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Romanov M, Sazanov A, Smirnov A. First century of chicken gene study and mapping – a look back and forward. WORLD POULTRY SCI J 2019. [DOI: 10.1079/wps20032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- M.N. Romanov
- Department of Microbiology and Molecular Genetics, 2209 Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824–4320, USA
| | - A.A. Sazanov
- All-Russian Institute of Animal Genetics and Breeding, Russian Academy of Agricultural Science, Moskovskoye shosse 55A, St Petersburg – Pushkin 189620, Russia
- Biological Research Institute, St Petersburg State University, Oranienbaumskoye shosse 2, St Petersburg – Stary Petergof 198504, Russia
| | - A.F. Smirnov
- All-Russian Institute of Animal Genetics and Breeding, Russian Academy of Agricultural Science, Moskovskoye shosse 55A, St Petersburg – Pushkin 189620, Russia
- Biological Research Institute, St Petersburg State University, Oranienbaumskoye shosse 2, St Petersburg – Stary Petergof 198504, Russia
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2
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Darris CE, Tyus JE, Kelley G, Ropelewski AJ, Nicholas HB, Wang X, Nahashon S. Molecular tools to support metabolic and immune function research in the Guinea Fowl (Numida meleagris). BMC Genomics 2015; 16:358. [PMID: 25948401 PMCID: PMC4432510 DOI: 10.1186/s12864-015-1520-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/10/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Guinea fowl (Numidia meleagris) production as an alternative source of meat and poultry has shown potential for economic viability. However, there has been little progress in characterizing the transcriptome of the guinea fowl. In this study RNA-sequencing and de novo transcriptome assembly of several Guinea fowl tissues (pancreas, hypothalamus, liver, bone marrow and bursa) which play key roles in regulating feed intake, satiety, and immune function was performed using Illumina's Hi-Seq 2000. RESULTS 74 million sequences were generated and assembled into 96,492 contigs using the Trinity software suite. Over 39,000 of these transcripts were found to have in silico translated protein sequences that are homologous to chicken protein sequences. Gene ontology analysis uncovered 416 transcripts with metabolic functions and 703 with immune function. CONCLUSION The transcriptome information presented here will support the development of molecular approaches to improve production efficiency of the guinea fowl and other avian species.
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Affiliation(s)
- Carl E Darris
- College of Agriculture, Human and Natural Sciences, Tennessee State University, Nashville, Tennessee, USA.
| | - James E Tyus
- College of Agriculture, Human and Natural Sciences, Tennessee State University, Nashville, Tennessee, USA.
| | - Gary Kelley
- College of Agriculture, Human and Natural Sciences, Tennessee State University, Nashville, Tennessee, USA.
| | - Alexander J Ropelewski
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
| | - Hugh B Nicholas
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
| | - Xiaofei Wang
- College of Agriculture, Human and Natural Sciences, Tennessee State University, Nashville, Tennessee, USA.
| | - Samuel Nahashon
- College of Agriculture, Human and Natural Sciences, Tennessee State University, Nashville, Tennessee, USA.
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Yang KT, Lin CY, Huang HL, Liou JS, Chien CY, Wu CP, Huang CW, Ou BR, Chen CF, Lee YP, Lin EC, Tang PC, Lee WC, Ding ST, Cheng WTK, Huang MC. Expressed transcripts associated with high rates of egg production in chicken ovarian follicles. Mol Cell Probes 2007; 22:47-54. [PMID: 17692502 DOI: 10.1016/j.mcp.2007.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Revised: 04/06/2007] [Accepted: 06/12/2007] [Indexed: 11/16/2022]
Abstract
The purpose of this study was to characterize differentially expressed transcripts associated with varying rates of egg production in Taiwan country chickens. Ovarian follicles were isolated from two strains of chicken which showed low (B) or high (L2) rates of egg production, then processed for RNA extraction and cDNA library construction. Three thousand and eight forty clones were randomly selected from the cDNA library and amplified by PCR, then used in microarray analysis. Differentially expressed transcripts (P<0.05, log(2)> or = 1.75) were sequenced, and aligned using GenBank. This analysis revealed 20 non-redundant sequences which corresponded to known transcripts. Eight transcripts were expressed at a higher level in ovarian tissue prepared from chicken strain B, and 12 transcripts were expressed at a higher level in L2 birds. These differential patterns of expression were confirmed by semi-quantitative RT-PCR. We show that transcripts of cyclin B2 (cycB2), ferritin heavy polypeptide 1 (FTH1), Gag-Pol polyprotein, thymosin beta4 (TB4) and elongation factor 1 alpha1 (EEF1A1) were enriched in B strain ovarian follicles. In contrast, thioredoxin (TXN), acetyl-CoA dehydrogenase long chain (ACADL), inhibitor of growth family member 4 (ING4) and annexin II (ANXA2) were expressed in at higher levels in the L2 strain. We suggest that our approach may lead to the isolation of effective molecular markers that can be used in selection programs in Taiwan country chickens.
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Affiliation(s)
- K T Yang
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
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Smith EJ, Shi L, Tu Z. Gallus gallus aggrecan gene-based phylogenetic analysis of selected avian taxonomic groups. Genetica 2005; 124:23-32. [PMID: 16011000 DOI: 10.1007/s10709-004-5184-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Mitochondrial DNA (mtDNA) sequences remain the most widely used for phylogenetic analysis in birds. A major limitation of mtDNA sequences, however, is that mitochondria genes are inherited as a single linkage group. Here we describe the use of a 540-bp DNA sequence corresponding to the G3 domain of Gallus gallus nuclear aggrecan gene (AGCI) for phylogenetic analysis of the main groups of Galliformes including Phasianidae, Numididae, and Odontophoridae. We also included species from Cracidae and Megapodiidae which are considered by some as Craciformes and others, including here as Galliformes. The uncorrected sequence divergence of the G3 fragments ranges from 1% among the grouses to 36% between some of the distant groups within Galliformes. These sequences contain 39-48% AT nucleotides and the ratios of transition versus transversion are above 1.5 in majority of the comparisons. Using G3 sequences from an Anseriform, Oxyura jamaicensis, as out-groups, phylogenetic trees were obtained using maximum parsimony and distance algorithms and bootstrap analyses. These trees were consistent with those described using Avian sarcoma and leucosis virus gag genes and those from amino acid sequences of hemoglobin and lysozyme c. Our data also support relationships among Galliformes which were defined using mtDNA sequences. In addition to the general support of the five main families of Galliformes, our data are also consistent with previous work that showed Francolinus africanus and Gallus gallus are in the same clade and that Tetraoninae is a well-supported monophyletic subfamily within Phasianidae. The results presented here suggest that the AGC1 sequences meet the criterion of novel nuclear DNA sequences that can be used to help resolve the relationships among Galliformes.
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Affiliation(s)
- Edward J Smith
- Department of Animal and Poultry Sciences, 2250 Litton-Reaves Hall, Virginia Tech, Blacksburg, VA 24061, USA.
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Smith EJ, Geng T, Long E, Pierson FW, Sponenberg DP, Larson C, Gogal R. Molecular analysis of the relatedness of five domesticated turkey strains. Biochem Genet 2005; 43:35-47. [PMID: 15859518 DOI: 10.1007/s10528-005-1065-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Our knowledge of the genetic relatedness among the eight existing domesticated turkey strains is limited. To begin to address this paucity, genetic relatedness among five turkey strains (Blue Slate, Bourbon Red, Narragansett, Royal Palm, and Spanish Black) was investigated using three molecular marker systems: randomly amplified polymorphic DNA (RAPD), microsatellite, and SNPs derived from a sequence tagged site and a cloned RAPD fragment. The RAPD analyses were based on five primers that revealed a total of 14 informative DNA fragments in all five populations. The microsatellite analyses involved two informative alleles from three primer-pairs. A total of nine SNPs were detected, one of which appeared to be strain specific. This SNP formed the basis of a PCR-RFLP genotyping procedure developed to distinguish one of the strains from the other four. Evidence from these analyses including the SNP-based RFLP-PCR suggests that Royal Palm is distinct from the other four strains, though more closely related to Narragansett. These data provide, for the first time, molecular evidence of the potential relationships among noncommercial domesticated turkey strains.
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Affiliation(s)
- Edward J Smith
- Comparative Genomics Lab, Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia 24061-0306, USA.
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Cosseddu GM, Perez-Enciso M, Fellous M, Vaiman D. Interspecific chromosome-wide transcription profiles reveal the existence of mammalian-specific and species-specific chromosome domains. J Mol Evol 2005; 59:317-28. [PMID: 15553087 DOI: 10.1007/s00239-004-2627-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A long-range exploration of expression levels through wide chromosome territories was carried out in three species (pig, cattle, and chicken) by aligning EST counts against the human genome. This strategy made it possible to produce expression profiles that were very similar between pig and cattle and that were significantly correlated with chicken levels of expression. In parallel with these alignments, we developed a statistical approach enabling us to screen genomic regions for both underexpression and overexpression at the chromosome level within a given species, as well as interspecifically. The observed correlations are indicative of the existence of interspecifically conserved domains of gene expression, not only for housekeeping genes (which are highly expressed), but also for regions where genes are significantly underexpressed. Furthermore, our strategy made it possible to point out regions that are differentially regulated between species. These expression data were crossed with available comparative mapping information for pigs and cattle, suggesting that coregulated regions are syntenic in various mammals.
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Burt DW, Morrice DR, Sewalem A, Smith J, Paton IR, Smith EJ, Bentley J, Hocking PM. Preliminary linkage map of the turkey (Meleagris gallopavo) based on microsatellite markers. Anim Genet 2004; 34:399-409. [PMID: 14687069 DOI: 10.1046/j.1365-2052.2003.01033.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The turkey is an agriculturally important species for which, until now, there is no published genetic linkage map based on microsatellite markers--still the markers most used in the chicken and other farm animals. In order to increase the number of markers on a turkey genetic linkage map we decided to map new microsatellite sequences obtained from a GT-enriched turkey genomic library. In different chicken populations more than 35-55% of microsatellites are polymorphic. In the turkey populations tested here, 43% of all turkey primers tested were found to be polymorphic, in both commercial and wild type turkeys. Twenty linkage groups (including the Z chromosome) containing 74 markers have been established, along with 37 other unassigned markers. This map will lay the foundations for further genetic mapping and the identification of genes and quantitative trait loci in this economically important species. Genome comparisons, based on genetic maps, with related species such as the chicken would then also be possible. All primer information, polymerase chain reaction (PCR) conditions, allele sizes and genetic linkage maps can be viewed at http://roslin.thearkdb.org/. The DNA is also available on request through the Roslin Institute.
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Affiliation(s)
- D W Burt
- Department of Genomics and Bioinformatics, Roslin Institute (Edinburgh), Roslin, Midlothian, UK.
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2002. [PMCID: PMC2447231 DOI: 10.1002/cfg.116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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