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Díaz-Matus de la Parra M, Inostroza K, Alcalde JA, Larama G, Bravo S. Characterization of the genetic diversity, structure, and admixture of 7 Chilean chicken breeds. Poult Sci 2024; 103:103238. [PMID: 38071783 PMCID: PMC10750188 DOI: 10.1016/j.psj.2023.103238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/04/2023] [Accepted: 10/23/2023] [Indexed: 12/29/2023] Open
Abstract
The Mapuche fowl is an autochthonous breed raised in Chile and represents an important zoogenetic resource for the local economy. This study aimed at investigating the genetic diversity, relationship and population structure of 96 local Chilean chickens derived from 3 ecotype of Mapuche fowl (Kollonka, Ketro, and Kollonka de aretes), 2 ecotype Chilean (Trintre, Cogote pelado) and 2 breeds (Light Brahma and Barred Plymouth Rock) using 12 microsatellite markers. In total, 113 alleles were detected in all populations, with a mean of 7.6 alleles per population. In all population chicken breeds, the observed and expected heterozygosity ranged from 0.91 to 0.98 and from 0.69 to 0.79. Furthermore, all populations showed significant deviations from Hardy-Weinberg expectations. Across each population, the global heterozygosity deficit (FIT) was -0.174, population differentiation index (FST) was 0.073, and the global inbreeding of individuals within breed (FIS) was -0.267. The phylogenetic relationships of chickens were examined using neighbor-joining trees constructed at the level of population. The highest Nei's standard genetic distance value of 0.559 was observed between Barred Plymouth Rock and Light Brahma, whereas the minimum value (0.099) was found between Kollonka and Trintre. The neighbor-joining tree constructed at population level revealed 2 main clusters, with Light Brahma, Barred Plymouth Rock, Ketro and Kollonka de aretes in 1 cluster, and Kollonka, Trintre and Cogote pelado breeds in the second cluster. Based on the results of the STRUCTURE analysis, the most likely number of clustering of the population evaluated was at K = 3, with Light Brahma and Barred Plymouth Rock breeds forming their own distinct clusters, while Kollonka, Ketro, Kollonka de aretes, Trintre and Cogote pelado breeds clustered together. This study represents the first report of genetic diversity in these populations in Chile. These results can be used as baseline genetic information for genetic conservation program, for instance, to control inbreeding and to implement further genetic studies in local Chilean chickens.
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Affiliation(s)
| | - Karla Inostroza
- Department of Agricultural and Aquacultural Sciences, Faculty of Natural Resources, Universidad Católica de Temuco, Temuco, Chile
| | - José Antonio Alcalde
- Department of Fruit Cultivation and Enology, Faculty of Agronomy and Forest Engineering, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Giovanni Larama
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco 4811230, Chile
| | - Silvana Bravo
- Institute of Animal Production, Faculty of Agricultural and Food Sciences, Universidad Austral de Chile, Valdivia, Chile; Center for Research on Volcanic Soils, Faculty of Agricultural and Food Sciences, Universidad Austral de Chile, Valdivia, Chile.
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Genetic Diversity and Population Structure of Local Chicken Ecotypes in Burkina Faso Using Microsatellite Markers. Genes (Basel) 2022; 13:genes13091523. [PMID: 36140691 PMCID: PMC9498515 DOI: 10.3390/genes13091523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/07/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
The objective of this study was to investigate the genetic diversity and population structure of local chicken ecotypes from Burkina Faso using microsatellite markers. A total of 71 individuals representing local chicken populations from the Centre-East (18), Centre-North (17), Sahel (18) and South-West (18) were used to estimate genetic diversity indices, population structure and phylogenetic relationships using 20 selected polymorphic microsatellite markers. The number of alleles, mean number of alleles, mean of observed and expected heterozygosity and polymorphic information content were 127, 6.35, 0.391, 0.521, 0.539 and 0.541, respectively. The estimated overall fixation index between loci (F), among populations (FIS) and inbreeding coefficient within chicken ecotypes were 0.239, 0.267 and 0.243, respectively. Analysis of the molecular variance revealed that 77% of the total genetic diversity was attributed to within-population variation and the remaining 1% and 22% were attributed to among-regions differentiation (FST) and among-individual differentiation (FIT), respectively. The highest pairwise genetic distance (0.026) was found between the local Konde ecotype and those from the Centre-North region while the lowest distance was observed between local chickens from the Sahel and the Centre-North regions (0.003). Neighbour-joining phylogenetic tree and principal component discriminant analyses confirmed the observed genetic distances between populations. The results show that local chickens in Burkina Faso have a rich genetic diversity with little differentiation between the studied populations. This study provides important information on measures of genetic diversity that could help in the design and implementation of future genetic improvement and conservation programs for local chickens in Burkina Faso.
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Roh HJ, Kim SC, Cho CY, Lee J, Jeon D, Kim DK, Kim KW, Afrin F, Ko YG, Lee JH, Batsaikhan S, Susanti T, Hegay S, Kongvongxay S, Gorkhali NA, Thi LAN, Thao TTT, Manikku L. Estimating genetic diversity and population structure of 22 chicken breeds in Asia using microsatellite markers. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2020; 33:1896-1904. [PMID: 32299162 PMCID: PMC7649407 DOI: 10.5713/ajas.19.0958] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/03/2020] [Indexed: 11/27/2022]
Abstract
Objective Estimating the genetic diversity and structures, both within and among chicken breeds, is critical for the identification and conservation of valuable genetic resources. In chickens, microsatellite (MS) marker polymorphisms have previously been widely used to evaluate these distinctions. Our objective was to analyze the genetic diversity and relationships among 22 chicken breeds in Asia based on allelic frequencies. Methods We used 469 genomic DNA samples from 22 chicken breeds from eight Asian countries (South Korea, KNG, KNB, KNR, KNW, KNY, KNO; Laos, LYO, LCH, LBB, LOU; Indonesia, INK, INS, ING; Vietnam, VTN, VNH; Mongolia, MGN; Kyrgyzstan, KGPS; Nepal, NPS; Sri Lanka, SBC) and three imported breeds (RIR, Rhode Island Red; WLG, White Leghorn; CON, Cornish). Their genetic diversity and phylogenetic relationships were analyzed using 20 MS markers. Results In total, 193 alleles were observed across all 20 MS markers, and the number of alleles ranged from 3 (MCW0103) to 20 (LEI0192) with a mean of 9.7 overall. The NPS breed had the highest expected heterozygosity (Hexp, 0.718±0.027) and polymorphism information content (PIC, 0.663±0.030). Additionally, the observed heterozygosity (Hobs) was highest in LCH (0.690±0.039), whereas WLG showed the lowest Hexp (0.372±0.055), Hobs (0.384±0.019), and PIC (0.325±0.049). Nei’s DA genetic distance was the closest between VTN and VNH (0.086), and farthest between KNG and MGN (0.503). Principal coordinate analysis showed similar results to the phylogenetic analysis, and three axes explained 56.2% of the variance (axis 1, 19.17%; 2, 18.92%; 3, 18.11%). STRUCTURE analysis revealed that the 22 chicken breeds should be divided into 20 clusters, based on the highest ΔK value (46.92). Conclusion This study provides a basis for future genetic variation studies and the development of conservation strategies for 22 chicken breeds in Asia.
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Affiliation(s)
- Hee-Jong Roh
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Seung-Chang Kim
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Chang-Yeon Cho
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Jinwook Lee
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Dayeon Jeon
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Dong-Kyo Kim
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Kwan-Woo Kim
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Fahmida Afrin
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Yeoung-Gyu Ko
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Jun-Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Solongo Batsaikhan
- Production and technology, National Centre for Livestock Genebank, Ulaanbaatar, 210349, Mongolia
| | - Triana Susanti
- Indonesia Research Institute for Animal Production, Bogor, 16720, Indonesia
| | - Sergey Hegay
- Institute of Biochemistry & Physiology, National Academy of Science of Kyrgyzstan, Bishkek, 720071, Kyrgyzstan
| | - Siton Kongvongxay
- Livestock Research Centre, Vientiane, 7170, Lao People's Democratic Republic
| | - Neena Amatya Gorkhali
- Animal Breeding Division, Nepal Agricultural Research Council, Kathmandu, 44600, Nepal
| | - Lan Anh Nguyen Thi
- Department of Animal Breeding and Genetics, Institute of Animal Sciences for Southern Vietnam, Binh Duong 75000, Vietnam
| | - Trinh Thi Thu Thao
- Department of Animal Breeding and Genetics, Institute of Animal Sciences for Southern Vietnam, Binh Duong 75000, Vietnam
| | - Lakmalie Manikku
- Department of Animal Production and Health, Veterinary Research Institute, Colombo, 20400, Sri Lanka
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Habimana R, Okeno TO, Ngeno K, Mboumba S, Assami P, Gbotto AA, Keambou CT, Nishimwe K, Mahoro J, Yao N. Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers. PLoS One 2020; 15:e0225084. [PMID: 32240167 PMCID: PMC7117670 DOI: 10.1371/journal.pone.0225084] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 03/08/2020] [Indexed: 11/19/2022] Open
Abstract
Rwanda has about 4.5 million of indigenous chicken (IC) that are very low in productivity. To initiate any genetic improvement programme, IC needs to be accurately characterized. The key purpose of this study was to ascertain the genetic diversity of IC in Rwanda using microsatellite markers. Blood samples of IC sampled from 5 agro-ecological zones were collected from which DNA was extracted, amplified by PCR and genotyped using 28 microsatellite markers. A total of 325 (313 indigenous and 12 exotic) chickens were genotyped and revealed a total number of 305 alleles varying between 2 and 22 with a mean of 10.89 per locus. One hundred eighty-six (186) distinct alleles and 60 private alleles were also observed. The frequency of private alleles was highest in samples from the Eastern region, whereas those from the North West had the lowest. The influx of genes was lower in the Eastern agro-ecological zone than the North West. The mean observed heterozygosity was 0.6155, whereas the average expected heterozygosity was 0.688. The overall inbreeding coefficient among the population was 0.040. Divergence from the Hardy-Weinberg equilibrium was significant (p<0.05) in 90% of loci in all the populations. The analysis of molecular variance revealed that about 92% of the total variation originated from variation within populations. Additionally, the study demonstrated that IC in Rwanda could be clustered into four gene groups. In conclusion, there was considerable genetic diversity in IC in Rwanda, which represents a crucial genetic resource that can be conserved or optimized through genetic improvement.
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Affiliation(s)
- Richard Habimana
- Animal Science and Veterinary Medicine, University of Rwanda, College of Agriculture, Nyagatare, Rwanda
- Department of Animal Science, Animal Breeding and Genomics Group, Egerton University, Nakuru, Kenya
| | - Tobias Otieno Okeno
- Department of Animal Science, Animal Breeding and Genomics Group, Egerton University, Nakuru, Kenya
| | - Kiplangat Ngeno
- Department of Animal Science, Animal Breeding and Genomics Group, Egerton University, Nakuru, Kenya
| | - Sylvere Mboumba
- Faculty of Agronomy and Biotechnologies, Masuku University of Science and Techniques, Franceville, Gabon
| | - Pauline Assami
- Biosciences eastern and central Africa, International Livestock Research Institute Hub, Nairobi, Kenya
| | - Anique Ahou Gbotto
- Laboratoire de genomique Fonctionnelle et Amélioration Génétique Université Nangui Abrogoua, Abidjan, Cote d'Ivoire
| | - Christian Tiambo Keambou
- Biosciences eastern and central Africa, International Livestock Research Institute Hub, Nairobi, Kenya
- Faculty of Agriculture and Veterinary medicine, University of Buea, Buea, Cameroon
| | - Kizito Nishimwe
- Animal Science and Veterinary Medicine, University of Rwanda, College of Agriculture, Nyagatare, Rwanda
| | - Janvier Mahoro
- Animal Science and Veterinary Medicine, University of Rwanda, College of Agriculture, Nyagatare, Rwanda
| | - Nasser Yao
- Biosciences eastern and central Africa, International Livestock Research Institute Hub, Nairobi, Kenya
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Islam MA, Osman SAM, Nishibori M. Genetic diversity of Bangladeshi native chickens based on complete sequence of mitochondrial DNA D-loop region. Br Poult Sci 2019; 60:628-637. [PMID: 31475858 DOI: 10.1080/00071668.2019.1655708] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
1. The aim of this study was to explore genetic diversity and possible origin of Bangladeshi (BD) native chickens. The complete mtDNA D-loop region was sequenced in 60 chickens representing five populations; naked neck, full feathered, Aseel, Hilly and autosomal dwarf. The 61 reference sequences representing different domestic chicken clades in China, India, Laos, Indonesia, Myanmar, and other Eurasian regions were included. The mtDNA D-loop sequence polymorphism and maternal origin of five BD populations were analysed.2. A total of 35 polymorphic sites, and 21 haplotypes were detected in 60 mtDNA D-loop sequences. The haplotype and nucleotide diversity of the five populations were 0.921 ± 0.018 and 0.0061 ± 0.0019, respectively. Both mtDNA network and phylogenetic analysis indicated four clades (four haplogroups) in BD populations (21 haplotypes) along with 61 reference haplotypes. Clade E contained the most individuals (20) and haplotypes (11) of BD chickens, followed by clade D (17, 6), clade C (12, 2) and clade F (11, 2), respectively.3. The higher number of unique haplotypes found in Yunnan, China, suggested that the origin of BD chickens was in this region. The haplotypes from different haplogroups were introduced in Bangladeshi chickens from India, China and Myanmar. The phylogenetic tree showed a close relationship of BD chickens with the clusters from India, China, Myanmar and Laos, and indicated the dispersion of BD chickens from these sources. The phylogenetic information revealed high genetic diversity of BD chickens because of their origin from different lineages with high genetic variation and distance, which was determined from four cluster and neighbour-joining trees.4. In conclusion, BD populations had high genetic diversity. The mtDNA network profiles and phylogenetic trees showed multiple maternal origins of BD chickens from India, China, Myanmar and Laos.
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Affiliation(s)
- M A Islam
- Department of Dairy and Poultry Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh.,Department of Bio-resource Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - S A M Osman
- Department of Bio-resource Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Department of Genetics, Faculty of Agriculture, Minia University, El Minia, Egypt
| | - M Nishibori
- Department of Bio-resource Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
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Carvalho D, Bonafé C, Rodriguez-Rodriguez M, Almeida M, Sarmento J, Britto F, Silva M. Variabilidade genética de 12 loci de microssatélites em galinhas crioulas Canela-Preta. ARQ BRAS MED VET ZOO 2018. [DOI: 10.1590/1678-4162-9675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
RESUMO Esta pesquisa foi realizada com o objetivo de se conhecer a variabilidade genética de 12 loci de microssatélites em galinhas crioulas Canela-Preta. Foram coletadas amostras de sangue de 118 galinhas crioulas Canela-Preta, provenientes de três municípios do estado do Piauí (Oeiras, Queimada Nova e Teresina). Após extração do DNA, foram utilizados marcadores para 12 loci de microssatélites: LEI0192, LEI0209, LEI0212, LEI0217, LEI0221, LEI0234, LEI0237, LEI0248, LEI0258, MCW0081, MCW0183 e MCW0213, que foram amplificados pela técnica de reação em cadeia da polimerase (PCR). Foram obtidos 408 alelos (somando os alelos dos 12 loci), com os fragmentos variando entre 50 e 460 pares de bases. O número de alelos variou de 15 (MCW0081) a 52 (LEI0212), com média de 31,5 alelos por locus. A média de heterozigosidade esperada e o conteúdo de informações polimórficas foram, respectivamente, 0,887 e 0,909. Foram observados desvios no equilíbrio de Hardy-Weinberg e valores positivos do índice de fixação com excesso de homozigotos. Os microssatélites utilizados mostraram-se polimórficos e podem ser usados para investigações genéticas em galinhas Canela-Preta. As galinhas dos plantéis avaliados apresentam grande variabilidade gênica, o que as qualifica como importante fonte de recursos genéticos e, consequentemente, faculta a utilização delas em programas de melhoramento genético animal.
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Fathi M, El-Zarei M, Al-Homidan I, Abou-Emera O. Genetic diversity of Saudi native chicken breeds segregating for naked neck and frizzle genes using microsatellite markers. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 31:1871-1880. [PMID: 29879833 PMCID: PMC6212745 DOI: 10.5713/ajas.18.0041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/07/2018] [Indexed: 11/27/2022]
Abstract
Objective Recently, there has been an increasing interest in conservation of native genetic resources of chicken on a worldwide basis. Most of the native chicken breeds are threatened by extinction or crossing with ecotypes. Methods Six Saudi native chicken breeds including black naked neck, brown frizzled, black, black barred, brown and gray were used in the current study. The aim of the current study was to evaluate genetic diversity, relationship and population structure of Saudi native chicken breeds based on 20 microsatellite markers. Results A total of 172 alleles were detected in Saudi native chicken breeds across all 20 microsatellite loci. The mean number of alleles per breed ranged from 4.35 in gray breed to 5.45 in normally feathered black with an average of 8.6 alleles. All breeds were characterized by a high degree of genetic diversity, with the lowest heterozygosity found in the brown breed (72%) and the greatest in the frizzled and black barred populations (78%). Higher estimate of expected heterozygosity (0.68) was found in both black breeds (normal and naked neck) compared to the other chicken populations. All studied breeds showed no inbreeding within breed (negative inbreeding coefficient [FIS]). The phylogenetic relationships of chickens were examined using neighbor-joining trees constructed at the level of breeds and individual samples. The neighbor-joining tree constructed at breed level revealed three main clusters, with naked neck and gray breeds in one cluster, and brown and frizzled in the second cluster leaving black barred in a separate one. Conclusion It could be concluded that the genetic information derived from the current study can be used as a guide for genetic improvement and conservation in further breeding programs. Our findings indicate that the Saudi native chicken populations have a rich genetic diversity and show a high polymorphism.
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Affiliation(s)
- Moataz Fathi
- Department of Animal Production and Breeding, College of Agriculture and Veterinary Medicine, Qassim University, Al-Qassim 51452, Saudi Arabia.,Department of Poultry Production, Faculty of Agriculture, Ain Shams University, Hadayek Shoubra 11241, Cairo, Egypt
| | - Mohamed El-Zarei
- Department of Animal Production and Breeding, College of Agriculture and Veterinary Medicine, Qassim University, Al-Qassim 51452, Saudi Arabia.,Department of Animal Production, Faculty of Agriculture, Suez Canal University 41522, Ismailia, Egypt
| | - Ibrahim Al-Homidan
- Department of Animal Production and Breeding, College of Agriculture and Veterinary Medicine, Qassim University, Al-Qassim 51452, Saudi Arabia
| | - Osama Abou-Emera
- Department of Animal Production and Breeding, College of Agriculture and Veterinary Medicine, Qassim University, Al-Qassim 51452, Saudi Arabia.,Department of Poultry Breeding, Animal Production Research Institute, Agriculture Research Center, Dokki, Giza 12618, Egypt
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Özdemir D, Cassandro M. Assessment of the population structure and genetic diversity of Denizli chicken subpopulations using SSR markers. ITALIAN JOURNAL OF ANIMAL SCIENCE 2017. [DOI: 10.1080/1828051x.2017.1384336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Demir Özdemir
- Teknik Bilimler Meslek Yüksekokulu, University of Akdeniz, Antalya, Turkey
| | - Martino Cassandro
- Dipartimento di Agronomia Animali Alimenti Risorse Naturali e Ambiente, University of Padova, Padova, Italy
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Meydan H, Jang CP, Yıldız MA, Weigend S. Maternal Origin of Turkish and Iranian Native Chickens Inferred from Mitochondrial DNA D-loop Sequences. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 29:1547-1554. [PMID: 27189637 PMCID: PMC5088373 DOI: 10.5713/ajas.15.1060] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 04/01/2016] [Accepted: 05/10/2016] [Indexed: 11/29/2022]
Abstract
To assess genetic diversity and maternal origin of Turkish and Iranian native chicken breeds, we analyzed the mtDNA D-loop sequences of 222 chickens from 2 Turkish (Denizli and Gerze) and 7 Iranian (White Marandi, Black Marandi, Naked Neck, Common Breed, Lari, West Azarbaijan, and New Hampshire) native chicken breeds, together with the available reference sequences of G. gallus gallus in GenBank. The haplotype diversity was estimated as 0.24±0.01 and 0.36±0.02 for Turkish and Iranian populations, respectively. In total, 19 haplotypes were observed from 24 polymorphic sites in Turkish and Iranian native chicken populations. Two different clades or haplogroups (A and E) were found in Turkish and Iranian chickens. Clade A haplotypes were found only in White Marandi, Common Breed and New Hampshire populations. Clade E haplotypes, which are quite common, were observed in Turkish and Iranian populations with 18 different haplotypes, of which Turkish and Iranian chickens, Clade E, haplotype 1 (TRIRE1) was a major haplotype with the frequency of 81.5% (181/222) across all breeds. Compared to red jungle fowl, Turkish and Iranian chicken breeds are closely related to each other. These results suggest that Turkish and Iranian chickens originated from the same region, the Indian subcontinent. Our results will provide reliable basic information for mtDNA haplotypes of Turkish and Iranian chickens and for studying the origin of domestic chickens.
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Affiliation(s)
- Hasan Meydan
- Department of Agricultural Biotechnology, Faculty of Agriculture, Akdeniz University, Antalya 07058, Turkey
| | - Cafer Pish Jang
- Department of Animal Science, Islamic Azad University of Maragheh, Maragheh 11369, Iran
| | - Mehmet Ali Yıldız
- Department of Animal Science, Faculty of Agriculture, Ankara University, Ankara 06100, Turkey
| | - Steffen Weigend
- Friedrich-Loeffler-Institut, Institute of Farm Animal Genetics, Mariensee, Neustadt D-31535, Germany
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The Expression of Nuclear Transcription Factor Kappa B (NF-κB) in the Case of Critically Ill Polytrauma Patients with Sepsis and Its Interactions with microRNAs. Biochem Genet 2016; 54:337-347. [PMID: 27003424 DOI: 10.1007/s10528-016-9727-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 03/14/2016] [Indexed: 12/22/2022]
Abstract
Critical polytrauma patients present a series of pathophysiological disturbances, biochemical and molecular dysfunction, which comprise to be the major cause of intensive care unit admission. In regard to molecular damage, there exists a series of factors, which all together contribute to the aggravation of the clinical status leading to increased mortality rate in these patients. One of the most important biochemical factors involved is the nuclear transcription factor B (NF-κB). Impaired NF-κB functioning is reflected on the clinical status of the patient through increased production of pro-inflammatory molecule, leading to multiple organ dysfunction syndrome. In addition to this, through microRNAs interactions, various pathophysiological as well as biochemical disturbances are produced, which altogether further reduce the patient's survival rate. In this paper, we would like to present the modifications seen in the expression of NF-κB in critically polytraumatized patients with sepsis. In additions to this, we would like to discuss the correlation between the microRNAs and its further implications in clinical status of these patients.
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Özdemir E, Altındağ A, Kandemir İ. Molecular diversity of some species belonging to the genus Daphnia O. F. Müller, 1785 (Crustacea: Cladocera) in Turkey. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:424-433. [PMID: 27159716 DOI: 10.3109/19401736.2015.1136303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Daphnia is a freshwater zooplankton species with controversial taxonomy due to its high morphological variation linked to environmental factors and inter-specific hybridization and polyploidy in some groups. The aim of the present study is to examine molecular diversity of some Daphnia species in Turkey and to establish DNA barcodes of Turkish Daphnia species. Sequence analysis was performed using 540 bp region of cytochrome oxidase subunit I gene of mitochondrial DNA. A total of 34 haplotypes have been identified for Turkey. Daphnia pulex complex was divided into two clades with 16.1% sequence divergence according to molecular taxonomy based on Kimura 2-parameter. The clade which was molecularly diverged from Daphnia pulex with 16.1% sequence divergence was found to show 99% similarity with Daphnia cf. pulicaria (sensu Alonso 1996) instead of Daphnia pulicaria Forbes, 1893. Furthermore, this study has contributed to Turkish zoogeography by demonstrating the distribution of Daphnia species in Turkey.
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Affiliation(s)
- Ebru Özdemir
- a Department of Molecular Biology and Genetics, Faculty of Science and Letters , University of Kafkas , Kars , Turkey.,b Department of Biology, Faculty of Science , University of Ankara , Ankara , Turkey
| | - Ahmet Altındağ
- b Department of Biology, Faculty of Science , University of Ankara , Ankara , Turkey
| | - İrfan Kandemir
- b Department of Biology, Faculty of Science , University of Ankara , Ankara , Turkey
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Anh NTL, Kunhareang S, Duangjinda M. Association of Chicken Growth Hormones and Insulin-like Growth Factor Gene Polymorphisms with Growth Performance and Carcass Traits in Thai Broilers. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:1686-95. [PMID: 26580435 PMCID: PMC4647076 DOI: 10.5713/ajas.15.0028] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 04/06/2015] [Accepted: 05/19/2015] [Indexed: 11/27/2022]
Abstract
Molecular marker selection has been an acceptable tool in the acceleration of the genetic response of desired traits to improve production performance in chickens. The crossbreds from commercial parent stock (PS) broilers with four Thai synthetic breeds; Kaen Thong (KT), Khai Mook Esarn (KM), Soi Nin (SN), and Soi Pet (SP) were used to study the association among chicken growth hormones (cGH) and the insulin-like growth factor (IGF-I) genes for growth and carcass traits; for the purpose of developing a suitable terminal breeding program for Thai broilers. A total of 408 chickens of four Thai broiler lines were genotyped, using polymerase chain reaction-restriction fragment length polymorphism methods. The cGH gene was significantly associated with body weight at hatching; at 4, 6, 8, 10 weeks of age and with average daily gain (ADG); during 2 to 4, 4 to 6, 0 to 6, 0 to 8, and 0 to 10 weeks of age in PS×KM chickens. For PS×KT populations, cGH gene showed significant association with body weight at hatching, and ADG; during 8 to 10 weeks of age. The single nucleotide polymorphism variant confirmed that allele G has positive effects for body weight and ADG. Within carcass traits, cGH revealed a tentative association within the dressing percentage. For the IGF-I gene polymorphism, there were significant associations with body weight at hatching; at 2, 4, and 6 weeks of age and ADG; during 0 to 2, 4 to 6, and 0 to 6 weeks of age; in all of four Thai broiler populations. There were tentative associations of the IGF-I gene within the percentages of breast muscles and wings. Thus, cGH gene may be used as a candidate gene, to improve growth traits of Thai broilers.
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Affiliation(s)
- Nguyen Thi Lan Anh
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Sajee Kunhareang
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand ; Research and Development Network Center for Animal Breeding (Native Chicken), Khon Kaen University, Khon Kaen 40002, Thailand
| | - Monchai Duangjinda
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand ; Research and Development Network Center for Animal Breeding (Native Chicken), Khon Kaen University, Khon Kaen 40002, Thailand
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Abebe AS, Mikko S, Johansson AM. Genetic diversity of five local Swedish chicken breeds detected by microsatellite markers. PLoS One 2015; 10:e0120580. [PMID: 25855978 PMCID: PMC4391840 DOI: 10.1371/journal.pone.0120580] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 01/27/2015] [Indexed: 11/19/2022] Open
Abstract
This study aimed at investigating the genetic diversity, relationship and population structure of 110 local Swedish chickens derived from five breeds (Gotlandshöna, Hedemorahöna, Öländsk dvärghöna, Skånsk blommehöna, and Bohuslän- Dals svarthöna, in the rest of the paper the shorter name Svarthöna is used) using 24 microsatellite markers. In total, one hundred thirteen alleles were detected in all populations, with a mean of 4.7 alleles per locus. For the five chicken breeds, the observed and expected heterozygosity ranged from 0.225 to 0.408 and from 0.231 to 0.515, with the lowest scores for the Svarthöna and the highest scores for the Skånsk blommehöna breeds, respectively. Similarly, the average within breed molecular kinship varied from 0.496 to 0.745, showing high coancestry, with Skånsk blommehöna having the lowest and Svarthöna the highest coancestry. Furthermore, all breeds showed significant deviations from Hardy-Weinberg expectations. Across the five breeds, the global heterozygosity deficit (FIT) was 0.545, population differentiation index (FST) was 0.440, and the global inbreeding of individuals within breed (FIS) was 0.187. The phylogenetic relationships of chickens were examined using neighbor-joining trees constructed at the level of breeds and individual samples. The neighbor-joining tree constructed at breed level revealed two main clusters, with Hedemorahöna and Öländsk dvärghöna breeds in one cluster, and Gotlandshöna and Svarthöna breeds in the second cluster leaving the Skånsk blommehöna in the middle. Based on the results of the STRUCTURE analysis, the most likely number of clustering of the five breeds was at K = 4, with Hedemorahöna, Gotlandshöna and Svarthöna breeds forming their own distinct clusters, while Öländsk dvärghöna and Skånsk blommehöna breeds clustered together. Losses in the overall genetic diversity of local Swedish chickens due to breeds extinction varied from -1.46% to -6.723%. The results of the current study can be used as baseline genetic information for genetic conservation program, for instance, to control inbreeding and to implement further genetic studies in local Swedish chickens.
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Affiliation(s)
- Abiye Shenkut Abebe
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sofia Mikko
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anna M. Johansson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
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ESFAHANI EFFATNASR, ESKANDARINASAB MORADPASHA, KHANIAN SAEEDESMAEIL, NIKMARD MEHDI, MOLAEE VAHID. Genetic diversity of a native chicken breed in Iran. J Genet 2014. [DOI: 10.1007/s12041-012-0139-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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16
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Suh S, Sharma A, Lee S, Cho CY, Kim JH, Choi SB, Kim H, Seong HH, Yeon SH, Kim DH, Ko YG. Genetic diversity and relationships of korean chicken breeds based on 30 microsatellite markers. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 27:1399-405. [PMID: 25178290 PMCID: PMC4150171 DOI: 10.5713/ajas.2014.14016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 03/21/2014] [Accepted: 06/03/2014] [Indexed: 11/27/2022]
Abstract
The effective management of endangered animal genetic resources is one of the most important concerns of modern breeding. Evaluation of genetic diversity and relationship of local breeds is an important factor towards the identification of unique and valuable genetic resources. This study aimed to analyze the genetic diversity and population structure of six Korean native chicken breeds (n = 300), which were compared with three imported breeds in Korea (n = 150). For the analysis of genetic diversity, 30 microsatellite markers from FAO/ISAG recommended diversity panel or previously reported microsatellite markers were used. The number of alleles ranged from 2 to 15 per locus, with a mean of 8.13. The average observed heterozygosity within native breeds varied between 0.46 and 0.59. The overall heterozygote deficiency (F IT) in native chicken was 0.234±0.025. Over 30.7% of F IT was contributed by within-population deficiency (F IS). Bayesian clustering analysis, using the STRUCTURE software suggested 9 clusters. This study may provide the background for future studies to identify the genetic uniqueness of the Korean native chicken breeds.
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Affiliation(s)
- Sangwon Suh
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Aditi Sharma
- Hanwoo Experiment Station, Pyeongchang 232-950, Korea
| | - Seunghwan Lee
- Hanwoo Experiment Station, Pyeongchang 232-950, Korea
| | - Chang-Yeon Cho
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Jae-Hwan Kim
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Seong-Bok Choi
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Hyun Kim
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Hwan-Hoo Seong
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | | | - Dong-Hun Kim
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Yeoung-Gyu Ko
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
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Seo DW, Hoque MR, Choi NR, Sultana H, Park HB, Heo KN, Kang BS, Lim HT, Lee SH, Jo C, Lee JH. Discrimination of korean native chicken lines using fifteen selected microsatellite markers. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 26:316-22. [PMID: 25049793 PMCID: PMC4093483 DOI: 10.5713/ajas.2012.12469] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 11/23/2012] [Accepted: 10/31/2012] [Indexed: 11/27/2022]
Abstract
In order to evaluate the genetic diversity and discrimination among five Korean native chicken lines, a total of 86 individuals were genotyped using 150 microsatellite (MS) markers, and 15 highly polymorphic MS markers were selected. Based on the highest value of the number of alleles, the expected heterozygosity (He) and polymorphic information content (PIC) for the selected markers ranged from 6 to 12, 0.466 to 0.852, 0.709 to 0.882 and 0.648 to 0.865, respectively. Using these markers, the calculated genetic distance (Fst), the heterozygote deficit among chicken lines (Fit) and the heterozygote deficit within chicken line (Fis) values ranged from 0.0309 to 0.2473, 0.0013 to 0.4513 and -0.1002 to 0.271, respectively. The expected probability of identity values in random individuals (PI), random half-sib (PI half-sibs ) and random sibs (PI sibs ) were estimated at 7.98×10(-29), 2.88×10(-20) and 1.25×10(-08), respectively, indicating that these markers can be used for traceability systems in Korean native chickens. The unrooted phylogenetic neighbor-joining (NJ) tree was constructed using 15 MS markers that clearly differentiated among the five native chicken lines. Also, the structure was estimated by the individual clustering with the K value of 5. The selected 15 MS markers were found to be useful for the conservation, breeding plan, and traceability system in Korean native chickens.
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Affiliation(s)
- D W Seo
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 305-764, Korea
| | - M R Hoque
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 305-764, Korea
| | - N R Choi
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 305-764, Korea
| | - H Sultana
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 305-764, Korea
| | - H B Park
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 305-764, Korea
| | - K N Heo
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 305-764, Korea
| | - B S Kang
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 305-764, Korea
| | - H T Lim
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 305-764, Korea
| | - S H Lee
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 305-764, Korea
| | - C Jo
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 305-764, Korea
| | - J H Lee
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 305-764, Korea
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Fonteque GV, Battilana J, Paludo E, Lima-Rosa CADV. Genetic polymorphism of fifteen microsatellite loci in Brazilian (blue-egg Caipira) chickens. PESQUISA VETERINÁRIA BRASILEIRA 2014. [DOI: 10.1590/s0100-736x2014000100016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The purpose of this study was to investigate the genetic polymorphism of fifteen microsatellites loci in Brazilian (blue-egg Caipira) chickens. Samples were collected from 100 blue eggs of Caipira chickens from rural properties in the city of Dois Lajeados, RS. After DNA extraction, the fragments related to molecular markers LEI0248, LEI0221, LEI0214, LEI0192, LEI0217, LEI0254, LEI0194, LEI0212, MCW0371, ADL0278, LEI0234, MCW0183, MCW0216, MCW0330 and MCW0081 were obtained by polymerase chain reaction (PCR). The statistical analysis were carried out with the softwares ARLEQUIN 3.5 version and CERVUS 3.0.3 version. The allelic and genotypic frequencies, deviations from Hardy-Weinberg equilibrium, estimates of observed (HO) and expected (HE) heterozygosity and polymorphic information content (PIC) were obtained for each marker locus. A total of 186 alleles from 15 loci were obtained, with sizes ranging of 83 to 490 base pairs. The medium number of alleles was 12.4, the HE was 0.76±0.14 and HO was 0.49±0.21 and PIC was 0.706. The first conclusion is that the microsatellites used are polymorphic and can be used to genetic studies in chickens. The second is that the "Caipira" chicken (blue eggs) population investigated has a great genic variability, which makes than an important source of genetic resources for future animal breeding programs.
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Suh S, Cho CY, Kim JH, Choi SB, Kim YS, Kim H, Seong HH, Lim HT, Cho JH, Ko YG. Analysis of Genetic Characteristics and Probability of Individual Discrimination in Korean Indigenous Chicken Brands by Microsatellite Marker. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2013. [DOI: 10.5187/jast.2013.55.3.185] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Choi NR, Hoque MR, Seo DW, Sultana H, Park HB, Lim HT, Heo KN, Kang BS, Jo C, Lee JH. ISAG-recommended Microsatellite Marker Analysis Among Five Korean Native Chicken Lines. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2012. [DOI: 10.5187/jast.2012.54.6.401] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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