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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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2
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Bypassing Mendel's First Law: Transmission Ratio Distortion in Mammals. Int J Mol Sci 2023; 24:ijms24021600. [PMID: 36675116 PMCID: PMC9863905 DOI: 10.3390/ijms24021600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Mendel's law of segregation states that the two alleles at a diploid locus should be transmitted equally to the progeny. A genetic segregation distortion, also referred to as transmission ratio distortion (TRD), is a statistically significant deviation from this rule. TRD has been observed in several mammal species and may be due to different biological mechanisms occurring at diverse time points ranging from gamete formation to lethality at post-natal stages. In this review, we describe examples of TRD and their possible mechanisms in mammals based on current knowledge. We first focus on the differences between TRD in male and female gametogenesis in the house mouse, in which some of the most well studied TRD systems have been characterized. We then describe known TRD in other mammals, with a special focus on the farmed species and in the peculiar common shrew species. Finally, we discuss TRD in human diseases. Thus far, to our knowledge, this is the first time that such description is proposed. This review will help better comprehend the processes involved in TRD. A better understanding of these molecular mechanisms will imply a better comprehension of their impact on fertility and on genome evolution. In turn, this should allow for better genetic counseling and lead to better care for human families.
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Madhavan SM, Konieczkowski M, Bruggeman LA, DeWalt M, Nguyen JK, O'Toole JF, Sedor JR. Essential role of Wtip in mouse development and maintenance of the glomerular filtration barrier. Am J Physiol Renal Physiol 2022; 323:F272-F287. [PMID: 35862649 PMCID: PMC9394782 DOI: 10.1152/ajprenal.00051.2022] [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: 03/02/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 11/22/2022] Open
Abstract
Wilms' tumor interacting protein (Wtip) has been implicated in cell junction assembly and cell differentiation and interacts with proteins in the podocyte slit diaphragm, where it regulates podocyte phenotype. To define Wtip expression and function in the kidney, we created a Wtip-deleted mouse model using β-galactosidase-neomycin (β-geo) gene trap technology. Wtip gene trap mice were embryonic lethal, suggesting additional developmental roles outside kidney function. Using β-geo heterozygous and normal mice, Wtip expression was identified in the developing kidneys, heart, and eyes. In the kidney, expression was restricted to podocytes, which appeared initially at the capillary loop stage coinciding with terminal podocyte differentiation. Heterozygous mice had an expected lifespan and showed no evidence of proteinuria or glomerular pathology. However, heterozygous mice were more susceptible to glomerular injury than wild-type littermates and developed more significant and prolonged proteinuria in response to lipopolysaccharide or adriamycin. In normal human kidneys, WTIP expression patterns were consistent with observations in mice and were lost in glomeruli concurrent with loss of synaptopodin expression in disease. Mechanistically, we identified the Rho guanine nucleotide exchange factor 12 (ARHGEF12) as a binding partner for WTIP. ARHGEF12 was expressed in human podocytes and formed high-affinity interactions through their LIM- and PDZ-binding domains. Our findings suggest that Wtip is essential for early murine embryonic development and maintaining normal glomerular filtration barrier function, potentially regulating slit diaphragm and foot process function through Rho effector proteins.NEW & NOTEWORTHY This study characterized dynamic expression patterns of Wilms' tumor interacting protein (Wtip) and demonstrates the novel role of Wtip in murine development and maintenance of the glomerular filtration barrier.
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Affiliation(s)
- Sethu M Madhavan
- Department of Medicine, The Ohio State University, Columbus, Ohio
| | | | - Leslie A Bruggeman
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, Ohio
- Department of Nephrology, Cleveland Clinic, Cleveland, Ohio
| | - Megan DeWalt
- Department of Medicine, The Ohio State University, Columbus, Ohio
| | - Jane K Nguyen
- Department of Pathology, Cleveland Clinic, Cleveland, Ohio
| | - John F O'Toole
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, Ohio
- Department of Nephrology, Cleveland Clinic, Cleveland, Ohio
| | - John R Sedor
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, Ohio
- Department of Nephrology, Cleveland Clinic, Cleveland, Ohio
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, Ohio
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4
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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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5
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Bergero R, Ellis P, Haerty W, Larcombe L, Macaulay I, Mehta T, Mogensen M, Murray D, Nash W, Neale MJ, O'Connor R, Ottolini C, Peel N, Ramsey L, Skinner B, Suh A, Summers M, Sun Y, Tidy A, Rahbari R, Rathje C, Immler S. Meiosis and beyond - understanding the mechanistic and evolutionary processes shaping the germline genome. Biol Rev Camb Philos Soc 2021; 96:822-841. [PMID: 33615674 PMCID: PMC8246768 DOI: 10.1111/brv.12680] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022]
Abstract
The separation of germ cell populations from the soma is part of the evolutionary transition to multicellularity. Only genetic information present in the germ cells will be inherited by future generations, and any molecular processes affecting the germline genome are therefore likely to be passed on. Despite its prevalence across taxonomic kingdoms, we are only starting to understand details of the underlying micro-evolutionary processes occurring at the germline genome level. These include segregation, recombination, mutation and selection and can occur at any stage during germline differentiation and mitotic germline proliferation to meiosis and post-meiotic gamete maturation. Selection acting on germ cells at any stage from the diploid germ cell to the haploid gametes may cause significant deviations from Mendelian inheritance and may be more widespread than previously assumed. The mechanisms that affect and potentially alter the genomic sequence and allele frequencies in the germline are pivotal to our understanding of heritability. With the rise of new sequencing technologies, we are now able to address some of these unanswered questions. In this review, we comment on the most recent developments in this field and identify current gaps in our knowledge.
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Affiliation(s)
- Roberta Bergero
- Institute of Evolutionary BiologyUniversity of EdinburghEdinburghEH9 3JTU.K.
| | - Peter Ellis
- School of BiosciencesUniversity of KentCanterburyCT2 7NJU.K.
| | | | - Lee Larcombe
- Applied Exomics LtdStevenage Bioscience CatalystStevenageSG1 2FXU.K.
| | - Iain Macaulay
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZU.K.
| | - Tarang Mehta
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZU.K.
| | - Mette Mogensen
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJU.K.
| | - David Murray
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJU.K.
| | - Will Nash
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZU.K.
| | - Matthew J. Neale
- Genome Damage and Stability Centre, School of Life SciencesUniversity of SussexBrightonBN1 9RHU.K.
| | | | | | - Ned Peel
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZU.K.
| | - Luke Ramsey
- The James Hutton InstituteInvergowrieDundeeDD2 5DAU.K.
| | - Ben Skinner
- School of Life SciencesUniversity of EssexColchesterCO4 3SQU.K.
| | - Alexander Suh
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJU.K.
- Department of Organismal BiologyUppsala UniversityNorbyvägen 18DUppsala752 36Sweden
| | - Michael Summers
- School of BiosciencesUniversity of KentCanterburyCT2 7NJU.K.
- The Bridge Centre1 St Thomas Street, London BridgeLondonSE1 9RYU.K.
| | - Yu Sun
- Norwich Medical SchoolUniversity of East AngliaNorwich Research Park, Colney LnNorwichNR4 7UGU.K.
| | - Alison Tidy
- School of BiosciencesUniversity of Nottingham, Plant Science, Sutton Bonington CampusSutton BoningtonLE12 5RDU.K.
| | | | - Claudia Rathje
- School of BiosciencesUniversity of KentCanterburyCT2 7NJU.K.
| | - Simone Immler
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJU.K.
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6
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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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7
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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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8
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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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9
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Woodruff RC, Balinski MA. Increase in viability due to the accumulation of X chromosome mutations in Drosophila melanogaster males. Genetica 2018; 146:323-328. [PMID: 29744733 DOI: 10.1007/s10709-018-0023-1] [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: 01/03/2018] [Accepted: 05/05/2018] [Indexed: 10/16/2022]
Abstract
To increase our understanding of the role of new X-chromosome mutations in adaptive evolution, single-X Drosophila melanogaster males were mated with attached-X chromosome females, allowing the male X chromosome to accumulate mutations over 28 generations. Contrary to our hypothesis that male viability would decrease over time, due to the accumulation and expression of X-linked recessive deleterious mutations in hemizygous males, viability significantly increased. This increase may be attributed to germinal selection and to new X-linked beneficial or compensatory mutations, possibly supporting the faster-X hypothesis.
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Affiliation(s)
- Ronny C Woodruff
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA.
| | - Michael A Balinski
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
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10
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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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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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Arnheim N, Calabrese P. Germline Stem Cell Competition, Mutation Hot Spots, Genetic Disorders, and Older Fathers. Annu Rev Genomics Hum Genet 2016; 17:219-43. [PMID: 27070266 DOI: 10.1146/annurev-genom-083115-022656] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Some de novo human mutations arise at frequencies far exceeding the genome average mutation rate. Examples include the common mutations at one or a few sites in the genes that cause achondroplasia, Apert syndrome, multiple endocrine neoplasia type 2B, and Noonan syndrome. These mutations are recurrent, provide a gain of function, are paternally derived, and are more likely to be transmitted as the father ages. Recent experiments have tested whether the high mutation frequencies are due to an elevated mutation rate per cell division, as expected, or to an advantage of the mutant spermatogonial stem cells over wild-type stem cells. The evidence, which includes the surprising discovery of testis mutation clusters, rules out the former model but not the latter. We propose how the mutations might alter spermatogonial stem cell function and discuss how germline selection contributes to the paternal age effect, the human mutational load, and adaptive evolution.
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Affiliation(s)
- Norman Arnheim
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California 90089-2910; ,
| | - Peter Calabrese
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California 90089-2910; ,
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Transmission ratio distortion: review of concept and implications for genetic association studies. Hum Genet 2012; 132:245-63. [PMID: 23242375 DOI: 10.1007/s00439-012-1257-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 12/04/2012] [Indexed: 12/31/2022]
Abstract
Transmission ratio distortion (TRD) occurs when one of the two alleles from either parent is preferentially transmitted to the offspring. This leads to a statistical departure from the Mendelian law of inheritance, which states that each of the two parental alleles is transmitted to offspring with a probability of 0.5. A number of mechanisms are thought to induce TRD such as meiotic drive, gametic competition, and embryo lethality. TRD has been extensively studied in animals, but the prevalence of TRD in humans remains largely unknown. Nevertheless, understanding the TRD phenomenon and taking it into consideration in many aspects of human genetics has potential benefits that have not been sufficiently emphasized in the current literature. In this review, we discuss the importance of TRD in three distinct but related fields of genetics: developmental genetics which studies the genetic abnormalities in zygotic and embryonic development, statistical genetics/genetic epidemiology which utilizes population study designs and statistical models to interpret the role of genes in human health, and population genetics which is concerned with genetic diversity in populations in an evolutionary context. From the perspective of developmental genetics, studying TRD leads to the identification of the processes and mechanisms for differential survival observed in embryos. As a result, it is a genetic force which affects allele frequency at the population, as well as, at the organismal level. Therefore, it has implications on genetic diversity of the population over time. From the perspective of genetic epidemiology, the TRD influence on a marker locus is a confounding factor which has to be adequately dealt with to correctly interpret linkage or association study results. These aspects are developed in this review. In addition to these theoretical notions, a brief summary of the empirical evidence of the TRD phenomenon in human and mouse studies is provided. The objective of our paper is to show the potentially important role of TRD in many areas of genetics, and to create an incentive for future research.
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Is genomics bad for you? Behav Brain Sci 2012; 35:364-5. [PMID: 23095385 DOI: 10.1017/s0140525x12000994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The plasticity of the genome complicates genetic causation but should be investigated from a functional perspective. Specific adaptive hypotheses are referenced in the target article, but it is also necessary to explain how the integrity of the genome is maintained despite processes that tend towards its diversification and degradation. These include the accumulation of deleterious changes and intragenomic conflict.
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Choi SK, Yoon SR, Calabrese P, Arnheim N. Positive selection for new disease mutations in the human germline: evidence from the heritable cancer syndrome multiple endocrine neoplasia type 2B. PLoS Genet 2012; 8:e1002420. [PMID: 22359510 PMCID: PMC3280958 DOI: 10.1371/journal.pgen.1002420] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 10/19/2011] [Indexed: 01/15/2023] Open
Abstract
Multiple endocrine neoplasia type 2B (MEN2B) is a highly aggressive thyroid cancer syndrome. Since almost all sporadic cases are caused by the same nucleotide substitution in the RET proto-oncogene, the calculated disease incidence is 100-200 times greater than would be expected based on the genome average mutation frequency. In order to determine whether this increased incidence is due to an elevated mutation rate at this position (true mutation hot spot) or a selective advantage conferred on mutated spermatogonial stem cells, we studied the spatial distribution of the mutation in 14 human testes. In donors aged 36-68, mutations were clustered with small regions of each testis having mutation frequencies several orders of magnitude greater than the rest of the testis. In donors aged 19-23 mutations were almost non-existent, demonstrating that clusters in middle-aged donors grew during adulthood. Computational analysis showed that germline selection is the only plausible explanation. Testes of men aged 75-80 were heterogeneous with some like middle-aged and others like younger testes. Incorporating data on age-dependent death of spermatogonial stem cells explains the results from all age groups. Germline selection also explains MEN2B's male mutation bias and paternal age effect. Our discovery focuses attention on MEN2B as a model for understanding the genetic and biochemical basis of germline selection. Since RET function in mouse spermatogonial stem cells has been extensively studied, we are able to suggest that the MEN2B mutation provides a selective advantage by altering the PI3K/AKT and SFK signaling pathways. Mutations that are preferred in the germline but reduce the fitness of offspring increase the population's mutational load. Our approach is useful for studying other disease mutations with similar characteristics and could uncover additional germline selection pathways or identify true mutation hot spots.
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Affiliation(s)
- Soo-Kyung Choi
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, United States of America
| | - Song-Ro Yoon
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, United States of America
| | - Peter Calabrese
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, United States of America
| | - Norman Arnheim
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, United States of America
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Folse HJ, Roughgarden J. DIRECT BENEFITS OF GENETIC MOSAICISM AND INTRAORGANISMAL SELECTION: MODELING COEVOLUTION BETWEEN A LONG-LIVED TREE AND A SHORT-LIVED HERBIVORE. Evolution 2011; 66:1091-113. [DOI: 10.1111/j.1558-5646.2011.01500.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Masel J, Lyttle DN. The consequences of rare sexual reproduction by means of selfing in an otherwise clonally reproducing species. Theor Popul Biol 2011; 80:317-22. [PMID: 21888925 DOI: 10.1016/j.tpb.2011.08.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 08/16/2011] [Accepted: 08/17/2011] [Indexed: 11/29/2022]
Abstract
Clonal reproduction of diploids leads to an increase in heterozygosity over time. A single round of selfing will then create new homozygotic genotypes. Given the same allele frequencies, heritable genetic variation is larger when there are more extreme, i.e. homozygotic genotypes. So after a long clonal expansion, one round of selfing increases heritable genetic variation, but any fully or partially recessive deleterious alleles simultaneously impose a fitness cost. Here we calculate that the cost of selfing in the yeast Saccharomyces is experienced only by a minority of zygotes. This allows a round of selfing to act as an evolutionary capacitor to unlock genetic variation previously found in a cryptic heterozygous form. We calculate the evolutionary consequences rather than the evolutionary causes of sex. We explore a range of parameter values describing sexual frequencies, focusing especially on the parameter values known for wild Saccharomyces. Our results are largely robust to many other parameter value choices, so long as meiosis is rare relative to the strength of selection on heterozygotes. Results may also be limited to organisms with a small number of genes. We therefore expect the same phenomenon in some other species with similar reproductive strategies.
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Affiliation(s)
- Joanna Masel
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
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18
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Understanding what determines the frequency and pattern of human germline mutations. Nat Rev Genet 2009; 10:478-88. [PMID: 19488047 DOI: 10.1038/nrg2529] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Surprising findings about human germline mutation have come from applying new technologies to detect rare mutations in germline DNA, from analysing DNA sequence divergence between humans and closely related species, and from investigating human polymorphic variation. In this Review we discuss how these approaches affect our current understanding of the roles of sex, age, mutation hot spots, germline selection and genomic factors in determining human nucleotide substitution mutation patterns and frequencies. To enhance our understanding of mutation and disease, more extensive molecular data on the human germ line with regard to mutation origin, DNA repair, epigenetic status and the effect of newly arisen mutations on gamete development are needed.
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Tannenbaum E. A comparison of sexual and asexual replication strategies in a simplified model based on the yeast life cycle. Theory Biosci 2008; 127:323-33. [DOI: 10.1007/s12064-008-0049-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Accepted: 07/08/2008] [Indexed: 11/29/2022]
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20
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Choi SK, Yoon SR, Calabrese P, Arnheim N. A germ-line-selective advantage rather than an increased mutation rate can explain some unexpectedly common human disease mutations. Proc Natl Acad Sci U S A 2008; 105:10143-8. [PMID: 18632557 PMCID: PMC2474563 DOI: 10.1073/pnas.0801267105] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Indexed: 11/18/2022] Open
Abstract
Two nucleotide substitutions in the human FGFR2 gene (C755G or C758G) are responsible for virtually all sporadic cases of Apert syndrome. This condition is 100-1,000 times more common than genomic mutation frequency data predict. Here, we report on the C758G de novo Apert syndrome mutation. Using data on older donors, we show that spontaneous mutations are not uniformly distributed throughout normal testes. Instead, we find foci where C758G mutation frequencies are 3-4 orders of magnitude greater than the remaining tissue. We conclude this nucleotide site is not a mutation hot spot even after accounting for possible Luria-Delbruck "mutation jackpots." An alternative explanation for such foci involving positive selection acting on adult self-renewing Ap spermatogonia experiencing the rare mutation could not be rejected. Further, the two youngest individuals studied (19 and 23 years old) had lower mutation frequencies and smaller foci at both mutation sites compared with the older individuals. This implies that the mutation frequency of foci increases as adults age, and thus selection could explain the paternal age effect for Apert syndrome and other genetic conditions. Our results, now including the analysis of two mutations in the same set of testes, suggest that positive selection can increase the relative frequency of premeiotic germ cells carrying such mutations, although individuals who inherit them have reduced fitness. In addition, we compared the anatomical distribution of C758G mutation foci with both new and old data on the C755G mutation in the same testis and found their positions were not correlated with one another.
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Affiliation(s)
- Soo-Kyung Choi
- Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089-2910
| | - Song-Ro Yoon
- Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089-2910
| | - Peter Calabrese
- Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089-2910
| | - Norman Arnheim
- Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089-2910
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21
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Affiliation(s)
- Hastings
- Institute of Cell, Animal and Population Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh EH9 3JT, Scotland, UK
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22
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Tannenbaum E, Fontanari JF. A quasispecies approach to the evolution of sexual replication in unicellular organisms. Theory Biosci 2008; 127:53-65. [DOI: 10.1007/s12064-008-0023-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Accepted: 01/18/2008] [Indexed: 10/22/2022]
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23
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Gasior SL, Preston G, Hedges DJ, Gilbert N, Moran JV, Deininger PL. Characterization of pre-insertion loci of de novo L1 insertions. Gene 2006; 390:190-8. [PMID: 17067767 PMCID: PMC1850991 DOI: 10.1016/j.gene.2006.08.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Revised: 08/21/2006] [Accepted: 08/22/2006] [Indexed: 10/24/2022]
Abstract
The human Long Interspersed Element-1 (LINE-1) and the Short Interspersed Element (SINE) Alu comprise 28% of the human genome. They share the same L1-encoded endonuclease for insertion, which recognizes an A+T-rich sequence. Under a simple model of insertion distribution, this nucleotide preference would lead to the prediction that the populations of both elements would be biased towards A+T-rich regions. Genomic L1 elements do show an A+T-rich bias. In contrast, Alu is biased towards G+C-rich regions when compared to the genome average. Several analyses have demonstrated that relatively recent insertions of both elements show less G+C content bias relative to older elements. We have analyzed the repetitive element and G+C composition of more than 100 pre-insertion loci derived from de novo L1 insertions in cultured human cancer cells, which should represent an evolutionarily unbiased set of insertions. An A+T-rich bias is observed in the 50 bp flanking the endonuclease target site, consistent with the known target site for the L1 endonuclease. The L1, Alu, and G+C content of 20 kb of the de novo pre-insertion loci shows a different set of biases than that observed for fixed L1s in the human genome. In contrast to the insertion sites of genomic L1s, the de novo L1 pre-insertion loci are relatively L1-poor, Alu-rich and G+C neutral. Finally, a statistically significant cluster of de novo L1 insertions was localized in the vicinity of the c-myc gene. These results suggest that the initial insertion preference of L1, while A+T-rich in the initial vicinity of the break site, can be influenced by the broader content of the flanking genomic region and have implications for understanding the dynamics of L1 and Alu distributions in the human genome.
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Affiliation(s)
- Stephen L. Gasior
- Tulane Cancer Center and Dept. of Epidemiology, Tulane University Health Sciences Center SL-66, 1430 Tulane Ave., New Orleans, LA 70112, Phone: (504) 988-6385, Fax: (504) 988-5516,
| | - Graeme Preston
- Tulane Cancer Center and Dept. of Epidemiology, Tulane University Health Sciences Center SL-66, 1430 Tulane Ave., New Orleans, LA 70112, Phone: (504) 988-6385, Fax: (504) 988-5516,
| | - Dale J. Hedges
- Tulane Cancer Center and Dept. of Epidemiology, Tulane University Health Sciences Center SL-66, 1430 Tulane Ave., New Orleans, LA 70112, Phone: (504) 988-6385, Fax: (504) 988-5516,
| | - Nicolas Gilbert
- Institut de Génétique Humaine, CNRS, UPR 1142, 141 rue de la Cardonille, 34396 Montpellier cedex 5, France
| | - John V. Moran
- Departments of Human Genetics and Internal Medicine, 1241 E. Catherine St., University of Michigan Medical School, Ann Arbor, Michigan 48109-0618
| | - Prescott L. Deininger
- Tulane Cancer Center and Dept. of Epidemiology, Tulane University Health Sciences Center SL-66, 1430 Tulane Ave., New Orleans, LA 70112, Phone: (504) 988-6385, Fax: (504) 988-5516,
- *Address for Correspondence: Tulane Cancer Center, SL66, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112, 504-988-6385,
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24
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Affiliation(s)
- John Jaenike
- Department of Biology, University of Rochester, Rochester, New York 14627; e-mail:
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25
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Weinberg HS, Korol AB, Kirzhner VM, Avivi A, Fahima T, Nevo E, Shapiro S, Rennert G, Piatak O, Stepanova EI, Skvarskaja E. Very high mutation rate in offspring of Chernobyl accident liquidators. Proc Biol Sci 2001; 268:1001-5. [PMID: 11375082 PMCID: PMC1088700 DOI: 10.1098/rspb.2001.1650] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Exposure to ionizing radiation has long been suspected to increase mutation load in humans. Nevertheless, such events as atomic bombing seem not to have yielded significant genetic defects. The Chernobyl accident created a different, long-term exposure to radiation. Clean-up teams (or 'liquidators') of the Chernobyl reactor are among those who received the highest doses, presumably in some combination of acute and chronic forms. In this study, children born to liquidator families (currently either in the Ukraine or Israel) conceived after (CA) parental exposure to radiation were screened for the appearance of new fragments using multi-site DNA fingerprinting. Their sibs conceived before (CB) exposure served as critical internal controls, in addition to external controls (non-exposed families). An unexpectedly high (sevenfold) increase in the number of new bands in CA individuals compared with the level seen in controls was recorded. A strong tendency for the number of new bands to decrease with elapsed time between exposure and offspring conception was established for the Ukrainian families. These results indicate that low doses of radiation can induce multiple changes in human germline DNA.
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Affiliation(s)
- H S Weinberg
- Institute of Evolution, University of Haifa, Haifa 31905, Israel
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26
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Rispe C, Moran NA. Accumulation of Deleterious Mutations in Endosymbionts: Muller’s Ratchet with Two Levels of Selection. Am Nat 2000; 156:425-441. [DOI: 10.1086/303396] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Girardet A, McPeek MS, Leeflang EP, Munier F, Arnheim N, Claustres M, Pellestor F. Meiotic segregation analysis of RB1 alleles in retinoblastoma pedigrees by use of single-sperm typing. Am J Hum Genet 2000; 66:167-75. [PMID: 10631148 PMCID: PMC1288323 DOI: 10.1086/302715] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/1999] [Accepted: 09/29/1999] [Indexed: 12/18/2022] Open
Abstract
In hereditary retinoblastoma, different epidemiological studies have indicated a preferential paternal transmission of mutant retinoblastoma alleles to offspring, suggesting the occurrence of a meiotic drive. To investigate this mechanism, we analyzed sperm samples from six individuals from five unrelated families affected with hereditary retinoblastoma. Single-sperm typing techniques were performed for each sample by study of two informative short tandem repeats located either in or close to the retinoblastoma gene (RB1). The segregation probability of mutant RB1 alleles in sperm samples was assessed by use of the SPERMSEG program, which includes experimental parameters, recombination fractions between the markers, and segregation parameters. A total of 2,952 single sperm from the six donors were analyzed. We detected a significant segregation distortion in the data as a whole (P=.0099) and a significant heterogeneity in the segregation rate across donors (.0092). Further analysis shows that this result can be explained by segregation distortion in favor of the normal allele in one donor only and that it does not provide evidence of a significant segregation distortion in the other donors. The segregation distortion favoring the mutant RB1 allele does not seem to occur during spermatogenesis, and, thus, meiotic drive may result either from various mechanisms, including a fertilization advantage or a better mobility in sperm bearing a mutant RB1 gene, or from the existence of a defectively imprinted gene located on the human X chromosome.
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Affiliation(s)
- A Girardet
- Laboratoire de Génétique Moléculaire, Institut de Biologie, and Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Unité Propre de Recherche 1142, 34060 Montpellier, France.
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28
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Affiliation(s)
- Alexey S. Kondrashov
- Section of Ecology and Systematics, Cornell University, Ithaca, New York; 14853 e-mail:
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29
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Population biology of bryozoans: correlates of sessile, colonial life histories in freshwater habitats. ACTA ACUST UNITED AC 1995. [DOI: 10.1007/bf02143202] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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30
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Munier FL, Arabien L, Flodman P, Spence MA, Pescia G, Rutz HP, Murphree AL. Putative non-Mendelian transmission of retinoblastoma in males: a phenotypic segregation analysis of 150 pedigrees. Hum Genet 1994; 94:484-90. [PMID: 7959681 DOI: 10.1007/bf00211012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In a previous genotypic study of eight families, we described paternal segregation distortion favoring the transmission of mutant alleles at the retinoblastoma gene locus (RB1). In the current study, we reviewed all published retinoblastoma pedigrees with defined ascertainment (n = 150), to determine whether the phenotypic segregation frequency at the RB1 locus is in general influenced by the sex of the transmitting parent. Segregation analysis under complete ascertainment revealed that 49.1% of the offspring of male transmitters were affected, while 44.3% of the offspring of female transmitters were affected. While this difference is not statistically significant, it is consistent with the previous findings. No significant sex distortion could be detected among the progeny of carrier fathers and mothers. In order to quantify the transmission ratio more precisely further prospective molecular genetic analysis is warranted. We propose a biological mechanism to account for a putative segregation distortion, namely that genetic recombination creates clones of spermatogonia that are homozygous for the mutant RB1 allele leading to a non-Mendelian ratio of sperm. This model can be experimentally tested using amplification of DNA from single sperm cells.
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Affiliation(s)
- F L Munier
- Division of Ophthalmology, Childrens Hospital, Los Angeles
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31
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Abstract
The inheritance of most genes is tightly controlled, governed by the rules of mendelian inheritance if nuclear or uniparental inheritance if cytoplasmic. A few notable genes and cytoplasmic genomes have escaped this regulation. Such genes may spread by increasing their own rate of transmission despite reducing host fitness and may be regarded as 'selfish'. Their population genetics are described and it appears they may impose a significant genetic load on the host population. Modern molecular techniques may enable similar loads to be imposed on pest species either by transferring selfish genes between species, or by linking deleterious genes to a selfish locus. Alternatively, 'modifier' genes that eliminate the virulent, or disease vectorial capacity, of the pest population may be introduced by linkage to a selfish locus. Selfish elements present in multiple copies may be preferable to single-copy elements as the former are capable of a larger reduction in host fitness. The practical application of these agents depends on five factors: (i) the rate of 'reversion' to a non-selfish form; (ii) the evolution of host repressor systems; (iii) their effect on host fitness, which determines their rate of invasion; (iv) the mechanism regulating host population size in the field; and (v) their ease of manipulation in the laboratory. The first two factors are the most uncertain in most systems, but should be amenable to experimental analysis. It is proposed that the development of such techniques may result in powerful new methods of population control which may be applied to both agricultural pests and disease vectors.
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Affiliation(s)
- I M Hastings
- Institute of Cell, Animal and Population Biology, University of Edinburgh, U.K
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Okamura B, Jones CS, Noble LR. Randomly amplified polymorphic DNA analysis of clonal population structure and geographic variation in a freshwater bryozoan. Proc Biol Sci 1993; 253:147-54. [PMID: 8397414 DOI: 10.1098/rspb.1993.0095] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The randomly amplified polymorphic DNA (RAPD) assay was used to identify genetic polymorphisms in three clonal populations of the freshwater bryozoan, Cristatella mucedo, a species with few useful biochemical genetic markers. Of the 19 decamer oligonucleotide primers screened, 13 gave clear, reproducible RAPD profiles. Clonal population structure was evident, and one clone was dominant at each site. Cluster analysis grouped populations from more distant localities separately (Thames Valley and Norfolk), whereas populations from the Thames Valley clustered together. However, even at the regional scale a high degree of relatedness pertained. This work is one of the first RAPD studies of natural populations, and demonstrates the suitability of the technique for examining population structure and geographic variation in clonal taxa.
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Hastings IM. Population genetic aspects of deleterious cytoplasmic genomes and their effect on the evolution of sexual reproduction. Genet Res (Camb) 1992; 59:215-25. [PMID: 1511870 DOI: 10.1017/s0016672300030500] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A conflict of interest may arise between intra-cellular genomes and their host cell. The example explicitly investigated is that of a 'selfish' mitochondrion which increases its own rate of replication at the cost of reduced metabolic activity which is deleterious to the host cell. The results apply to deleterious cytoplasmic agents in general, such as intracellular parasites. Numerical simulation suggests that selfish mitochondria are able to invade an isogamous sexual population and are capable of reducing its fitness to below 5% of that prior to their invasion. Their spread is enhanced by decreasing the number of mitotic divisions between meioses, and this may constitute a significant constraint on the evolution of lifecycles. The presence of such deleterious cytoplasmic agents favours a nuclear mutation whose expression prevents cytoplasm from the other gamete entering the zygote at fertilization, resulting in uniparental inheritance of cytoplasm. Such a mutation appears physiologically plausible and can increase in frequency despite its deleterious effect in halving the amount of cytoplasm in the zygote. It is suggested that these were the conditions under which anisogamy evolved. These results have implications for the evolution of sexual reproduction. Standard theory suggests there is no immediate cost of sex, a twofold cost being incurred later as anisogamy evolves. The analysis described here predicts a large, rapid reduction in fitness associated with isogamous sexual reproduction, due to the spread of deleterious cytoplasmic agents with fitness only subsequently rising to a maximum twofold cost as uniparental inheritance of cytoplasm and anisogamy evolve.
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Affiliation(s)
- I M Hastings
- Institute of Cell, Animal and Population Biology, University of Edinburgh, Scotland
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