1
|
Teterina AA, Willis JH, Lukac M, Jovelin R, Cutter AD, Phillips PC. Genomic diversity landscapes in outcrossing and selfing Caenorhabditis nematodes. PLoS Genet 2023; 19:e1010879. [PMID: 37585484 PMCID: PMC10461856 DOI: 10.1371/journal.pgen.1010879] [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: 12/28/2022] [Revised: 08/28/2023] [Accepted: 07/21/2023] [Indexed: 08/18/2023] Open
Abstract
Caenorhabditis nematodes form an excellent model for studying how the mode of reproduction affects genetic diversity, as some species reproduce via outcrossing whereas others can self-fertilize. Currently, chromosome-level patterns of diversity and recombination are only available for self-reproducing Caenorhabditis, making the generality of genomic patterns across the genus unclear given the profound potential influence of reproductive mode. Here we present a whole-genome diversity landscape, coupled with a new genetic map, for the outcrossing nematode C. remanei. We demonstrate that the genomic distribution of recombination in C. remanei, like the model nematode C. elegans, shows high recombination rates on chromosome arms and low rates toward the central regions. Patterns of genetic variation across the genome are also similar between these species, but differ dramatically in scale, being tenfold greater for C. remanei. Historical reconstructions of variation in effective population size over the past million generations echo this difference in polymorphism. Evolutionary simulations demonstrate how selection, recombination, mutation, and selfing shape variation along the genome, and that multiple drivers can produce patterns similar to those observed in natural populations. The results illustrate how genome organization and selection play a crucial role in shaping the genomic pattern of diversity whereas demographic processes scale the level of diversity across the genome as a whole.
Collapse
Affiliation(s)
- Anastasia A. Teterina
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
- Center of Parasitology, Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
| | - John H. Willis
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Matt Lukac
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Richard Jovelin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Asher D. Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Patrick C. Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| |
Collapse
|
2
|
Abstract
Sex differences in overall recombination rates are well known, but little theoretical or empirical attention has been given to how and why sexes differ in their recombination landscapes: the patterns of recombination along chromosomes. In the first scientific review of this phenomenon, we find that recombination is biased toward telomeres in males and more uniformly distributed in females in most vertebrates and many other eukaryotes. Notable exceptions to this pattern exist, however. Fine-scale recombination patterns also frequently differ between males and females. The molecular mechanisms responsible for sex differences remain unclear, but chromatin landscapes play a role. Why these sex differences evolve also is unclear. Hypotheses suggest that they may result from sexually antagonistic selection acting on coding genes and their regulatory elements, meiotic drive in females, selection during the haploid phase of the life cycle, selection against aneuploidy, or mechanistic constraints. No single hypothesis, however, can adequately explain the evolution of sex differences in all cases. Sex-specific recombination landscapes have important consequences for population differentiation and sex chromosome evolution.
Collapse
Affiliation(s)
- Jason M. Sardell
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
| |
Collapse
|
3
|
Cahoon CK, Libuda DE. Leagues of their own: sexually dimorphic features of meiotic prophase I. Chromosoma 2019; 128:199-214. [PMID: 30826870 PMCID: PMC6823309 DOI: 10.1007/s00412-019-00692-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/28/2019] [Accepted: 02/05/2019] [Indexed: 01/12/2023]
Abstract
Meiosis is a conserved cell division process that is used by sexually reproducing organisms to generate haploid gametes. Males and females produce different end products of meiosis: eggs (females) and sperm (males). In addition, these unique end products demonstrate sex-specific differences that occur throughout meiosis to produce the final genetic material that is packaged into distinct gametes with unique extracellular morphologies and nuclear sizes. These sexually dimorphic features of meiosis include the meiotic chromosome architecture, in which both the lengths of the chromosomes and the requirement for specific meiotic axis proteins being different between the sexes. Moreover, these changes likely cause sex-specific changes in the recombination landscape with the sex that has the longer chromosomes usually obtaining more crossovers. Additionally, epigenetic regulation of meiosis may contribute to sexually dimorphic recombination landscapes. Here we explore the sexually dimorphic features of both the chromosome axis and crossing over for each stage of meiotic prophase I in Mus musculus, Caenorhabditis elegans, and Arabidopsis thaliana. Furthermore, we consider how sex-specific changes in the meiotic chromosome axes and the epigenetic landscape may function together to regulate crossing over in each sex, indicating that the mechanisms controlling crossing over may be different in oogenesis and spermatogenesis.
Collapse
Affiliation(s)
- Cori K Cahoon
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1370 Franklin Boulevard, Eugene, OR, 97403-1229, USA
| | - Diana E Libuda
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1370 Franklin Boulevard, Eugene, OR, 97403-1229, USA.
| |
Collapse
|
4
|
Abstract
Sexual reproduction requires the production of haploid gametes (sperm and egg) with only one copy of each chromosome; fertilization then restores the diploid chromosome content in the next generation. This reduction in genetic content is accomplished during a specialized cell division called meiosis, in which two rounds of chromosome segregation follow a single round of DNA replication. In preparation for the first meiotic division, homologous chromosomes pair and synapse, creating a context that promotes formation of crossover recombination events. These crossovers, in conjunction with sister chromatid cohesion, serve to connect the two homologs and facilitate their segregation to opposite poles during the first meiotic division. During the second meiotic division, which is similar to mitosis, sister chromatids separate; the resultant products are haploid cells that become gametes. In Caenorhabditis elegans (and most other eukaryotes) homologous pairing and recombination are required for proper chromosome inheritance during meiosis; accordingly, the events of meiosis are tightly coordinated to ensure the proper execution of these events. In this chapter, we review the seminal events of meiosis: pairing of homologous chromosomes, the changes in chromosome structure that chromosomes undergo during meiosis, the events of meiotic recombination, the differentiation of homologous chromosome pairs into structures optimized for proper chromosome segregation at Meiosis I, and the ultimate segregation of chromosomes during the meiotic divisions. We also review the regulatory processes that ensure the coordinated execution of these meiotic events during prophase I.
Collapse
Affiliation(s)
- Kenneth J Hillers
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA 93407, United States
| | - Verena Jantsch
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter,1030 Vienna, Austria
| | | | - Judith L Yanowitz
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, United States
| |
Collapse
|
5
|
Jaramillo-Lambert A, Engebrecht J. A single unpaired and transcriptionally silenced X chromosome locally precludes checkpoint signaling in the Caenorhabditis elegans germ line. Genetics 2010; 184:613-28. [PMID: 20008570 PMCID: PMC2845332 DOI: 10.1534/genetics.109.110338] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 12/07/2009] [Indexed: 12/26/2022] Open
Abstract
In many organisms, female and male meiosis display extensive sexual dimorphism in the temporal meiotic program, the number and location of recombination events, sex chromosome segregation, and checkpoint function. We show here that both meiotic prophase timing and germ-line apoptosis, one output of checkpoint signaling, are dictated by the sex of the germ line (oogenesis vs. spermatogenesis) in Caenorhabditis elegans. During oogenesis in feminized animals (fem-3), a single pair of asynapsed autosomes elicits a checkpoint response, yet an unpaired X chromosome fails to induce checkpoint activation. The single X in males and fem-3 worms is a substrate for the meiotic recombination machinery and repair of the resulting double strand breaks appears to be delayed compared with worms carrying paired X chromosomes. Synaptonemal complex axial HORMA domain proteins, implicated in repair of meiotic double strand breaks (DSBs) and checkpoint function, are assembled and disassembled on the single X similarly to paired chromosomes, but the central region component, SYP-1, is not loaded on the X chromosome in males. In fem-3 worms some X chromosomes achieve nonhomologous self-synapsis; however, germ cells with SYP-1-positive X chromosomes are not preferentially protected from apoptosis. Analyses of chromatin and X-linked gene expression indicate that a single X, unlike asynapsed X chromosomes or autosomes, maintains repressive chromatin marks and remains transcriptionally silenced and suggests that this state locally precludes checkpoint signaling.
Collapse
Affiliation(s)
- Aimee Jaramillo-Lambert
- Department of Molecular and Cellular Biology, Genetics Graduate Group, University of California, Davis, California 95616, USA.
| | | |
Collapse
|
6
|
Joshi N, Barot A, Jamison C, Börner GV. Pch2 links chromosome axis remodeling at future crossover sites and crossover distribution during yeast meiosis. PLoS Genet 2009; 5:e1000557. [PMID: 19629172 PMCID: PMC2708914 DOI: 10.1371/journal.pgen.1000557] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Accepted: 06/10/2009] [Indexed: 01/10/2023] Open
Abstract
Segregation of homologous chromosomes during meiosis I depends on appropriately positioned crossovers/chiasmata. Crossover assurance ensures at least one crossover per homolog pair, while interference reduces double crossovers. Here, we have investigated the interplay between chromosome axis morphogenesis and non-random crossover placement. We demonstrate that chromosome axes are structurally modified at future crossover sites as indicated by correspondence between crossover designation marker Zip3 and domains enriched for axis ensemble Hop1/Red1. This association is first detected at the zygotene stage, persists until double Holliday junction resolution, and is controlled by the conserved AAA+ ATPase Pch2. Pch2 further mediates crossover interference, although it is dispensable for crossover formation at normal levels. Thus, interference appears to be superimposed on underlying mechanisms of crossover formation. When recombination-initiating DSBs are reduced, Pch2 is also required for viable spore formation, consistent with further functions in chiasma formation. pch2Δ mutant defects in crossover interference and spore viability at reduced DSB levels are oppositely modulated by temperature, suggesting contributions of two separable pathways to crossover control. Roles of Pch2 in controlling both chromosome axis morphogenesis and crossover placement suggest linkage between these processes. Pch2 is proposed to reorganize chromosome axes into a tiling array of long-range crossover control modules, resulting in chiasma formation at minimum levels and with maximum spacing. In the germ line of sexually reproducing organisms, haploid gametes are generated from diploid precursor cells by a specialized cell division called meiosis. Reduction by half of chromosome numbers during the first meiotic division depends on genetic exchange, resulting in the formation of crossovers. Without crossovers, pairs of homologous chromosomes frequently fail to separate, resulting in unbalanced gametes with a surplus or deficit of individual chromosomes. Along a given chromosome, crossovers form in different locations in different cells, but distribution of crossovers within each cell is controlled in two ways: first, at least one crossover is formed along each homolog pair, irrespective of size; second, a crossover in a given interval reduces the frequency of crossovers in adjacent chromosome regions. Here, we identify functions of the evolutionarily conserved protein Pch2 in suppressing additional crossovers in adjacent regions and ensuring homolog segregation under certain conditions. Pch2 further controls the assembly of chromosome axis protein Hop1 at future crossover sites. Our findings reveal that chromosome axes undergo structural changes at the same positions where crossovers occur. Thus, axis remodeling and crossover placement are linked via Pch2.
Collapse
Affiliation(s)
- Neeraj Joshi
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America
| | - Aekam Barot
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America
| | - Christine Jamison
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America
| | - G. Valentin Börner
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America
- * E-mail:
| |
Collapse
|
7
|
Cutter AD, Dey A, Murray RL. Evolution of the Caenorhabditis elegans genome. Mol Biol Evol 2009; 26:1199-234. [PMID: 19289596 DOI: 10.1093/molbev/msp048] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A fundamental problem in genome biology is to elucidate the evolutionary forces responsible for generating nonrandom patterns of genome organization. As the first metazoan to benefit from full-genome sequencing, Caenorhabditis elegans has been at the forefront of research in this area. Studies of genomic patterns, and their evolutionary underpinnings, continue to be augmented by the recent push to obtain additional full-genome sequences of related Caenorhabditis taxa. In the near future, we expect to see major advances with the onset of whole-genome resequencing of multiple wild individuals of the same species. In this review, we synthesize many of the important insights to date in our understanding of genome organization and function that derive from the evolutionary principles made explicit by theoretical population genetics and molecular evolution and highlight fertile areas for future research on unanswered questions in C. elegans genome evolution. We call attention to the need for C. elegans researchers to generate and critically assess nonadaptive hypotheses for genomic and developmental patterns, in addition to adaptive scenarios. We also emphasize the potential importance of evolution in the gonochoristic (female and male) ancestors of the androdioecious (hermaphrodite and male) C. elegans as the source for many of its genomic and developmental patterns.
Collapse
Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology and the Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada.
| | | | | |
Collapse
|
8
|
Abstract
Caenorhabditis elegans is an important experimental organism for the study of recombination during meiosis. A variety of techniques have been developed for the measurement of meiotic recombination in C. elegans, ranging from traditional genetic measures to direct cytological determination of chiasma frequency. Here, we provide methods for some of the varied approaches used for the study of meiotic recombination in these tiny but powerful worms.
Collapse
Affiliation(s)
- Kenneth J Hillers
- Biological Sciences, California Polytechnic State University, San Luis Obispo, CA, USA
| | | |
Collapse
|
9
|
Lim JGY, Stine RRW, Yanowitz JL. Domain-specific regulation of recombination in Caenorhabditis elegans in response to temperature, age and sex. Genetics 2008; 180:715-26. [PMID: 18780748 PMCID: PMC2567375 DOI: 10.1534/genetics.108.090142] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Accepted: 08/03/2008] [Indexed: 11/18/2022] Open
Abstract
It is generally considered that meiotic recombination rates increase with temperature, decrease with age, and differ between the sexes. We have reexamined the effects of these factors on meiotic recombination in the nematode Caenorhabditis elegans using physical markers that encompass >96% of chromosome III. The only difference in overall crossover frequency between oocytes and male sperm was observed at 16 degrees . In addition, crossover interference (CI) differs between the germ lines, with oocytes displaying higher CI than male sperm. Unexpectedly, our analyses reveal significant changes in crossover distribution in the hermaphrodite oocyte in response to temperature. This feature appears to be a general feature of C. elegans chromosomes as similar changes in response to temperature are seen for the X chromosome. We also find that the distribution of crossovers changes with age in both hermaphrodites and females. Our observations indicate that it is the oocytes from the youngest mothers-and not the oldest-that showed a different pattern of crossovers. Our data enhance the emerging hypothesis that recombination in C. elegans, as in humans, is regulated in large chromosomal domains.
Collapse
Affiliation(s)
- Jaclyn G Y Lim
- Department of Biology, Goucher College, Baltimore, Maryland 21204, USA
| | | | | |
Collapse
|
10
|
Abstract
The faithful segregation of homologous chromosomes during meiosis is dependent on the formation of physical connections (chiasma) that form following reciprocal exchange of DNA molecules during meiotic recombination. Here we review the current knowledge in the Caenorhabditis elegans meiotic recombination field. We discuss recent developments that have improved our understanding of the crucial steps that must precede the initiation and propagation of meiotic recombination. We summarize the pathways that impact on meiotic prophase entry and the current understanding of how chromosomes reorganize and interact to promote homologous chromosome pairing and subsequent synapsis. We pay particular attention to the mechanisms that contribute to meiotic DNA double-strand break (DSB) formation and strand exchange processes, and how the C. elegans system compares with other model organisms. Finally, we highlight current and future areas of research that are likely to further our understanding of the meiotic recombination process.
Collapse
Affiliation(s)
- Tatiana Garcia-Muse
- DNA Damage Response Laboratory, Clare Hall Laboratories, Cancer Research UK, Blanch Lane, South Mimms, EN6 3LD, UK
| | | |
Collapse
|
11
|
Nelson MN, Nixon J, Lydiate DJ. Genome-wide analysis of the frequency and distribution of crossovers at male and female meiosis in Sinapis alba L. (white mustard). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:31-43. [PMID: 15902398 DOI: 10.1007/s00122-005-1961-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2004] [Accepted: 02/14/2005] [Indexed: 05/02/2023]
Abstract
We present the first genetic linkage maps of Sinapis alba (white mustard) and a rigorous analysis of sex effects on the frequency and distribution of crossovers at meiosis in this species. Sex-averaged maps representing recombination in two highly heterozygous parents were aligned to give a consensus map consisting of 382 loci defined by restriction fragment length polymorphisms and arranged in 12 linkage groups with no unlinked markers. The loci were distributed in a near-random manner across the genome, and there was little evidence of segregation distortion. From these dense maps, a subset of spaced informative markers was used to establish recombination frequencies assayed separately in male and female gametes and derived from two distinct genetic backgrounds. Analyses of 746 gametes indicated that recombination frequencies were greater in male gametes, with the greatest differences near the ends of linkage groups. Genetic background had a lesser effect on recombination frequencies, with no discernible pattern in the distribution of such differences. The possible causes of sex differences in recombination frequency and the implications for plant breeding are discussed.
Collapse
|
12
|
Kato KK, Palmer RG. Molecular mapping of four ovule lethal mutants in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 108:577-85. [PMID: 14610643 DOI: 10.1007/s00122-003-1482-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2003] [Accepted: 09/10/2003] [Indexed: 05/24/2023]
Abstract
We report genetic mapping of four soybean ovule lethal mutants, PS-1, PS-2, PS-3, and PS-4, which had been identified as female partial-sterile mutants from a gene-tagging study. The four mutants had been classified into two mutation classes: (1) PS-1-sporophytic mutation affects sporophytically expressed genes; and (2) PS-2, PS-3, and PS-4 mutants-female gametophyte-specific mutations affect gametophytically expressed genes and are transmitted through the male, but not the female gametes. Molecular mapping demonstrated that these four mutant genes and previously reported female-partial sterile gene, Fsp1, are located independently on soybean molecular linkage groups (MLG-) using SSR markers. PS-1, designated as Fsp2 and Genetic Type Collection number T364, is located between SSR markers Satt170 and Satt363 on MLG-C2 and linked by 13.9 cM and 12.1 cM, respectively. PS-2, designated as Fsp3 and Genetic Type Collection number T365H, is located between SSR markers Satt538 and Satt429 on MLG-A2 and linked by 13.3 cM and 25.4 cM, respectively. PS-3, designated as Fsp4 and Genetic Type Collection number T366H, is located on the terminus of MLG-F and linked to Sat 152 by 13.1 cM. PS-4, designated as Fsp5 and Genetic Type Collection number T367H, is located between SSR markers Satt324 and Satt138 on MLG-G and linked by 19.6 cM and 7.5 cM, respectively. SSR markers adjacent to Fsp3, Fsp4, and Fsp5 were distorted from a 1:2:1 ratio and fit a 1:1 ratio. The segregation distortions of SSR markers adjacent to Fsp3, Fsp4, and Fsp5 are in support of male, but not female transmission of the Fsp3, Fsp4, and Fsp5 gametes.
Collapse
Affiliation(s)
- K K Kato
- Department of Crop Science, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, 080-8555, Hokkaido, Japan
| | | |
Collapse
|
13
|
Meneely PM, Farago AF, Kauffman TM. Crossover distribution and high interference for both the X chromosome and an autosome during oogenesis and spermatogenesis in Caenorhabditis elegans. Genetics 2002; 162:1169-77. [PMID: 12454064 PMCID: PMC1462340 DOI: 10.1093/genetics/162.3.1169] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Regulation of both the number and the location of crossovers during meiosis is important for normal chromosome segregation. We used sequence-tagged site polymorphisms to examine the distribution of all crossovers on the X chromosome during oogenesis and on one autosome during both oogenesis and spermatogenesis in Caenorhabditis elegans. The X chromosome has essentially one crossover during oogenesis, with only three possible double crossover exceptions among 220 recombinant X chromosomes. All three had one of the two crossovers in the same chromosomal interval, suggesting that crossovers in that interval do not cause interference. No other interval was associated with double crossovers. Very high interference was also found on an autosome during oogenesis, implying that each chromosome has only one crossover during oogenesis. During spermatogenesis, recombination on this autosome was reduced by approximately 30% compared to oogenesis, but the relative distribution of the residual crossovers was only slightly different. In contrast to previous results with other autosomes, no double crossover chromosomes were observed. Despite an increased frequency of nonrecombinant chromosomes, segregation of a nonrecombinant autosome during spermatogenesis appears to occur normally. This indicates that an achiasmate segregation system helps to ensure faithful disjunction of autosomes during spermatogenesis.
Collapse
Affiliation(s)
- Philip M Meneely
- Department of Biology, Haverford College, Pennsylvania 19041, USA.
| | | | | |
Collapse
|
14
|
Park C, Frank MT, Lewin HA. Fine-mapping of a region of variation in recombination rate on BTA23 to the D23S22-D23S23 interval using sperm typing and meiotic breakpoint analysis. Genomics 1999; 59:143-9. [PMID: 10409425 DOI: 10.1006/geno.1999.5869] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Meiotic recombination rate (theta) within chromosome segments of similar physical size is known to vary widely throughout the genome. This variation has a genetic component, occurring between the sexes and among individuals of the same sex. We reported previously the existence of variation in theta between males in the DYA-PRL interval on bovine chromosome 23 (BTA23). This region contains the bovine major histocompatibility complex and has been shown to contain recombination hotspots in humans and mice. The aim of this study was to map more finely the interval(s) on BTA23 where variation in theta occurs using sperm typing and meiotic breakpoint analysis. By adding a marker (DRB3) between DYA and PRL, the DYA-PRL interval was subdivided into two adjacent intervals, thus permitting evaluation and comparison of theta among five bulls. Significant variation in theta was found for both intervals; theta(DYA-DRB3) ranged from 13.2 to 28.1%, and theta(DRB3-PRL) ranged from 2.4 to 13.0%. The variation in theta was individual- and region-specific. A meiotic breakpoint strategy employing PCR amplification products from recombinant sperm was then used to refine the chromosomal location associated with variation in theta within the DYA-DRB3 interval. The subinterval D23S22-D23S23 exhibited the greatest degree of variation among bulls having high and low theta within the DYA-DRB3 interval. To confirm this result, theta(D23S22-D23S23) was directly evaluated in three additional randomly chosen bulls using sperm typing. The region showing variation in theta was narrowed to the D23S22-D23S23 subinterval, ranging from 4.6 to 9.2%. Identification of the molecular basis for variation in theta may be useful for map-dependent applications, such as marker-assisted selection and positional cloning of genes affecting physiologically important traits.
Collapse
Affiliation(s)
- C Park
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | | | | |
Collapse
|
15
|
del Cerro AL, Fernández A, Santos JL. Chiasma localization, heterochromatin and synaptonemal complexes in the grasshopper Pyrgomorpha conica. Chromosome Res 1996; 4:69-75. [PMID: 8653273 DOI: 10.1007/bf02254948] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Surface-spread synaptonemal complexes and chiasma distributions in spermatocytes with different C-banding patterns and chiasma distributions in oocytes were analyzed in the grasshopper Pyrgomorpha conica. Male meiosis was characterized by a proximal/distal chiasma localization and complete pairing of homologous chromosomes at pachytene. However, there were indications of a relationship between the frequency and location of pairing initiation sites and chiasma distribution. The presence of a proximal supernumerary segment in a medium-sized chromosome does not increase the mean cell chiasma frequency of carrier individuals compared with those lacking it but may modify chiasma distribution in at least some carrier bivalents. This effect could be related to heterosynapsis in the region near the segment. Mean cell chiasma frequency was significantly lower in females than in males. Females also showed altered chiasma distributions compared with males, with fewer proximal chiasmata and more interstitial and distal chiasmata.
Collapse
Affiliation(s)
- A L del Cerro
- Departamento de Genética, Universidad Complutense, Madrid, Spain
| | | | | |
Collapse
|
16
|
Devaux P, Kilian A, Kleinhofs A. Comparative mapping of the barley genome with male and female recombination-derived, doubled haploid populations. MOLECULAR & GENERAL GENETICS : MGG 1995; 249:600-8. [PMID: 8544825 DOI: 10.1007/bf00418029] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Male (anther culture) and female (Hordeum bulbosum) derived, doubled haploid populations were used to map the barley genome and thus determine the different recombination rates occurring during meiosis in the F1 hybrid donor plants. The anther culture-derived (male recombination) population showed an 18% overall increase in recombination rate. This increased recombination rate was observed for every chromosome and most of the chromosome arms. Examination of linkage distances between individual markers revealed eight segments with significantly higher recombination in the anther culture-derived population, and one in the Hordeum bulbosum-derived population. Very strong distortions of single locus segregations were observed in the anther culture-derived population, but map distances were not affected significantly by these distortions. There were 1.047 and 0.912 recombinations per chromosome in the anther culture and Hordeum bulbosum-derived doubled haploid populations, respectively.
Collapse
Affiliation(s)
- P Devaux
- Department of Crop and Soil Sciences, Washington State University, Pullman 99164-6420, USA
| | | | | |
Collapse
|
17
|
Zetka MC, Rose AM. Mutant rec-1 eliminates the meiotic pattern of crossing over in Caenorhabditis elegans. Genetics 1995; 141:1339-49. [PMID: 8601478 PMCID: PMC1206871 DOI: 10.1093/genetics/141.4.1339] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Meiotic crossovers are not randomly distributed along the chromosome. In Caenorhabditis elegans the central portions of the autosomes have relatively few crossovers compared to the flanking regions. We have measured the frequency of crossing over for several intervals across chromosome I in strains mutant for rec-1. The chromosome is approximately 50 map units in both wild-type and rec-1 homozygotes, however, the distribution of exchanges is very different in rec-1. Map distances expand across the gene cluster and contract near the right end of the chromosome, resulting in a genetic map more consistent with the physical map. Mutations in two other genes, him-6 and him-14, also disrupted the distribution of exchanges. Unlike rec-1, individuals homozygous for him-6 and him-14 had an overall reduction in the amount of crossing over accompanied by a high frequency of nondisjunction and reduced egg hatching. In rec-1; him-6 and rec-1; him-14 homozygotes the frequency of crossing over was characteristic of the Him mutant phenotype, whereas the distribution of the reduced number of exchanges was characteristic of the Rec-1 pattern. It appears that these gene products play a role in establishing the meiotic pattern of exchange events.
Collapse
Affiliation(s)
- M C Zetka
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | | |
Collapse
|
18
|
Barnes TM, Kohara Y, Coulson A, Hekimi S. Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans. Genetics 1995; 141:159-79. [PMID: 8536965 PMCID: PMC1206715 DOI: 10.1093/genetics/141.1.159] [Citation(s) in RCA: 169] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The genetic map of each Caenorhabditis elegans chromosome has a central gene cluster (less pronounced on the X chromosome) that contains most of the mutationally defined genes. Many linkage group termini also have clusters, though involving fewer loci. We examine the factors shaping the genetic map by analyzing the rate of recombination and gene density across the genome using the positions of cloned genes and random cDNA clones from the physical map. Each chromosome has a central gene-dense region (more diffuse on the X) with discrete boundaries, flanked by gene-poor regions. Only autosomes have reduced rates of recombination in these gene-dense regions. Cluster boundaries appear discrete also by recombination rate, and the boundaries defined by recombination rate and gene density mostly, but not always, coincide. Terminal clusters have greater gene densities than the adjoining arm but similar recombination rates. Thus, unlike in other species, most exchange in C. elegans occurs in gene-poor regions. The recombination rate across each cluster is constant and similar; and cluster size and gene number per chromosome are independent of the physical size of chromosomes. We propose a model of how this genome organization arose.
Collapse
Affiliation(s)
- T M Barnes
- Department of Biology, McGill University, Montréal, Quebec, Canada
| | | | | | | |
Collapse
|
19
|
Ellis RE, Kimble J. The fog-3 gene and regulation of cell fate in the germ line of Caenorhabditis elegans. Genetics 1995; 139:561-77. [PMID: 7713418 PMCID: PMC1206367 DOI: 10.1093/genetics/139.2.561] [Citation(s) in RCA: 107] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
In the nematode Caenorhabditis elegans, germ cells normally adopt one of three fates: mitosis, spermatogenesis or oogenesis. We have identified and characterized the gene fog-3, which is required for germ cells to differentiate as sperm rather than as oocytes. Analysis of double mutants suggests that fog-3 is absolutely required for spermatogenesis and acts at the end of the regulatory hierarchy controlling sex determination for the germ line. By contrast, mutations in fog-3 do not alter the sexual identity of other tissues. We also have characterized the null phenotype of fog-1, another gene required for spermatogenesis; we demonstrate that it too controls the sexual identity of germ cells but not of other tissues. Finally, we have studied the interaction of these two fog genes with gld-1, a gene required for germ cells to undergo oogenesis rather than mitosis. On the basis of these results, we propose that germ-cell fate might be controlled by a set of inhibitory interactions among genes that specify one of three fates: mitosis, spermatogenesis or oogenesis. Such a regulatory network would link the adoption of one germ-cell fate to the suppression of the other two.
Collapse
Affiliation(s)
- R E Ellis
- Howard Hughes Medical Institute, Laboratory of Molecular Biology, Madison, Wisconsin, USA
| | | |
Collapse
|
20
|
Abstract
The many features that have made the hermaphroditic nematode Caenorhabditis elegans a good model system for studying development have also attracted investigators to the study of meiosis. Genetic analysis suggests that in C. elegans there are two types of chromosomal sites required for proper meiotic function. The first is needed early in meiosis for recombination and segregation. The second is involved in the mechanisms that establish the normal frequency and distribution of exchange. Genes whose products may interact with these sites have been identified by mutant analysis. Study of these mutations in the nematode is enhancing our general understanding of meiotic functions.
Collapse
Affiliation(s)
- M Zetka
- Institute of Zoology, University of Fribourg, Pérolles, Switzerland
| | | |
Collapse
|
21
|
McKim KS, Peters K, Rose AM. Two types of sites required for meiotic chromosome pairing in Caenorhabditis elegans. Genetics 1993; 134:749-68. [PMID: 8349107 PMCID: PMC1205513 DOI: 10.1093/genetics/134.3.749] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Previous studies have shown that isolated portions of Caenorhabditis elegans chromosomes are not equally capable of meiotic exchange. These results led to the proposal that a homolog recognition region (HRR), defined as the region containing those sequences enabling homologous chromosomes to pair and recombine, is localized near one end of each chromosome. Using translocations and duplications we have localized the chromosome I HRR to the right end. Whereas the other half of chromosome I did not confer any ability for homologs to pair and recombine, deficiencies in this region dominantly suppressed recombination to the middle of the chromosome. These deletions may have disrupted pairing mechanisms that are secondary to and require an HRR. Thus, the processes of pairing and recombination appear to utilize at least two chromosomal elements, the HRR and other pairing sites. For example, terminal sequences from other chromosomes increase the ability of free duplications to recombine with their normal homologs, suggesting that telomere-associated sequences, homologous or nonhomologous, play a role in facilitating meiotic exchange. Recombination can also initiate at internal sites separated from the HRR by chromosome rearrangement, such as deletions of the unc-54 region of chromosome I. When crossing over was suppressed in a region of chromosome I, compensatory increases were observed in other regions. Thus, the presence of the HRR enabled recombination to occur but did not determine the distribution of the crossover events. It seems most likely that there are multiple initiation sites for recombination once homolog recognition has been achieved.
Collapse
Affiliation(s)
- K S McKim
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | | | | |
Collapse
|
22
|
Abstract
The rearrangement hIn1(I) was isolated as a crossover suppressor for the right end of linkage group (LG) I. By inducing genetic markers on this crossover suppressor and establishing the gene order in the homozygote, hIn1(I) was demonstrated to be the first genetically proven inversion in Caenorhabditis elegans. hIn1(I) extensively suppresses recombination in heterozygotes in the right arm of chromosome I from unc-75 to unc-54. This suppression is associated with enhancement of recombination in other regions of the chromosome. The enhancement observed maintains the normal distribution of events but does not extend to other chromosomes. The genetic distance of chromosome I in inversion heterozygotes approaches 50 map units (m.u.), approximately equal to one chiasma per meiosis. This value is maintained in hIn1(I)/szT1(I;X) heterozygotes indicating that small homologous regions can pair and recombine efficiently. hIn1(I)/hT2(I;III) heterozygotes share no uninverted homologous regions and segregate randomly, suggesting the importance of chiasma formation in proper segregation of chromosomes. The genetic distance of chromosome I in these heterozygotes is less that 1 m.u., indicating that crossing over can be suppressed along an entire chromosome. Since one of our goals was to develop an efficient balancer for the right end of LGI, the effectiveness of hIn1(I) as a balancer was tested by isolating and maintaining lethal mutations. The meiotic behaviour of hIn1(I) is consistent with other genetic and cytogenetic data suggesting the meiotic chromosomes are monocentric. Rare recombinants bearing duplications and deficiencies of chromosome I were recovered from hIn1(I) heterozygotes, leading to the proposal the inversion was paracentric.
Collapse
Affiliation(s)
- M C Zetka
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | | |
Collapse
|
23
|
Haack H, Hodgkin J. Tests for parental imprinting in the nematode Caenorhabditis elegans. MOLECULAR & GENERAL GENETICS : MGG 1991; 228:482-5. [PMID: 1896016 DOI: 10.1007/bf00260643] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The mutation him-6 (e1423) leads to generalized chromosomal nondisjunction during meiosis in oogenesis and spermatogenesis of C. elegans. As a result, gametes nullisomic or disomic for each of the six chromosomes occur at appreciable frequency. Crosses utilizing marked him-6 strains were used to generate and identify exceptional euploid progeny which had received both homologues of a marked autosome either from the male parent or from the female parent. Examples of all ten possible exceptions were identified and found to be viable and fertile. These results (together with previous data for the X chromosome) indicate that major chromosomal imprinting effects do not occur during gametogenesis in this organism.
Collapse
Affiliation(s)
- H Haack
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | |
Collapse
|