Regions Of Non-homologous Chromosomes Research Articles

Advancement in controlling meiotic recombination for plant breeding

Meiotic recombination (Crossover) that takes place during gamete formation in all the sexually reproducing organisms creates genetic diversity which is very important for crop improvement and the evolution of new varieties when natural and artificial selection act upon this. Research spotlight from the year focused on the potential of tinkering with the mechanism of meiotic recombination to generate genetic diversity for crop improvement and plant breeding purposes. Several approaches are applied to increase CO frequency, alter CO distribution and induce COs between non-homologous chromosomal regions and how to practically apply these in breeding programs. In this review, we describe how altering meiotic recombination frequency could be beneficial for plant breeding and their practical applications for crop improvement.

Manipulation of crossover frequency and distribution for plant breeding

The crossovers (COs) that occur during meiotic recombination lead to genetic diversity upon which natural and artificial selection can act. The potential of tinkering with the mechanisms of meiotic recombination to increase the amount of genetic diversity accessible for breeders has been under the research spotlight for years. A wide variety of approaches have been proposed to increase CO frequency, alter CO distribution and induce COs between non-homologous chromosomal regions. For most of these approaches, translational biology will be crucial for demonstrating how these strategies can be of practical use in plant breeding. In this review, we describe how tinkering with meiotic recombination could benefit plant breeding and give concrete examples of how these strategies could be implemented into breeding programs.

Identification and characterization of a subtelomeric satellite DNA in Callitrichini monkeys

Repetitive DNAs are abundant fast evolving components of eukaryotic genomes, which often possess important structural and functional roles. Despite their ubiquity, repetitive DNAs are poorly studied when compared to the genic fraction of genomes. Here, we took advantage of the availability of the sequenced genome of the common marmoset Callithrix jacchus to assess its satellite DNAs (satDNAs) and their distribution in Callitrichini. Firstly, we performed similarity-based clustering, repeat identification, and classification using RepeatExplorer with whole-genome shotgun Illumina reads from a male C. jacchus. After clustering analysis, we identified a satDNA composed by 171 bp motifs, named MarmoSAT, which composes 1.09 % of the C. jacchus genome. Multiple sequence alignments were performed using Muscle 4.0. The MEGA software version 5.05 was used for the calculation of genetic distances and construction of Neighbor-Joining (NJ) trees. Chromosome preparations were obtained from fibroblast cultures of one male of each C. penicillata, C. geoffroyi, Callimico goeldii and Mico argentatus. We performed CBG-banding and fluorescence in situ hybridization (FISH) using alpha and MarmoSAT satDNAs and telomeric sequences as probes. Finally, we investigated the transcription of MarmoSAT in several tissues of C. jacchus using the RNA-seq data generated by the Non-Human Primate Reference Transcriptome Resource. FISH on chromosomes of species from Callithrichini showed that MarmoSAT had a subtelomeric location. In addition to the common monomeric form we found that MarmoSAT was also organized in higher-order repeats of 338 bp in C. goeldii. Our phylogenetic analyses showed that MarmoSAT repeats from C. jacchus lack chromosome-specific features, suggesting exchange events among subterminal regions of non-homologous chromosomes. MarmoSAT is transcribed in several tissues of C. jacchus, with the highest transcription levels in spleen, thymus and heart. The transcription profile and subtelomeric location suggest that MarmoSAT may be involved in the regulation of telomerase and modulation of telomeric chromatin. Agências financiadoras: CNPq, CAPES, FAPEMIG

Flow cytometry and cytogenetic tools in eucalypts: genome size variation × karyotype stability

The eucalypts comprise a group of woody plants used in commercial forest plantations owing to their high growth rates, adaptability to various ecological conditions and multiple applications. Despite the enormous amount of molecular data available for eucalypts, a basic understanding of the nature of its genome still requires information regarding the DNA amount in the genus. In this work, we estimated the genome size and base composition of 25 eucalypt species. With a comparative karyotype approach, we aimed to identify possible chromosomal alterations correlated with the genome size variation. Classical cytogenetic and genomic in situ hybridization experiments were conducted for this purpose. The studied species showed genome size ranging from 2C = 0.91 (Corymbia intermedia) to 2C = 1.37 pg (Eucalyptus paniculata) and AT/CG ratios varying from AT = 61.3 (Eucalyptus urophylla) to AT = 62.85% (C. intermedia). Comparative karyotype analysis revealed no remarkable differences in chromosome number (2n = 22) or morphology among eucalypt species despite considerable differences in nuclear DNA content. The genome in situ hybridization method did not distinguish non-homologous chromosomal regions of Eucalyptus baileyana and Corymbia citriodora, despite the difference of 0.45 pg between their genome sizes. The results found in the present work corroborate the consideration of small and dispersed DNA changes as the main cause of genome size variation in eucalypts.

Identification and characterization of a subtelomeric satellite DNA in Callitrichini monkeys.

Repetitive DNAs are abundant fast-evolving components of eukaryotic genomes, which often possess important structural and functional roles. Despite their ubiquity, repetitive DNAs are poorly studied when compared with the genic fraction of genomes. Here, we took advantage of the availability of the sequenced genome of the common marmoset Callithrix jacchus to assess its satellite DNAs (satDNAs) and their distribution in Callitrichini. After clustering analysis of all reads and comparisons by similarity, we identified a satDNA composed by 171 bp motifs, named MarmoSAT, which composes 1.09% of the C. jacchus genome. Fluorescent in situ hybridization on chromosomes of species from the genera Callithrix, Mico and Callimico showed that MarmoSAT had a subtelomeric location. In addition to the common monomeric, we found that MarmoSAT was also organized in higher-order repeats of 338 bp in Callimico goeldii. Our phylogenetic analyses showed that MarmoSAT repeats from C. jacchus lack chromosome-specific features, suggesting exchange events among subterminal regions of non-homologous chromosomes. MarmoSAT is transcribed in several tissues of C. jacchus, with the highest transcription levels in spleen, thymus and heart. The transcription profile and subtelomeric location suggest that MarmoSAT may be involved in the regulation of telomerase and modulation of telomeric chromatin.

Analysis of genome-wide contacts of forum terminus in Drosophila S2 cells

Stable contacts between the regions of nonhomologous chromosomes have long been known from earlycytogenetic studies [1–5]; however, their nature is stillnot sufficiently studied. In recent years, new techniques specifically designed for a more accurate analysis of threedimensional structures of the chromosomes in the nucleus and to identify chromosomalregions that are close enough to each other were developed [6, 7]. These methods ar e based on the fixation ofchromatin structures by treatment with formaldehyde,Cleavage of DNA with an appropriate restrictionenzyme, and subsequent ligation of the sticky ends ofadjacent DNA fragments. Elegant methods for subsequent truncation of recombinant DNA molecules,their amplification by PCR, and analysis of the products by deep sequencing were proposed. Thus, it ispossible to reveal all the possible interactions of aselected region of the genome with other areas.Previously, we have obtained data indicating thatthe expression of

Chromosomes of three freshwater stingrays (Rajiformes Potamotrygonidae) from the Rio Negro basin, Amazon, Brazil

Potamotrygonidae is the representative family of South American freshwater elasmobranchs. It is a monophyletic group containing 20 species grouped into three genera. Three species belonging to two genera of this family were collected from the middle Negro River, Amazonas, Brazil, and studied cytogenetically: Paratrygon aiereba, Potamotrygon motoro and Potamotrygon orbignyi. Paratrygon aiereba presented 2n = 90 chromosomes and 4M+2SM+10ST+74A. Both species of Potamotrygon presented 2n = 66 chromosomes and differed in their chromosomal formulas: P. motoro had 18M+12SM+10ST+26A and P. orbignyi had 22M+10SM+8ST+26A. No sex heteromorphism was detected. The Fundamental Number (FN) was 106 for the three species. A system of multiple NORs was found in the three species, but with interspecific differences in terms of location and position of the active Ag-NORs sites. Paratrygon aiereba presented only four sites on the short arms of two chromosomal pairs, both in terminal regions. Potamotrygon motoro presented seven sites, on the long and short arms, all in terminal regions of non-homologous chromosomes; P. orbignyi presented eight sites on the long arms, all in terminal regions, of non-homologous chromosomes. The constitutive heterochromatin was in pericentromeric regions of all chromosomes, and no significant interspecific difference was found in relation to this marker.

Quasi-linkage: a confounding factor in linkage analysis of complex diseases?

Human linkage analysis is based on the assumption that unlinked genomic loci, particularly loci located on non-homologous chromosomes, segregate independently during meiosis. An exception to this rule is the phenomenon of quasi-linkage (QL) that describes the non-random segregation of non-homologous chromosomes, which can undermine the basic concept of linkage. Molecular mechanisms of QL are not clear; however, observations in mice and plants suggest a possible affinity between non-homologous chromosomal regions containing repetitive or like sequences. QL has not been investigated in humans. As QL may generate false linkages in genome scans of complex diseases, we sought to determine whether genomic loci detected in such genome scans exhibit QL. A number of individual markers showing linkage to schizophrenia, asthma, multiple sclerosis, inflammatory bowel disease and type-1 diabetes were tested for QL in a pairwise linkage analysis against all other markers exhibiting evidence for linkage in each specific study. The Marshfield genotype dataset of eight CEPH families was used for this purpose. The best QL lod scores generated from the analysis were within the range of the "lukewarm" lod scores reported in the majority of linkage studies for complex disorders. In addition, we performed a genome-wide QL analysis on the Marshfield family database which detected eight QL lod scores >6. The replication of the best Marshfield QL scores was performed using the deCODE families and although none of the eight pairs demonstrated independent evidence for QL, three pairs generated maximal lod scores of 0.11, 0.3, and 1.51. In conclusion, although complex disease relevant markers did not produce high QL lod scores, the general phenomenon of QL in humans cannot be excluded and potentially can be a confounding factor in genetic studies of complex traits.

Chromosome Pairing Does Not Contribute to Nuclear Architecture in Vegetative Yeast Cells

There are several reports of a closer-than-random colocalization of homologous chromosomes in the vegetative nuclei of diploid budding yeast. Here, we studied by fluorescence in situ hybridization (FISH) the nuclear distribution of chromosomes and found a slight tendency toward closer proximity between homologous (allelic) loci than between any nonhomologous chromosomal regions. We show that most of this preferential association is not due to vegetative (also known as somatic) pairing but is caused by the polar orientation of interphase chromosomes (Rabl orientation). We quantified the occasional loss of detectable fluorescence signals that is inherent to the FISH method. Signal loss leads to the occurrence of a single signal that may be misinterpreted as the close association of two homologous chromosomal sites. The nuclear distribution of homologous loci, when corrected for the influence of nuclear architecture and methodological faults, was not different or was only marginally different from a random relative positioning as predicted by computer simulation. We discuss here several possibilities for the residual homologous proximity that do not invoke homology-dependent vegetative pairing, and we conclude that, in diploid budding yeast, constitutive vegetative pairing is a negligible factor for the organization of the interphase nucleus.

Genetic and molecular analysis of Aspergillus nidulans transformants obtained by the biolistic process

Twenty transformants obtained by transforming the argB strain of Aspergillus nidulans by the biolistic process were analysed in detail. Eight lost the Arg+ phenotype very frequently and the other 12 were mitotically stable, even after 15 successive subculturing. To analyse the integration events, the mitotically stable transformants were submited to genetic and molecular analyses; 16.7% resulted from the integration of the transforming DNA in tandem with the chromosomal argB locus, 8.3% showed replacement of the argB mutation by wild type allele, 41.7% showed transforming DNA integrated into nonhomologous chromosomal regions at chromosome III, and 33.3% showed transforming DNA integrated into nonhomologous chromosomal regions at chromosomes others than III. Among the mitotically stable transformants, the frequency of integration into nonhomologous sites was higher by the biolistic process than that reported by the literature for protoplast-mediated transformation.Key words: Aspergillus nidulans, fungal transformation, biolistic gene transfer, gene integration, argB gene.

Stable length polymorphism of up to 260 kb at the tip of the short arm of human chromosome 16

We have completed a long-range restriction map of the terminal region of the short arm of human chromosome 16 (16p13.3) by physically linking a distal genetic locus (α-globin) with two recently isolated probes to telomere-associated repeats (TelBam3.4 and TelBam11). Comparison of 47 chromosomes has revealed major polymorphic length variation in this region: we have Identified three alleles in which the α-globin genes lie 170 kb, 350 kb, or 430 kb from the telomere. The two most common alleles contain different terminal segments, starting 145 kb distal to the α-globin genes. Beyond this boundary these alleles are non-homologous, yet each contains sequences related to other (different) chromosome termini. This chromosome size polymorphism has probably arisen by occasional exchanges between the subtelomeric regions of nonhomologous chromosomes; analogous length variation is likely to be present at other human telomeres.

Genetic and molecular characterization of argB+ transformants of Aspergillus nidulans.

Thirty-three argB- to argB+ transformants of Aspergillus nidulans have been subjected to genetic and molecular analysis. Two showed high levels of mitotic instability although it is suggested that this is a consequence of heterokaryosis rather than instability of the transformation event. Most transformants resulted from the integration of the transforming DNA in tandem with the chromosomal argB locus. The maximum number of inserted sequences was two, to generate three copies of the argB locus. The other main transformant type showed replacement of the argB- mutation by the wild-type allele present on the transforming plasmid. Transformants were also recovered in which the transforming DNA had integrated into non-homologous chromosomal regions. Selfed or hybrid cleistothetica from all transformants, except the gene replacement types gave arginine requiring recombinants. Most transformants showed low levels of meiotic instability. Others displayed varying levels which in some cases differed between selfed and hybrid cleistotheticia. There was some correlation between meiotic instability and the nature of the transformation event. Diploid parasexual and aneuploid analysis located the integrated DNA in each transformant to chromosome III. Two transformants were isolated as heterozygous diploids. A third diploid was isolated as a stable mitotic segregant from one of the mitotically unstable transformants.

Evidence against somatic association in hexaploid wheat

In mitotic interphase nuclei, nucleolus-organizing regions of homologous chromosomes lay no closer to each other than nucleolus-organizing regions of non-homologous chromosomes. — Mitotic metaphase studies of distances between satellites and also between telocentrics showed no greater nearness of homologues than of non-homologues. — These studies fail to support the concept of somatic association in hexaploid wheat.