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Morgan AP, Payseur BA. Genetic background affects the strength of crossover interference in house mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596233. [PMID: 38854148 PMCID: PMC11160618 DOI: 10.1101/2024.05.28.596233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Meiotic recombination is required for faithful chromosome segregation in most sexually reproducing organisms and shapes the distribution of genetic variation in populations. Both the overall rate and the spatial distribution of crossovers vary within and between species. Adjacent crossovers on the same chromosome tend to be spaced more evenly than expected at random, a phenomenon known as crossover interference. Although interference has been observed in many taxa, the factors that influence the strength of interference are not well understood. We used house mice (Mus musculus), a well-established model system for understanding recombination, to study the effects of genetics and age on recombination rate and interference in the male germline. We analyzed crossover positions in 503 progeny from reciprocal F1 hybrids between inbred strains representing the three major subspecies of house mice. Consistent with previous studies, autosomal alleles from M. m. musculus tend to increase recombination rate, while inheriting a M. m. musculus X chromosome decreases recombination rate. Old males transmit an average of 0.6 more crossovers per meiosis (5.0%) than young males, though the effect varies across genetic backgrounds. We show that the strength of crossover interference depends on genotype, providing a rare demonstration that interference evolves over short timescales. Differences between reciprocal F1s suggest that X-linked factors modulate the strength of interference. Our findings motivate additional comparisons of interference among recently diverged species and further examination of the role of paternal age in determining the number and positioning of crossovers.
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Affiliation(s)
- Andrew P Morgan
- Department of Medicine, University of North Carolina, Chapel Hill, NC
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin, Madison, WI
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Wen H, Johnson JS, Freitas PHF, Maskal JM, Gloria LS, Araujo AC, Pedrosa VB, Tiezzi F, Maltecca C, Huang Y, Schinckel AP, Brito LF. Longitudinal genomic analyses of automatically-recorded vaginal temperature in lactating sows under heat stress conditions based on random regression models. Genet Sel Evol 2023; 55:95. [PMID: 38129768 PMCID: PMC10734178 DOI: 10.1186/s12711-023-00868-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Automatic and continuous recording of vaginal temperature (TV) using wearable sensors causes minimal disruptions to animal behavior and can generate data that enable the evaluation of temporal body temperature variation under heat stress (HS) conditions. However, the genetic basis of TV in lactating sows from a longitudinal perspective is still unknown. The objectives of this study were to define statistical models and estimate genetic parameters for TV in lactating sows using random regression models, and identify genomic regions and candidate genes associated with HS indicators derived from automatically-recorded TV. RESULTS Heritability estimates for TV ranged from 0.14 to 0.20 over time (throughout the day and measurement period) and from 0.09 to 0.18 along environmental gradients (EG, - 3.5 to 2.2, which correspond to dew point values from 14.87 to 28.19 ˚C). Repeatability estimates of TV over time and along EG ranged from 0.57 to 0.66 and from 0.54 to 0.77, respectively. TV measured from 12h00 to 16h00 had moderately high estimates of heritability (0.20) and repeatability (0.64), indicating that this period might be the most suitable for recording TV for genetic selection purposes. Significant genotype-by-environment interactions (GxE) were observed and the moderately high estimates of genetic correlations between pairs of extreme EG indicate potential re-ranking of selection candidates across EG. Two important genomic regions on chromosomes 10 (59.370-59.998 Mb) and16 (21.548-21.966 Mb) were identified. These regions harbor the genes CDC123, CAMK1d, SEC61A2, and NUDT5 that are associated with immunity, protein transport, and energy metabolism. Across the four time-periods, respectively 12, 13, 16, and 10 associated genomic regions across 14 chromosomes were identified for TV. For the three EG classes, respectively 18, 15, and 14 associated genomic windows were identified for TV, respectively. Each time-period and EG class had uniquely enriched genes with identified specific biological functions, including regulation of the nervous system, metabolism and hormone production. CONCLUSIONS TV is a heritable trait with substantial additive genetic variation and represents a promising indicator trait to select pigs for improved heat tolerance. Moderate GxE for TV exist, indicating potential re-ranking of selection candidates across EG. TV is a highly polygenic trait regulated by a complex interplay of physiological, cellular and behavioral mechanisms.
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Affiliation(s)
- Hui Wen
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Jay S Johnson
- USDA-ARS Livestock Behavior Research Unit, West Lafayette, IN, USA
| | - Pedro H F Freitas
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Jacob M Maskal
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Leonardo S Gloria
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Andre C Araujo
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Victor B Pedrosa
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
- Department of Agriculture, Food, Environment and Forestry, University of Florence, Florence, Italy
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | | | - Allan P Schinckel
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA.
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Brekke C, Berg P, Gjuvsland AB, Johnston SE. Recombination rates in pigs differ between breeds, sexes and individuals, and are associated with the RNF212, SYCP2, PRDM7, MEI1 and MSH4 loci. Genet Sel Evol 2022; 54:33. [PMID: 35596132 PMCID: PMC9123673 DOI: 10.1186/s12711-022-00723-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 04/25/2022] [Indexed: 12/01/2022] Open
Abstract
Background Recombination is a fundamental part of mammalian meiosis that leads to the exchange of large segments of DNA between homologous chromosomes and is therefore an important driver of genetic diversity in populations. In breeding populations, understanding recombination is of particular interest because it can break up unfavourable linkage phases between alleles and produce novel combinations of alleles that could be exploited in selection. In this study, we used dense single nucleotide polymorphism (SNP) genotype data and pedigree information to analyse individual and sex-specific variation and genetic architecture of recombination rates within and between five commercially selected pig breeds. Results In agreement with previous studies, recombination rates were higher in females than in males for all breeds and for all chromosomes, except 1 and 13, for which male rates were slightly higher. Total recombination rate differed between breeds but the pattern of recombination along the chromosomes was well conserved across breeds for the same sex. The autosomal linkage maps spanned a total length of 1731 to 1887 cM for males and of 2231 to 2515 cM for females. Estimates of heritability for individual autosomal crossover count ranged from 0.04 to 0.07 for males and from 0.08 to 0.11 for females. Fourteen genomic regions were found to be associated with individual autosomal crossover count. Of these, four were close to or within candidate genes that have previously been associated with individual recombination rates in pigs and other mammals, namely RNF212, SYCP2 and MSH4. Two of the identified regions included the PRDM7 and MEI1 genes, which are known to be involved in meiosis but have not been previously associated with variation in individual recombination rates. Conclusions This study shows that genetic variation in autosomal recombination rate persists in domesticated species under strong selection, with differences between closely-related breeds and marked differences between the sexes. Our findings support results from other studies, i.e., that individual crossover counts are associated with the RNF212, SYCP2 and MSH4 genes in pig. In addition, we have found two novel candidate genes associated with the trait, namely PRDM7 and MEI1. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00723-9.
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Affiliation(s)
- Cathrine Brekke
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Oluf Thesens vei 6, 1433, Ås, Norway.
| | - Peer Berg
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Oluf Thesens vei 6, 1433, Ås, Norway
| | | | - Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
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Shen B, Freebern E, Jiang J, Maltecca C, Cole JB, Liu GE, Ma L. Effect of Temperature and Maternal Age on Recombination Rate in Cattle. Front Genet 2021; 12:682718. [PMID: 34354736 PMCID: PMC8329537 DOI: 10.3389/fgene.2021.682718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/28/2021] [Indexed: 11/16/2022] Open
Abstract
Meiotic recombination is a fundamental biological process that facilitates meiotic division and promotes genetic diversity. Recombination is phenotypically plastic and affected by both intrinsic and extrinsic factors. The effect of maternal age on recombination rates has been characterized in a wide range of species, but the effect’s direction remains inconclusive. Additionally, the characterization of temperature effects on recombination has been limited to model organisms. Here we seek to comprehensively determine the impact of genetic and environmental factors on recombination rate in dairy cattle. Using a large cattle pedigree, we identified maternal recombination events within 305,545 three-generation families. By comparing recombination rate between parents of different ages, we found a quadratic trend between maternal age and recombination rate in cattle. In contrast to either an increasing or decreasing trend in humans, cattle recombination rate decreased with maternal age until 65 months and then increased afterward. Combining recombination data with temperature information from public databases, we found a positive correlation between environmental temperature during fetal development of offspring and recombination rate in female parents. Finally, we fitted a full recombination rate model on all related factors, including genetics, maternal age, and environmental temperatures. Based on the final model, we confirmed the effect of maternal age and environmental temperature during fetal development of offspring on recombination rate with an estimated heritability of 10% (SE = 0.03) in cattle. Collectively, we characterized the maternal age and temperature effects on recombination rate and suggested the adaptation of meiotic recombination to environmental stimuli in cattle. Our results provided first-hand information regarding the plastic nature of meiotic recombination in a mammalian species.
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Affiliation(s)
- Botong Shen
- Department of Animal and Avian Sciences, University of Maryland, College Park, College Park, MD, United States
| | - Ellen Freebern
- Department of Animal and Avian Sciences, University of Maryland, College Park, College Park, MD, United States
| | - Jicai Jiang
- Department of Animal and Avian Sciences, University of Maryland, College Park, College Park, MD, United States.,Department of Animal Science, North Carolina State University, Raleigh, NC, United States
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, United States
| | - John B Cole
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, United States
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, United States
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, College Park, MD, United States
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Johnsson M, Whalen A, Ros-Freixedes R, Gorjanc G, Chen CY, Herring WO, de Koning DJ, Hickey JM. Genetic variation in recombination rate in the pig. Genet Sel Evol 2021; 53:54. [PMID: 34171988 PMCID: PMC8235837 DOI: 10.1186/s12711-021-00643-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/02/2021] [Indexed: 11/10/2022] Open
Abstract
Background Meiotic recombination results in the exchange of genetic material between homologous chromosomes. Recombination rate varies between different parts of the genome, between individuals, and is influenced by genetics. In this paper, we assessed the genetic variation in recombination rate along the genome and between individuals in the pig using multilocus iterative peeling on 150,000 individuals across nine genotyped pedigrees. We used these data to estimate the heritability of recombination and perform a genome-wide association study of recombination in the pig. Results Our results confirmed known features of the recombination landscape of the pig genome, including differences in genetic length of chromosomes and marked sex differences. The recombination landscape was repeatable between lines, but at the same time, there were differences in average autosome-wide recombination rate between lines. The heritability of autosome-wide recombination rate was low but not zero (on average 0.07 for females and 0.05 for males). We found six genomic regions that are associated with recombination rate, among which five harbour known candidate genes involved in recombination: RNF212, SHOC1, SYCP2, MSH4 and HFM1. Conclusions Our results on the variation in recombination rate in the pig genome agree with those reported for other vertebrates, with a low but nonzero heritability, and the identification of a major quantitative trait locus for recombination rate that is homologous to that detected in several other species. This work also highlights the utility of using large-scale livestock data to understand biological processes. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00643-0.
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Affiliation(s)
- Martin Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK. .,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 750 07, Uppsala, Sweden.
| | - Andrew Whalen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK
| | - Roger Ros-Freixedes
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK.,Departament de Ciència Animal, Universitat de Lleida-Agrotecnio-CERCA Center, Lleida, Spain
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK
| | - Ching-Yi Chen
- Pig Improvement Company, Genus plc, 100 Bluegrass Commons Blvd., Ste2200, Hendersonville, TN, 37075, USA
| | - William O Herring
- Pig Improvement Company, Genus plc, 100 Bluegrass Commons Blvd., Ste2200, Hendersonville, TN, 37075, USA
| | - Dirk-Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 750 07, Uppsala, Sweden
| | - John M Hickey
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK
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