Chromosome Banding and Heterochromatin in Vicia Faba

<p>This study documents the distribution of bands in Vicia faba root-tip chromosomes as shown by acid treatment, quinacrine mustard fluorescence, various forms of Giemsa banding and orcein banding methods, and demonstrates the coincidence of these bands with the position of heterochromatin as shown by cold treatment and late replication. Heterochromatin in the large metacentric M chromosome is located in two areas: (a) around the centromere and (b) adjacent to the secondary constriction. The latter is not late-replicating but is judged to represent classical nucleolus-associated heterochromatin. Heterochromatin in the smaller sub-telocentric S chromosomes is located in the intercalary and proximal areas of their long arms and in the short arm of two chromosomes. The variable expression of particular chromosome segments with different banding techniques testifies to certain differences between heterochromatic regions and emphasizes the existence of several classes of heterochromatin. In situ molecular hybridization of labelled complementary RNA to chromosomal DNA indicates the presence of repetitive DNA in both euchromatin and heterochromatin of the V. faba genome.</p>

Chromosome Banding and Heterochromatin in Vicia Faba

<p>This study documents the distribution of bands in Vicia faba root-tip chromosomes as shown by acid treatment, quinacrine mustard fluorescence, various forms of Giemsa banding and orcein banding methods, and demonstrates the coincidence of these bands with the position of heterochromatin as shown by cold treatment and late replication. Heterochromatin in the large metacentric M chromosome is located in two areas: (a) around the centromere and (b) adjacent to the secondary constriction. The latter is not late-replicating but is judged to represent classical nucleolus-associated heterochromatin. Heterochromatin in the smaller sub-telocentric S chromosomes is located in the intercalary and proximal areas of their long arms and in the short arm of two chromosomes. The variable expression of particular chromosome segments with different banding techniques testifies to certain differences between heterochromatic regions and emphasizes the existence of several classes of heterochromatin. In situ molecular hybridization of labelled complementary RNA to chromosomal DNA indicates the presence of repetitive DNA in both euchromatin and heterochromatin of the V. faba genome.</p>

Cytological and Cytogenetical Studies on Normal and Interchange Allium Triquetrum

<p>Interchanges (otherwise known as segmental chromosome interchanges or reciprocal translocations), involving exchanges of segments of nonhomologous chromosomes, have been studied extensively in plants. Probably the earliest observations were those of Gates (1903) on a ring of chromosomes at meiosis in Oenothera rubrinervis. Belling's reports of sterility in hybrids amongst certain velvet beans (Stizolobium) were later attributed to an interchange of chromosome segments (Belling, 1925). More clearly defined early cases were provided by McClintock's (1930) cytological demonstrations of interchanges in maize. Burnham's (1956) review indicates a sizable accumulation of data in plants. The researches in maize by Brink, McClintock and Burnham, and others, are by far the most extensive, and these data have contributed much to our present understanding of many cytological processes, particularly synapsis, chiasma formation and orientation phenomena.</p>

Cytological and Cytogenetical Studies on Normal and Interchange Allium Triquetrum

<p>Interchanges (otherwise known as segmental chromosome interchanges or reciprocal translocations), involving exchanges of segments of nonhomologous chromosomes, have been studied extensively in plants. Probably the earliest observations were those of Gates (1903) on a ring of chromosomes at meiosis in Oenothera rubrinervis. Belling's reports of sterility in hybrids amongst certain velvet beans (Stizolobium) were later attributed to an interchange of chromosome segments (Belling, 1925). More clearly defined early cases were provided by McClintock's (1930) cytological demonstrations of interchanges in maize. Burnham's (1956) review indicates a sizable accumulation of data in plants. The researches in maize by Brink, McClintock and Burnham, and others, are by far the most extensive, and these data have contributed much to our present understanding of many cytological processes, particularly synapsis, chiasma formation and orientation phenomena.</p>

PATRIOT: A Pipeline for Tracing Identity-by-Descent for Chromosome Segments to Improve Genomic Prediction in Self-Pollinating Crop Species

The lowering genotyping cost is ushering in a wider interest and adoption of genomic prediction and selection in plant breeding programs worldwide. However, improper conflation of historical and recent linkage disequilibrium between markers and genes restricts high accuracy of genomic prediction (GP). Multiple ancestors may share a common haplotype surrounding a gene, without sharing the same allele of that gene. This prevents parsing out genetic effects associated with the underlying allele of that gene among the set of ancestral haplotypes. We present “Parental Allele Tracing, Recombination Identification, and Optimal predicTion” (i.e., PATRIOT) approach that utilizes marker data to allow for a rapid identification of lines carrying specific alleles, increases the accuracy of genomic relatedness and diversity estimates, and improves genomic prediction. Leveraging identity-by-descent relationships, PATRIOT showed an improvement in GP accuracy by 16.6% relative to the traditional rrBLUP method. This approach will help to increase the rate of genetic gain and allow available information to be more effectively utilized within breeding programs.

Trends in genetic diversity and the effect of inbreeding in American Angus cattle under genomic selection

Background While the adoption of genomic evaluations in livestock has increased genetic gain rates, its effects on genetic diversity and accumulation of inbreeding have raised concerns in cattle populations. Increased inbreeding may affect fitness and decrease the mean performance for economically important traits, such as fertility and growth in beef cattle, with the age of inbreeding having a possible effect on the magnitude of inbreeding depression. The purpose of this study was to determine changes in genetic diversity as a result of the implementation of genomic selection in Angus cattle and quantify potential inbreeding depression effects of total pedigree and genomic inbreeding, and also to investigate the impact of recent and ancient inbreeding. Results We found that the yearly rate of inbreeding accumulation remained similar in sires and decreased significantly in dams since the implementation of genomic selection. Other measures such as effective population size and the effective number of chromosome segments show little evidence of a detrimental effect of using genomic selection strategies on the genetic diversity of beef cattle. We also quantified pedigree and genomic inbreeding depression for fertility and growth. While inbreeding did not affect fertility, an increase in pedigree or genomic inbreeding was associated with decreased birth weight, weaning weight, and post-weaning gain in both sexes. We also measured the impact of the age of inbreeding and found that recent inbreeding had a larger depressive effect on growth than ancient inbreeding. Conclusions In this study, we sought to quantify and understand the possible consequences of genomic selection on the genetic diversity of American Angus cattle. In both sires and dams, we found that, generally, genomic selection resulted in decreased rates of pedigree and genomic inbreeding accumulation and increased or sustained effective population sizes and number of independently segregating chromosome segments. We also found significant depressive effects of inbreeding accumulation on economically important growth traits, particularly with genomic and recent inbreeding.

Mesoscale Simulation of Bacterial Chromosome and Cytoplasmic Nanoparticles in Confinement

In this study we investigated, using a simple polymer model of bacterial chromosome, the subdiffusive behaviors of both cytoplasmic particles and various loci in different cell wall confinements. Non-Gaussian subdiffusion of cytoplasmic particles as well as loci were obtained in our Langevin dynamic simulations, which agrees with fluorescence microscope observations. The effects of cytoplasmic particle size, locus position, confinement geometry, and density on motions of particles and loci were examined systematically. It is demonstrated that the cytoplasmic subdiffusion can largely be attributed to the mechanical properties of bacterial chromosomes rather than the viscoelasticity of cytoplasm. Due to the randomly positioned bacterial chromosome segments, the surrounding environment for both particle and loci is heterogeneous. Therefore, the exponent characterizing the subdiffusion of cytoplasmic particle/loci as well as Laplace displacement distributions of particle/loci can be reproduced by this simple model. Nevertheless, this bacterial chromosome model cannot explain the different responses of cytoplasmic particles and loci to external compression exerted on the bacterial cell wall, which suggests that the nonequilibrium activity, e.g., metabolic reactions, play an important role in cytoplasmic subdiffusion.

DNA Organization along Pachytene Chromosome Axes and Its Relationship with Crossover Frequencies

During meiosis, the number of crossovers vary in correlation to the length of prophase chromosome axes at the synaptonemal complex stage. It has been proposed that the regular spacing of the DNA loops, along with the close relationship of the recombination complexes and the meiotic axes are at the basis of this covariation. Here, we use a cytogenomic approach to investigate the relationship between the synaptonemal complex length and the DNA content in chicken oocytes during the pachytene stage of the first meiotic prophase. The synaptonemal complex to DNA ratios of specific chromosomes and chromosome segments were compared against the recombination rates obtained by MLH1 focus mapping. The present results show variations in the DNA packing ratios of macro- and microbivalents and also between regions within the same bivalent. Chromosome or chromosome regions with higher crossover rates form comparatively longer synaptonemal complexes than expected based on their DNA content. These observations are compatible with the formation of higher number of shorter DNA loops along meiotic axes in regions with higher recombination levels.