1
|
Non-Mendelian segregation and transmission drive of B chromosomes. Chromosome Res 2022; 30:217-228. [DOI: 10.1007/s10577-022-09692-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/11/2022] [Accepted: 04/11/2022] [Indexed: 11/03/2022]
|
2
|
Carioscia SA, Weaver KJ, Bortvin AN, Pan H, Ariad D, Bell AD, McCoy RC. A method for low-coverage single-gamete sequence analysis demonstrates adherence to Mendel's first law across a large sample of human sperm. eLife 2022; 11:76383. [PMID: 36475543 PMCID: PMC9844984 DOI: 10.7554/elife.76383] [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: 12/14/2021] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
Recently published single-cell sequencing data from individual human sperm (n=41,189; 969-3377 cells from each of 25 donors) offer an opportunity to investigate questions of inheritance with improved statistical power, but require new methods tailored to these extremely low-coverage data (∼0.01× per cell). To this end, we developed a method, named rhapsodi, that leverages sparse gamete genotype data to phase the diploid genomes of the donor individuals, impute missing gamete genotypes, and discover meiotic recombination breakpoints, benchmarking its performance across a wide range of study designs. We then applied rhapsodi to the sperm sequencing data to investigate adherence to Mendel's Law of Segregation, which states that the offspring of a diploid, heterozygous parent will inherit either allele with equal probability. While the vast majority of loci adhere to this rule, research in model and non-model organisms has uncovered numerous exceptions whereby 'selfish' alleles are disproportionately transmitted to the next generation. Evidence of such 'transmission distortion' (TD) in humans remains equivocal in part because scans of human pedigrees have been under-powered to detect small effects. After applying rhapsodi to the sperm data and scanning for evidence of TD, our results exhibited close concordance with binomial expectations under balanced transmission. Together, our work demonstrates that rhapsodi can facilitate novel uses of inferred genotype data and meiotic recombination events, while offering a powerful quantitative framework for testing for TD in other cohorts and study systems.
Collapse
Affiliation(s)
- Sara A Carioscia
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Kathryn J Weaver
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Andrew N Bortvin
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Hao Pan
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Daniel Ariad
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Avery Davis Bell
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
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.
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Casellas J, Cañas-Álvarez JJ, González-Rodríguez A, Puig-Oliveras A, Fina M, Piedrafita J, Molina A, Díaz C, Baró JA, Varona L. Bayesian analysis of parent-specific transmission ratio distortion in seven Spanish beef cattle breeds. Anim Genet 2016; 48:93-96. [PMID: 27650416 DOI: 10.1111/age.12509] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2016] [Indexed: 01/09/2023]
Abstract
Transmission ratio distortion (TRD) is the departure from the expected Mendelian ratio in offspring, a poorly investigated biological phenomenon in livestock species. Given the current availability of specific parametric methods for the analysis of segregation data, this study focused on the screening of TRD in 602 402 single nucleotide polymorphisms covering all autosomal chromosomes in seven Spanish beef cattle breeds. On average, 0.13% (n = 786) and 0.01% (n = 29) of genetic markers evidenced sire- or dam-specific TRD respectively. There were no single nucleotide polymorphisms accounting for both sire- and dam-specific TRD at the same time, and only one marker (rs43147474) accounted for (sire-specific) TRD in all seven breeds. It must be noted that rs43147474 is located in the fourth intronic region of the GTP-binding protein 10 gene, and this locus has been previously linked to the maintenance of mitochondria and nucleolar architectures. Alternatively, other candidate genes surround this hot-spot for sire-specific TRD in the cattle genome, and they are related to embryonic and postnatal lethality as well as prostate cancer, among others. This research characterized the distribution of TRD in the bovine genome, highlighting heterogeneous results when comparing across breeds.
Collapse
Affiliation(s)
- J Casellas
- Grup de Recerca en Millora Genètica Molecular Veterinària, Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - J J Cañas-Álvarez
- Grup de Recerca en Remugants, Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - A González-Rodríguez
- Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013, Zaragoza, Spain
| | - A Puig-Oliveras
- Grup de Recerca en Millora Genètica Molecular Veterinària, Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - M Fina
- Grup de Recerca en Remugants, Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - J Piedrafita
- Grup de Recerca en Remugants, Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - A Molina
- MERAGEM, Universidad de Córdoba, 14071, Córdoba, Spain
| | - C Díaz
- Departamento de Mejora Genética Animal, INIA, 28040, Madrid, Spain
| | - J A Baró
- Departamento de Ciencias Agroforestales, Universidad de Valladolid, 34004, Palencia, Spain
| | - L Varona
- Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013, Zaragoza, Spain
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Didion JP, Morgan AP, Yadgary L, Bell TA, McMullan RC, Ortiz de Solorzano L, Britton-Davidian J, Bult CJ, Campbell KJ, Castiglia R, Ching YH, Chunco AJ, Crowley JJ, Chesler EJ, Förster DW, French JE, Gabriel SI, Gatti DM, Garland T, Giagia-Athanasopoulou EB, Giménez MD, Grize SA, Gündüz İ, Holmes A, Hauffe HC, Herman JS, Holt JM, Hua K, Jolley WJ, Lindholm AK, López-Fuster MJ, Mitsainas G, da Luz Mathias M, McMillan L, Ramalhinho MDGM, Rehermann B, Rosshart SP, Searle JB, Shiao MS, Solano E, Svenson KL, Thomas-Laemont P, Threadgill DW, Ventura J, Weinstock GM, Pomp D, Churchill GA, Pardo-Manuel de Villena F. R2d2 Drives Selfish Sweeps in the House Mouse. Mol Biol Evol 2016; 33:1381-95. [PMID: 26882987 PMCID: PMC4868115 DOI: 10.1093/molbev/msw036] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A selective sweep is the result of strong positive selection driving newly occurring or standing genetic variants to fixation, and can dramatically alter the pattern and distribution of allelic diversity in a population. Population-level sequencing data have enabled discoveries of selective sweeps associated with genes involved in recent adaptations in many species. In contrast, much debate but little evidence addresses whether “selfish” genes are capable of fixation—thereby leaving signatures identical to classical selective sweeps—despite being neutral or deleterious to organismal fitness. We previously described R2d2, a large copy-number variant that causes nonrandom segregation of mouse Chromosome 2 in females due to meiotic drive. Here we show population-genetic data consistent with a selfish sweep driven by alleles of R2d2 with high copy number (R2d2HC) in natural populations. We replicate this finding in multiple closed breeding populations from six outbred backgrounds segregating for R2d2 alleles. We find that R2d2HC rapidly increases in frequency, and in most cases becomes fixed in significantly fewer generations than can be explained by genetic drift. R2d2HC is also associated with significantly reduced litter sizes in heterozygous mothers, making it a true selfish allele. Our data provide direct evidence of populations actively undergoing selfish sweeps, and demonstrate that meiotic drive can rapidly alter the genomic landscape in favor of mutations with neutral or even negative effects on overall Darwinian fitness. Further study will reveal the incidence of selfish sweeps, and will elucidate the relative contributions of selfish genes, adaptation and genetic drift to evolution.
Collapse
Affiliation(s)
- John P Didion
- Department of Genetics, The University of North Carolina at Chapel Hill Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill Carolina Center for Genome Science, The University of North Carolina at Chapel Hill
| | - Andrew P Morgan
- Department of Genetics, The University of North Carolina at Chapel Hill Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill Carolina Center for Genome Science, The University of North Carolina at Chapel Hill
| | - Liran Yadgary
- Department of Genetics, The University of North Carolina at Chapel Hill Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill Carolina Center for Genome Science, The University of North Carolina at Chapel Hill
| | - Timothy A Bell
- Department of Genetics, The University of North Carolina at Chapel Hill Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill Carolina Center for Genome Science, The University of North Carolina at Chapel Hill
| | - Rachel C McMullan
- Department of Genetics, The University of North Carolina at Chapel Hill Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill Carolina Center for Genome Science, The University of North Carolina at Chapel Hill
| | - Lydia Ortiz de Solorzano
- Department of Genetics, The University of North Carolina at Chapel Hill Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill Carolina Center for Genome Science, The University of North Carolina at Chapel Hill
| | - Janice Britton-Davidian
- Institut des Sciences de l'Evolution, Université De Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | | | - Karl J Campbell
- Island Conservation, Puerto Ayora, Galápagos Island, Ecuador School of Geography, Planning & Environmental Management, The University of Queensland, St Lucia, QLD, Australia
| | - Riccardo Castiglia
- Department of Biology and Biotechnologies "Charles Darwin", University of Rome "La Sapienza", Rome, Italy
| | - Yung-Hao Ching
- Department of Molecular Biology and Human Genetics, Tzu Chi University, Hualien City, Taiwan
| | | | - James J Crowley
- Department of Genetics, The University of North Carolina at Chapel Hill
| | | | - Daniel W Förster
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany
| | - John E French
- National Toxicology Program, National Institute of Environmental Sciences, NIH, Research Triangle Park, NC
| | - Sofia I Gabriel
- Department of Animal Biology & CESAM - Centre for Environmental and Marine Studies, Faculty of Sciences, University of Lisbon, Lisboa, Portugal
| | | | | | | | - Mabel D Giménez
- Instituto de Biología Subtropical, CONICET - Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| | - Sofia A Grize
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - İslam Gündüz
- Department of Biology, Faculty of Arts and Sciences, University of Ondokuz Mayis, Samsun, Turkey
| | - Andrew Holmes
- Laboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD
| | - Heidi C Hauffe
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'adige, TN, Italy
| | - Jeremy S Herman
- Department of Natural Sciences, National Museums Scotland, Edinburgh, United Kingdom
| | - James M Holt
- Department of Computer Science, The University of North Carolina at Chapel Hill
| | - Kunjie Hua
- Department of Genetics, The University of North Carolina at Chapel Hill
| | | | - Anna K Lindholm
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | | | - George Mitsainas
- Section of Animal Biology, Department of Biology, University of Patras, Patras, Greece
| | - Maria da Luz Mathias
- Department of Animal Biology & CESAM - Centre for Environmental and Marine Studies, Faculty of Sciences, University of Lisbon, Lisboa, Portugal
| | - Leonard McMillan
- Department of Computer Science, The University of North Carolina at Chapel Hill
| | - Maria da Graça Morgado Ramalhinho
- Department of Animal Biology & CESAM - Centre for Environmental and Marine Studies, Faculty of Sciences, University of Lisbon, Lisboa, Portugal
| | - Barbara Rehermann
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD
| | - Stephan P Rosshart
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY
| | - Meng-Shin Shiao
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Emanuela Solano
- Department of Biology and Biotechnologies "Charles Darwin", University of Rome "La Sapienza", Rome, Italy
| | | | | | - David W Threadgill
- Department of Veterinary Pathobiology, Texas A&M University, College Station Department of Molecular and Cellular Medicine, Texas A&M University, College Station
| | - Jacint Ventura
- Departament de Biologia Animal, de Biologia Vegetal y de Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Daniel Pomp
- Department of Genetics, The University of North Carolina at Chapel Hill Carolina Center for Genome Science, The University of North Carolina at Chapel Hill
| | | | - Fernando Pardo-Manuel de Villena
- Department of Genetics, The University of North Carolina at Chapel Hill Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill Carolina Center for Genome Science, The University of North Carolina at Chapel Hill
| |
Collapse
|
9
|
Dai B, Guo H, Huang C, Ahmed MM, Lin Z. Identification and Characterization of Segregation Distortion Loci on Cotton Chromosome 18. FRONTIERS IN PLANT SCIENCE 2016; 7:2037. [PMID: 28149299 PMCID: PMC5242213 DOI: 10.3389/fpls.2016.02037] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 12/20/2016] [Indexed: 05/11/2023]
Abstract
Segregation distortion is commonly detected via genetic mapping and this phenomenon has been reported in many species. However, the genetic causes of the segregation distortion regions in a majority of species are still unclear. To genetically dissect the SD on chromosome 18 in cotton, eight reciprocal backcross populations and two F2 populations were developed. Eleven segregation distortion loci (SDL) were detected in these ten populations. Comparative analyses among populations revealed that SDL18.1 and SDL18.9 were consistent with male gametic competition; whereas SDL18.4 and SDL18.11 reflected female gametic selection. Similarly, other SDL could reflect zygotic selection. The surprising finding was that SDL18.8 was detected in all populations, and the direction was skewed towards heterozygotes. Consequently, zygotic selection or heterosis could represent the underlying genetic mechanism for SDL18.8. Among developed introgression lines, SDL18.8 was introgressed as a heterozygote, further substantiating that a heterozygote state was preferred under competition. Six out of 11 SDL on chromosome 18 were dependent on the cytoplasmic environment. These results indicated that different SDL showed varying responses to the cytoplasmic environment. Overall, the results provided a novel strategy to analyze the molecular mechanisms, which could be further exploited in cotton interspecific breeding programs.
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Gulevich R, Oskina I, Ilyina O, Herbeck Y, Plyusnina I, Trut L. The non- agoutimutation in Norway rats ( Rattus norvegicus) selected for behavior. CAN J ZOOL 2013. [DOI: 10.1139/cjz-2012-0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The frequency of aa homozygous descendants was studied in crosses of Aa heterozygous Norway rat (Rattus norvegicus (Berkenhout, 1769)) parents selected for tame and aggressive behavior. First, Aa heterozygotes were obtained in crosses between tame homozygotes for the wild-type allele (AA) and aggressive homozygotes for the non-agouti allele (aa). The most tame and the most aggressive descendants were selected from the progeny of the Aa genotype by using the glove test. Then Aa rats were crossed among tame and among aggressive descendants, and the AA and Aa genotypes of grey descendants were identified by polymerase chain reactions (PCR). The segregation of descendants into the AA, Aa, and aa genotypes was cumulatively analyzed in five generations of selection with regard to the phenotypic manifestation of tame and aggressive behavior in their parents. The frequency of aa descendants in the progeny of mothers with low aggressive behavior scores was less than expected and less than in the progeny of mothers with high aggressive behavior scores.
Collapse
Affiliation(s)
- R. Gulevich
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, pr. Lavrentyeva 10, Novosibirsk 630090, Russia
| | - I. Oskina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, pr. Lavrentyeva 10, Novosibirsk 630090, Russia
| | - O. Ilyina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, pr. Lavrentyeva 10, Novosibirsk 630090, Russia
| | - Yu. Herbeck
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, pr. Lavrentyeva 10, Novosibirsk 630090, Russia
| | - I. Plyusnina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, pr. Lavrentyeva 10, Novosibirsk 630090, Russia
| | - L. Trut
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, pr. Lavrentyeva 10, Novosibirsk 630090, Russia
| |
Collapse
|
12
|
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.
Collapse
|
13
|
Abstract
The Collaborative Cross Consortium reports here on the development of a unique genetic resource population. The Collaborative Cross (CC) is a multiparental recombinant inbred panel derived from eight laboratory mouse inbred strains. Breeding of the CC lines was initiated at multiple international sites using mice from The Jackson Laboratory. Currently, this innovative project is breeding independent CC lines at the University of North Carolina (UNC), at Tel Aviv University (TAU), and at Geniad in Western Australia (GND). These institutions aim to make publicly available the completed CC lines and their genotypes and sequence information. We genotyped, and report here, results from 458 extant lines from UNC, TAU, and GND using a custom genotyping array with 7500 SNPs designed to be maximally informative in the CC and used a novel algorithm to infer inherited haplotypes directly from hybridization intensity patterns. We identified lines with breeding errors and cousin lines generated by splitting incipient lines into two or more cousin lines at early generations of inbreeding. We then characterized the genome architecture of 350 genetically independent CC lines. Results showed that founder haplotypes are inherited at the expected frequency, although we also consistently observed highly significant transmission ratio distortion at specific loci across all three populations. On chromosome 2, there is significant overrepresentation of WSB/EiJ alleles, and on chromosome X, there is a large deficit of CC lines with CAST/EiJ alleles. Linkage disequilibrium decays as expected and we saw no evidence of gametic disequilibrium in the CC population as a whole or in random subsets of the population. Gametic equilibrium in the CC population is in marked contrast to the gametic disequilibrium present in a large panel of classical inbred strains. Finally, we discuss access to the CC population and to the associated raw data describing the genetic structure of individual lines. Integration of rich phenotypic and genomic data over time and across a wide variety of fields will be vital to delivering on one of the key attributes of the CC, a common genetic reference platform for identifying causative variants and genetic networks determining traits in mammals.
Collapse
|
14
|
Quantitative trait locus analysis of stage-specific inbreeding depression in the Pacific oyster Crassostrea gigas. Genetics 2011; 189:1473-86. [PMID: 21940682 DOI: 10.1534/genetics.111.131854] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inbreeding depression and genetic load have been widely observed, but their genetic basis and effects on fitness during the life cycle remain poorly understood, especially for marine animals with high fecundity and high, early mortality (type-III survivorship). A high load of recessive mutations was previously inferred for the Pacific oyster Crassostrea gigas, from massive distortions of zygotic, marker segregation ratios in F(2) families. However, the number, genomic location, and stage-specific onset of mutations affecting viability have not been thoroughly investigated. Here, we again report massive distortions of microsatellite-marker segregation ratios in two F(2) hybrid families, but we now locate the causative deleterious mutations, using a quantitative trait locus (QTL) interval-mapping model, and we characterize their mode of gene action. We find 14-15 viability QTL (vQTL) in the two families. Genotypic frequencies at vQTL generally suggest selection against recessive or partially recessive alleles, supporting the dominance theory of inbreeding depression. No epistasis was detected among vQTL, so unlinked vQTL presumably have independent effects on survival. For the first time, we track segregation ratios of vQTL-linked markers through the life cycle, to determine their stage-specific expression. Almost all vQTL are absent in the earliest life stages examined, confirming zygotic viability selection; vQTL are predominantly expressed before the juvenile stage (90%), mostly at metamorphosis (50%). We estimate that, altogether, selection on vQTL caused 96% mortality in these families, accounting for nearly all of the actual mortality. Thus, genetic load causes substantial mortality in inbred Pacific oysters, particularly during metamorphosis, a critical developmental transition warranting further investigation.
Collapse
|