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Malinovskaya LP, Tishakova KV, Bikchurina TI, Slobodchikova AY, Torgunakov NY, Torgasheva AA, Tsepilov YA, Volkova NA, Borodin PM. Negative heterosis for meiotic recombination rate in spermatocytes of the domestic chicken Gallus gallus. Vavilovskii Zhurnal Genet Selektsii 2021; 25:661-668. [PMID: 34782886 PMCID: PMC8558918 DOI: 10.18699/vj21.075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 11/24/2022] Open
Abstract
Benef its and costs of meiotic recombination are a matter of discussion. Because recombination breaks
allele combinations already tested by natural selection and generates new ones of unpredictable f itness, a high
recombination rate is generally benef icial for the populations living in a f luctuating or a rapidly changing environment
and costly in a stable environment. Besides genetic benef its and costs, there are cytological effects of recombination,
both positive and negative. Recombination is necessary for chromosome synapsis and segregation. However,
it involves a massive generation of double-strand DNA breaks, erroneous repair of which may lead to germ
cell death or various mutations and chromosome rearrangements. Thus, the benef its of recombination (generation
of new allele combinations) would prevail over its costs (occurrence of deleterious mutations) as long as the population
remains suff iciently heterogeneous. Using immunolocalization of MLH1, a mismatch repair protein, at the
synaptonemal complexes, we examined the number and distribution of recombination nodules in spermatocytes
of two chicken breeds with high (Pervomai) and low (Russian Crested) recombination rates and their F1 hybrids and
backcrosses. We detected negative heterosis for recombination rate in the F1 hybrids. Backcrosses to the Pervomai
breed were rather homogenous and showed an intermediate recombination rate. The differences in overall recombination
rate between the breeds, hybrids and backcrosses were mainly determined by the differences in the crossing
over number in the seven largest macrochromosomes. The decrease in recombination rate in F1 is probably
determined by diff iculties in homology matching between the DNA sequences of genetically divergent breeds. The
suppression of recombination in the hybrids may impede gene f low between parapatric populations and therefore
accelerate their genetic divergence.
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Affiliation(s)
- L P Malinovskaya
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | - T I Bikchurina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A Yu Slobodchikova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N Yu Torgunakov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Torgasheva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Y A Tsepilov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N A Volkova
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Moscow region, Russia
| | - P M Borodin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Pazhayam NM, Turcotte CA, Sekelsky J. Meiotic Crossover Patterning. Front Cell Dev Biol 2021; 9:681123. [PMID: 34368131 PMCID: PMC8344875 DOI: 10.3389/fcell.2021.681123] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/28/2021] [Indexed: 12/02/2022] Open
Abstract
Proper number and placement of meiotic crossovers is vital to chromosome segregation, with failures in normal crossover distribution often resulting in aneuploidy and infertility. Meiotic crossovers are formed via homologous repair of programmed double-strand breaks (DSBs). Although DSBs occur throughout the genome, crossover placement is intricately patterned, as observed first in early genetic studies by Muller and Sturtevant. Three types of patterning events have been identified. Interference, first described by Sturtevant in 1915, is a phenomenon in which crossovers on the same chromosome do not occur near one another. Assurance, initially identified by Owen in 1949, describes the phenomenon in which a minimum of one crossover is formed per chromosome pair. Suppression, first observed by Beadle in 1932, dictates that crossovers do not occur in regions surrounding the centromere and telomeres. The mechanisms behind crossover patterning remain largely unknown, and key players appear to act at all scales, from the DNA level to inter-chromosome interactions. There is also considerable overlap between the known players that drive each patterning phenomenon. In this review we discuss the history of studies of crossover patterning, developments in methods used in the field, and our current understanding of the interplay between patterning phenomena.
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Affiliation(s)
- Nila M. Pazhayam
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Carolyn A. Turcotte
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jeff Sekelsky
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Veller C, Edelman NB, Muralidhar P, Nowak MA. Variation in Genetic Relatedness Is Determined by the Aggregate Recombination Process. Genetics 2020; 216:985-994. [PMID: 33109528 PMCID: PMC7768252 DOI: 10.1534/genetics.120.303680] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/21/2020] [Indexed: 12/25/2022] Open
Abstract
The genomic proportion that two relatives share identically by descent-their genetic relatedness-can vary depending on the history of recombination and segregation in their pedigree. Previous calculations of the variance of genetic relatedness have defined genetic relatedness as the proportion of total genetic map length (cM) shared by relatives, and have neglected crossover interference and sex differences in recombination. Here, we consider genetic relatedness as the proportion of the total physical genome (bp) shared by relatives, and calculate its variance for general pedigree relationships, making no assumptions about the recombination process. For the relationships of grandparent-grandoffspring and siblings, the variance of genetic relatedness is a simple decreasing function of [Formula: see text], the average proportion of locus pairs that recombine in meiosis. For general pedigree relationships, the variance of genetic relatedness is a function of metrics analogous to [Formula: see text] Therefore, features of the aggregate recombination process that affect [Formula: see text] and analogs also affect variance in genetic relatedness. Such features include the number of chromosomes and heterogeneity in their size, the number of crossovers and their spatial organization along chromosomes, and sex differences in recombination. Our calculations help to explain several recent observations about variance in genetic relatedness, including that it is reduced by crossover interference (which is known to increase [Formula: see text]). Our methods further allow us to calculate the neutral variance of ancestry among F2s in a hybrid cross, enabling precise statistical inference in F2-based tests for various kinds of selection.
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Affiliation(s)
- Carl Veller
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Nathaniel B Edelman
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Pavitra Muralidhar
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Martin A Nowak
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
- Department of Mathematics, Harvard University, Cambridge, Massachusetts 02138
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Veller C, Kleckner N, Nowak MA. A rigorous measure of genome-wide genetic shuffling that takes into account crossover positions and Mendel's second law. Proc Natl Acad Sci U S A 2019; 116:1659-1668. [PMID: 30635424 PMCID: PMC6358705 DOI: 10.1073/pnas.1817482116] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Comparative studies in evolutionary genetics rely critically on evaluation of the total amount of genetic shuffling that occurs during gamete production. Such studies have been hampered by the absence of a direct measure of this quantity. Existing measures consider crossing-over by simply counting the average number of crossovers per meiosis. This is qualitatively inadequate, because the positions of crossovers along a chromosome are also critical: a crossover toward the middle of a chromosome causes more shuffling than a crossover toward the tip. Moreover, traditional measures fail to consider shuffling from independent assortment of homologous chromosomes (Mendel's second law). Here, we present a rigorous measure of genome-wide shuffling that does not suffer from these limitations. We define the parameter [Formula: see text] as the probability that the alleles at two randomly chosen loci are shuffled during gamete production. This measure can be decomposed into separate contributions from crossover number and position and from independent assortment. Intrinsic implications of this metric include the fact that [Formula: see text] is larger when crossovers are more evenly spaced, which suggests a selective advantage of crossover interference. Utilization of [Formula: see text] is enabled by powerful emergent methods for determining crossover positions either cytologically or by DNA sequencing. Application of our analysis to such data from human male and female reveals that (i) [Formula: see text] in humans is close to its maximum possible value of 1/2 and that (ii) this high level of shuffling is due almost entirely to independent assortment, the contribution of which is ∼30 times greater than that of crossovers.
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Affiliation(s)
- Carl Veller
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138;
| | - Martin A Nowak
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138
- Department of Mathematics, Harvard University, Cambridge, MA 02138
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Zawierta M, Biecek P, Waga W, Cebrat S. The role of intragenomic recombination rate in the evolution of population's genetic pool. Theory Biosci 2007; 125:123-32. [PMID: 17412291 DOI: 10.1016/j.thbio.2007.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In a simple computer model of population evolution, we have shown that frequency of recombination between haplotypes during the gamete production influences the effectiveness of the reproduction strategy. High recombination rates keeps the fraction of defective alleles low while low recombination rate or uneven distributed recombination spots change the strategy of genomes' evolution and result in the accumulation of heterozygous loci in the genomes. Even short fragment of chromosome with restricted recombination influences the genetic structure of neighboring regions.
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Affiliation(s)
- Marta Zawierta
- Department of Genomics, Wrocław University, ul. Przybyszewskiego 63/77, 51-148 Wrocław, Poland
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Esch E. Estimation of gametic frequencies from F2 populations using the EM algorithm and its application in the analysis of crossover interference in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:100-109. [PMID: 15841356 DOI: 10.1007/s00122-005-1998-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2004] [Accepted: 03/07/2005] [Indexed: 05/24/2023]
Abstract
The gametes produced in meiosis provide information on the frequency of recombination and also on the interdependence of recombination events, i.e. interference. Using F(2) individuals, it is not possible in all cases to derive the gametes, which have fused, and which provide the information about interference unequivocally when three or more segregating markers are considered simultaneously. Therefore, a method was developed to estimate the gametic frequencies using a maximum likelihood approach together with the expectation maximisation algorithm. This estimation procedure was applied to F(2) mapping data from rice (Oryza sativa L.) to carry out a genome-wide analysis of crossover interference. The distribution of the coefficient of coincidence in dependence on the recombination fraction revealed for all chromosomes increasing positive interference with decreasing interval size. For some chromosomes this mutual inhibition of recombination was not so strong in small intervals. The centromere had a significant effect on interference. The positive interference found in the chromosome arms were reduced significantly when the intervals considered spanned the centromere. Two chromosomes even demonstrated independent recombination and slightly negative interference for small intervals including the centromere. Different marker densities had no effect on the results. In general, interference depended on the frequency of recombination events in relation to the physical length. The strength of the centromere effect on interference seemed to depend on the strength of recombination suppression around the centromere.
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Affiliation(s)
- E Esch
- Abteilung Angewandte Genetik, Universität Hannover, Herrenhäuser Strasse 2, 30419 Hannover, Germany.
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Dumas D, Britton-Davidian J. Chromosomal rearrangements and evolution of recombination: comparison of chiasma distribution patterns in standard and robertsonian populations of the house mouse. Genetics 2002; 162:1355-66. [PMID: 12454079 PMCID: PMC1462339 DOI: 10.1093/genetics/162.3.1355] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The effects of chromosomal rearrangements on recombination rates were tested by the analysis of chiasma distribution patterns in wild house mice. Males and females of two chromosomal races from Tunisia differing by nine pairs of Robertsonian (Rb) fusions (standard all-acrocentric, 2N = 40 and 2N = 22) were studied. A significant decrease in chiasma number (CN) was observed in Rb mice compared to standard ones for both sexes. The difference in CN was due to a reduction in the number of proximal chiasmata and was associated with an overall more distal redistribution. These features were related to distance of chiasmata to the centromere, suggesting that the centromere effect was more pronounced in Rb fusions than in acrocentric chromosomes. These modifications were interpreted in terms of structural meiotic constraints, although genic factors were likely involved in patterning the observed differences between sexes within races. Thus, the change in chromosomal structure in Rb mice was associated with a generalized decrease in recombination due to a reduction in diploid number, a lower CN, and a decrease in the efficiency of recombination. The effects of such modifications on patterns of genic diversity are discussed in the light of models of evolution of recombination.
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Affiliation(s)
- David Dumas
- Laboratoire Génétique et Environnement, Institut des Sciences de l'Evolution (UMR 5554), Université Montpellier II, cc 065, 34095 Montpellier Cedex 5, France.
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