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Huang L, Guo Q, Wu Y, Jiang Y, Bai H, Wang Z, Chen G, Chang G. Carcass traits, proximate composition, amino acid and fatty acid profiles, and mineral contents of meat from Cherry Valley, Chinese crested, and crossbred ducks. Anim Biotechnol 2023; 34:2459-2466. [PMID: 35816470 DOI: 10.1080/10495398.2022.2096625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Duck meat is known for its taste and high nutritive value. To preserve local genetic diversity while maintaining commercial viability, we obtained a crossbreed (CB) between high-performing Cherry Valley (CV) and traditional Chinese crested (CC) ducks. We compared carcass traits and meat quality characteristics of CB and parental breeds. Meat from the above ducks at their respective marketable ages was evaluated for proximate composition, amino acid and fatty acid profiles, and selected mineral content. The live weights, carcass weights, and breast muscle percentage of CB were higher than CC but lower than CV; the leg muscle of CB was lower than CV and CC. CB had higher intramuscular fat content than CV; its collagen content was lower than CC but higher than CV in breast and thigh muscles. Additionally, the saturated fatty acid content of CB muscle was lower than CV and higher than CC. CB contained more monounsaturated fatty acids than CV and CC. Zn content was higher in CB breast than CV and CC. CB, obtained by crossing CV and CC, has partial advantages over both the breeds suggesting that these characteristics aligned with standards to breed ducks with high-quality meat.
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Affiliation(s)
- Lan Huang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Qixin Guo
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Yun Wu
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Yong Jiang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Hao Bai
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Zhixiu Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Guohong Chen
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Guobin Chang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
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Chen H, Luo K, Wang C, Xuan R, Zheng S, Tang H, Li Y, Xiong Y, Wu Y, Wang L, Ouyang J, Yan X. Genomic characteristics and selection signals of Zhongshan ducks. Animal 2023; 17:100797. [PMID: 37121157 DOI: 10.1016/j.animal.2023.100797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 03/20/2023] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
The Zhongshan duck (ZSP) is a duck breed indigenous to China and is known for its moderate body size, strong disease resistance, tender meat, and little subcutaneous fat. However, the genomic basis of such excellent breeding characteristics remains poorly understood. Therefore, we generated whole-genomes of 58 ZSPs and 180 other indigenous Chinese ducks (60 Jinding ducks, 60 Shan Partridge ducks, and 60 Liancheng white ducks) and identified 10 560 032 single nucleotide polymorphisms and 1 334 893 structural variants. Based on genetic diversity and population structure indices, our results confirm that the ZSP is a unique germplasm resource. In addition, three reproduction-related genes (i.e., OAZ, AMH, and RLF) were located in highly differentiated regions between the ZSP and the other three duck breeds (Jinding duck; Liancheng White duck; Shan Partridge duck), suggesting that these genes may have a strong influence on egg production. Among these genes, AMH may have introgressed from an unknown species of the Anatidae family. We also identified other significant genes in the significantly differentiated window (i.e., 1% cut-off), some of which are responsible for growth and development (SEMA5B and MIB1), metabolism (EDEM3 and Xylb), skeletal system morphogenesis (bglap and MGP), and egg shape (ITPR2). These findings highlight the genetic characteristics of the ZSP that shape an array of its morphological traits. Overall, this study should facilitate a more fine-scale approach towards improving the ZSP and other indigenous ducks in China and even all over the world.
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Zhang Y, Bao Q, Cao Z, Bian Y, Zhang Y, Cao Z, Chen G, Xu Q. Chinese Domestic Ducks Evolved from Mallard Duck (Anas platyrhynchos) and Spot-Billed Duck (A. zonorhyncha). Animals (Basel) 2023; 13:ani13071156. [PMID: 37048411 PMCID: PMC10093112 DOI: 10.3390/ani13071156] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/19/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
China has a rich genetic resource in its 34 domestic duck breeds. In order to detect the genetic diversity and explore the origin of these indigenous duck populations, the mitochondrial DNA (mtDNA) control region was sequenced and analyzed for 208 individual ducks, including 22 domestic breeds, wild Mallards ducks, Eastern spot-billed ducks, White Muscovy ducks, and Black Muscovy ducks. The haplotype diversity (Hd) was 0.653 and the average nucleotide diversity (Pi) was 0.005, indicating moderate genetic diversity. Sixty haplotypes were detected, and the maximum-likelihood (ML) phylogenetic tree and median-joining (MJ) network were generated from the sequence analyses. In this study, haplotypes from the Mallard duck (Anas platyrhynchos) were detected in most of the Chinese domestic duck breeds. In addition, the Eastern spot-billed duck (A. zonorhyncha) H8 haplotype was detected in two duck breeds. Only two haplotypes were found in Muscovy ducks, suggesting low genetic diversity within this population. The sequence and haplotype analyses revealed that both A. platyrhynchos and A. zonorhyncha contributed to the evolution of domestic ducks in China.
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Affiliation(s)
- Yang Zhang
- Key Laboratory for Evaluation and Utilization of Poultry Genetic Resources of Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China
| | - Qiang Bao
- Key Laboratory for Evaluation and Utilization of Poultry Genetic Resources of Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China
| | - Zhi Cao
- Key Laboratory for Evaluation and Utilization of Poultry Genetic Resources of Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China
| | - Youqing Bian
- Jiangsu Sci-Tech Demonstration Garden of Modern Animal Husbandy, Taizhou 225300, China
| | - Yu Zhang
- Key Laboratory for Evaluation and Utilization of Poultry Genetic Resources of Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China
| | - Zhengfeng Cao
- Key Laboratory for Evaluation and Utilization of Poultry Genetic Resources of Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China
| | - Guohong Chen
- Key Laboratory for Evaluation and Utilization of Poultry Genetic Resources of Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Qi Xu
- Key Laboratory for Evaluation and Utilization of Poultry Genetic Resources of Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China
- Correspondence: ; Tel.: +86-0514-87997206
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Jia Y, Qiu G, Cao C, Wang X, Jiang L, Zhang T, Geng Z, Jin S. Mitochondrial genome and phylogenetic analysis of Chaohu duck. Gene 2022; 851:147018. [DOI: 10.1016/j.gene.2022.147018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/13/2022] [Accepted: 10/25/2022] [Indexed: 11/04/2022]
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5
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Adeola AC, Sola-Ojo FE, Opeyemi YA, Oguntunji AO, Nneji LM, Ewuola MK, Bello SF, Olaniyi WA, Adesoji AT, Karuno AP, Sanke OJ, Daniel EL. Genetic diversity and population structure of muscovy duck ( Cairina moschata) from Nigeria. PeerJ 2022; 10:e13236. [PMID: 35444865 PMCID: PMC9014852 DOI: 10.7717/peerj.13236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/17/2022] [Indexed: 01/15/2023] Open
Abstract
The domestic Muscovy duck (Cairina moschata) provide unique genetic resources patterned by both tropical environmental conditions and human activities, the evaluation of their genetic diversity and population structure will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the variation in mtDNA cytochrome b and nuclear DNA CYP2U1 sequences of 378 Nigerian Muscovy ducks (comprising of 287 de novo and 91 downloaded) plus 80 published sequences of Muscovy ducks from India. The results showed high haplotype diversity (0.800 ± 0.023) among Nigerian Muscovy duck populations with 91 distinct haplotypes for the nuclear DNA CYP2U1 gene but low (0.266 ± 0.033) for cytochrome b with 31 haplotypes. The median-joining networks of both markers grouped Nigerian Muscovy ducks into two; the first group consisting of only Nigerian Muscovy duck populations, and the second group Nigerian with Indian populations. Neutrality test results indicated that Nigerian populations experienced recent population expansion and/or genetic hitchhiking. A geographic signal was absent in line with previously studied poultry species in Nigeria. The most prominent haplotype dominated across all regions in Nigeria, which may be due to extensive genetic intermixing except for the Indian population (F ST = 0.02550, P = 0.01075). This indicated low genetic differentiation between and within Nigerian Muscovy duck as revealed by the suitability of the nuclear DNA CYP2U1 gene.
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Affiliation(s)
- Adeniyi C. Adeola
- Molecular Evolution and Genome Diversity, State Key Laboratory of Genetic Resources & Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, Yunnan, China,Centre for Biotechnology Research, Bayero University, Kano, Nigeria
| | - Foluke E. Sola-Ojo
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, Kwara, Nigeria
| | - Yusuf A. Opeyemi
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, Kwara, Nigeria
| | - Abel O. Oguntunji
- Department of Animal Science and Fisheries Management, Bowen University, Iwo, Osun, Nigeria
| | - Lotanna Micah Nneji
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States
| | - Muslim K. Ewuola
- Animal Breeding and Genetics Unit/Department of Animal Science, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Semiu F. Bello
- Department of Animal Genetics/Breeding and Reproduction/College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Wasiu A. Olaniyi
- Department of Animal Science, Faculty of Agriculture, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Adeosun T. Adesoji
- Department of Agricultural Education, Federal College of Education, Bichi, Kano, Nigeria
| | - Alex P. Karuno
- Molecular Evolution and Genome Diversity, State Key Laboratory of Genetic Resources & Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Oscar J. Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Taraba, Nigeria
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Wang R, Sun J, Han H, Huang Y, Chen T, Yang M, Wei Q, Wan H, Liao Y. Whole-genome resequencing reveals genetic characteristics of different duck breeds from the Guangxi region in China. G3-GENES GENOMES GENETICS 2021; 11:6156632. [PMID: 33677537 PMCID: PMC8759808 DOI: 10.1093/g3journal/jkab054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/17/2021] [Indexed: 11/15/2022]
Abstract
Distinctive indigenous duck (Anas platyrhynchos) populations of Guangxi, China, evolved due to the geographical, cultural, and environmental variability of this region. To investigate the genetic diversity and population structure of the indigenous ducks of Guangxi, 78 individuals from eight populations were collected and sequenced by whole-genome resequencing with an average depth of ∼9.40×. The eight indigenous duck populations included four breeds and four resource populations. Moreover, the genome data of 47 individuals from two typical meat-type breeds and two native egg-type breeds were obtained from a public database. Calculation of heterozygosity, nucleotide diversity (π), Tajima’s D, and FST indicated that the Guangxi populations were characterized by higher genetic diversity and lower differentiation than meat-type breeds. The highest diversity was observed in the Xilin-Ma ducks. Principal component, structure, and phylogenetic tree analyses revealed the relationship between the indigenous duck populations of Guangxi. A mild degree of differentiation was observed among the Guangxi populations, although three populations were closer to the meat or egg breeds. Indigenous populations are famous for their special flavor, small body size, and slow growth rates. Selective sweep analysis revealed the candidate genes and pathways associated with these growth traits. Our findings provide a valuable source of information regarding genetic diversity, population conservation, and genome-associated breeding of ducks.
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Affiliation(s)
- Ran Wang
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, Guangdong 518120, China.,ShenZhen Engineering Laboratory for Genomics-Assisted Animal Breeding, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Junli Sun
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530001, China
| | - Hu Han
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, Guangdong 518120, China.,ShenZhen Engineering Laboratory for Genomics-Assisted Animal Breeding, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Yingfei Huang
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530001, China
| | - Tao Chen
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, Guangdong 518120, China.,ShenZhen Engineering Laboratory for Genomics-Assisted Animal Breeding, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Manman Yang
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, Guangdong 518120, China.,ShenZhen Engineering Laboratory for Genomics-Assisted Animal Breeding, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Qiang Wei
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, Guangdong 518120, China.,ShenZhen Engineering Laboratory for Genomics-Assisted Animal Breeding, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Huofu Wan
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530001, China
| | - Yuying Liao
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530001, China.,Guangxi Veterinary Research Institute, Nanning, Guangxi 530001, China
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De AK, Sawhney S, Bhattacharya D, Sujatha T, Sunder J, Ponraj P, Ravi SK, Mondal S, Malakar D, Kundu A. Origin, genetic diversity and evolution of Andaman local duck, a native duck germplasm of an insular region of India. PLoS One 2021; 16:e0245138. [PMID: 33561119 PMCID: PMC7872295 DOI: 10.1371/journal.pone.0245138] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 12/23/2020] [Indexed: 11/29/2022] Open
Abstract
Domestic ducks are of paramount importance as a cheap source of protein in rural India. Andaman local duck (ALD) is an indigenous avian genetic resource of Andaman and Nicobar islands (ANI) and is mainly distributed in Middle and Northern parts of these islands. Negligence has brought this breed on the edge of extinction necessitating immediate conservation efforts. Here, we report the genetic diversity, population structure and matrilineal genetic root of ALD. Partial mtDNA D-loop sequences were analyzed in 71 ALD samples and analysis revealed 19 polymorphic sites and 13 haplotypes. Estimated haplotype (Hd ± SD) and nucleotide diversity (π ± SD) were 0.881 ± 0.017 and 0.00897 ± 0.00078 respectively. The high genetic diversity of ALD indicates introgression of genetic material from other local duck breeds. In addition, it can be postulated that ALD bearing high genetic diversity has strong ability to adapt to environmental changes and can withstand impending climate change. Phylogenetic and network analysis indicate that ALD falls under Eurasian clade of mallard and ALD forms three clusters; one cluster is phylogenetically close to Southeast Asian countries, one close to Southern part of mainland India and the third one forms an independent cluster. Therefore, ALD might have migrated either from Southeast Asian countries which enjoy a close cultural bondage with ANI from time immemorial or from Southern part of India. The independent cluster may have evolved locally in these islands and natural selection pressure imposed by environmental conditions might be the driving force for evaluation of these duck haplotypes; which mimics Darwin's theory of natural selection. The results of the study will be beneficial for formulating future breeding programme and conservation strategy towards sustainable development of the duck breed.
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Affiliation(s)
- Arun Kumar De
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Sneha Sawhney
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Debasis Bhattacharya
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - T. Sujatha
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Jai Sunder
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Perumal Ponraj
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - S. K. Ravi
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Samiran Mondal
- Department of Veterinary Pathology, West Bengal University of Animal and Fishery Sciences, Kolkata, West Bengal, India
| | - Dhruba Malakar
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana, India
| | - A. Kundu
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
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Zhang Y, Wang L, Bian Y, Wang Z, Xu Q, Chang G, Chen G. Marginal diversity analysis of conservation of Chinese domestic duck breeds. Sci Rep 2019; 9:13141. [PMID: 31511604 PMCID: PMC6739371 DOI: 10.1038/s41598-019-49652-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/29/2019] [Indexed: 11/24/2022] Open
Abstract
The present study aimed to systematically evaluate the genetic diversity of Chinese domestic duck breeds and ensure the most effective allocation and usage of conservation funds. We first performed an analysis of DNA genetic distance in 21 duck breeds by measuring short tandem repeats. Then, we calculated the extinction probability, contribution rate, and marginal diversity for each breed. The results showed that the extinction rate of the Zhongshan duck, Guangxi duck, and Ji'an duck were the highest at 0.67, 0.59, and 0.59, respectively, and that of the Linwu duck, Jinding duck, and Gaoyou duck were the lowest at 0.15, 0.18, and 0.19, respectively. The current diversity of populations was 7.72 and the expected diversity in five hundred years is 5.14 ± 1.15. The marginal diversity of the Chinese Muscovy duck was the largest (-2.20), accounting for 42.61% of the expected diversity, followed by the Guangxi duck (-0.49, 9.44%), whereas the Jinding duck was the smallest (-0.12; 2.32%). The protection potency of the Chinese Muscovy duck was the largest (0.61), followed by Guangxi duck (0.29), whereas the Jinding duck was the smallest (0.02). This study provides a reference for determining the conservation priority of Chinese domestic duck breeds or genetic resources.
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Affiliation(s)
- Yang Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, People's Republic of China.
| | - Laidi Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, People's Republic of China
| | - Youqing Bian
- Jiangsu Sci-tech Demonstration Garden of Modern Animal Husbandy, Taizhou, 225300, Jiangsu, People's Republic of China
| | - Zhaoshan Wang
- Jiangsu Eco Food Company Limited, Suqian, 223600, Jiangsu, People's Republic of China
| | - Qi Xu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, People's Republic of China
| | - Guobin Chang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, People's Republic of China
| | - Guohong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, People's Republic of China
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Padilla-Jacobo G, Cano-Camacho H, López-Zavala R, Cornejo-Pérez ME, Zavala-Páramo MG. Evolutionary history of Mexican domesticated and wild Meleagris gallopavo. Genet Sel Evol 2018; 50:19. [PMID: 29665772 PMCID: PMC5905111 DOI: 10.1186/s12711-018-0388-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 04/02/2018] [Indexed: 02/08/2023] Open
Abstract
Background The distribution of the wild turkey (Meleagris gallopavo) extends from Mexico to southeastern Canada and to the eastern and southern regions of the USA. Six subspecies have been described based on morphological characteristics and/or geographical variations in wild and domesticated populations. In this paper, based on DNA sequence data from the mitochondrial D-loop, we investigated the genetic diversity and structure, genealogical relationships, divergence time and demographic history of M. gallopavo populations including domesticated individuals. Results Analyses of 612 wild and domesticated turkey mitochondrial D-loop sequences, including 187 that were collected for this study and 425 from databases, revealed 64 haplotypes with few mutations, some of which are shared between domesticated and wild turkeys. We found a high level of haplotype and nucleotide diversity, which suggests that the total population of this species is large and stable with an old evolutionary history. The results of genetic differentiation, haplotype network, and genealogical relationships analyses revealed three main genetic groups within the species: mexicana as a population relict (C1), merriami (C2), and mexicana/intermedia/silvestris/osceola (C3). Haplotypes detected in domesticated turkeys belong to group C3. Estimates of divergence times agree with range expansion and diversification events of the relict population of M. gallopavo in northwestern Mexico during the Pliocene–Pleistocene and Pleistocene–Holocene boundaries. Demographic reconstruction showed that an expansion of the population occurred 110,000 to 130,000 years ago (Kya), followed by a stable period 100 Kya and finally a decline ~ 10 Kya (Pleistocene–Holocene boundary). In Mexico, the Trans-Mexican Volcanic Belt may be responsible for the range expansion of the C3 group. Two haplotypes with different divergence times, MGMDgoB/MICH1 and MICH2, are dominant in domesticated and commercial turkeys. Conclusions During the Pleistocene, a large and stable population of M. gallopavo covered a wide geographic distribution from the north to the center of America (USA and Mexico). The mexicana, merriami, and mexicana/intermedia/silvestris/osceola genetic groups originated after divergence and range expansion from northwestern Mexico during the Pliocene–Pleistocene and Pleistocene–Holocene boundaries. Old and new maternal lines of the mexicana/intermedia/silvestris/osceola genetic group were distributed within the Trans-Mexican Volcanic Belt where individuals were captured for domestication. Two haplotypes are the main founder maternal lines of domesticated turkeys. Electronic supplementary material The online version of this article (10.1186/s12711-018-0388-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gabriela Padilla-Jacobo
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Km. 9.5 Carretera Morelia-Zinapécuaro, Posta Veterinaria, C.P. 58000, Tarímbaro, Michoacán, Mexico
| | - Horacio Cano-Camacho
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Km. 9.5 Carretera Morelia-Zinapécuaro, Posta Veterinaria, C.P. 58000, Tarímbaro, Michoacán, Mexico
| | - Rigoberto López-Zavala
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma de Tamaulipas, Km. 5, Carretera a Cd. Mante S/S, C.P. 87276, Ciudad Victoria, Tamaulipas, Mexico
| | - María E Cornejo-Pérez
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Km. 9.5 Carretera Morelia-Zinapécuaro, Posta Veterinaria, C.P. 58000, Tarímbaro, Michoacán, Mexico
| | - María G Zavala-Páramo
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Km. 9.5 Carretera Morelia-Zinapécuaro, Posta Veterinaria, C.P. 58000, Tarímbaro, Michoacán, Mexico.
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10
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Gene expression patterns in Korean native ducks ( Anas platyrhynchos) with different apparent metabolisable energy (AME) levels. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.05.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Gaur U, Tantia MS, Mishra B, Bharani Kumar ST, Vijh RK, Chaudhury A. Mitochondrial D-loop analysis for uncovering the population structure and genetic diversity among the indigenous duck (Anas platyrhynchos) populations of India. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:212-219. [PMID: 28116946 DOI: 10.1080/24701394.2016.1267158] [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: 10/20/2022]
Abstract
The indigenous domestic duck (Anas platyrhynchos domestica) which is domesticated from Mallard (Anas platyrhynchos) contributes significantly to poor farming community in coastal and North Eastern regions of India. For conservation and maintenance of indigenous duck populations it is very important to know the existing genetic diversity and population structure. To unravel the population structure and genetic diversity among the five indigenous duck populations of India, the mitochondrial D-loop sequences of 120 ducks were analyzed. The sequence analysis by comparison of mtDNA D-loop region (470 bp) of five Indian duck populations revealed 25 mitochondrial haplotypes. Pairwise FST value among populations was 0.4243 (p < .01) and the range of nucleotide substitution per site (Dxy) between the five Indian duck populations was 0.00034-0.00555, and the net divergence (Da) was 0-0.00355. The phylogenetic analysis in the present study unveiled three clades. The analysis revealed genetic continuity among ducks of coastal region of the country which formed a separate group from the ducks of the inland area. Both coastal as well as the land birds revealed introgression of the out group breed Khaki Campbell, which is used for breed improvement programs in India. The observations revealed very less selection and a single matrilineal lineage of indigenous domestic ducks.
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Affiliation(s)
- Uma Gaur
- a National Bureau of Animal Genetic Resources , Karnal , India.,b Department of Bio & Nano Technology , Guru Jambheshwar University of Science and Technology , Hisar , India
| | | | - Bina Mishra
- c Indian Veterinary Research Institute , Izatnagar , India
| | - Settypalli Tirumala Bharani Kumar
- d Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications , International Atomic Energy Agency , Vienna , Austria
| | | | - Ashok Chaudhury
- b Department of Bio & Nano Technology , Guru Jambheshwar University of Science and Technology , Hisar , India
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Kameshpandian P, Thomas S, Nagarajan M. Genetic diversity and relationship of Indian Muscovy duck populations. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:165-169. [PMID: 28034341 DOI: 10.1080/24701394.2016.1261851] [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: 10/20/2022]
Abstract
Assessment of genetic diversity within and between populations is a prerequisite for sustainable utilization of domestic species. The domestic Muscovy duck (Cairina moschata) is an economically important species around the world for its unique meat taste and low-caloric content. It is one of the important domestic species in India as it ensures food security to the rural sectors. In this study, we have analyzed the genetic diversity and relationship of four Muscovy duck populations collected from different states (Assam, Mizoram, Odisha and Kerala) of India using mtDNA cytochrome b and nuclear DNA CYP2U1 genes. The results showed low genetic diversity among populations for both the genes. Kerala population showed significant genetic differences from the other three populations. The median joining network of cytochrome b gene suggested that the domestic Muscovy ducks present in India are the product of a single domestication event and probably introduced to India several years ago, as reported elsewhere. This study has also showed the suitability of nuclear DNA CYP2U1 gene in genetic diversity analysis.
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Affiliation(s)
- Paramasivam Kameshpandian
- a Department of Genomic Science, School of Biological Sciences , Central University of Kerala , Kasaragod , Kerala , India
| | - Subhash Thomas
- a Department of Genomic Science, School of Biological Sciences , Central University of Kerala , Kasaragod , Kerala , India
| | - Muniyandi Nagarajan
- a Department of Genomic Science, School of Biological Sciences , Central University of Kerala , Kasaragod , Kerala , India
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13
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Chen L, Luo J, Li JX, Li JJ, Wang DQ, Tian Y, Lu LZ. Transcriptome analysis of adiposity in domestic ducks by transcriptomic comparison with their wild counterparts. Anim Genet 2015; 46:299-307. [PMID: 25917302 DOI: 10.1111/age.12294] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2015] [Indexed: 01/28/2023]
Abstract
Excessive adiposity is a major problem in the duck industry, but its molecular mechanisms remain unknown. Genetic comparisons between domestic and wild animals have contributed to the exploration of genetic mechanisms responsible for many phenotypic traits. Significant differences in body fat mass have been detected between domestic and wild ducks. In this study, we used the Peking duck and Anas platyrhynchos as the domestic breed and wild counterpart respectively and performed a transcriptomic comparison of abdominal fat between the two breeds to comprehensively analyze the transcriptome basis of adiposity in ducks. We obtained approximately 350 million clean reads; assembled 61 250 transcripts, including 23 699 novel ones; and identified alternative 5' splice sites, alternative 3' splice sites, skipped exons and retained intron as the main alternative splicing events. A differential expression analysis between the two breeds showed that 753 genes exhibited differential expression. In Peking ducks, some lipid metabolism-related genes (IGF2, FABP5, BMP7, etc.) and oncogenes (RRM2, AURKA, CYR61, etc.) were upregulated, whereas genes related to tumor suppression and immunity (TNFRSF19, TNFAIP6, IGSF21, NCF1, etc.) were downregulated, suggesting adiposity might closely associate with tumorigenesis in ducks. Furthermore, 280 576 single-nucleotide variations were found differentiated between the two breeds, including 8641 non-synonymous ones, and some of the non-synonymous ones were found enriched in genes involved in lipid-associated and immune-associated pathways, suggesting abdominal fat of the duck undertakes both a metabolic function and immune-related function. These datasets enlarge our genetic information of ducks and provide valuable resources for analyzing mechanisms underlying adiposity in ducks.
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Affiliation(s)
- L Chen
- Institute of Animal Sciences and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
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14
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Heikkinen ME, Ruokonen M, Alexander M, Aspi J, Pyhäjärvi T, Searle JB. Relationship between wild greylag and European domestic geese based on mitochondrial DNA. Anim Genet 2015; 46:485-97. [PMID: 26096191 DOI: 10.1111/age.12319] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2015] [Indexed: 11/30/2022]
Abstract
The origins of the European domestic goose are uncertain. The available information comes from archaeological findings and historical literature, but genetic evidence has hitherto been scarce. The domestic goose in Europe is derived from the greylag goose (Anser anser), but it is not known where the initial domestication took place and which of the two subspecies of greylag goose was ancestral. We aimed to determine the amount and geographical distribution of genetic diversity in modern populations of greylag geese as well as in different breeds of the domestic goose to make inferences about goose domestication. We studied DNA sequence variation in the mitochondrial control region of greylag geese from multiple populations across Europe and western Asia as well as specimens of domestic geese representing 18 modern breeds and individuals not belonging to any recognised breed. Our results show notable differences in genetic diversity between different greylag goose populations and the presence of six mitochondrial haplogroups which show a degree of geographical partitioning. The genetic diversity of the domestic goose is low, with 84% of sampled individuals having one of two major closely related haplotypes, suggesting that modern European domestic geese may derive from a narrow genetic base. The site of domestication remains unresolved, but domestic geese in Turkey were unusually diverse, indicating the importance of further sampling in the vicinity of the eastern Mediterranean and the Near East. There appears to be past or ongoing hybridisation between greylags and domestic geese in particular areas, consistent with field observations.
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Affiliation(s)
- M E Heikkinen
- Genetics and Physiology Unit, University of Oulu, Oulu, 90014, Finland
| | - M Ruokonen
- Genetics and Physiology Unit, University of Oulu, Oulu, 90014, Finland
| | - M Alexander
- Department of Archaeology, University of York, York, YO10 5DD, United Kingdom
| | - J Aspi
- Genetics and Physiology Unit, University of Oulu, Oulu, 90014, Finland
| | - T Pyhäjärvi
- Genetics and Physiology Unit, University of Oulu, Oulu, 90014, Finland
| | - J B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853, USA
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15
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Investigating the puzzling genetic structure of mallard populations (Anas platyrhynchos L.) in Italy. EUR J WILDLIFE RES 2014. [DOI: 10.1007/s10344-014-0876-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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16
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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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18
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Volkovsky DV, Kulikova IV, Gerasimov YN, Zhuravlev YN. Genetic diversity of Anser albifrons Scopoli, 1769 and Anser fabalis Latham, 1787 in the Russian Far East. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413040169] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Hou ZC, Yang FX, Qu LJ, Zheng JX, Brun JM, Basso B, Pitel F, Yang N, Xu GY. Genetic structure of Eurasian and North American mallard ducks based on mtDNA data. Anim Genet 2011; 43:352-5. [PMID: 22486512 DOI: 10.1111/j.1365-2052.2011.02248.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To elucidate the origin and genetic structure of the domesticated duck in Eurasia and North America, we sequenced 114 duck D-loop sequences and retrieved 489 D-loop sequences from GenBank. In total, 603 ducks including 50 duck breeds/populations from eight countries (China, France, Russia, India, Kazakhstan, Mongolia, Thailand and USA) were used in this study. One hundred and thirty-four haplotypes and 81 variable sites were detected. H49 was the predominant haplotype, which was considered to be the same dominant haplotype found in the previous studies, and was found in 309 birds. The smallest values for both genetic differentiation index (F(ST), 0.04156) and the number of the net nucleotide substitutions between two populations (D(A), 0.00018) were observed between Eurasian domestic ducks and Eurasian mallards. No geography, breed or population clusters were observed in the Eurasian domestic ducks and mallards. Five haplotypes were shared by USA mallards and Eurasian domestic duck/Eurasian mallards. Only one haplotype (H49) was shared by Eurasian domestic ducks and China spot-billed ducks. By combining phylogenetic analyses, haplotype network profile, genetic distances and shared haplotypes, we can draw two major conclusions: (i) Eurasian and North American mallards show a clear geographic distribution pattern; (ii) Eurasian domestic ducks are derived from the Eurasian mallards, not from the spot-billed ducks.
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Affiliation(s)
- Z-C Hou
- National Engineering Laboratory for Animal Breeding and Ministry of Agriculture, China Agricultural University, Beijing, China
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20
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Li HF, Zhu WQ, Song WT, Shu JT, Han W, Chen KW. Origin and genetic diversity of Chinese domestic ducks. Mol Phylogenet Evol 2010; 57:634-40. [PMID: 20674751 DOI: 10.1016/j.ympev.2010.07.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Revised: 06/02/2010] [Accepted: 07/20/2010] [Indexed: 11/18/2022]
Abstract
China is particularly rich in duck genetic resources. In order to reveal the genetic diversity and origin of Chinese domestic duck, the 667 bp control region of mitochondrial DNA of 238 domestic ducks from 26 indigenous breeds, 25 wild mallards and nine spot-billed ducks were sequenced and analyzed them together with the published data for 12 mallards and nine spot-billed ducks. The haplotype diversity (Hd, 0.645) and average nucleotide diversity (Pi, 0.115%) indicate low genetic diversity of Chinese domestic ducks. The NJ phylogenetic tree and reduced median-joining network chart were constructed using a total of 72 haplotypes. The genetic contribution of mallard (Anas platyrhynchos) can be detected in most of Chinese indigenous duck breeds and that of spot-billed duck (Anas zonorhyncha) can also be detected in few Chinese indigenous duck breeds. The results indicated that the Chinese domestic ducks mainly derived from mallard (A. platyrhynchos) and few derived from spot-billed duck (A. zonorhyncha).
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Affiliation(s)
- Hui-Fang Li
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou 225003, PR China.
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Chen SY, He DQ, Liu YP. Low Genetic Variability of Domestic Muscovy Duck (Cairina moschata) in China Revealed by Mitochondrial DNA Control Region Sequences. Biochem Genet 2009; 47:734-8. [DOI: 10.1007/s10528-009-9272-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2008] [Accepted: 06/26/2009] [Indexed: 10/20/2022]
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