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Huang HL, Cheng YS. A novel minisequencing single-nucleotide polymorphism marker of the lysozyme gene detects high hatchability of Tsaiya ducks (Anas platyrhynchos). Theriogenology 2014; 82:1113-20. [DOI: 10.1016/j.theriogenology.2014.07.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 07/16/2014] [Accepted: 07/22/2014] [Indexed: 10/25/2022]
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De Marco MA, Valentini A, Foni E, Savarese MC, Cotti C, Chiapponi C, Raffini E, Donatelli I, Delogu M. Is there a relation between genetic or social groups of mallard ducks and the circulation of low pathogenic avian influenza viruses? Vet Microbiol 2014; 170:418-24. [PMID: 24690373 DOI: 10.1016/j.vetmic.2014.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 02/21/2014] [Accepted: 03/03/2014] [Indexed: 11/19/2022]
Abstract
We investigated the circulation dynamics of low pathogenic avian influenza viruses (LPAIVs) in the mallard (Anas platyrhynchos) reservoir in Italy. In particular, we evaluated the temporal distribution of virologic findings by combining virus isolation data with a new population genetic-based study approach. Thus, during 11 consecutive sampling periods (wintering periods between 1993/94 and 2003/04), categorised into 40 sampling sub-periods, cloacal swab samples were collected from 996 wild and 16 captive-reared mallards, to be screened by RT-PCR before attempting influenza A virus isolation in embryonated eggs. Forty-eight LPAIVs were isolated from wild mallards and antigenically characterised by haemagglutination-inhibition and neuraminidase-inhibition assays. When considering LPAIV antigenic subtypes in which more than one mallard tested virus isolation positive (H1N1, n. 22; H2N3, n. 2; H5N3, n. 2; H6N5, n. 3; H6N8, n. 2; H7N3, n. 3; H11N6, n. 5), at least two birds infected with a specific HN subtype clustered within one same sampling sub-period. In the context of the novel population genetic approach, total DNA was extracted from a subset of 16 captive-reared and 65 wild ducks (2000/01 and 2001/02 sampling periods) to assess genetic diversity by amplified fragment length polymorphisms (AFLP) markers. Analyses of AFLP results showed that captive-reared mallards clustered together, whereas two main independent clusters characterised the distribution pattern of most wild mallards. Within this subset of samples, nearly identical H7N3 LPAIV strains were isolated from two wild mallards belonging to the same genetic cluster. Blood sera were also collected from the above subset of mallards and examined for antibodies to the homologous H7N3 virus strain. Four out of six wild mallards testing H7N3-seropositive by haemagglutination-inhibition assay (2001/02 period) belonged to the genetic cluster including H7N3 virus shedding ducks. Overall, our data raise the possibility of an enhanced transmission and circulation of LPAIVs in genetic or social groups of wild mallards, gathered in flocks possibly related by parentage and/or geographic origin.
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Affiliation(s)
- Maria A De Marco
- Laboratory of Genetics, Institute for Environmental Protection and Research, Via Ca' Fornacetta, 40064 Ozzano Emilia, BO, Italy.
| | - Alessio Valentini
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Via S. Camillo de Lellis, 01100 Viterbo, Italy
| | - Emanuela Foni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Via dei Mercati, 43126 Parma, Italy
| | - Maria C Savarese
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Via S. Camillo de Lellis, 01100 Viterbo, Italy
| | - Claudia Cotti
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra, 40064 Ozzano Emilia, BO, Italy
| | - Chiara Chiapponi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Via dei Mercati, 43126 Parma, Italy
| | - Elisabetta Raffini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Via del Limite, 48022 Lugo, RA, Italy
| | - Isabella Donatelli
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Viale Regina Elena, 00161 Rome, Italy
| | - Mauro Delogu
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra, 40064 Ozzano Emilia, BO, Italy
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SULANDART SRI, ZEIN MOCHSYAMSULARIFIN. Application of Two Molecular Sexing Methods for Indonesian Bird Species: Implication for Captive Breeding Programs in Indonesia. HAYATI JOURNAL OF BIOSCIENCES 2012. [DOI: 10.4308/hjb.19.4.183] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Chen CC, Liu YS, Cheng CC, Wang CL, Liao MH, Tseng CN, Chang HW. High-throughput sex identification by melting curve analysis in blue-breasted quail and chicken. Theriogenology 2012; 77:1951-8. [PMID: 22341710 DOI: 10.1016/j.theriogenology.2011.12.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 11/12/2011] [Accepted: 12/04/2011] [Indexed: 01/17/2023]
Abstract
The objective was to develop a high-throughput method of identifying sex in both Coturnix chinensis and Gallus gallus, which would be useful for biomedical research and hatcheries. Because chromo-helicase-DNA binding protein (CHD)-based Griffiths P2/P8 primers do not produce polymerase chain reaction (PCR) products with distinguishable sex-specific curves in melting curve analysis (MCA), these primers are unsuitable for high throughput application in either species. Conserved regions were identified by basic local alignment search tool (BLAST) analyses of cloned CHD-Z and CHD-W genes of C. chinensis. Based on sequence alignment, a female-specific CHD-W primer (W-cot-F1) and a female/male (or CHD-W/CHD-Z)-common primer (ZW-cot-F1) were redesigned for use in combination with the Griffiths P2 primer for MCA-based PCR reaction. In C. chinensis and G. gallus, W-cot-F1/P2 and ZW-cot-F1/P2 had amplicon lengths of 315/318 and 114 base pairs and melting temperatures (Tm) of approximately 79.5 °C to 80 °C and approximately 78.5 °C to 79°C, respectively. Thus, MCA distinguished sex based on two distinct Tm peaks in females versus only one Tm peak in males. The MCA-based real-time PCR combined with the proposed primer redesign provided a high-throughput method of identifying sex in C. chinensis and G. gallus.
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Affiliation(s)
- C-C Chen
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
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Widespread amplification of amplified fragment length polymorphisms (AFLPs) in marine Antarctic animals. Polar Biol 2011. [DOI: 10.1007/s00300-011-1139-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Li D, Cui H, Wang C, Ling S, Huang Z, Zhang H. A fast and effective method to perform paternity testing for Wolong giant pandas. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11434-011-4571-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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High-throughput gender identification of three Columbidae species using melting curve analysis. Theriogenology 2010; 75:73-9.e1-4. [PMID: 20833415 DOI: 10.1016/j.theriogenology.2010.07.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 07/17/2010] [Accepted: 07/19/2010] [Indexed: 11/21/2022]
Abstract
The objective was to perform high-throughput gender identification of three Columbidae species (Columba livia, Columba pulchricollis, and Streptopelia tranquebarica). Although the chromo-helicase-DNA binding protein (CHD)-based Griffiths P2/P8 primer set resolved the amplicon products of these species in 3% agarose gel electrophoresis, it was unsuitable for molecular gender identification using the melting curve analysis (MCA) curve for high-throughput analysis. After sequencing the CHD-Z and CHD-W genes for these species, we redesigned a female-specific CHD-W primer (dove-W) and a female/male (or CHD-Z/CHD-W)-common primer (dove-ZW) to combine with the Griffiths P2 primer to generate two PCR amplicons with different lengths (P2/dove-W and P2/dove-ZW for 252- and 104-bp, respectively). Melting temperature (Tm) values for P2/dove-W and P2/dove-ZW amplicons were determined and resolved in MCA at approximately 79.0∼79.5 and 77.5 °C, respectively. Accordingly, females contained two Tm peaks, whereas males contained one. In conclusion, melting curve analysis (MCA) using our proposed primer sets was a robust gender identification method for the three Columbidae species tested.
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Li X, Zhu Y, Liu P, Zhuge Z, Su G, Wang J. Assessment of genetic diversity in Chinese eared pheasant using fluorescent-AFLP markers. Mol Phylogenet Evol 2010; 57:429-33. [PMID: 20595068 DOI: 10.1016/j.ympev.2010.05.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 05/25/2010] [Indexed: 11/17/2022]
Abstract
The eared pheasant consists of four species: white eared pheasant (Crossoptilon crossoptilon), Tibetan eared pheasant (Crossoptilon harmani), blue eared pheasant (Crossoptilon auritum), and brown eared pheasant (Crossoptilon mantchuricum). These species are found only in China, and are also on the list of the world's threatened species. In this paper, 74 individuals from the four eared pheasant species were assessed for population genetic diversity by means of fluorescent-AFLP markers. A total of 429 AFLP peaks were amplified by 11 pairs of fluorescent EcoRI/TaqI primer combinations. Out of all markers, 329 AFLPs were polymorphic. Each primer combination produced in reactions from 19 to 72 fragments and the polymorphic peaks percentage ranged from 53.33% to 86.11% with an average of 74.36% polymorphic bands. Genetic distance between species and genetic diversity within species were evaluated using Jaccard's similarity coefficients (SC) and the corresponding dendrogram. It was found that there was a moderate genetic distance between the four species (SC=0.674-0.832). Brown eared pheasant was genetically closely related to blue eared pheasant (SC=0.832), while white eared pheasant was more closely related to Tibetan eared pheasant (SC=0.812). Genetic diversity was lower in brown eared pheasant (SC=0.913) and Tibetan eared pheasant (SC=0.903) than in white eared pheasant (SC=0.832) and blue eared pheasant (SC=0.853).
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Affiliation(s)
- Xiujuan Li
- College of Veterinary Medicine, China Agricultural University, Beijing, PR China
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HARA K, WATABE H, SASAZAKI S, MUKAI F, MANNEN H. Development of SNP markers for individual identification and parentage test in a Japanese Black cattle population. Anim Sci J 2010; 81:152-7. [DOI: 10.1111/j.1740-0929.2009.00720.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Chou TC, Yao CT, Su SH, Hung YC, Chen WS, Cheng CC, Tseng CN, Wang HM, Chou YC, Li SSL, Gu DL, Chang HW. Validation of Spilornis cheela hoya TaqMan probes for potential gender identification of many Accipitridae species. Theriogenology 2009; 73:404-11. [PMID: 19959218 DOI: 10.1016/j.theriogenology.2009.09.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 09/15/2009] [Accepted: 09/19/2009] [Indexed: 11/20/2022]
Abstract
The objective of this study was to test the hypothesis that genders of Accipitridae species, with the same or similar sequences to our previously proposed Spilornis cheela hoya (S. c. hoya) chromo-helicase-DNA binding protein (CHD)-W-specific and CHD-ZW-common TaqMan probes, can be successfully determined. Eight species of Accipitridae with known genders were collected. After PCR, TA cloning, sequencing, and alignment analyses, sequence length differences of Griffiths P2/P8 PCR amplicons between CHD-Z and CHD-W genes ranged from 2 to 19 bp for these Accipitridae species, and they were unsolved in 3% agarose gel. Using our previous proposed S. c. hoya TaqMan probes, the genders of Circaetus gallicus, completely homologous to the sequences for these CHD probes, were successfully identified. With one nucleotide difference to S. c. hoya CHD-W-specific probe, gender identification of Accipiter gularis, Accipiter soloensis, Accipiter trivirgatus, Accipiter virgatus, and Butastur indicus were validated. With two nucleotide differences in the CHD-W-specific probe and one nucleotide difference in the CHD-ZW-common probe, Pernis ptilorhyncus also performed well for gender identification. In conclusion, the S. c. hoyaCHD probes, coupled with the Griffiths P2/P8 primers, were validated to provide accurate and high-throughput gender identification for many Accipitridae species.
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Affiliation(s)
- T-C Chou
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
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Huang CW, Cheng YS, Rouvier R, Yang KT, Wu CP, Huang HL, Huang MC. Duck (Anas platyrhynchos) linkage mapping by AFLP fingerprinting. Genet Sel Evol 2009; 41:28. [PMID: 19291328 PMCID: PMC2666072 DOI: 10.1186/1297-9686-41-28] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2009] [Accepted: 03/17/2009] [Indexed: 11/10/2022] Open
Abstract
Amplified fragment length polymorphism (AFLP) with multicolored fluorescent molecular markers was used to analyze duck (Anas platyrhynchos) genomic DNA and to construct the first AFLP genetic linkage map. These markers were developed and genotyped in 766 F2 individuals from six families from a cross between two different selected duck lines, brown Tsaiya and Pekin. Two hundred and ninety-six polymorphic bands (64% of all bands) were detected using 18 pairs of fluorescent TaqI/EcoRI primer combinations. Each primer set produced a range of 7 to 29 fragments in the reactions, and generated on average 16.4 polymorphic bands. The AFLP linkage map included 260 co-dominant markers distributed in 32 linkage groups. Twenty-one co-dominant markers were not linked with any other marker. Each linkage group contained three to 63 molecular markers and their size ranged between 19.0 cM and 171.9 cM. This AFLP linkage map provides important information for establishing a duck chromosome map, for mapping quantitative trait loci (QTL mapping) and for breeding applications.
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Affiliation(s)
- Chang-Wen Huang
- Department of Animal Science, National Chung Hsing University, 250 Kuo-Kung Road, Taichung 402, Taiwan
- Institute of Cellular and Organism Biology, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 115, Taiwan
| | - Yu-Shin Cheng
- Livestock Research Institute, Council of Agriculture, Hsin-Hua, Tainan 712, Taiwan
| | - Roger Rouvier
- Institut National de la Recherche Agronomique, Station d'Amélioration Génétique des Animaux, Centre de Recherches de Toulouse, BP52627, F31326 Castanet-Tolosan Cedex, France
| | - Kuo-Tai Yang
- Department of Animal Science, National Chung Hsing University, 250 Kuo-Kung Road, Taichung 402, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 115, Taiwan
| | - Chean-Ping Wu
- Department of Animal Science, National Chung Hsing University, 250 Kuo-Kung Road, Taichung 402, Taiwan
- Department of Animal Science, National Chiayi University, 300 Syuefu Road, Chiayi 600, Taiwan
| | - Hsiu-Lin Huang
- Department of Animal Science, National Chung Hsing University, 250 Kuo-Kung Road, Taichung 402, Taiwan
| | - Mu-Chiou Huang
- Department of Animal Science, National Chung Hsing University, 250 Kuo-Kung Road, Taichung 402, Taiwan
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Chang HW, Cheng CA, Gu DL, Chang CC, Su SH, Wen CH, Chou YC, Chou TC, Yao CT, Tsai CL, Cheng CC. High-throughput avian molecular sexing by SYBR green-based real-time PCR combined with melting curve analysis. BMC Biotechnol 2008; 8:12. [PMID: 18269737 PMCID: PMC2259332 DOI: 10.1186/1472-6750-8-12] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Accepted: 02/12/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Combination of CHD (chromo-helicase-DNA binding protein)-specific polymerase chain reaction (PCR) with electrophoresis (PCR/electrophoresis) is the most common avian molecular sexing technique but it is lab-intensive and gel-required. Gender determination often fails when the difference in length between the PCR products of CHD-Z and CHD-W genes is too short to be resolved. RESULTS Here, we are the first to introduce a PCR-melting curve analysis (PCR/MCA) to identify the gender of birds by genomic DNA, which is gel-free, quick, and inexpensive. Spilornis cheela hoya (S. c. hoya) and Pycnonotus sinensis (P. sinensis) were used to illustrate this novel molecular sexing technique. The difference in the length of CHD genes in S. c. hoya and P. sinensis is 13-, and 52-bp, respectively. Using Griffiths' P2/P8 primers, molecular sexing failed both in PCR/electrophoresis of S. c. hoya and in PCR/MCA of S. c. hoya and P. sinensis. In contrast, we redesigned sex-specific primers to yield 185- and 112-bp PCR products for the CHD-Z and CHD-W genes of S. c. hoya, respectively, using PCR/MCA. Using this specific primer set, at least 13 samples of S. c. hoya were examined simultaneously and the Tm peaks of CHD-Z and CHD-W PCR products were distinguished. CONCLUSION In this study, we introduced a high-throughput avian molecular sexing technique and successfully applied it to two species. This new method holds a great potential for use in high throughput sexing of other avian species, as well.
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Affiliation(s)
- Hsueh-Wei Chang
- Faculty of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan.
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