Chromosome-autonomous feedback downregulates meiotic DSB competence upon synaptonemal complex formation

The number of DNA double-strand breaks (DSBs) initiating meiotic recombination is elevated in Saccharomyces cerevisiae mutants that are globally defective in forming crossovers and synaptonemal complex (SC), a protein scaffold juxtaposing homologous chromosomes. These mutants thus appear to lack a negative feedback loop that inhibits DSB formation when homologs engage one another. This feedback is predicted to be chromosome autonomous, but this has not been tested. Moreover, what chromosomal process is recognized as "homolog engagement" remains unclear. To address these questions, we evaluated effects of homolog engagement defects restricted to small portions of the genome using karyotypically abnormal yeast strains with a homeologous chromosome V pair, monosomic V, or trisomy XV. We found that homolog-engagement-defective chromosomes incurred more DSBs, concomitant with prolonged retention of the DSB-promoting protein Rec114, while the rest of the genome remained unaffected. SC-deficient, crossover-proficient mutants ecm11 and gmc2 experienced increased DSB numbers diagnostic of homolog engagement defects. These findings support the hypothesis that SC formation provokes DSB protein dissociation, leading in turn to loss of a DSB competent state. Our findings show that DSB number is regulated in a chromosome-autonomous fashion and provide insight into how homeostatic DSB controls respond to aneuploidy during meiosis.

A low resolution epistasis mapping approach to identify chromosome arm interactions in allohexaploid wheat

1AbstractEpistasis is an important contributor to genetic variance, even in inbred populations where it is present as additive by additive interactions. Testing for epistasis presents a multiple testing problem as the search space for modest numbers of markers is large. Additionally, single markers do not necessarily track functional units of interacting chromatin as well as haplotype based methods do. To harness the power of multiple markers while drastically minimizing the number of tests conducted, we present a low resolution test for epistatic interactions across whole chromosome arms. Two additive genetic covariance matrices are constructed from markers on two different chromosome arms. The Hadamard product of these additive covariance matrices is then used to produce the additive by additive epistasis covariance matrix between the two chromosome arms. The covariance matrices are subsequently used to estimate an epistatic interaction variance parameter in a mixed model framework, while correcting for background additive and epistatic effects. We find significant epistatic interactions for 2% of interactions tested for four agronomic traits in a population of winter wheat. Interactions across homeologous chromosome arms were identified, but were less abundant than other interaction chromosome arm pairs. Of these, homeologous chromosome arm pair 4BL and 4DL showed a strong relationship between the product of their additive effects and the interaction effect that may be indicative of functional redundancy. Several chromosome arms were involved in many interactions across the genome, suggesting that they may contain important large effect regulatory factors. The differential patterns of epistasis across different traits suggests that detection of epistatic interactions is robust when correcting for background additive and epistatic effects in the population. The low resolution epistasis mapping method presented here identifies important epistatic interactions with a limited number of statistical tests at the cost of relatively lower precision.

Genetic variation in a complex polyploid: unveiling the dynamic allelic features of sugarcane

BackgroundSugarcane (Saccharum spp.) is highly polyploid and aneuploid. Modern cultivars are derived from hybridization between S. officinarum and S. spontaneum. This combination results in a genome exhibiting variable ploidy among different loci, a huge genome size (approximately 10 Gb) and a high content of repetitive regions. Gene expression mechanisms are poorly understood in these cultivars. An approach using genomic, transcriptomic and genetic mapping can improve our knowledge of the behavior of genetics in sugarcane.ResultsThe hypothetical HP600 and centromere protein C (CENP-C) genes from sugarcane were used to elucidate the allelic expression and genomic and genetic behavior of this complex polyploid. The genomically side-by-side genes HP600 and CENP-C were found in two different homeologous chromosome groups with ploidies of eight and ten. The first region (Region01) was a Sorghum bicolor ortholog with all haplotypes of HP600 and CENP- C expressed, but HP600 exhibited an unbalanced haplotype expression. The second region (Region02) was a scrambled sugarcane sequence formed from different noncollinear genes containing duplications of HP600 and CENP-C (paralogs). This duplication occurred before the Saccharum genus formation and after the separation of sorghum and sugarcane, resulting in a nonexpressed HP600 pseudogene and a recombined fusion version of CENP-C and orthologous gene Sobic.003G299500 with at least two chimerical gene haplotypes expressed. The genetic map construction supported the difficulty of mapping markers located in duplicated regions of complex polyploid genomes.ConclusionAll these findings describe a low synteny region in sugarcane, formed by events occurring in all members of the Saccharum genus. Additionally, evidence of duplicated and truncate gene expression and the behavior of genetic markers in a duplicated region was found. Thus, we describe the complexity involved in sugarcane genetics and genomics and allelic dynamics, which can be useful for understanding the complex polyploid genome.

EVIDENCIA DE LA ESTABILIDAD CARIOTÍPICA DURANTE LA DIVERGENCIA EVOLUTIVA ENTRE Paralabrax maculatofasciatus Y P. nebulifer (PERCIFORMES: SERRANIDAE)

La información sobre la estructura cromosómica es básica dentro del conocimiento biológico de cualquier especie y fundamental para la comprensión de fenómenos citogenéticos que subyacen a procesos fisiológicos, ontogénicos y evolutivos. En este último ámbito, el conocimiento del grado de similitud de los cromosomas de especies filogenéticamente cercanas complementa la información necesaria para plantear hipótesis causales sobre procesos de divergencia evolutiva. El objetivo del presente estudio fue determinar la similitud citogenética entre Paralabrax maculatofasciatus y P. nebulifer, especies filogenéticamente cercanas que se distribuyen en el Pacífico oriental, mediante la comparación del número, tipo y tamaño de los cromosomas. El examen de células mitóticas de eleuteroembriones en ambas especies mostró un cariotipo constituido por 48 cromosomas acrocéntricos (2n = 48A; número fundamental = 48), sin la presencia de cromosomas heteromórficos. No se detectaron diferencias significativas entre especies, tanto en el tamaño promedio, como en la longitud relativa (LR) de los pares cromosómicos homeólogos que presentaron un valor máximo de 4 μm (LR = 5.5 %; par 1) y un mínimo de 1.7 μm (LR = 2.3 %; par 24). Este cariotipo es considerado ancestral dentro del Orden Perciformes y está presente en la mayoría de las especies de la Familia Serranidae. Con base en estos resultados se sustenta la hipótesis de que la divergencia evolutiva entre P. maculatofasciatus y P. nebulifer se originó a través del establecimiento de barreras reproductivas precopulatorias sin alteración cariotípica ni formación de barreras postcopulatorias, tanto precigóticas como postcigóticas. Evidencen of karyotypic stasis during the evolutionary divergence between Paralabrax maculatofasciatus and P. nebulifer (Perciformes: Serranidae) Information on chromosome structure is basic within the biological knowledge of any species and fundamental to the understanding of the cytogenetic phenomena underlying physiological, ontogenic and evolutionary processes. Knowledge on the degree of similarity of chromosomes in phylogenetically close species supplements the necessary information to raise causal hypotheses on the processes of evolutionary divergence. The objective of this study was to determine the cytogenetic similarity between Paralabrax maculatofasciatus and P. nebulifer, closely (phylogenetically) related species distributed in the Eastern Pacific, by comparing number, type and size of chromosomes of these taxa. The examination of mitotic cells from eleutheroembryos of both species showed a karyotype consisting of 48 acrocentric chromosomes (2n = 48A; fundamental number = 48), without the presence of heteromorphic chromosomes. No significant differences between species were observed in size and relative length (RL) of homeologous chromosome pairs which showed maximum and minimum values of 4 μm (RL = 5.5 %; pair 1) and 1.7 μm (RL = 2.3 %; pair 24), respectively. This karyotype is considered ancestral within the Order Perciformes and is present in most of the species of the Family Serranidae. The results found in this study supported the hypothesis that evolutionary divergence between P. maculatofasciatus and P. nebulifer occurred through the establishment of pre-mating reproductive barriers, without karyotype modification or formation of post-mating barriers, either pre-zygotic or post-zygotic.

Identification of a 5S rDNA spacer type specific to Triticum urartu and wheats containing the T. urartu genome

A PCR system was designed to amplify 5S spacer rDNA specifically from homeologous chromosome 1 in a variety of species representative of the Aegilops and Triticum genera. Two polymerase chain reaction (PCR) primer combinations were used, one of which appears to be apomorphic in nature and specific to chromosome 1A in Triticum urartu and tetraploid and hexaploid wheats containing the AA genome donated by T. urartu. The value of studying single repeat types to investigate the molecular evolution of 5S-rDNA arrays is considered. Key words: 5S rDNA, polymerase chain reaction, Triticum, wheat.

Recognition of Homeology by the Wheat Ph1 Locus

Chromosome 1Am of Triticum monococcum is closely homeologous to T. aestivum chromosome 1A but recombines with it little in the presence of the wheat suppressor of homeologous chromosome pairing, Ph1. In the absence of Ph1, the two chromosomes recombine as if they were completely homologous. Chromosomes having either terminal or interstitial segments of chromosome 1Am in 1A were constructed and their recombination with 1A was investigated in the presence of Ph1. No recombination was detected in the homeologous (1Am/1A) segments, irrespective of whether terminally or interstitially positioned in a chromosome, whereas the levels of recombination in the juxtaposed homologous (1A/1A) segments was normal or close to normal relative to completely homologous 1A chromosomes. These observations show that Ph1 does not regulate chromosome pairing by premeiotic chromosome alignment and a mitotic spindle-centromere interaction, as has been suggested, but processes homology along the entire length of chromosomes.