Crossing over in the oogenesis of Gallus gallus domesticus chickens: periodicity in the distribution of chiasmata over the length of chromosomes

The periodic occurrence of chiasmata was studied in lampbrush chromosomes of the chicken (Gallus gallus domesticus). It was shown that the most probable interference distance in chicken macrobivalents 1-3 corresponded to 24.48 Mb. The distance at which absolute interference is observed in chicken macrochromosomes varies from 5.75 to 9.02 Mb.     

Estimation of the Minimal Size of Chicken Gallus gallus domesticusMicrochromosomes via Pulsed-Field Electrophoresis

The karyotype of the chicken Gallus gallus domesticuswas studied by means of pulsed-field electrophoresis. An electrokaryogram was obtained for the microchromosomal (MI) portion of the chicken genome. Chicken MIs were separated into two fractions. A fraction with a higher mobility included MIs sized 3.4–4.8 Mb; the lower size limit of a less mobile fraction corresponded to MIs of approximately 5 Mb. The smallest MI in the chicken karyotype was estimated at 3.4 ±0.25 Mb.     

Determination of the minimum size of Gallus gallus domesticus chicken microchromosome by a pulse electrophoresis method]

The karyotype of the chicken Gallus gallus domesticus was studied by means of pulsed-field electrophoresis. An electrokaryogram was obtained for the microchromosomal (MI) portion of the chicken genome. Chicken MIs were separated into two fractions. A fraction with a higher mobility included MIs sized 3.4-4.8 Mb; the lower size limit of a less mobile fraction corresponded to MIs of approximately 5 Mb. The smallest MI in the chicken karyotype was estimated at 3.4 +/- 0.25 Mb.     

Variation in the ratio of physical to genetic distance in intervals adjacent to theMla locus on barley chromosome 1H

Variants of the pulsed-field gel electrophoresis technique were used in conjunction with two-dimensional DNA gel electrophoresis (2-DDGE) to determine the ratio of physical to genetic distance in two genetically defined intervals on barley chromosome 1H.2-DDGE analysis demonstrated that two loci that define a 0.3 cM interval, as determined by hybridization with BCD249, reside on a single 450-kbMluI fragment. This result indicates a maximum ratio of physical to genetic distance in this interval of 1500 kb/cM as compared to 3.7–4.2 Mb/cM for the barley genome as a whole. High molecular weight (HMW) DNA restricted withNotI and probed sequentially with MWG068 and BCD249 yield diffuse bands at approximately 2.8 Mb and 3.0 Mb in the C.I. 16151 and C.I. 16155 parental lines, respectively. These results suggest the maximum ratio of physical to genetic distance in the interval defined by these probes is 7.8 Mb/cM. unique HMW DNA restriction fragment length polymorphisms (RFLP) were attributed to the presence of recombination breakpoints. Data from the recombination breakpoint analysis were used to estimate a ratio of physical to genetic distance of 2.5 Mb/cM in theXbcd249.2-Xmwg068 interval and 0.465 Mb/cM in theXbcd249.1-Xbcd249.2 interval. Both physical linkage and recombination breakpoint analysis indicate theXbcd249.1-Xbcd249.2 interval is approximately five-fold smaller, physically, than theXbcd249.2-Xmwg068 interval.     

Crossover interference underlies sex differences in recombination rates

In many organisms, recombination rates differ between the two sexes. Here we show that in mice, this is because of a shorter genomic interference distance in females than in males, measured in Mb. However, the interference distance is the same in terms of bivalent length. We propose a model in which the interference distance in the two sexes reflects the compaction of chromosomes at the pachytene stage of meiosis.     

A compact cartilaginous fish model genome

The genomes of several vertebrates, including six mammals, the chicken, Xenopus and four ray-finned fishes have been sequenced or are currently being sequenced to provide a better understanding of the human genome through comparative analysis. However, this list does not include cartilaginous fishes, which are the most basal living jawed vertebrates [1]. The genomes of the current ‘popular’ cartilaginous fishes such as the nurse shark, dogfish, and horn shark are larger than the human genome (∼3800 Mb to 7000 Mb) [2], and are not attractive for whole-genome sequencing. Here, we report the characterization of the relatively small genome (1200 Mb) of a cartilaginous fish, the elephant fish (Callorhinchus milii), and propose it as a model for whole-genome sequencing.     

A high‐density linkage map enables a second‐generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution

Detailed linkage and recombination rate maps are necessary to use the full potential of genome sequencing and population genomic analyses. We used a custom collared flycatcher 50 K SNP array to develop a high‐density linkage map with 37 262 markers assigned to 34 linkage groups in 33 autosomes and the Z chromosome. The best‐order map contained 4215 markers, with a total distance of 3132 cM and a mean genetic distance between markers of 0.12 cM . Facilitated by the array being designed to include markers from most scaffolds, we obtained a second‐generation assembly of the flycatcher genome that approaches full chromosome sequences (N50 super‐scaffold size 20.2 Mb and with 1.042 Gb (of 1.116 Gb) anchored to and mostly ordered and oriented along chromosomes). We found that flycatcher and zebra finch chromosomes are entirely syntenic but that inversions at mean rates of 1.5–2.0 event (6.6–7.5 Mb) per My have changed the organization within chromosomes, rates high enough for inversions to potentially have been involved with many speciation events during avian evolution. The mean recombination rate was 3.1 cM /Mb and correlated closely with chromosome size, from 2 cM /Mb for chromosomes >100 Mb to >10 cM /Mb for chromosomes <10 Mb. This size dependence seemed entirely due to an obligate recombination event per chromosome; if 50 cM was subtracted from the genetic lengths of chromosomes, the rate per physical unit DNA was constant across chromosomes. Flycatcher recombination rate showed similar variation along chromosomes as chicken but lacked the large interior recombination deserts characteristic of zebra finch chromosomes.     

Draft Genome Sequence of Lactobacillus gigeriorum CRBIP 24.85T,Isolated from a Chicken Crop

We report the draft genome of the strain Lactobacillus gigeriorum CRBIP 24.85^T, isolated from a chicken crop. The total length of the 60 scaffolds is about 1.9 Mb, with a GC content of 38% and 2,062 protein-coding sequences (CDS).     

A radiation hybrid map of chicken chromosome 15

We have constructed a radiation hybrid (RH) map of chicken chromosome (GGA) 15. This map can be used as a resource to efficiently map genes to this chromosome. The map has been developed using a 6000 rad chicken-hamster whole-genome radiation hybrid panel (ChickRH6). In total, six microsatellite loci, 18 sequence tagged sites (STSs) from BAC end sequences and 11 genes were typed on the panel. The initial framework map comprised eight markers, and an additional 23 markers were then added to generate the final map. The total map length was 334 centiRay6000 (cR6000). The estimated retention frequency for the data set was 18%. Using an estimated physical length of 21 Mb, the ratio between cR6000 and physical distance over GGA15 was estimated to be 0.063 Mb/cR6000. The present map increases the marker density and the marker resolution on GGA15 and enables fast mapping of new chicken genes homologous to genes from human chromosomes 12 and 22.     

Lampbrush Chromosomes in the Japanese Quail Coturnix coturnix japonica: Cytological Map of Macrochromosomes and Meiotic Crossing-over Frequency in Females

Cytological map of lampbrush macrobivalents of the Japanese quail (Coturnix coturnix japonica) were constructed. Investigation of chiasmata allowed to estimate the frequency of reciprocal genetic recombination (crossing over) in Japanese quail female meiosis. The total chiasma number in bivalents of Japanese quail oocyte nuclei was determined to be 53–58. Macrobivalents 1–5 and Z of the Japanese quail had on average 3.3 chiasmata per bivalent, and microbivalents, 1.0–1.1 chiasmata per bivalent. The chiasmata (crossover) frequency in Japanese quail females was lower than in chicken. In macrochromosomes of Japanese quail females, one crossover occurred per 43.9 Mb, and in chicken, per 30.0 Mb. Judging from chiasma frequency, the genetic length of the Japanese quail genome is likely to be 2650–2900 cM. Crossover frequency in the species was 0.023 per Mb in macrobivalents and 0.07–0.08 Mb in microbivalents and for the total genome, 0.041 crossing over per Mb. The genetic length of one Mb (recombination rate ) in female Japanese quails was 1.14 cM in macrochromosomes, 3.60–4.12 cM in microchromosomes, and about 1.96–2.15 cM averaged over the genome.     

Reducing the interval of a growth QTL on chromosome 4 in laying hens

In our previous research, we identified a QTL with an interval of 3.4 Mb for growth on chicken chromosome (GGA) 4 in an advanced intercross population of an initial cross between the New Hampshire inbred line (NHI) and the White Leghorn inbred line (WL77). In the current study, an association analysis was performed in a population of purebred white layers (WLA) with White Leghorn origin. Genotypic data of 130 SNPs within the previously identified 3.4‐Mb region were obtained using a 60K SNP chip. In total, 24 significant SNPs (LOD ≥ 4.44) on GGA4 were detected for daily weigh gain from 8 to 14 weeks and two SNPs (LOD ≥ 4.80) for body weight at 14 weeks. The QTL interval was reduced by 1.9 Mb to an interval of 1.5 Mb (74.6–76.1 Mb) that harbors 15 genes. Furthermore, to identify additional loci for chicken growth, a genome‐wide association study (GWAS) was carried out in a WLA population. The GWAS identified an additional QTL on GGA6 for body weight at six weeks (19.8–21.2 Mb). Our findings showed that by using a WLA population we were able to further reduce the QTL confidence interval previously detected using a NHI × WL77 advanced intercross population.     

The chicken (Gallus gallus) Z chromosome contains at least three nonlinear evolutionary strata

Birds have female heterogamety with Z and W sex chromosomes. These evolved from different autosomal precursor chromosomes than the mammalian X and Y. However, previous work has suggested that the pattern and process of sex chromosome evolution show many similarities across distantly related organisms. Here we show that stepwise restriction of recombination between the protosex chromosomes of birds has resulted in regions of the chicken Z chromosome showing discrete levels of divergence from W homologs (gametologs). The 12 genes analyzed fall into three levels of estimated divergence values, with the most recent divergence (d_S = 0.18–0.21) displayed by 6 genes in a region on the Z chromosome corresponding to the interval 1–11 Mb of the assembled genome sequence. Another 4 genes show intermediate divergence (d_S = 0.27–0.38) and are located in the interval 16–53 Mb. Two genes (at positions 42 and 50 Mb) with higher d_S values are located proximal to the most distal of the 4 genes with intermediate divergence, suggesting an inversion event. The distribution of genes and their divergence indicate at least three evolutionary strata, with estimated times for cessation of recombination between Z and W of 132–150 (stratum 1), 71–99 (stratum 2), and 47–57 (stratum 3) million years ago. An inversion event, or some other form of intrachromosomal rearrangement, subsequent to the formation of strata 1 and 2 has scrambled the gene order to give rise to the nonlinear arrangement of evolutionary strata currently seen on the chicken Z chromosome. These observations suggest that the progressive restriction of recombination is an integral feature of sex chromosome evolution and occurs also in systems of female heterogamety.     

Molecular analysis of irradiation-induced and spontaneous deletion mutants at a disease resistance locus inLactuca sativa

The major cluster of disease resistance genes in lettuce (Lactuca sativa) contains at least nine downy mildew resistance genes (Dm) spanning a genetic distance of 20 cM and a physical distance of at least 6 Mb. Nine molecular markers that were genetically tightly linked toDm3 were used to analyze nine independent deletion mutants and construct a map of the region surroundingDm3. This analysis identified a linear order of deletion breakpoints and markers along the chromosome. There was no evidence for chromosomal rearrangements associated with the deletions. The region is not highly recombinagenic and the deletion breakpoints provided greater genetic resolution than meiotic recombinants. The region contains a mixture of high- and low-copy-number sequences; no single-copy sequences were detected. Three markers hybridized to low-copy-number families of sequences that are duplicated predominantly close toDm3. This was not true for sequences related to the triose-phosphate isomerase gene; these had been shown previously to be linked toDm3, as well as to two independent clusters ofDm genes, and elsewhere in the genome. Two spontaneous mutants ofDm3 were identified; several markers flankingDm3 are absent in one of these two mutants. The stability of theDm3 region was also studied by analyzing the genotypes of diverse related cultivars. The 1.5 Mb region surroundingDm3 has remained stable through many generations of breeding with and without selection forDm3 activity.     

Chromosome-level genome assembly of Japanese chestnut (Castanea crenata Sieb. et Zucc.) reveals conserved chromosomal segments in woody rosids

Japanese chestnut (Castanea crenata Sieb. et Zucc.), unlike other Castanea species, is resistant to most diseases and wasps. However, genomic data of Japanese chestnut that could be used to determine its biotic stress resistance mechanisms have not been reported to date. In this study, we employed long-read sequencing and genetic mapping to generate genome sequences of Japanese chestnut at the chromosome level. Long reads (47.7 Gb; 71.6× genome coverage) were assembled into 781 contigs, with a total length of 721.2 Mb and a contig N50 length of 1.6 Mb. Genome sequences were anchored to the chestnut genetic map, comprising 14,973 single nucleotide polymorphisms (SNPs) and covering 1,807.8 cM map distance, to establish a chromosome-level genome assembly (683.8 Mb), with 69,980 potential protein-encoding genes and 425.5 Mb repetitive sequences. Furthermore, comparative genome structure analysis revealed that Japanese chestnut shares conserved chromosomal segments with woody plants, but not with herbaceous plants, of rosids. Overall, the genome sequence data of Japanese chestnut generated in this study is expected to enhance not only its genetics and genomics but also the evolutionary genomics of woody rosids.     

Identification and functional characterization of copy number variations in diverse chicken breeds

Background

The detection and functional characterization of genomic structural variations are important for understanding the landscape of genetic variation in the chicken. A recently recognized aspect of genomic structural variation, called copy number variation (CNV), is gaining interest in chicken genomic studies. The aim of the present study was to investigate the pattern and functional characterization of CNVs in five characteristic chicken breeds, which will be important for future studies associating phenotype with chicken genome architecture.

Results

Using a commercial 385 K array-based comparative genomic hybridization (aCGH) genome array, we performed CNV discovery using 10 chicken samples from four local Chinese breeds and the French breed Houdan chicken. The female Anka broiler was used as a reference. A total of 281 copy number variation regions (CNVR) were identified, covering 12.8 Mb of polymorphic sequences or 1.07% of the entire chicken genome. The functional annotation of CNVRs indicated that these regions completely or partially overlapped with 231 genes and 1032 quantitative traits loci, suggesting these CNVs have important functions and might be promising resources for exploring differences among various breeds. In addition, we employed quantitative PCR (qPCR) to further validate several copy number variable genes, such as prolactin receptor, endothelin 3 (EDN3), suppressor of cytokine signaling 2, CD8a molecule, with important functions, and the results suggested that EDN3 might be a molecular marker for the selection of dark skin color in poultry production. Moreover, we also identified a new CNVR (chr24: 3484617–3512275), encoding the sortilin-related receptor gene, with copy number changes in only black-bone chicken.

Conclusions

Here, we report a genome-wide analysis of the CNVs in five chicken breeds using aCGH. The association between EDN3 and melanoblast proliferation was further confirmed using qPCR. These results provide additional information for understanding genomic variation and related phenotypic characteristics.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-934) contains supplementary material, which is available to authorized users.     

Self Crowding of Globular Proteins Studied by Small-Angle X-Ray Scattering

Small-angle x-ray scattering (SAXS) was used to study the behavior of equine metmyoglobin (Mb) and bovine pancreatic trypsin inhibitor (BPTI) at concentrations up to 0.4 and 0.15 g/mL, respectively, in solutions also containing 50% D₂O and 1 M urea. For both proteins, significant effects because of interference between x-rays scattered by different molecules (interparticle interference) were observed, indicating nonideal behavior at high concentrations. The experimental data were analyzed by comparison of the observed scattering profiles with those predicted by crystal structures of the proteins and a hard-sphere fluid model used to represent steric exclusion effects. The Mb scattering data were well fit by the hard-sphere model using a sphere radius of 18 Å, only slightly smaller than that estimated from the three-dimensional structure (20 Å). In contrast, the scattering profiles for BPTI in phosphate buffer displayed substantially less pronounced interparticle interference than predicted by the hard-sphere model and the radius estimated from the known structure of the protein (15 Å). Replacing the phosphate buffer with 3-(N-morpolino)propane sulfonic acid (MOPS) led to increased interparticle interference, consistent with a larger effective radius and suggesting that phosphate ions may mediate attractive intermolecular interactions, as observed in some BPTI crystal structures, without the formation of stable oligomers. The scattering data were also used to estimate second virial coefficients for the two proteins: 2.0 ×10^-4 cm³mol/g² for Mb in phosphate buffer, 1.6 ×10^-4 cm³mol/g² for BPTI in phosphate buffer and 9.2 ×10^-4 cm³mol/g² for BPTI in MOPS. The results indicate that the behavior of Mb, which is nearly isoelectric under the conditions used, is well described by the hard-sphere model, but that of BPTI is considerably more complex and is likely influenced by both repulsive and attractive electrostatic interactions. The hard-sphere model may be a generally useful tool for the analysis of small-angle scattering data from concentrated macromolecular solutions.     

A meiotically reproducible chromosome length polymorphism in the ascomycete fungus Ophiostoma ulmi (sensu lato)

We have followed the transmission of Ophiostoma ulmis.l. chromosome length polymorphisms (CLPs) into the F₂ generation to determine the reproducibility of a genome rearrangement culminating in the conversion of a 1.0 Mb chromosome into a 800 kb chromosome. The 1.0 Mb chromosome in strain CESS16K is thus far unique among O. ulmi s.l. wild-type strains, as no other wild-type strains have been observed with chromosomes smaller than 2.3 Mb. It has been previously shown that the 1.0 Mb chromosome is mitotically stable, carries at least one normally expressed gene, and is transmitted through meiosis. In this study, a series of crosses were performed to further elucidate the pattern of inheritance of the 1.0 Mb chromosome and the process of conversion of the 1.0 Mb species to 800 kb. In crosses where the 1.0 Mb chromosome was allowed to pair with itself or with the 800 kb chromosome, all progeny inherited a copy of the 1.0 Mb or 800 kb form, further demonstrating the A-type nature of these small chromosomes. When a cross was repeated between the strains CESS16K (1.0 Mb chromosome) and FG245B^r-O (no 1.0 Mb or 800 kb chromosome), the occurrence of a 800 kb chromosome was observed in 9% of the progeny. A reciprocal cross between an 800 kb strain and a strain with no 800 kb or 1.0 Mb chromosome was conducted, and a progeny strain containing a 1.0 Mb chromosome was recovered. The reproducibility and reciprocality of the 1.0 Mb to 800 kb chromosome conversion demonstrates that meiotic processes are responsible for this CLP, and that O. ulmi s.l. strains with various divergent genome architectures can remain sexually compatible.     

Maximum likelihood estimation of linkage and interference from tetrad data

Maximum likelihood equations have been derived for estimation of map distance and interference from two-point and ranked tetrad data. The estimators have been applied to data from Saccharomyces cerevisiae and Schizosaccharomyces pombe. S. cerevisiae consistently shows quite strong interference over the mapped genome. In striking contrast, S. pombe consistently shows much weaker interference and many crosses exhibit negative interference. In neither species was there a conspicuous tendency for intervals spanning a centromere to show less interference than those that did not. Since the amount of recombination per microgram of DNA in the two species is similar, the difference in interference characteristics seems to be a reflection of some fundamental difference in the recombination process of the two species.