Definition of the zebrafish genome using flow cytometry and cytogenetic mapping

<p>Abstract</p> <p>Background</p> <p>The zebrafish (<it>Danio rerio</it>) is an important vertebrate model organism system for biomedical research. The syntenic conservation between the zebrafish and human genome allows one to investigate the function of human genes using the zebrafish model. To facilitate analysis of the zebrafish genome, genetic maps have been constructed and sequence annotation of a reference zebrafish genome is ongoing. However, the duplicative nature of teleost genomes, including the zebrafish, complicates accurate assembly and annotation of a representative genome sequence. Cytogenetic approaches provide "anchors" that can be integrated with accumulating genomic data.</p> <p>Results</p> <p>Here, we cytogenetically define the zebrafish genome by first estimating the size of each linkage group (LG) chromosome using flow cytometry, followed by the cytogenetic mapping of 575 bacterial artificial chromosome (BAC) clones onto metaphase chromosomes. Of the 575 BAC clones, 544 clones localized to apparently unique chromosomal locations. 93.8% of these clones were assigned to a specific LG chromosome location using fluorescence <it>in situ </it>hybridization (FISH) and compared to the LG chromosome assignment reported in the zebrafish genome databases. Thirty-one BAC clones localized to multiple chromosomal locations in several different hybridization patterns. From these data, a refined second generation probe panel for each LG chromosome was also constructed.</p> <p>Conclusion</p> <p>The chromosomal mapping of the 575 large-insert DNA clones allows for these clones to be integrated into existing zebrafish mapping data. An accurately annotated zebrafish reference genome serves as a valuable resource for investigating the molecular basis of human diseases using zebrafish mutant models.</p

Research Note: Association of single nucleotide polymorphism of AKT3 with egg production traits in White Muscovy ducks (Cairina moschata).

Prior studies on transcriptomes of hypothalamus and ovary revealed that AKT3 is one of the candidate genes that might affect egg production in White Muscovy ducks. The role of AKT3 in the uterus during reproductive processes cannot be overemphasized. However, functional role of this gene in the tissues and on egg production traits of Muscovy ducks remains unknown. To identify the relationship between AKT3 and egg production traits in ducks, relative expression profile was first examined prior to identifying the variants within AKT3 that may underscore egg production traits [age at first egg (AFE), number of eggs at 300 d (N300D), and number of eggs at 59 wk (N59W)] in 549 ducks. The mRNA expression of AKT3 gene in high producing (HP) ducks was significantly higher than low producing (LP) ducks in the ovary, oviduct, and hypothalamus (P \u3c 0.05 or 0.001). Three variants in AKT3 (C-3631A, C-3766T, and C-3953T) and high linkage block between C-3766T and C-3953T which are significantly (P \u3c 0.05) associated with N300D and N59W were discovered. This study elucidates novel knowledge on the molecular mechanism of AKT3 that might be regulating egg production traits in Muscovy ducks

First record of Foulassi Screeching Frog, Arthroleptis adelphus (Perret, 1966) (Anura, Arthroleptidae, Arthroleptinae), from Nigeria, with notes on its phylogenetic position

We report the first known occurrence of the Foulassi Screeching Frog, Arthroleptis adelphus (Perret, 1966), from Nigeria. A specimen of A. adelphus was collected during herpetological survey work conducted in Cross River National Park, south-eastern Nigeria. Morphometrics and mitochondrial 16S rRNA gene confirm identity of the specimen. Matrilineal genealogy reveals a sister relationship of A. adelphus from Nigeria with individuals from south-western Cameroon. Genetic analysis further shows geographic structuring and divergence among populations of A. adelphus from the Guineo&amp;ndash;Congolian forest region. We offer updates to the IUCN geographic range of A. adelphus

The study of selection signature and its applications on identification of candidate genes using whole genome sequencing data in chicken—a review

ABSTRACT: Chicken is a major source of protein for the increasing human population and is useful for research purposes. There are almost 1,600 distinct regional breeds of chicken across the globe, among which a large body of genetic and phenotypic variations has been accumulated due to extensive natural and artificial selection. Moreover, natural selection is a crucial force for animal domestication. Several approaches have been adopted to detect selection signatures in different breeds of chicken using whole genome sequencing (WGS) data including integrated haplotype score (iHS), cross-populated extend haplotype homozygosity test (XP-EHH), fixation index (FST), cross-population composite likelihood ratio (XP-CLR), nucleotide diversity (Pi), and others. In addition, gene enrichment analyses are utilized to determine KEGG pathways and gene ontology (GO) terms related to traits of interest in chicken. Herein, we review different studies that have adopted diverse approaches to detect selection signatures in different breeds of chicken. This review systematically summarizes different findings on selection signatures and related candidate genes in chickens. Future studies could combine different selection signatures approaches to strengthen the quality of the results thereby providing more affirmative inference. This would further aid in deciphering the importance of selection in chicken conservation for the increasing human population

MULTIVARIATE ANALYSES OF DETERMINANTS OF EXOTIC DUCK ADOPTION IN SOUTH-WEST NIGERIA: IMPLICATION ON INDIGENOUS DUCK GENETIC RESOURCES

Poultry products contribute substantial proportion of animal protein consumed in Nigeria. These products are derived from both indigenous and exotic breeds of available species. The present study investigated the determinants of adoption of exotic ducks in south-west Nigeria through the application of classification regression tree (CRT) and binary logistic regression (BLR) model. Besides, the implication of adoption of improved breeds of duck on indigenous duck genetic resources was also considered. Multi-stage, stratified and cluster sampling methods were used to collect primary data from 524 respondents through structured questionnaires in three south-west states of Nigeria. About half (51.50%) of respondents indicated interest to adopt exotic ducks. In addition, the results of CRT (risk value = 33.6) and BLR (X2=0.727, P=0.197) were in consonance and both multivariate statistical techniques identified consumption of duck products followed by duck keeping as the principal determinants of exotic duck adopters among the respondents. The two principal indicators of potential exotic duck adopters could aid in guiding animal breeders, extension agents and stakeholders involved in animal agriculture in identifying potential adopter of exotic ducks in south-west Nigeria. Considering the expressed interest of the respondents to adopt improved breeds of ducks, this suggests the need for concerted effort of animal breeders and other stake holders involved in livestock production to guard against possible ‘genetic erosion’ of the valuable germplasm inherent in indigenous ducks via neglect through conservation

Definition of the zebrafish genome using flow cytometry and cytogenetic mapping-1

<p><b>Copyright information:</b></p><p>Taken from "Definition of the zebrafish genome using flow cytometry and cytogenetic mapping"</p><p>http://www.biomedcentral.com/1471-2164/8/195</p><p>BMC Genomics 2007;8():195-195.</p><p>Published online 27 Jun 2007</p><p>PMCID:PMC1925092.</p><p></p> syntenic with a previously mapped BAC clone probe, zK007C07, which localizes to the short arm (p arm) of LG chromosome 3, (labeled in orange, denoted by orange arrows). One BAC clone, zK110G19 (labeled in red), was observed to have two signals on the same chromosome, LG chromosome 4. The primary signal is on 4p with a secondary signal in the heterochromatic region of 4q. LG chromosome 4 is denoted by red arrows. Seventeen clones had signals on two non-homologous chromosomes. For example, zC211K08 (labeled in orange) localized to the p arm of LG chromosome 22 and to the q arm heterochromatic region of LG chromosome 4 (denoted by orange arrows). The near-telomeric marker for the q arm of LG chromosome 22, zC118M01, is labeled in green (denoted by green arrows) and the near-telomeric marker for the p arm of LG chromosome 4, zK030C13, is labeled in white (denoted by white arrows). Five BAC clones were pan-centromeric, such as zK171K22 (labeled in orange). Five BAC clones were peri-centromeric. For example, zK120I24 (labeled in orange) localized to the p arm and near the centromere of LG chromosome 7 (denoted by orange arrows), the p arm and near the centromere of an unknown chromosome, and near the centromere of multiple chromosomes. The near-telomeric marker for the q arm of LG chromosome 7, zC128L16, is labeled in green (denoted by green arrows)

Definition of the zebrafish genome using flow cytometry and cytogenetic mapping-0

<p><b>Copyright information:</b></p><p>Taken from "Definition of the zebrafish genome using flow cytometry and cytogenetic mapping"</p><p>http://www.biomedcentral.com/1471-2164/8/195</p><p>BMC Genomics 2007;8():195-195.</p><p>Published online 27 Jun 2007</p><p>PMCID:PMC1925092.</p><p></p>sh chromosomes. Flow-peaks contained in the oval represent the zebrafish chromosomes (see B for the chromosomal composition of each peak). The largest zebrafish LG chromosomes (5 and 7) were slightly larger than human chromosome 18 (76.12 Mb) and the smallest zebrafish LG chromosomes (22 and 25) were similar to the size of human chromosome 21 (46.94 Mb). Thus, human chromosomes 18 and 21 were chosen as references (labeled in the karyogram). A flow karyogram of the zebrafish chromosome preparation. LG chromosomes ranged in size from 42.2 to 77.9 Mb and the LG chromosomes composing each peak are denoted. The similarity of size resulted in only LG chromosomes 3, 4, and 24 separating into distinct peaks. The remaining nine peaks contained 2 to 5 chromosomes

Definition of the zebrafish genome using flow cytometry and cytogenetic mapping-2

<p><b>Copyright information:</b></p><p>Taken from "Definition of the zebrafish genome using flow cytometry and cytogenetic mapping"</p><p>http://www.biomedcentral.com/1471-2164/8/195</p><p>BMC Genomics 2007;8():195-195.</p><p>Published online 27 Jun 2007</p><p>PMCID:PMC1925092.</p><p></p>as observed to have only homozygous signals near the centromere of LG chromosome 3q. zK188H10, which consistently localized near the middle of LG chromosome 3p, is labeled in green. Three hybridization patterns were observed for zK167C09 in metaphase preparations from AB embryos including homozygous signals near the centromere of LG chromosome 3q, homozygous signals located medially on LG chromosome 3p, and a heterozygous state. The heterozygous pattern is depicted in this image with zK167C09 labeled in red and zK188H10, which consistently hybridized medially on LG chromosome 3p, labeled in green. White arrows denote LG chromosome 3 in and

Definition of the zebrafish genome using flow cytometry and cytogenetic mapping-3

<p><b>Copyright information:</b></p><p>Taken from "Definition of the zebrafish genome using flow cytometry and cytogenetic mapping"</p><p>http://www.biomedcentral.com/1471-2164/8/195</p><p>BMC Genomics 2007;8():195-195.</p><p>Published online 27 Jun 2007</p><p>PMCID:PMC1925092.</p><p></p>gion, which made finding a near-telomeric marker probe difficult for this chromosome arm. zC079A18 (labeled in orange) was established as a near-telomeric marker probe for the q arm of LG chromosome 4 (denoted by orange arrows). Also shown is the near-centromeric marker for LG chromosome 4, zC091G03, (labeled in white, denoted by white arrows) and BAC clone zC207E19, which localizes to the heterochromatic region of the long arm of LG chromosome 4 (labeled in green, denoted by green arrows)

Definition of the zebrafish genome using flow cytometry and cytogenetic mapping-4

<p><b>Copyright information:</b></p><p>Taken from "Definition of the zebrafish genome using flow cytometry and cytogenetic mapping"</p><p>http://www.biomedcentral.com/1471-2164/8/195</p><p>BMC Genomics 2007;8():195-195.</p><p>Published online 27 Jun 2007</p><p>PMCID:PMC1925092.</p><p></p>sh chromosomes. Flow-peaks contained in the oval represent the zebrafish chromosomes (see B for the chromosomal composition of each peak). The largest zebrafish LG chromosomes (5 and 7) were slightly larger than human chromosome 18 (76.12 Mb) and the smallest zebrafish LG chromosomes (22 and 25) were similar to the size of human chromosome 21 (46.94 Mb). Thus, human chromosomes 18 and 21 were chosen as references (labeled in the karyogram). A flow karyogram of the zebrafish chromosome preparation. LG chromosomes ranged in size from 42.2 to 77.9 Mb and the LG chromosomes composing each peak are denoted. The similarity of size resulted in only LG chromosomes 3, 4, and 24 separating into distinct peaks. The remaining nine peaks contained 2 to 5 chromosomes