Molecular cytogenetic resources for chromosome 4 and comparative analysis of phylogenetic chromosome IV in great apes

We have generated a panel of 55 somatic cell hybrids retaining fragments of human chromosome 4. Each hybrid has been characterized cytogenetically by FISH and molecularly by 37 STSs, evenly spaced along the chromosome. The panel can be exploited to map subregionally DNA sequences on chromosome 4 and to generate partial chromosome paints useful in the characterization of chromosomal rearrangements involving this chromosome. Furthermore, a panel of 84 YACs mapping on chromosome 4 has been characterized by FISH. A subset of this panel is recognized by STSs used in the somatic cell hybrid characterization. In this way a correlation between the genetic and the physical maps can be established. These resources have been used to investigate the conservation of the phylogenetic chromosome IV in great apes. The results indicate that all the pericentric inversions that differentiate chromosome IV in these species are distinct and that one of the breakpoints frequently lies very close to the centromere. In 4 instances, the YAC containing the breakpoint was identified. The breakpoint in IVq of PTR and MMU lies in the same YAC, suggesting that this breakpoint has been utilized twice in the evolutionary history of this chromosome.     

Harvest of red-legged partridge in central Spain

A basic rule to attain sustainable use of harvested resources is to adjust take to availability. Populations of red-legged partridges in Spain have decreased in recent decades, and releases of farm-bred partridges to improve short-term availability are increasingly common. We used questionnaires and bird surveys to assess whether harvest was related to availability of wild partridges or intensity of farm-bred partridge releases. We studied 50 hunting estates, including 6 administratively labeled as intensive (with few numerical and temporal restrictions to releases). In addition, we considered hunting pressure (number of hunters × hunting days/km²) and habitat as explanatory variables in the analyses. In intensive estates, annual harvest was exclusively related to release intensity, indicating that in these estates hunting is detached from natural resources and approaches an industrial activity based on external inputs. In non-intensive estates, harvest was affected by wild stock availability, walked-up shooting pressure, and habitat (greater harvest in estates with more Mediterranean shrubland). In these estates, releases did not increase annual harvest, and can be considered an inefficient practice. Additionally, the relationship between abundance estimates and harvest disappeared in estates with low partridge abundance estimates, suggesting possibilities for overharvesting in a large proportion of estates. Increasing the abundance of wild red-legged partridge through techniques like habitat management, and improving the adjustment of harvest to availability, may be a good strategy to increase long-term harvest in non-intensive estates. Additionally, Government and managers must create ways to segregate and label the estates where only wild red-legged partridges are managed from those where releases are used, to reduce ecological costs of management decisions. © 2012 The Wildlife Society.     

Sanitary risks of red-legged partridge releases: introduction of parasites

We studied the helminth community and body condition of 99 hunter-harvested red-legged partridges (Alectoris rufa) from Ciudad Real (Central Spain). Forty-six were sampled in two game estates where an important number of farm-reared red-legged partridges are released yearly. The remaining 53 were obtained from natural wild populations adjacent to one of the estates with releases. Four nematode species (Heterakis gallinarum, Aonchoteca caudinflata, Eucoleus contortus and Cheilospirura gruveli) and two cestode species (Raillietina (R.) tetragona and Skryabinia bolivari) were identified. The managed areas showed higher parasite diversity, with higher prevalences and intensities for all helminths found. Three of these species were typical of farm-bred partridges and two of these, A. caundinflata and S. bolivari, were found parasitizing adult partridges. This suggests introduction of these helminths into the breeding population of managed states. The birds sampled in the nonmanaged estates showed a better body condition, but no relation with parasite infection was found. Our results suggest that the release of farm-reared red-legged partridges, a strategy that is becoming a common practice in Spanish hunting areas, poses risk to wild populations because of introducing parasites. However, these results also suggest that simply stopping releases may be a good way to remove locally those parasites from populations, as the establishment of the introduced parasites seems limited.     

A comparative cytogenetic study of chromosome homology between chicken and Japanese quail

In order to construct a chicken (Gallus gallus) cytogenetic map, we isolated 134 genomic DNA clones as new cytogenetic markers from a chicken cosmid DNA library, and mapped these clones to chicken chromosomes by fluorescence in situ hybridization. Forty-five and 89 out of 134 clones were localized to macrochromosomes and microchromosomes, respectively. The 45 clones, which localized to chicken macrochromosomes (Chromosomes 1-8 and the Z chromosome) were used for comparative mapping of Japanese quail (Coturnix japonica). The chromosome locations of the DNA clones and their gene orders in Japanese quail were quite similar to those of chicken, while Japanese quail differed from chicken in chromosomes 1, 2, 4 and 8. We specified the breakpoints of pericentric inversions in chromosomes 1 and 2 by adding mapping data of 13 functional genes using chicken cDNA clones. The presence of a pericentric inversion was also confirmed in chromosome 8. We speculate that more than two rearrangements are contained in the centromeric region of chromosome 4. All 30 clones that mapped to chicken microchromosomes also localized to Japanese quail microchromosomes, suggesting that chromosome homology is highly conserved between chicken and Japanese quail and that few chromosome rearrangements occurred in the evolution of the two species.     

Daily variations of blood biochemical parameters in the red-legged partridge (Alectoris rufa)

The study of blood chemistry provides important information about many aspects of the biology and physiology of animals. It is known that many factors can influence the results of such analyses. A proper knowledge of these effects is necessary to correctly interpret the results. In this paper, we analyzed the daily variations of blood biochemical parameters of 32 captive red-legged partridges (Alectoris rufa) of both sexes to test the effect of the daily cycle on these parameters. We found daily variation in glucose, cholesterol, uric acid, triglycerides, and calcium, but not in total protein and creatinine. A sex effect was only significant in uric acid. The most reliable data were those obtained from blood samples collected in midday hours. Hence, this time is suggested for blood-sampling in future studies.     

Ectoparasite ticks and chewing lice of red-legged partridge,Alectoris rufa,in Spain

During the 1992-1993 and 1993-1994 shooting seasons, 212 wild red-legged partridge, Alectoris rufa (Galliformes: Phaisanide) were captured in 18 Spanish provinces and examined for chewing lice and ticks. Three tick species and six species of chewing lice were found. Ticks (Acari: Ixodidae) Haemaphysalis punctata Canestrini & Fanzago, Hyalomma lusitanicum Koch and Ixodes frontalis Panzer were found at the lowest prevalence (1.4% overall tick prevalence). The louse (Mallophaga) species, Goniodes dispar Burmeister (Goniodidae) (52.8%) and Cuclotogaster obscurior Hopkins (Philopteridae) (28.8%) were the most prevalent, while Goniocotes obscurus Giebel (Philopteridae) (10.8%), Menopon pallens Clay (Menoponidae) (7.5%) and Menacanthus lyali Rodriguez et al. (Menoponidae) (3.3%) were found at medium to low prevalence. Columbicola columbae columbae Linnaeus (Philopteridae) was found at the lowest prevalence (0.5%). The intensity of C. obscurior and overall intensity of all lice species were directly related to the environmental mean temperature and the Normalized Difference Vegetation Index (NDVI), whereas intensity of G. dispar was directly related to NDVI only. The intensity of G. dispar, C. obscurior, all louse intensity, and louse species richness were higher in male than female birds. Intensity of each louse species, all louse intensity and louse species richness were inversely associated with the nutritional index. No relationship was observed between bird age and louse intensity or species richness.     

Molecular cytogenetic investigation of chromosome composition and transmission in sugarcane

Modern sugarcane cultivars (Saccharum spp., 2n = 100–120) are complex polyploids derived from interspecific hybridization performed a century ago between the sugar-producing species S. officinarum L. and the wild species S. spontaneum L. Using genomic in situ hybridization, we revealed that between 15 and 27.5% of the genome of modern cultivars is derived from S. spontaneum, including 10–23% of entire chromosomes from this wild species and 8–13% chromosomes derived from interspecific recombination. We confirmed the occurrence of 2n + n transmission in crosses and first backcrosses between these two species and demonstrated that this also can occur in crosses between S. officinarum and modern cultivars. We analysed five S. officinarum clones with more than 80 chromosomes and demonstrated that they were derived from interspecific hybridization supporting the classical view that this species is characterized by 2n = 80. We also illustrated the complementarities between molecular cytogenetics and genetic mapping approaches for analysing complex genomes.     

Molecular cytogenetic assignment of genes to bovine chromosome 5

Seven genes were assigned by molecular cytogenetic methods to bovine chromosome 5. To accomplish this, specific primers were either publicly available or were designed from highly conserved regions of the publicly available mammalian gene sequences. The identity of the amplified segments was verified by sequencing and alignment with the published sequences. The optimized primers that amplified the desired bovine genes were used for screening a bovine bacterial artificial chromosome library. The positive clones were localized to a specific band of bovine chromosome 5 by fluorescence in situ hybridization. The genes HOXC4, SP1 and IGFBP6 were localized to band q21, COL2A1 was localized to bands q21-q23, IGF1 was localized to band q26, MB to band q31 and the gene CYP2D6 was localized to band q35. The cytogenetic assignment of SP1, IGFBP6, COL2A1, IGF1, MB and CYP2D6 is first reported here and the assignment of HOXC4 refines the previous assignment of this gene. The identification and localization of these genes further support the development of the human to bovine comparative map through characterizing the homologous segments conserved in the evolution of these species. This information will be useful for the future localization of genes that affect economically important traits in bovines.     

Chromosome homology between chicken (Gallus gallus domesticus) and the red-legged partridge (Alectoris rufa); evidence of the occurrence of a neocentromere during evolution

Chromosome-specific paints from macrochromosomes 1-9 and Z of the chicken were hybridised to metaphases of the red-legged partridge and revealed no inter-chromosomal rearrangements. The results from chromosome painting are similar to previous studies on the Japanese quail but different from findings in guinea fowl and several species of pheasant. The difference in centromere position in chicken and partridge chromosome 4, previously assumed to be the result of an inversion, was confirmed. However, FISH mapping of BAC clones from chicken chromosome 4 revealed that the order of loci was the same in both species, indicating the occurrence of a neocentromere during divergence.     

Molecular cytogenetic characterization of ring chromosome 4 in a female having a chromosomally normal child

We present the clinical and molecular findings of mosaic ring chromosome 4. The patient was referred to us for infertility and short stature. Results of three repeated cytogenetic analyses from lymphocytes showed a similar mosaic karyotype with multiple cell-lines [46,XX,r(4)/45,XX,-4/46,XX,dic r(4)/47,XX,r(4),+r(4)/46,XX]. FISH showed deletion of the 4p subtelomeric region and the 4q telomeric region from the ring chromosome 4. The breakpoints were mapped using molecular analysis. Parental karyotypes were normal. During the course of this study, the patient became pregnant without assisted reproductive technology. The result of amniocentesis performed at 16 weeks gestation showed a normal karyotype. Delivery was uncomplicated. This is the first report, to our knowledge, of the presence of ring chromosome 4 having various mosaic conditions in a female having a chromosomally normal fetus.     

Correlates of helminth community in the red-legged partridge (Alectoris rufa L.) in Spain

Between 1992 and 1996, 587 wild red-legged partridges (Alectoris rufa) from 16 Spanish provinces were examined to study the variations of helminth communities in this game species across a broad geographical area. The survey revealed 13 species of helminth parasites. Dicrocoelium sp.. Rhabdometra nigropunctata, and Cheilospirura gruweli were the most common species, whereas Raillietina bolivari, Choanotaenia infundibulum, Tetrameres sp., and Capillaria anatis were the most rare. Subulura suctoria, Heterakis gallinarum, Heterakis tenuicaudata, Capillaria contorta, Trichostrongylus tenuis, and Raillietina tetragona occurred with intermediate frequencies. The abundance of C. gruweli, S. suctoria, H. tenuicaudata, T. tenuis, and R. tetragona was inversely correlated to latitude and directly correlated to yearly mean temperature, whereas the abundance of Dicrocoelium sp. was directly correlated to latitude and inversely correlated to yearly mean temperature. The abundance of R. tetragona was inversely correlated to latitude and yearly mean humidity. The number of helminths per partridge and the number of helminth species per partridge were lower in young birds than in adults. Partridge body condition was inversely correlated to abundance of C. contorta. Richer infracommunities were linked to richer component communities. At the infracommunity level, total number of helminths per partridge and number of helminth species per partridge were inversely correlated to latitude and directly correlated to yearly mean temperature. At the component community level, both species richness and diversity (Simpson's index) were inversely correlated to latitude and directly correlated to mean temperature. Across the broad geographical range of the study area, the helminth parasite communities of red-legged partridges had marked geographical variation in their structure. Our results suggest that this variation is determined by the distribution of both intermediate and definitive hosts. We discuss the implications of this variation for the hypothesis that supplementary releases of captive-bred partridges for sport hunting can affect the helminth fauna of wild red-legged partridges.     

Predation of simulated red-legged partridge nests in big game estates from South Central Spain

Over the past few decades, the wild boar has been undergoing an expansion in Europe, which may have negatively affected small game populations and particularly red-legged partridges. We aim to evaluate the red-legged partridge nest predation by wild boar at high boar abundances by placing artificial nests in nine big game estates. Predation rates were compared between nests placed in fenced controlled plots with no wild boar access (but accessible to other predators) and open plots in which the wild boar gains access. The proportion of nests and eggs predated was significantly lower in wild boar exclusion areas, recording a predation rate of 50 % for the nests and 38 % for the eggs in these areas, whereas in the presence of wild boar, the predation rate was 80 % for the nests and 58 % for the eggs. Moreover, the wild boar was identified as the main nest predator in unfenced areas, accounting for 36 and 48 % of the predated nests and eggs respectively. This study sheds light on the wild boar predation on nests of the red-legged partridges.     

Molecular cytogenetic definition of the chicken genome: the first complete avian karyotype

Chicken genome mapping is important for a range of scientific disciplines. The ability to distinguish chromosomes of the chicken and other birds is thus a priority. Here we describe the molecular cytogenetic characterization of each chicken chromosome using chromosome painting and mapping of individual clones by FISH. Where possible, we have assigned the chromosomes to known linkage groups. We propose, on the basis of size, that the NOR chromosome is approximately the size of chromosome 22; however, we suggest that its original assignment of 16 should be retained. We also suggest a definitive chromosome classification system and propose that the probes developed here will find wide utility in the fields of developmental biology, DT40 studies, agriculture, vertebrate genome organization, and comparative mapping of avian species.     

The effects of fasting and refeeding on biochemical parameters in the red-legged partridge (Alectoris rufa)

Every year, about three million farm-reared red-legged partridges are released in Spain for hunting purposes, most of them for restocking where the success is very low. Some factors such as the sudden shift from abundant commercial energy-rich diet to natural food and absence of experience at looking for natural food resources could cause a rapid physical deterioration, being more vulnerable to predation and disease. To determine fasting capacity in red-legged partridges, we fasted 32 birds during 4 days and then we refed them, collecting blood samples and body masses during the experiment. Red-legged partridges entered in the third critic phase of fasting, in which body proteins became the main energetic source, after 48 h of fasting. The fasting period caused an average loss of 17% of their initial body mass and only attained a 93.6% of their initial body mass after 24 days of refeeding. The limited capacity to resist fasting in the red-legged partridge could be one of the reasons for the low success in restocking, mainly in those where neither supplementary feeding nor acclimation period is allowed for birds before they are finally released.     

Molecular cytogenetic analysis reveals the existence of two independent neo-XY sex chromosome systems in Anatolian Pamphagidae grasshoppers

Background

Neo-XY sex chromosome determination is a rare event in short horned grasshoppers, but it appears with unusual frequency in the Pamphagidae family. The neo-Y chromosomes found in several species appear to have undergone heterochromatinization and degradation, but this subject needs to be analyzed in other Pamphagidae species. We perform here karyotyping and molecular cytogenetic analyses in 12 Pamphagidae species from the center of biodiversity of this group in the previously-unstudied Anatolian plateau.

Results

The basal karyotype for the Pamphagidae family, consisting of 18 acrocentric autosomes and an acrocentric X chromosome (2n♂?=?19, X0; 2n♀?=?20, XX), was found only in G. adaliae. The karyotype of all other studied species consisted of 16 acrocentric autosomes and a neo-XY sex chromosome system (2n♂♀?=?18, neo-XX♀/neo-XY♂). Two different types of neo-Y chromosomes were found. One of them was typical for three species of the Glyphotmethis genus, and showed a neo-Y chromosome being similar in size to the XR arm of the neo-X, with the addition of two small subproximal interstitial C-blocks. The second type of the neo-Y chromosome was smaller and more heterochromatinized than the XR arm, and was typical for all Nocarodeini species studied. The chromosome distribution of C-positive regions and clusters of ribosomal DNA (rDNA) and telomeric repeats yielded additional information on evolution of these neo-XY systems.

Conclusion

Most Pamphagidae species in the Anatolian region were found to have neo-XY sex chromosome systems, belonging to two different evolutionary lineages, marked by independent X-autosome fusion events occurred within the Trinchinae and Pamphaginae subfamilies. The high density of species carrying neo-XY systems in the Anatolian region, and the different evolutionary stage for the two lineages found, one being older than the other, indicates that this region has a long history of neo-XY sex chromosome formation.

     

Parasites, condition, immune responsiveness and carotenoid-based ornamentation in male red-legged partridge Alectoris rufa

Sexual ornaments might indicate better condition, fewer parasites or a greater immune responsiveness. Carotenoid-based ornaments are common sexual signals of birds and often influence mate choice. Skin or beaks pigmented by carotenoids can change colour rapidly, and could be particularly useful as honest indicators of an individual's current condition and/or health. This is because carotenoids must be acquired through diet and/or allocation for ornamental coloration might be to the detriment of self-maintenance needs. Here, we investigated whether the carotenoid-based coloration of eye rings and beak of male red-legged partridges Alectoris rufa predicted condition (mass corrected for size), parasite load (more specifically infection by coccidia, a main avian intestinal parasite) or a greater immune responsiveness (swelling response to a plant lectin, phytohaemagluttinin, or PHA). Redness of beak and eye rings positively correlated with plasma carotenoid levels. Also, males in better condition had fewer coccidia, more circulating carotenoids and a greater swelling response to PHA. Carotenoid-based ornamentation predicted coccidia abundance and immune responsiveness (redder males had fewer coccidia and greater swelling response to PHA), but was only weakly positively related to condition. Thus, the carotenoid pigmentation of beak and eye rings reflected the current health status of individuals. Our results are consistent with the hypothesis that allocation trade-offs (carotenoid use for ornamentation versus parasite defence needs) might ensure reliable carotenoid-based signalling.     

Molecular cytogenetic characterization of Roegneria ciliaris chromosome additions in common wheat

The development of alien addition lines is important both for transferring useful genes from related species into common wheat and for studying the relationship between alien chromosomes and those of wheat. Roegneria ciliaris (2n=4x=28, S^cS^cY^cY^c) is reported to be a potential source of resistance to wheat scab, which may be useful in wheat improvement. The amphiploid common wheat-R. ciliaris and BC₁F₇ or BC₂F₆ derivatives were screened by C-banding, genomic in situ hybridization (GISH), fluorescent in situ hybridization (FISH) and restriction fragment length polymorphism (RFLP) for the presence of R. ciliaris chromatin introgressed into wheat. Six lines were identified as disomic chromosome additions (DA), one as a ditelosomic addition (Dt), two as double disomic additions (dDA) and one as a monosomic chromosome addition (MA). RFLP analysis using wheat homoeologous group-specific clones indicated that the R. ciliaris chromosomes involved in these lines belong to groups 1, 2, 3, 5 and 7. The genomic affinities of the added R. ciliaris chromosomes were determined by FISH analysis using the repetitive sequence pCbTaq4.14 as a probe. These data suggest that the R. ciliaris chromosomes in five lines belong to the S^c genome. Based on the molecular cytogenetic data, the lines are designated as DA2S^c#1, Dt2S^c#1L, DA3S^c#1, dDA1S^c#2+5Y^c#1, DA5Y^c#1, DA7S^c#1, DA7Y^c#1 and MA?Y^c#1. Based on the present and previous work, 8 of the 14 chromosomes of R. ciliaris have been transferred into wheat.     

Molecular cytogenetic evidence of rearrangements on the Y chromosome of the threespine stickleback fish

To identify the processes shaping vertebrate sex chromosomes during the early stages of their evolution, it is necessary to study systems in which genetic sex determination was recently acquired. Previous cytogenetic studies suggested that threespine stickleback fish (Gasterosteus aculeatus) do not have a heteromorphic sex chromosome pair, although recent genetic studies found evidence of an XY genetic sex-determination system. Using fluorescence in situ hybridization (FISH), we report that the threespine stickleback Y chromosome is heteromorphic and has suffered both inversions and deletion. Using the FISH data, we reconstruct the rearrangements that have led to the current physical state of the threespine stickleback Y chromosome. These data demonstrate that the threespine Y is more degenerate than previously thought, suggesting that the process of sex chromosome evolution can occur rapidly following acquisition of a sex-determining region.     

Molecular cytogenetic analysis of eight inversion duplications of human chromosome 13q that each contain a neocentromere

Neocentromeres are fully functional centromeres that have arisen in previously noncentromeric chromosomal locations on rearranged chromosomes. The formation of neocentromeres results in the mitotic stability of chromosomal fragments that do not contain endogenous centromeres and that would normally be lost. Here we describe a unique collection of eight independent patient-derived cell lines, each of which contains a neocentromere on a supernumerary inversion duplication of a portion of human chromosome 13q. Findings in these patients reveal insight into the clinical manifestations associated with polysomy for portions of chromosome 13q. The results of FISH and immunofluorescent analysis of the neocentromeres in these chromosomes confirm the lack of alpha-satellite DNA and the presence of CENtromere proteins (CENP)-C, -E, and hMAD2. The positions of the inversion breakpoints in these chromosomes have been placed onto the physical map of chromosome 13, by means of FISH mapping with cosmid probes. These cell lines define, within chromosome 13q, at least three distinct locations where neocentromeres have formed, with five independent neocentromeres in band 13q32, two in band 13q21, and one in band 13q31. The results of examination of the set of 40 neocentromere-containing chromosomes that have thus far been described, including the 8 neocentromere-containing chromosomes from chromosome 13q that are described in the present study, suggest that chromosome 13q has an increased propensity for neocentromere formation, relative to some other human chromosomes. These neocentromeres will provide the means for testing hypotheses about sequence requirements for human centromere formation.     

Molecular and cytogenetic characterization of radiation hybrids specific for human chromosome 16.

Two hundred and twenty-three radiation hybrids retaining random fragments of human chromosome 16 were isolated during two successive experiments in HAT medium and screened with a total of 38 DNA probes, corresponding to anonymous DNA or gene sequences localized on chromosome 16. The presence of single or multiple human chromosomal fragments in a small subset of these hybrids was determined using in situ hybridization with total human DNA. The results confirm that individual radiation hybrids are often heterogeneous with respect to the retention and distribution of human fragments, as already suggested by their characterization with DNA probes. A number of these 223 radiation hybrids, whose detailed characterization has not been previously reported, represent a resource for the rapid isolation of new DNA markers or coding sequences from specific regions of chromosome 16 where human disease genes are already known to map.