, following allelic transmission from mothers who are heterozygous carriers to their offspring, was performed. A preferential transmission of the mutant allele to male offspring (58% of males inherited the mutant allele) was found; however, the bias was not statistically significant (P=0.29; χ2 test).
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Affiliation(s)
- Mariano Stabile
- Zygote Center, Center for Genetics, Prenatal Diagnosis, Fertility, I-84131 Salerno, Italy
| | - Davide Colavito
- Research & Innovation s.r.l. (R&I Genetics), I-35127 Padova, Italy
| | - Elda Del Giudice
- Research & Innovation s.r.l. (R&I Genetics), I-35127 Padova, Italy
| | - Anna F Rispoli
- Zygote Center, Center for Genetics, Prenatal Diagnosis, Fertility, I-84131 Salerno, Italy
| | - Marina C Ingenito
- Zygote Center, Center for Genetics, Prenatal Diagnosis, Fertility, I-84131 Salerno, Italy
| | - Anna K Naumova
- Departments of Obstetrics and Gynecology and Human Genetics, Research Institute of the McGill University Health Centre (RI-MUHC), McGill University, Montreal, Quebec H4A 3J1, Canada
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20
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Casellas J, Id-Lahoucine S, Cánovas A. Discriminating between allele- and genotype-specific transmission ratio distortion. Anim Genet 2020; 51:847-854. [PMID: 32996622 DOI: 10.1111/age.13007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2020] [Indexed: 11/30/2022]
Abstract
Transmission ratio distortion (TRD) is defined as the observed deviation from the expected Mendelian inheritance of alleles from heterozygous parents. This phenomenon is attributed to various biological mechanisms acting on germ cells, embryos or fetuses, or even in early postnatal life. Current statistical approaches typically use two independent parametrizations assuming that TRD relies on allele- or genotype-related mechanisms, although they have never been tested and compared. This study compared allele- and genotype-related TRD models on simulated datasets with 1000 genotyped offspring and real data from 168 sire-dam-offspring beef cattle trios. The analysis of simulated datasets favored the true model of analysis in most cases (>93%), and a low percentage of missidentification occurred under (almost) null dominance (genotype-related model) or similar and moderate-to-low sire- and dam-specific TRD parameters (allele-related model). Moreover, the correlation between simulated and predicted distortion parameters was high (>0.97) under the true model. The comparison of allele- and genotype-related TRD models is an appealing tool to infer the biological source of TRD (i.e. haploid vs. diploid cells) when screening the whole genome. The analysis of beef cattle data corroborated a TRD region previously reported in chromosome 4, although discarding allele-related mechanisms and favoring the genotype-related model as the more reliable one. The results of this study highlight the relevance of implementing and comparing different parametrizations to capture all kinds of TRD, and to compare them using appropriate statistical methods.
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Affiliation(s)
- J Casellas
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - S Id-Lahoucine
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.,Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - A Cánovas
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
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Maternal Transmission Ratio Distortion in Two Iberian Pig Varieties. Genes (Basel) 2020; 11:genes11091050. [PMID: 32899475 PMCID: PMC7563664 DOI: 10.3390/genes11091050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 12/30/2022] Open
Abstract
Transmission ratio distortion (TRD) is defined as the allele transmission deviation from the heterozygous parent to the offspring from the expected Mendelian genotypic frequencies. Although TRD can be a confounding factor in genetic mapping studies, this phenomenon remains mostly unknown in pigs, particularly in traditional breeds (i.e., the Iberian pig). We aimed to describe the maternal TRD prevalence and its genomic distribution in two Iberian varieties. Genotypes from a total of 247 families (dam and offspring) of Entrepelado (n = 129) and Retinto (n = 118) Iberian varieties were analyzed. The offspring were sired by both ungenotyped purebred Retinto and Entrepelado Iberian boars, regardless of the dam variety used. After quality control, 16,246 single-nucleotide polymorphisms (SNPs) in the Entrepelado variety and 9744 SNPs in the Retinto variety were analyzed. Maternal TRD was evaluated by a likelihood ratio test under SNP-by-SNP, adapting a previous model solved by Bayesian inference. Results provided 68 maternal TRD loci (TRDLs) in the Entrepelado variety and 24 in the Retinto variety (q < 0.05), with mostly negative TRD values, increasing the transmission of the minor allele. In addition, both varieties shared ten common TRDLs. No strong evidence of biological effects was found in genes with TRDLs. However, some biological processes could be affected by TRDLs, such as embryogenesis at different levels and lipid metabolism. These findings could provide useful insight into the genetic mechanisms to improve the swine industry, particularly in traditional breeds.
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22
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Mogessie B. Advances and surprises in a decade of oocyte meiosis research. Essays Biochem 2020; 64:263-275. [PMID: 32538429 DOI: 10.1042/ebc20190068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 12/30/2022]
Abstract
Eggs are produced from progenitor oocytes through meiotic cell division. Fidelity of meiosis is critical for healthy embryogenesis - fertilisation of aneuploid eggs that contain the wrong number of chromosomes is a leading cause of genetic disorders including Down's syndrome, human embryo deaths and infertility. Incidence of meiosis-related oocyte and egg aneuploidies increases dramatically with advancing maternal age, which further complicates the 'meiosis problem'. We have just emerged from a decade of meiosis research that was packed with exciting and transformative research. This minireview will focus primarily on studies of mechanisms that directly influence chromosome segregation.
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Affiliation(s)
- Binyam Mogessie
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
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23
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Davies NM, Howe LJ, Brumpton B, Havdahl A, Evans DM, Davey Smith G. Within family Mendelian randomization studies. Hum Mol Genet 2020; 28:R170-R179. [PMID: 31647093 DOI: 10.1093/hmg/ddz204] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 01/08/2023] Open
Abstract
Mendelian randomization (MR) is increasingly used to make causal inferences in a wide range of fields, from drug development to etiologic studies. Causal inference in MR is possible because of the process of genetic inheritance from parents to offspring. Specifically, at gamete formation and conception, meiosis ensures random allocation to the offspring of one allele from each parent at each locus, and these are unrelated to most of the other inherited genetic variants. To date, most MR studies have used data from unrelated individuals. These studies assume that genotypes are independent of the environment across a sample of unrelated individuals, conditional on covariates. Here we describe potential sources of bias, such as transmission ratio distortion, selection bias, population stratification, dynastic effects and assortative mating that can induce spurious or biased SNP-phenotype associations. We explain how studies of related individuals such as sibling pairs or parent-offspring trios can be used to overcome some of these sources of bias, to provide potentially more reliable evidence regarding causal processes. The increasing availability of data from related individuals in large cohort studies presents an opportunity to both overcome some of these biases and also to evaluate familial environmental effects.
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Affiliation(s)
- Neil M Davies
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, United Kingdom.,Population Health Sciences, Bristol Medical School, University of Bristol, Barley House, Oakfield Grove, Bristol, BS8 2BN, United Kingdom
| | - Laurence J Howe
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, United Kingdom.,Population Health Sciences, Bristol Medical School, University of Bristol, Barley House, Oakfield Grove, Bristol, BS8 2BN, United Kingdom
| | - Ben Brumpton
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, United Kingdom.,K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway.,Clinic of Thoracic and Occupational Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Alexandra Havdahl
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, United Kingdom.,Nic Waals Institute, Lovisenberg Diaconal Hospital, Oslo, Norway.,Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway
| | - David M Evans
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, United Kingdom.,University of Queensland Diamantina Institute, University of Queensland, Brisbane, 4102, Australia
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, United Kingdom.,Population Health Sciences, Bristol Medical School, University of Bristol, Barley House, Oakfield Grove, Bristol, BS8 2BN, United Kingdom
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24
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Snanoudj S, Molin A, Colson C, Coudray N, Paulien S, Mittre H, Gérard M, Schaefer E, Goldenberg A, Bacchetta J, Odent S, Naudion S, Demeer B, Faivre L, Gruchy N, Kottler ML, Richard N. Maternal Transmission Ratio Distortion of GNAS Loss-of-Function Mutations. J Bone Miner Res 2020; 35:913-919. [PMID: 31886927 DOI: 10.1002/jbmr.3948] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 12/09/2019] [Accepted: 12/14/2019] [Indexed: 12/14/2022]
Abstract
Pseudohypoparathyroidism type 1A (PHP1A) and pseudopseudohypoparathyroidism (PPHP) are two rare autosomal dominant disorders caused by loss-of-function mutations in the imprinted Guanine Nucleotide Binding Protein, Alpha Stimulating Activity (GNAS) gene, coding Gs α. PHP1A is caused by mutations in the maternal allele and results in Albright's hereditary osteodystrophy (AHO) and hormonal resistance, mainly to the parathormone (PTH), whereas PPHP, with AHO features and no hormonal resistance, is linked to mutations in the paternal allele. This study sought to investigate parental transmission of GNAS mutations. We conducted a retrospective study in a population of 204 families with 361 patients harboring GNAS mutations. To prevent ascertainment bias toward a higher proportion of affected children due to the way in which data were collected, we excluded from transmission analysis all probands in the ascertained sibships. After bias correction, the distribution ratio of the mutated alleles was calculated from the observed genotypes of the offspring of nuclear families and was compared to the expected ratio of 50% according to Mendelian inheritance (one-sample Z-test). Sex ratio, phenotype of the transmitting parent, and transmission depending on the severity of the mutation were also analyzed. Transmission analysis was performed in 114 nuclear families and included 250 descendants. The fertility rates were similar between male and female patients. We showed an excess of transmission from mother to offspring of mutated alleles (59%, p = .022), which was greater when the mutations were severe (61.7%, p = .023). Similarly, an excess of transmission was found when the mother had a PHP1A phenotype (64.7%, p = .036). By contrast, a Mendelian distribution was observed when the mutations were paternally inherited. Higher numbers of females within the carriers, but not in noncarriers, were also observed. The mother-specific transmission ratio distortion (TRD) and the sex-ratio imbalance associated to PHP1A point to a role of Gs α in oocyte biology or embryogenesis, with implications for genetic counseling. © 2019 American Society for Bone and Mineral Research.
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Affiliation(s)
- Sarah Snanoudj
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Arnaud Molin
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Cindy Colson
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Nadia Coudray
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Sylvie Paulien
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Hervé Mittre
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Marion Gérard
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Elise Schaefer
- Department of Genetics, CHU de Strasbourg, Strasbourg, France
| | | | - Justine Bacchetta
- Department of Pediatric Nephrology, Rheumatology and Dermatology, CHU de Lyon, Bron, France
| | - Sylvie Odent
- Department of Genetics, CHU de Rennes, Rennes, France
| | - Sophie Naudion
- Department of Genetics, CHU de Bordeaux, Bordeaux, France
| | | | | | - Nicolas Gruchy
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Marie-Laure Kottler
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Nicolas Richard
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
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25
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Fishman L, McIntosh M. Standard Deviations: The Biological Bases of Transmission Ratio Distortion. Annu Rev Genet 2019; 53:347-372. [DOI: 10.1146/annurev-genet-112618-043905] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The rule of Mendelian inheritance is remarkably robust, but deviations from the equal transmission of alternative alleles at a locus [a.k.a. transmission ratio distortion (TRD)] are also commonly observed in genetic mapping populations. Such TRD reveals locus-specific selection acting at some point between the diploid heterozygous parents and progeny genotyping and therefore can provide novel insight into otherwise-hidden genetic and evolutionary processes. Most of the classic selfish genetic elements were discovered through their biasing of transmission, but many unselfish evolutionary and developmental processes can also generate TRD. In this review, we describe methodologies for detecting TRD in mapping populations, detail the arenas and genetic interactions that shape TRD during plant and animal reproduction, and summarize patterns of TRD from across the genetic mapping literature. Finally, we point to new experimental approaches that can accelerate both detection of TRD and characterization of the underlying genetic mechanisms.
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Affiliation(s)
- Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA
| | - Mariah McIntosh
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA
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26
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Bosch J, Mestre J, Baiges C, Martínez JE, Calvo JF, Jiménez‐Franco MV. Colour plumage polymorphism in the Booted Eagle: inheritance pattern and temporal stability of the morph frequencies. J Zool (1987) 2019. [DOI: 10.1111/jzo.12666] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- J. Bosch
- Cra. de Navarcles 43, Santpedor Barcelona Spain
| | - J. Mestre
- Departament de Territori i Sostenibilitat Parc Natural dels Ports Tarragona Spain
| | - C. Baiges
- Departament de Territori i Sostenibilitat Parc Natural dels Ports Tarragona Spain
| | - J. E. Martínez
- Departamento de Ecología e Hidrología Universidad de Murcia Murcia Spain
- Bonelli′s Eagle Study and Conservation Group Murcia Spain
| | - J. F. Calvo
- Departamento de Ecología e Hidrología Universidad de Murcia Murcia Spain
| | - M. V. Jiménez‐Franco
- Departamento de Biología Aplicada Universidad Miguel Hernández Elche, Alicante Spain
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27
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Id-Lahoucine S, Cánovas A, Jaton C, Miglior F, Fonseca PAS, Sargolzaei M, Miller S, Schenkel FS, Medrano JF, Casellas J. Implementation of Bayesian methods to identify SNP and haplotype regions with transmission ratio distortion across the whole genome: TRDscan v.1.0. J Dairy Sci 2019; 102:3175-3188. [PMID: 30738671 DOI: 10.3168/jds.2018-15296] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 12/08/2018] [Indexed: 12/12/2022]
Abstract
Realized deviations from the expected Mendelian inheritance of alleles from heterozygous parents have been previously reported in a broad range of organisms (i.e., transmission ratio distortion; TRD). Various biological mechanisms affecting gametes, embryos, fetuses, or even postnatal offspring can produce patterns of TRD. However, knowledge about its prevalence and potential causes in livestock species is still scarce. Specific Bayesian models have been recently developed for the analyses of TRD for biallelic loci, which accommodated a wide range of population structures, enabling TRD investigation in livestock populations. The parameterization of these models is flexible and allows the study of overall (parent-unspecific) TRD and sire- and dam-specific TRD. This research aimed at deriving Bayesian models for fitting TRD on the basis of haplotypes, testing the models for both haplotype- and SNP-based methods in simulated data and actual Holstein genotypes, and developing a specific software for TRD analyses. Results obtained on simulated data sets showed that the statistical power of the analysis increased with sample size of trios (n), proportion of heterozygous parents, and the magnitude of the TRD. On the other hand, the statistical power to detect TRD decreased with the number of alleles at each loci. Bayesian analyses showed a strong Pearson correlation coefficient (≥0.97) between simulated and estimated TRD that reached the significance level of Bayes factor ≥10 for both single-marker and haplotype analyses when n ≥ 25. Moreover, the accuracy in terms of the mean absolute error decreased with the increase of the sample size and increased with the number of alleles at each loci. Using real data (55,732 genotypes of Holstein trios), SNP- and haplotype-based distortions were detected with overall TRD, sire-TRD, or dam-TRD, showing different magnitudes of TRD and statistical relevance. Additionally, the haplotype-based method showed more ability to capture TRD compared with individual SNP. To discard possible random TRD in real data, an approximate empirical null distribution of TRD was developed. The program TRDscan v.1.0 was written in Fortran 2008 language and provides a powerful statistical tool to scan for TRD regions across the whole genome. This developed program is freely available at http://www.casellas.info/files/TRDscan.zip.
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Affiliation(s)
- S Id-Lahoucine
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph N1G 2W1, Ontario, Canada; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona, Spain.
| | - A Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph N1G 2W1, Ontario, Canada
| | - C Jaton
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph N1G 2W1, Ontario, Canada; The Semex Alliance, Guelph N1G 3Z2, Ontario, Canada
| | - F Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph N1G 2W1, Ontario, Canada; Canadian Dairy Network, Guelph N1K 1E5, Ontario, Canada
| | - P A S Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph N1G 2W1, Ontario, Canada; Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - M Sargolzaei
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph N1G 2W1, Ontario, Canada; HiggsGene Solutions Inc., Guelph N1G 4S7, Ontario, Canada
| | - S Miller
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph N1G 2W1, Ontario, Canada; Angus Genetics Inc., St. Joseph, MO 64506
| | - F S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph N1G 2W1, Ontario, Canada
| | - J F Medrano
- Department of Animal Science, University of California-Davis, Davis 95616
| | - J Casellas
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona, Spain
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28
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Do Gametes Woo? Evidence for Their Nonrandom Union at Fertilization. Genetics 2018; 207:369-387. [PMID: 28978771 DOI: 10.1534/genetics.117.300109] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/10/2017] [Indexed: 12/18/2022] Open
Abstract
A fundamental tenet of inheritance in sexually reproducing organisms such as humans and laboratory mice is that gametes combine randomly at fertilization, thereby ensuring a balanced and statistically predictable representation of inherited variants in each generation. This principle is encapsulated in Mendel's First Law. But exceptions are known. With transmission ratio distortion, particular alleles are preferentially transmitted to offspring. Preferential transmission usually occurs in one sex but not both, and is not known to require interactions between gametes at fertilization. A reanalysis of our published work in mice and of data in other published reports revealed instances where any of 12 mutant genes biases fertilization, with either too many or too few heterozygotes and homozygotes, depending on the mutant gene and on dietary conditions. Although such deviations are usually attributed to embryonic lethality of the underrepresented genotypes, the evidence is more consistent with genetically-determined preferences for specific combinations of egg and sperm at fertilization that result in genotype bias without embryo loss. This unexpected discovery of genetically-biased fertilization could yield insights about the molecular and cellular interactions between sperm and egg at fertilization, with implications for our understanding of inheritance, reproduction, population genetics, and medical genetics.
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29
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Affiliation(s)
- Claire Infante-Rivard
- Department of Epidemiology, Biostatistics and Occupational Health, Faculty of Medicine, McGill University, Montréal, QC, Canada
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30
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Linkage Map of Lissotriton Newts Provides Insight into the Genetic Basis of Reproductive Isolation. G3-GENES GENOMES GENETICS 2017; 7:2115-2124. [PMID: 28500054 PMCID: PMC5499121 DOI: 10.1534/g3.117.041178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Linkage maps are widely used to investigate structure, function, and evolution of genomes. In speciation research, maps facilitate the study of the genetic architecture of reproductive isolation by allowing identification of genomic regions underlying reduced fitness of hybrids. Here we present a linkage map for European newts of the Lissotriton vulgaris species complex, constructed using two families of F2 L. montandoni × L. vulgaris hybrids. The map consists of 1146 protein-coding genes on 12 linkage groups, equal to the haploid chromosome number, with a total length of 1484 cM (1.29 cM per marker). It is notably shorter than two other maps available for salamanders, but the differences in map length are consistent with cytogenetic estimates of the number of chiasmata per chromosomal arm. Thus, large salamander genomes do not necessarily translate into long linkage maps, as previously suggested. Consequently, salamanders are an excellent model to study evolutionary consequences of recombination rate variation in taxa with large genomes and a similar number of chromosomes. A complex pattern of transmission ratio distortion (TRD) was detected: TRD occurred mostly in one family, in one breeding season, and was clustered in two genomic segments. This is consistent with environment-dependent mortality of individuals carrying L. montandoni alleles in these two segments and suggests a role of TRD blocks in reproductive isolation. The reported linkage map will empower studies on the genomic architecture of divergence and interactions between the genomes of hybridizing newts.
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31
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Huang LO, Infante-Rivard C, Labbe A. Analysis of case-parent trios for imprinting effect using a loglinear model with adjustment for sex-of-parent-specific transmission ratio distortion. Hum Genet 2017. [PMID: 28631064 DOI: 10.1007/s00439-017-1824-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Transmission ratio distortion (TRD) is a phenomenon where parental transmission of disease allele to the child does not follow the Mendelian inheritance ratio. TRD occurs in a sex-of-parent-specific or non-sex-of-parent-specific manner. An offset computed from the transmission probability of the minor allele in control-trios can be added to the loglinear model to adjust for TRD. Adjusting the model removes the inflation in the genotype relative risk (RR) estimate and Type 1 error introduced by non-sex-of-parent-specific TRD. We now propose to further extend this model to estimate an imprinting parameter. Some evidence suggests that more than 1% of all mammalian genes are imprinted. In the presence of imprinting, for example, the offspring inheriting an over-transmitted disease allele from the parent with a higher expression level in a neighboring gene is over-represented in the sample. TRD mechanisms such as meiotic drive and gametic competition occur in a sex-of-parent-specific manner. Therefore, sex-of-parent-specific TRD (ST) leads to over-representation of maternal or paternal alleles in the affected child. As a result, ST may bias the imprinting effect when present in the sample. We propose a sex-of-parent-specific transmission offset in adjusting the loglinear model to account for ST. This extended model restores the correct RR estimates for child and imprinting effects, adjusts for inflation in Type 1 error, and improves performance on sensitivity and specificity compared to the original model without ST offset. We conclude that to correctly interpret the association signal of an imprinting effect, adjustment for ST is necessary to ensure valid conclusions.
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Affiliation(s)
- Lam Opal Huang
- Section for Metabolic Genetics, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Universitetsparken 1, 1st floor, DIKU, 2100, København Ø, Denmark.
| | - Claire Infante-Rivard
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, H3A 1A2, Canada
| | - Aurélie Labbe
- Department of Decision Sciences, HEC Montréal, Montreal, QC, H3T 2A7, Canada
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32
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The Slavic NBN Founder Mutation: A Role for Reproductive Fitness? PLoS One 2016; 11:e0167984. [PMID: 27936167 PMCID: PMC5148078 DOI: 10.1371/journal.pone.0167984] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 11/23/2016] [Indexed: 01/21/2023] Open
Abstract
The vast majority of patients with Nijmegen Breakage Syndrome (NBS) are of Slavic origin and carry a deleterious deletion (c.657del5; rs587776650) in the NBN gene on chromosome 8q21. This mutation is essentially confined to Slavic populations and may thus be considered a Slavic founder mutation. Notably, not a single parenthood of a homozygous c.657del5 carrier has been reported to date, while heterozygous carriers do reproduce but have an increased cancer risk. These observations seem to conflict with the considerable carrier frequency of c.657del5 of 0.5% to 1% as observed in different Slavic populations because deleterious mutations would be eliminated quite rapidly by purifying selection. Therefore, we propose that heterozygous c.657del5 carriers have increased reproductive success, i.e., that the mutation confers heterozygote advantage. In fact, in our cohort study of the reproductive history of 24 NBS pedigrees from the Czech Republic, we observed that female carriers gave birth to more children on average than female non-carriers, while no such reproductive differences were observed for males. We also estimate that c.657del5 likely occurred less than 300 generations ago, thus supporting the view that the original mutation predated the historic split and subsequent spread of the ‘Slavic people’. We surmise that the higher fertility of female c.657del5 carriers reflects a lower miscarriage rate in these women, thereby reflecting the role of the NBN gene product, nibrin, in the repair of DNA double strand breaks and their processing in immune gene rearrangements, telomere maintenance, and meiotic recombination, akin to the previously described role of the DNA repair genes BRCA1 and BRCA2.
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Bhatnagar SR, Greenwood CMT, Labbe A. Assessing transmission ratio distortion in extended families: a comparison of analysis methods. BMC Proc 2016; 10:197-202. [PMID: 27980636 PMCID: PMC5133486 DOI: 10.1186/s12919-016-0030-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A statistical departure from Mendel's law of segregation is known as transmission ratio distortion. Although well documented in many other organisms, the extent of transmission ratio distortion and its influence in the human genome remains incomplete. Using Genetic Analysis Workshop 19 whole genome sequence data from 20 large Mexican American pedigrees, our goal was to identify potentially distorted regions in the genome using family-based association methods such as the transmission disequilibrium test, the pedigree disequilibrium test, and the family-based association test. Preliminary results showed an unusually high number of transmission ratio distortion signals identified by the transmission disequilibrium test, but this phenomenon could not be replicated by the pedigree disequilibrium test or family-based association test. Applying these tests to different subsets of the data, we found the transmission disequilibrium test to be very sensitive to imputed genotypes. Regression analysis of transmission ratio distortion test p values controlling for minor allele frequency and quality control checks showed that Hardy Weinberg p values are associated with this inflation. Although the transmission disequilibrium test appears confounded by imputation of single nucleotide polymorphisms, the pedigree disequilibrium test and family-based association test seem to offer more robust alternatives when searching for transmission ratio distortion loci in whole genome sequence data from extended families.
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Affiliation(s)
- Sahir R. Bhatnagar
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, 1020 Pine Avenue West, Montreal, QC H3A 1A2 Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Ste. Catherine, Montreal, QC H3T 1E2 Canada
| | - Celia M. T. Greenwood
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, 1020 Pine Avenue West, Montreal, QC H3A 1A2 Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Ste. Catherine, Montreal, QC H3T 1E2 Canada
- Departments of Oncology and Human Genetics, McGill University, Montreal, QC Canada
| | - Aurélie Labbe
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, 1020 Pine Avenue West, Montreal, QC H3A 1A2 Canada
- Department of Psychiatry, McGill University, Montreal, QC Canada
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Huang LO, Infante-Rivard C, Labbe A. Analysis of Case-Parent Trios Using a Loglinear Model with Adjustment for Transmission Ratio Distortion. Front Genet 2016; 7:155. [PMID: 27630667 PMCID: PMC5005337 DOI: 10.3389/fgene.2016.00155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/16/2016] [Indexed: 01/16/2023] Open
Abstract
Transmission of the two parental alleles to offspring deviating from the Mendelian ratio is termed Transmission Ratio Distortion (TRD), occurs throughout gametic and embryonic development. TRD has been well-studied in animals, but remains largely unknown in humans. The Transmission Disequilibrium Test (TDT) was first proposed to test for association and linkage in case-trios (affected offspring and parents); adjusting for TRD using control-trios was recommended. However, the TDT does not provide risk parameter estimates for different genetic models. A loglinear model was later proposed to provide child and maternal relative risk (RR) estimates of disease, assuming Mendelian transmission. Results from our simulation study showed that case-trios RR estimates using this model are biased in the presence of TRD; power and Type 1 error are compromised. We propose an extended loglinear model adjusting for TRD. Under this extended model, RR estimates, power and Type 1 error are correctly restored. We applied this model to an intrauterine growth restriction dataset, and showed consistent results with a previous approach that adjusted for TRD using control-trios. Our findings suggested the need to adjust for TRD in avoiding spurious results. Documenting TRD in the population is therefore essential for the correct interpretation of genetic association studies.
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Affiliation(s)
- Lam O. Huang
- Department of Epidemiology, Biostatistics and Occupational Health, McGill UniversityMontréal, QC, Canada
| | - Claire Infante-Rivard
- Department of Epidemiology, Biostatistics and Occupational Health, McGill UniversityMontréal, QC, Canada
| | - Aurélie Labbe
- Department of Epidemiology, Biostatistics and Occupational Health, McGill UniversityMontréal, QC, Canada
- Department of Psychiatry, McGill UniversityMontréal, QC, Canada
- Douglas Mental Health University InstituteMontréal, QC, Canada
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Ducret V, Gaigher A, Simon C, Goudet J, Roulin A. Sex-specific allelic transmission bias suggests sexual conflict at MC1R. Mol Ecol 2016; 25:4551-63. [PMID: 27480981 DOI: 10.1111/mec.13781] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/20/2016] [Accepted: 07/21/2016] [Indexed: 02/03/2023]
Abstract
Sexual conflict arises when selection in one sex causes the displacement of the other sex from its phenotypic optimum, leading to an inevitable tension within the genome - called intralocus sexual conflict. Although the autosomal melanocortin-1-receptor gene (MC1R) can generate colour variation in sexually dichromatic species, most previous studies have not considered the possibility that MC1R may be subject to sexual conflict. In the barn owl (Tyto alba), the allele MC1RWHITE is associated with whitish plumage coloration, typical of males, and the allele MC1RRUFOUS is associated with dark rufous coloration, typical of females, although each sex can express any phenotype. Because each colour variant is adapted to specific environmental conditions, the allele MC1RWHITE may be more strongly selected in males and the allele MC1RRUFOUS in females. We therefore investigated whether MC1R genotypes are in excess or deficit in male and female fledglings compared with the expected Hardy-Weinberg proportions. Our results show an overall deficit of 7.5% in the proportion of heterozygotes in males and of 12.9% in females. In males, interannual variation in assortative pairing with respect to MC1R explained the year-specific deviations from Hardy-Weinberg proportions, whereas in females, the deficit was better explained by the interannual variation in the probability of inheriting the MC1RWHITE or MC1RRUFOUS allele. Additionally, we observed that sons inherit the MC1RRUFOUS allele from their fathers on average slightly less often than expected under the first Mendelian law. Transmission ratio distortion may be adaptive in this sexually dichromatic species if males and females are, respectively, selected to display white and rufous plumages.
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Affiliation(s)
- Valérie Ducret
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne, CH-1015, Switzerland.
| | - Arnaud Gaigher
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne, CH-1015, Switzerland
| | - Céline Simon
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne, CH-1015, Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne, CH-1015, Switzerland
| | - Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne, CH-1015, Switzerland
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Itoh H, Berthet M, Fressart V, Denjoy I, Maugenre S, Klug D, Mizusawa Y, Makiyama T, Hofman N, Stallmeyer B, Zumhagen S, Shimizu W, Wilde AAM, Schulze-Bahr E, Horie M, Tezenas du Montcel S, Guicheney P. Asymmetry of parental origin in long QT syndrome: preferential maternal transmission of KCNQ1 variants linked to channel dysfunction. Eur J Hum Genet 2015; 24:1160-6. [PMID: 26669661 DOI: 10.1038/ejhg.2015.257] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 10/30/2015] [Accepted: 11/15/2015] [Indexed: 11/09/2022] Open
Abstract
Transmission distortion of disease-causing alleles in long QT syndrome (LQTS) has been reported, suggesting a potential role of KCNQ1 and KCNH2 in reproduction. This study sought to investigate parental transmission in LQTS families according to ethnicity, gene loci (LQT1-3: KCNQ1, KCNH2, and SCN5A) or severity of channel dysfunction. We studied 3782 genotyped members from 679 European and Japanese LQTS families (2748 carriers). We determined grandparental and parental origins of variant alleles in 1903 children and 624 grandchildren, and the grandparental origin of normal alleles in healthy children from 44 three-generation control families. LQTS alleles were more of maternal than paternal origin (61 vs 39%, P<0.001). The ratio of maternally transmitted alleles in LQT1 (66%) was higher than in LQT2 (56%, P<0.001) and LQT3 (57%, P=0.03). Unlike the Mendelian distribution of grandparental alleles seen in control families, variant grandparental LQT1 and LQT2 alleles in grandchildren showed an excess of maternally transmitted grandmother alleles. For LQT1, maternal transmission differs according to the variant level of dysfunction with 68% of maternal transmission for dominant negative or unknown functional consequence variants vs 58% for non-dominant negative and variants leading to haploinsufficiency, P<0.01; however, for LQT2 or LQT3 this association was not significant. An excess of disease-causing alleles of maternal origin, most pronounced in LQT1, was consistently found across ethnic groups. This observation does not seem to be linked to an imbalance in transmission of the LQTS subtype-specific grandparental allele, but to the potential degree of potassium channel dysfunction.
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Affiliation(s)
- Hideki Itoh
- INSERM, UMR S1166, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S1166, Paris, France.,Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Otsu, Japan
| | - Myriam Berthet
- INSERM, UMR S1166, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S1166, Paris, France.,Institute of Cardiometabolism and Nutrition, ICAN, Pitié-Salpêtrière Hospital, Paris, France
| | - Véronique Fressart
- INSERM, UMR S1166, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S1166, Paris, France.,Institute of Cardiometabolism and Nutrition, ICAN, Pitié-Salpêtrière Hospital, Paris, France.,AP-HP, Groupe Hospitalier Pitié-Salpétrière, Service de Biochimie Métabolique, UF Cardiogénétique et Myogénétique Moléculaire et Cellulaire, Paris, France
| | - Isabelle Denjoy
- INSERM, UMR S1166, Paris, France.,Cardiology Department, AP-HP, Hôpital Bichat, Paris, France
| | - Svetlana Maugenre
- INSERM, UMR S1166, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S1166, Paris, France.,Institute of Cardiometabolism and Nutrition, ICAN, Pitié-Salpêtrière Hospital, Paris, France
| | - Didier Klug
- Hôpital Cardiologique de Lille, CHRU, Service de cardiologie A, Lille, France
| | - Yuka Mizusawa
- AMC Heart Center, Department of Clinical and Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Takeru Makiyama
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Nynke Hofman
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Birgit Stallmeyer
- Department of Cardiovascular Medicine, Institute for Genetics of Heart Diseases (IfGH), University Hospital Münster, Münster, Germany
| | - Sven Zumhagen
- Department of Cardiovascular Medicine, Institute for Genetics of Heart Diseases (IfGH), University Hospital Münster, Münster, Germany
| | - Wataru Shimizu
- Division of Arrhythmia and Electrophysiology, Department of Cardiovascular Medicine, National Cerebral and Cardiovascular Center, Suita, Japan.,Division of Cardiology, Department of Internal Medicine, Nippon Medical School, Tokyo, Japan
| | - Arthur A M Wilde
- AMC Heart Center, Department of Clinical and Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Eric Schulze-Bahr
- Department of Cardiovascular Medicine, Institute for Genetics of Heart Diseases (IfGH), University Hospital Münster, Münster, Germany.,Interdisciplinary Centre for Clinical Research (IZKF) of the University of Münster, Münster, Germany
| | - Minoru Horie
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Otsu, Japan
| | - Sophie Tezenas du Montcel
- Biostatistics Unit, AP-HP, Groupe Hospitalier Pitié-Salpêtrière Charles-Foix, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France
| | - Pascale Guicheney
- INSERM, UMR S1166, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S1166, Paris, France.,Institute of Cardiometabolism and Nutrition, ICAN, Pitié-Salpêtrière Hospital, Paris, France
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Case LK, Wall EH, Osmanski EE, Dragon JA, Saligrama N, Zachary JF, Lemos B, Blankenhorn EP, Teuscher C. Copy number variation in Y chromosome multicopy genes is linked to a paternal parent-of-origin effect on CNS autoimmune disease in female offspring. Genome Biol 2015; 16:28. [PMID: 25886764 PMCID: PMC4396973 DOI: 10.1186/s13059-015-0591-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 01/20/2015] [Indexed: 12/11/2022] Open
Abstract
Background The prevalence of some autoimmune diseases is greater in females compared with males, although disease severity is often greater in males. The reason for this sexual dimorphism is unknown, but it may reflect negative selection of Y chromosome-bearing sperm during spermatogenesis or male fetuses early in the course of conception/pregnancy. Previously, we showed that the sexual dimorphism in experimental autoimmune encephalomyelitis (EAE) is associated with copy number variation (CNV) in Y chromosome multicopy genes. Here, we test the hypothesis that CNV in Y chromosome multicopy genes influences the paternal parent-of-origin effect on EAE susceptibility in female mice. Results We show that C57BL/6 J consomic strains of mice possessing an identical X chromosome and CNV in Y chromosome multicopy genes exhibit sperm head abnormalities and female-biased sex ratio. This is consistent with X-Y intragenomic conflict arising from an imbalance in CNV between homologous X:Y chromosome multicopy genes. These males also display paternal transmission of EAE to female offspring and differential loading of microRNAs within the sperm nucleus. Furthermore, in humans, families of probands with multiple sclerosis similarly exhibit a female-biased sex ratio, whereas families of probands affected with non-sexually dimorphic autoimmune diseases exhibit unbiased sex ratios. Conclusions These findings provide evidence for a mechanism at the level of the male gamete that contributes to the sexual dimorphism in EAE and paternal parent-of-origin effects in female mice, raising the possibility that a similar mechanism may contribute to the sexual dimorphism in multiple sclerosis. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0591-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laure K Case
- Department of Medicine, University of Vermont, Given Medical Building C317, Burlington, VT, 05405, USA.
| | - Emma H Wall
- Department of Medicine, University of Vermont, Given Medical Building C317, Burlington, VT, 05405, USA.
| | - Erin E Osmanski
- Department of Medicine, University of Vermont, Given Medical Building C317, Burlington, VT, 05405, USA.
| | - Julie A Dragon
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, 05405, USA.
| | - Naresha Saligrama
- Department of Medicine, University of Vermont, Given Medical Building C317, Burlington, VT, 05405, USA. .,Current address: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - James F Zachary
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA.
| | - Bernardo Lemos
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, 02115, USA.
| | - Elizabeth P Blankenhorn
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19129, USA.
| | - Cory Teuscher
- Department of Medicine, University of Vermont, Given Medical Building C317, Burlington, VT, 05405, USA. .,Department of Pathology, University of Vermont, Burlington, VT, 05405, USA.
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38
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Didion JP, Morgan AP, Clayshulte AMF, Mcmullan RC, Yadgary L, Petkov PM, Bell TA, Gatti DM, Crowley JJ, Hua K, Aylor DL, Bai L, Calaway M, Chesler EJ, French JE, Geiger TR, Gooch TJ, Garland T, Harrill AH, Hunter K, McMillan L, Holt M, Miller DR, O'Brien DA, Paigen K, Pan W, Rowe LB, Shaw GD, Simecek P, Sullivan PF, Svenson KL, Weinstock GM, Threadgill DW, Pomp D, Churchill GA, Pardo-Manuel de Villena F. A multi-megabase copy number gain causes maternal transmission ratio distortion on mouse chromosome 2. PLoS Genet 2015; 11:e1004850. [PMID: 25679959 PMCID: PMC4334553 DOI: 10.1371/journal.pgen.1004850] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 10/24/2014] [Indexed: 12/29/2022] Open
Abstract
Significant departures from expected Mendelian inheritance ratios (transmission ratio distortion, TRD) are frequently observed in both experimental crosses and natural populations. TRD on mouse Chromosome (Chr) 2 has been reported in multiple experimental crosses, including the Collaborative Cross (CC). Among the eight CC founder inbred strains, we found that Chr 2 TRD was exclusive to females that were heterozygous for the WSB/EiJ allele within a 9.3 Mb region (Chr 2 76.9 - 86.2 Mb). A copy number gain of a 127 kb-long DNA segment (designated as responder to drive, R2d) emerged as the strongest candidate for the causative allele. We mapped R2d sequences to two loci within the candidate interval. R2d1 is located near the proximal boundary, and contains a single copy of R2d in all strains tested. R2d2 maps to a 900 kb interval, and the number of R2d copies varies from zero in classical strains (including the mouse reference genome) to more than 30 in wild-derived strains. Using real-time PCR assays for the copy number, we identified a mutation (R2d2WSBdel1) that eliminates the majority of the R2d2WSB copies without apparent alterations of the surrounding WSB/EiJ haplotype. In a three-generation pedigree segregating for R2d2WSBdel1, the mutation is transmitted to the progeny and Mendelian segregation is restored in females heterozygous for R2d2WSBdel1, thus providing direct evidence that the copy number gain is causal for maternal TRD. We found that transmission ratios in R2d2WSB heterozygous females vary between Mendelian segregation and complete distortion depending on the genetic background, and that TRD is under genetic control of unlinked distorter loci. Although the R2d2WSB transmission ratio was inversely correlated with average litter size, several independent lines of evidence support the contention that female meiotic drive is the cause of the distortion. We discuss the implications and potential applications of this novel meiotic drive system.
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Affiliation(s)
- John P. Didion
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Andrew P. Morgan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Amelia M.-F. Clayshulte
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Rachel C. Mcmullan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Liran Yadgary
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Petko M. Petkov
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Timothy A. Bell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Daniel M. Gatti
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - James J. Crowley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kunjie Hua
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - David L. Aylor
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Ling Bai
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mark Calaway
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | | | - John E. French
- National Toxicology Program, National Institute of Environmental Sciences, NIH, Research Triangle Park, North Carolina, United States of America
| | - Thomas R. Geiger
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Terry J. Gooch
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Theodore Garland
- Department of Biology, University of California Riverside, Riverside, California, United States of America
| | - Alison H. Harrill
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Kent Hunter
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Leonard McMillan
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Matt Holt
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Darla R. Miller
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Deborah A. O'Brien
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kenneth Paigen
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Wenqi Pan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lucy B. Rowe
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Ginger D. Shaw
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Petr Simecek
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Patrick F. Sullivan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Karen L Svenson
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - George M. Weinstock
- Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America
| | - David W. Threadgill
- Department of Veterinary Pathobiology and Department of Molecular and Cellular Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Daniel Pomp
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | | | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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Abstract
Current statistical approaches to investigate the nature and magnitude of transmission ratio distortion (TRD) are scarce and restricted to the most common experimental designs such as F2 populations and backcrosses. In this article, we describe a new Bayesian approach to check TRD within a given biallelic genetic marker in a diploid species, providing a highly flexible framework that can accommodate any kind of population structure. This model relies on the genotype of each offspring and thus integrates all available information from either the parents' genotypes or population-specific allele frequencies and yields TRD estimates that can be corroborated by the calculation of a Bayes factor (BF). This approach has been evaluated on simulated data sets with appealing statistical performance. As a proof of concept, we have also tested TRD in a porcine population with five half-sib families and 352 offspring. All boars and piglets were genotyped with the Porcine SNP60 BeadChip, whereas genotypes from the sows were not available. The SNP-by-SNP screening of the pig genome revealed 84 SNPs with decisive evidences of TRD (BF > 100) after accounting for multiple testing. Many of these regions contained genes related to biological processes (e.g., nucleosome assembly and co-organization, DNA conformation and packaging, and DNA complex assembly) that are critically associated with embryonic viability. The implementation of this method, which overcomes many of the limitations of previous approaches, should contribute to fostering research on TRD in both model and nonmodel organisms.
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40
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Kawakami T, Backström N, Burri R, Husby A, Olason P, Rice AM, Ålund M, Qvarnström A, Ellegren H. Estimation of linkage disequilibrium and interspecific gene flow in Ficedula flycatchers by a newly developed 50k single-nucleotide polymorphism array. Mol Ecol Resour 2014; 14:1248-60. [PMID: 24784959 PMCID: PMC4368375 DOI: 10.1111/1755-0998.12270] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 04/14/2014] [Accepted: 04/25/2014] [Indexed: 12/30/2022]
Abstract
With the access to draft genome sequence assemblies and whole-genome resequencing data from population samples, molecular ecology studies will be able to take truly genome-wide approaches. This now applies to an avian model system in ecological and evolutionary research: Old World flycatchers of the genus Ficedula, for which we recently obtained a 1.1 Gb collared flycatcher genome assembly and identified 13 million single-nucleotide polymorphism (SNP)s in population resequencing of this species and its sister species, pied flycatcher. Here, we developed a custom 50K Illumina iSelect flycatcher SNP array with markers covering 30 autosomes and the Z chromosome. Using a number of selection criteria for inclusion in the array, both genotyping success rate and polymorphism information content (mean marker heterozygosity = 0.41) were high. We used the array to assess linkage disequilibrium (LD) and hybridization in flycatchers. Linkage disequilibrium declined quickly to the background level at an average distance of 17 kb, but the extent of LD varied markedly within the genome and was more than 10-fold higher in ‘genomic islands’ of differentiation than in the rest of the genome. Genetic ancestry analysis identified 33 F1 hybrids but no later-generation hybrids from sympatric populations of collared flycatchers and pied flycatchers, contradicting earlier reports of backcrosses identified from much fewer number of markers. With an estimated divergence time as recently as <1 Ma, this suggests strong selection against F1 hybrids and unusually rapid evolution of reproductive incompatibility in an avian system.
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Affiliation(s)
- Takeshi Kawakami
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
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Mosinger B, Redding KM, Parker MR, Yevshayeva V, Yee KK, Dyomina K, Li Y, Margolskee RF. Genetic loss or pharmacological blockade of testes-expressed taste genes causes male sterility. Proc Natl Acad Sci U S A 2013; 110:12319-24. [PMID: 23818598 PMCID: PMC3725061 DOI: 10.1073/pnas.1302827110] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
TAS1R taste receptors and their associated heterotrimeric G protein gustducin are involved in sugar and amino acid sensing in taste cells and in the gastrointestinal tract. They are also strongly expressed in testis and sperm, but their functions in these tissues were previously unknown. Using mouse models, we show that the genetic absence of both TAS1R3, a component of sweet and amino acid taste receptors, and the gustducin α-subunit GNAT3 leads to male-specific sterility. To gain further insight into this effect, we generated a mouse model that expressed a humanized form of TAS1R3 susceptible to inhibition by the antilipid medication clofibrate. Sperm formation in animals without functional TAS1R3 and GNAT3 is compromised, with malformed and immotile sperm. Furthermore, clofibrate inhibition of humanized TAS1R3 in the genetic background of Tas1r3(-/-), Gnat3(-/-) doubly null mice led to inducible male sterility. These results indicate a crucial role for these extraoral "taste" molecules in sperm development and maturation. We previously reported that blocking of human TAS1R3, but not mouse TAS1R3, can be achieved by common medications or chemicals in the environment. We hypothesize that even low levels of these compounds can lower sperm count and negatively affect human male fertility, which common mouse toxicology assays would not reveal. Conversely, we speculate that TAS1R3 and GNAT3 activators may help infertile men, particularly those that are affected by some of the mentioned inhibitors and/or are diagnosed with idiopathic infertility involving signaling pathway of these receptors.
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