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Wolc A, Lisowski M, Grajewski B, Lewko L, Szwaczkowski T. Inter and intra population genetic variability in ducks under conservation programs. Poult Sci 2024; 103:104136. [PMID: 39208486 PMCID: PMC11399794 DOI: 10.1016/j.psj.2024.104136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 07/15/2024] [Accepted: 07/24/2024] [Indexed: 09/04/2024] Open
Abstract
This study focuses on estimation of the inter and intra population genetic variability of 6 duck populations. Microsatellite loci were used to assess the genetic variation and population structure of 6 duck populations under a conservation program in Poland. DNA polymorphism was assessed using 24 microsatellite markers and 50 individuals from each population. Polymorphism information content (PIC), heterozygosity with 2 estimators of genetic differentiation (FST and GST), and Nei's standard genetic distance were calculated. The results showed that these 6 endangered duck populations showed high genetic polymorphism. Observed heterozygosity within populations ranged from 0.14 to 0.83, with the average value of 0.58. PIC within populations ranged from 0.038 (P-8 and P-9 lines) to 0.89 (LsA line). Average number of alleles in the studied populations ranged from 4.5 (KhO-1 line) to 7.3 (LsA line). Based on the results, the pairs of lines LsA: P-33 and P-8: P-9 were found to be the most related; and the most genetically distant group was KhO-1 line, which originated as a cross between Khaki Campbell with Orpington duck.
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Affiliation(s)
- Anna Wolc
- Department of Animal Science, Iowa State University, Ames, IA 50010, USA; Hy-Line International, Dallas Center, IA 50063, USA
| | - Mirosław Lisowski
- Department of Reproductive Biotechnology and Cryoconservation, National Research Institute of Animal Production, 32-083 Balice, Poland
| | - Bartosz Grajewski
- Department of Reproductive Biotechnology and Cryoconservation, National Research Institute of Animal Production, 32-083 Balice, Poland
| | - Lidia Lewko
- Department of Poultry Breeding, National Research Institute of Animal Production, 32-083 Balice, Poland
| | - Tomasz Szwaczkowski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637 Poznan, Poland.
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Wang K, Hua G, Li J, Yang Y, Zhang C, Yang L, Hu X, Scheben A, Wu Y, Gong P, Zhang S, Fan Y, Zeng T, Lu L, Gong Y, Jiang R, Sun G, Tian Y, Kang X, Hu H, Li W. Duck pan-genome reveals two transposon insertions caused bodyweight enlarging and white plumage phenotype formation during evolution. IMETA 2024; 3:e154. [PMID: 38868520 PMCID: PMC10989122 DOI: 10.1002/imt2.154] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 11/07/2023] [Indexed: 06/14/2024]
Abstract
Structural variations (SVs) are a major source of domestication and improvement traits. We present the first duck pan-genome constructed using five genome assemblies capturing ∼40.98 Mb new sequences. This pan-genome together with high-depth sequencing data (∼46.5×) identified 101,041 SVs, of which substantial proportions were derived from transposable element (TE) activity. Many TE-derived SVs anchoring in a gene body or regulatory region are linked to duck's domestication and improvement. By combining quantitative genetics with molecular experiments, we, for the first time, unraveled a 6945 bp Gypsy insertion as a functional mutation of the major gene IGF2BP1 associated with duck bodyweight. This Gypsy insertion, to our knowledge, explains the largest effect on bodyweight among avian species (27.61% of phenotypic variation). In addition, we also examined another 6634 bp Gypsy insertion in MITF intron, which triggers a novel transcript of MITF, thereby contributing to the development of white plumage. Our findings highlight the importance of using a pan-genome as a reference in genomics studies and illuminate the impact of transposons in trait formation and livestock breeding.
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Affiliation(s)
- Kejun Wang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Guoying Hua
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Jingyi Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Intelligent Husbandry Department, College of Animal Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yu Yang
- Wuhan Academy of Agricultural ScienceWuhanChina
| | - Chenxi Zhang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Lan Yang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Xiaoyu Hu
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Armin Scheben
- Simons Center for Quantitative BiologyCold Spring Harbor LaboratoryCold Spring HarborNew YorkUSA
| | - Yanan Wu
- Department of preventive veterinary medicine, College of Veterinary MedicineHenan Agricultural UniversityZhengzhouChina
- International Joint Research Center for National Animal ImmunologyZhengzhouHenanChina
| | - Ping Gong
- Wuhan Academy of Agricultural ScienceWuhanChina
| | - Shuangjie Zhang
- Quality Safety and Processing LaboratoryJiangsu Institute of Poultry SciencesYangzhouChina
| | - Yanfeng Fan
- Quality Safety and Processing LaboratoryJiangsu Institute of Poultry SciencesYangzhouChina
| | - Tao Zeng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Animal Husbandry and Veterinary ScienceZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Lizhi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Animal Husbandry and Veterinary ScienceZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Yanzhang Gong
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Intelligent Husbandry Department, College of Animal Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Ruirui Jiang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Guirong Sun
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Yadong Tian
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Xiangtao Kang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Haifei Hu
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding and Guangdong Rice Engineering LaboratoryGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Wenting Li
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
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Gu H, Wen J, Zhao X, Zhang X, Ren X, Cheng H, Qu L. Evolution, Inheritance, and Strata Formation of the W Chromosome in Duck (Anas platyrhynchos). Genome Biol Evol 2023; 15:evad183. [PMID: 37931036 PMCID: PMC10630070 DOI: 10.1093/gbe/evad183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 11/08/2023] Open
Abstract
The nonrecombining female-limited W chromosome is predicted to experience unique evolutionary processes. Difficulties in assembling W chromosome sequences have hindered the identification of duck W-linked sequences and their evolutionary footprint. To address this, we conducted three initial contig-level genome assemblies and developed a rigorous pipeline by which to successfully expand the W-linked data set, including 11 known genes and 24 newly identified genes. Our results indicate that the W chromosome expression may not be subject to female-specific selection; a significant convergent pattern of upregulation associated with increased female-specific selection was not detected. The genetic stability of the W chromosome is also reflected in the strong evolutionary correlation between it and the mitochondria; the complete consistency of the cladogram topology constructed from their gene sequences proves the shared maternal coevolution. By detecting the evolutionary trajectories of W-linked sequences, we have found that recombination suppression started in four distinct strata, of which three were conserved across Neognathae. Taken together, our results have revealed a unique evolutionary pattern and an independent stratum evolutionary pattern for sex chromosomes.
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Affiliation(s)
- Hongchang Gu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Junhui Wen
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiurong Zhao
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xinye Zhang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xufang Ren
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huan Cheng
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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He Y, Zhang M, Dai C, Yu L. Comparison of the Gut Microbial Communities of Domestic and Wild Mallards ( Anas platyrhynchos) Based on High-Throughput Sequencing Technology. Animals (Basel) 2023; 13:2956. [PMID: 37760356 PMCID: PMC10525502 DOI: 10.3390/ani13182956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Mallards (Anas platyrhynchos) are currently one of the most popular species in rare bird breeding in several southern provinces of China, but there have been no studies comparing the gut microbial communities of domestic and wild mallards. In this study, 16S rRNA gene high-throughput sequencing technology was used to compare the composition and diversity of gut microbial communities in domestic and wild mallards. Alpha diversity analysis showed significant differences in gut microbial communities between the two groups of mallards, and the diversity and richness of gut microbial communities were significantly higher in wild mallards than in domestic mallards. Beta diversity analysis showed that the two groups of stool samples were mostly separated on the principal coordinate analysis (PCoA) plot. In domestic mallards, Firmicutes (68.0% ± 26.5%) was the most abundant bacterial phylum, followed by Proteobacteria (24.5% ± 22.9%), Bacteroidetes (3.1% ± 3.2%), Fusobacteria (2.2% ± 5.9%), and Actinobacteria (1.1% ± 1.8%). The dominant bacterial phyla in wild mallards were Firmicutes (79.0% ± 10.2%), Proteobacteria (12.9% ± 9.5%), Fusobacteria (3.4% ± 2.5%), and Bacteroidetes (2.8% ± 2.4%). At the genus level, a total of 10 dominant genera (Streptococcus, Enterococcus, Clostridium, Lactobacillus, Soilbacillus, Bacillus, Acinetobacter, Comamonas, Shigella, and Cetobacterium) with an average relative abundance greater than 1% were detected in the fecal samples of both groups. The average relative abundance of five potential pathogenic genera (Streptococcus, Enterococcus, Acinetobacter, Comamonas, and Shigella) was higher in domestic mallards than in wild mallards. The enrichment of pathogenic bacteria in the intestinal tract of domestic mallards should be of sufficient concern.
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Affiliation(s)
- Yaoyin He
- Animal Science and Technology College, Guangxi University, Nanning 530004, China; (Y.H.); (M.Z.)
| | - Minghui Zhang
- Animal Science and Technology College, Guangxi University, Nanning 530004, China; (Y.H.); (M.Z.)
| | - Chuanyin Dai
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin 541006, China;
| | - Lijiang Yu
- Animal Science and Technology College, Guangxi University, Nanning 530004, China; (Y.H.); (M.Z.)
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Melkikh AV. Mutations, sex, and genetic diversity: New arguments for partially directed evolution. Biosystems 2023; 229:104928. [PMID: 37172758 DOI: 10.1016/j.biosystems.2023.104928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/18/2023] [Accepted: 05/09/2023] [Indexed: 05/15/2023]
Abstract
A review of the theories of the existence of sexes, genetic diversity, and the distribution of mutations among organisms shows that all these concepts are not a product of random evolution and cannot be explained within the framework of Darwinism. Most mutations are the result of the genome acting on itself. This is an organized process that is implemented very differently in different species, in different places in the genome. Because of the fact that it is not random, this process must be directed and regulated, albeit with complex and not fully understood laws. This means that an additional reason must be included in order to model such mutations during evolution. The assumption of directionality must not only be explicitly included in evolutionary theory but must also occupy a central place in it. In this study an updated model of partially directed evolution is constructed, which is capable of qualitatively explaining the indicated features of evolution. Experiments are described that can confirm or disprove the proposed model.
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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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Lin R, Li J, Yang Y, Yang Y, Chen J, Zhao F, Xiao T. Genome-Wide Population Structure Analysis and Genetic Diversity Detection of Four Chinese Indigenous Duck Breeds from Fujian Province. Animals (Basel) 2022; 12:ani12172302. [PMID: 36078022 PMCID: PMC9454422 DOI: 10.3390/ani12172302] [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: 07/18/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary The aim of this study was to conduct a genome-wide comparative analysis of four indigenous Chinese duck breeds (Jinding, Liancheng white, Putian black, and Shanma ducks) from Fujian Province, to understand their genetic diversity and population structure. Population parameters showed that the four indigenous breeds were separated groups. Five genomic regions are presented as hotspots of autozygosity among these indigenous duck breeds, with candidate genes involved in muscle growth, pigmentation, and neuroregulation. Genomic information may play a vital role in the improvement of conservation strategies. Abstract The assessment of population genetic structure is the basis for understanding the genetic information of indigenous breeds and is important for the protection and management of indigenous breeds. However, the population genetic differentiation of many local breeds still remains unclear. Here, we performed a genome-wide comparative analysis of Jinding, Liancheng white, Putian black, and Shanma ducks based on the genomic sequences using RAD sequencing to understand their population structure and genetic diversity. The population parameters showed that there were obvious genetic differences among the four indigenous breeds, which were separated groups. Among them, Liancheng white and Shanma ducks may come from the same ancestor because the phylogenetic tree forms three tree trunks. In addition, during the runs of homozygosity (ROH), we found that the average inbreeding coefficient of Liancheng white and Putian black ducks was the lowest and the highest, respectively. Five genomic regions were considered to be the hotspots of autozygosity among these indigenous duck breeds, and the candidate genes involved a variety of potential variations, such as muscle growth, pigmentation, and neuroregulation. These findings provide insights into the further improvement and conservation of Fujian duck breeds.
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Zhou H, Yang Y, Wang L, Ye S, Liu J, Gong P, Qian Y, Zeng H, Chen X. Integrated multi-omic data reveal the potential molecular mechanisms of the nutrition and flavor in Liancheng white duck meat. Front Genet 2022; 13:939585. [PMID: 36046229 PMCID: PMC9421069 DOI: 10.3389/fgene.2022.939585] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/14/2022] [Indexed: 12/01/2022] Open
Abstract
The Liancheng white (LW) duck is one of the most valued Chinese indigenous poultry breeds. Its meat is rich in nutrients and has distinct flavors, but the molecular mechanisms behind them are unknown. To address this issue, we measured and compared multi-omic data (genome, transcriptome, and metabolome) of breast meat from LW ducks and the Mianyang Shelduck (MS) ducks. We found that the LW duck has distinct breed-specific genetic features, including numerous mutant genes with differential expressions associated with amino acid metabolism and transport activities. The metabolome driven by genetic materials was also seen to differ between the two breeds. For example, several amino acids that are beneficial for human health, such as L-Arginine, L-Ornithine, and L-lysine, were found in considerably higher concentrations in LW muscle than in MS duck muscle (p < 0.05). SLC7A6, a mutant gene, was substantially upregulated in the LW group (p < 0.05), which may lead to excessive L-arginine and L-ornithine accumulation in LW duck meat through transport regulation. Further, guanosine monophosphate (GMP), an umami-tasting molecule, was considerably higher in LW muscle (p < 0.05), while L-Aspartic acid was significantly abundant in MS duck meat (p < 0.05), showing that the LW duck has a different umami formation. Overall, this study contributed to our understanding of the molecular mechanisms driving the enriched nutrients and distinct umami of LW duck meat, which will provide a useful reference for duck breeding.
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Affiliation(s)
- Hao Zhou
- Insitute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, China
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Yang
- Insitute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, China
| | - Lixia Wang
- Insitute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, China
| | - Shengqiang Ye
- Insitute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, China
| | - Jiajia Liu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Gong
- Insitute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, China
| | - Yunguo Qian
- Insitute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, China
| | - Huijun Zeng
- Wuhan Institute for Food and Cosmetic Control, Wuhan, China
- Key Laboratory of Edible Oil Quality and Safety for State Market Regulation, Wuhan, China
- *Correspondence: Huijun Zeng, ; Xing Chen,
| | - Xing Chen
- Insitute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, China
- *Correspondence: Huijun Zeng, ; Xing Chen,
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Xu K, Lin C, Zhang X, Guo H. The complete mitochondrial genome of Anas zonorhyncha (Swinhoe, 1866) (Anatidae: Anas). Mitochondrial DNA B Resour 2022; 7:696-697. [PMID: 35493718 PMCID: PMC9045757 DOI: 10.1080/23802359.2022.2064246] [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] [Indexed: 11/24/2022] Open
Abstract
The complete mitochondrial genome of Anas zonorhyncha was first reported. The length of the entire mitochondrial genome was 16,605 base pairs, including 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a D-loop region. A phylogenetic tree of A. zonorhyncha was constructed with a group of related species in the family of Anatidae, indicating a close genetic relationship between A. zonorhyncha and A. poecilorhyncha.
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Affiliation(s)
- Kuo Xu
- School of Biological Science, The University of Edinburgh, Edinburgh, UK
| | - Chuyu Lin
- Shenzhen Zhong Nong Jing Yue Biotech Company Limited, Shenzhen, China
| | - Xinyuan Zhang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Huabing Guo
- Forest Inventory and Planning Institute of Jilin Province, Changchun, China
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Zhu T, Qi X, Chen Y, Wang L, Lv X, Yang W, Zhang J, Li K, Ning Z, Jiang Z, Qu L. Positive selection of skeleton-related genes during duck domestication revealed by whole genome sequencing. BMC Ecol Evol 2021; 21:165. [PMID: 34488647 PMCID: PMC8419914 DOI: 10.1186/s12862-021-01894-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 08/20/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Domestication alters several phenotypic, neurological, and physiological traits in domestic animals compared to those in their wild ancestors. Domestic ducks originated from mallards, and some studies have shown that spot-billed ducks may have also made minor genetic contributions to domestication. Compared with the two ancestral species, domestic ducks generally differ in body size and bone morphology. In this study, we performed both genomic and transcriptomic analyses to identify candidate genes for elucidating the genetic mechanisms underlying phenotypic variation. METHODS In this study, the duck genome data from eight domestic breeds and two wild species were collected to study the genetic changes during domestication. And the transcriptome data of different tissues from wild ducks and seven domestic ducks were used to reveal the expression difference between wild and domestic ducks. RESULTS Using fixation index (Fst) algorithm and transcriptome data, we found that the genes related to skeletal development had high Fst values in wild and domestic breeds, and the differentially expressed genes were mainly enriched in the ossification pathway. Our data strongly suggest that the skeletal systems of domestic ducks were changed to adapt to artificial selection for larger sizes. In addition, by combining the genome and transcriptome data, we found that some Fst candidate genes exhibited different expression patterns, and these genes were found to be involved in digestive, immune, and metabolic functions. CONCLUSIONS A wide range of phenotypic differences exists between domestic and wild ducks. Through both genome and transcriptome analyses, we found that genes related to the skeletal system in domestic ducks were strongly selected. Our findings provide new insight into duck domestication and selection effects during the domestication.
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Affiliation(s)
- Tao Zhu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Yuanmingyuan West Road 2#, Beijing, 100193, China
| | - Xin Qi
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Yuanmingyuan West Road 2#, Beijing, 100193, China
| | - Yu Chen
- Beijing General Station of Animal Husbandry, Beiyuan Road 15A#, Beijing, 100107, China
| | - Liang Wang
- Beijing General Station of Animal Husbandry, Beiyuan Road 15A#, Beijing, 100107, China
| | - Xueze Lv
- Beijing General Station of Animal Husbandry, Beiyuan Road 15A#, Beijing, 100107, China
| | - Weifang Yang
- Beijing General Station of Animal Husbandry, Beiyuan Road 15A#, Beijing, 100107, China
| | - Jianwei Zhang
- Beijing General Station of Animal Husbandry, Beiyuan Road 15A#, Beijing, 100107, China
| | - Kaiyang Li
- Beijing General Station of Animal Husbandry, Beiyuan Road 15A#, Beijing, 100107, China
| | - Zhonghua Ning
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Yuanmingyuan West Road 2#, Beijing, 100193, China
| | - Zhihua Jiang
- Department of Animal Sciences, Center for Reproductive Biology, Veterinary and Biomedical Research Building, Washington State University, Pullman, Washington, 647010, USA
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Yuanmingyuan West Road 2#, Beijing, 100193, China.
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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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13
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Feng P, Zeng T, Yang H, Chen G, Du J, Chen L, Shen J, Tao Z, Wang P, Yang L, Lu L. Whole-genome resequencing provides insights into the population structure and domestication signatures of ducks in eastern China. BMC Genomics 2021; 22:401. [PMID: 34058976 PMCID: PMC8165772 DOI: 10.1186/s12864-021-07710-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 05/12/2021] [Indexed: 01/03/2023] Open
Abstract
Background Duck is an ancient domesticated animal with high economic value, used for its meat, eggs, and feathers. However, the origin of indigenous Chinese ducks remains elusive. To address this question, we performed whole-genome resequencing to first explore the genetic relationship among variants of these domestic ducks with their potential wild ancestors in eastern China, as well as understand how the their genomes were shaped by different natural and artificial selective pressures. Results Here, we report the resequencing of 60 ducks from Chinese spot-billed ducks (Anas zonorhyncha), mallards (Anas platyrhnchos), Fenghua ducks, Shaoxing ducks, Shanma ducks and Cherry Valley Pekin ducks of eastern China (ten from each population) at an average effective sequencing depth of ~ 6× per individual. The results of population and demographic analysis revealed a deep phylogenetic split between wild (Chinese spot-billed ducks and mallards) and domestic ducks. By applying selective sweep analysis, we identified that several candidate genes, important pathways and GO categories associated with artificial selection were functionally related to cellular adhesion, type 2 diabetes, lipid metabolism, the cell cycle, liver cell proliferation, and muscle functioning in domestic ducks. Conclusion Genetic structure analysis showed a close genetic relationship of Chinese spot-billed ducks and mallards, which supported that Chinese spot-billed ducks contributed to the breeding of domestic ducks. During the long history of artificial selection, domestic ducks have developed a complex biological adaptation to captivity. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07710-2.
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Affiliation(s)
- Peishi Feng
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China.,Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Tao Zeng
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hua Yang
- Institute of Quality and Standards for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guohong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jinping Du
- Institute of Animal Husbandry and Veterinary Science, Hubei Academy of Agricultural Science, Wuhan, China
| | - Li Chen
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Junda Shen
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhenrong Tao
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ping Wang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China.
| | - Lin Yang
- College of Animal Science, South China Agricultural University, Guangzhou, China.
| | - Lizhi Lu
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
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14
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Jiang F, Lin R, Xiao C, Xie T, Jiang Y, Chen J, Ni P, Sung WK, Han J, Du X, Li S. Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations. Genet Sel Evol 2021; 53:35. [PMID: 33849442 PMCID: PMC8042899 DOI: 10.1186/s12711-021-00627-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 03/26/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The most prolific duck genetic resource in the world is located in Southeast/South Asia but little is known about the domestication and complex histories of these duck populations. RESULTS Based on whole-genome resequencing data of 78 ducks (Anas platyrhynchos) and 31 published whole-genome duck sequences, we detected three geographic distinct genetic groups, including local Chinese, wild, and local Southeast/South Asian populations. We inferred the demographic history of these duck populations with different geographical distributions and found that the Chinese and Southeast/South Asian ducks shared similar demographic features. The Chinese domestic ducks experienced the strongest population bottleneck caused by domestication and the last glacial maximum (LGM) period, whereas the Chinese wild ducks experienced a relatively weak bottleneck caused by domestication only. Furthermore, the bottleneck was more severe in the local Southeast/South Asian populations than in the local Chinese populations, which resulted in a smaller effective population size for the former (7100-11,900). We show that extensive gene flow has occurred between the Southeast/South Asian and Chinese populations, and between the Southeast Asian and South Asian populations. Prolonged gene flow was detected between the Guangxi population from China and its neighboring Southeast/South Asian populations. In addition, based on multiple statistical approaches, we identified a genomic region that included three genes (PNPLA8, THAP5, and DNAJB9) on duck chromosome 1 with a high probability of gene flow between the Guangxi and Southeast/South Asian populations. Finally, we detected strong signatures of selection in genes that are involved in signaling pathways of the nervous system development (e.g., ADCYAP1R1 and PDC) and in genes that are associated with morphological traits such as cell growth (e.g., IGF1R). CONCLUSIONS Our findings provide valuable information for a better understanding of the domestication and demographic history of the duck, and of the gene flow between local duck populations from Southeast/South Asia and China.
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Affiliation(s)
- Fan Jiang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Ruiyi Lin
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 People’s Republic of China
| | - Changyi Xiao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Tanghui Xie
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Yaoxin Jiang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Jianhai Chen
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Institute for Systems Genetics, West China Hospital, Auspiciousness Peace Center, Gaopeng Avenue, Wuhou District, Chengdu, 610041 People’s Republic of China
| | - Pan Ni
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Wing-Kin Sung
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Department of Computer Science, National University of Singapore, Singapore, 117417 Singapore
| | - Jianlin Han
- International Livestock Research Institute (ILRI), Nairobi, Kenya
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, People’s Republic of China
| | - Xiaoyong Du
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Shijun Li
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun, 130118 People’s Republic of China
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15
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Liu D, Fan W, Xu Y, Yu S, Liu W, Guo Z, Huang W, Zhou Z, Hou S. Genome-wide association studies demonstrate that TASP1 contributes to increased muscle fiber diameter. Heredity (Edinb) 2021; 126:991-999. [PMID: 33767369 DOI: 10.1038/s41437-021-00425-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 03/01/2021] [Accepted: 03/09/2021] [Indexed: 12/13/2022] Open
Abstract
Muscle fiber diameter is an economically important trait because it affects meat yield and quality. However, the genetic basis underlying muscle fiber diameter has not been determined. In this study, we collected THREE muscular histological phenotypes in 479 ducks from an F2 segregating population generated by mallard × Pekin duck crosses. We performed genome-wide association studies (GWAS) and identified a quantitative trait locus (QTL) significantly associated with muscle fiber diameter on chromosome 3. Then, we discovered the selection signatures using the fixation index among 40 mallards and 30 Pekin ducks in this QTL region. Furthermore, we characterized the recombination event in this QTL region and identified a 6-kb block located on TASP1 that was significantly associated with muscle fiber diameter. Finally, five SNPs were screened as potential causative mutations within the 6-kb block. In conclusion, we demonstrated that TASP1 contributes to an increase in muscle fiber diameter, which helps to characterize muscle development and contributes to the genetic improvement of meat yield and quality in livestock.
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Affiliation(s)
- Dapeng Liu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Animal Nutrition; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Wenlei Fan
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, PR China
| | - Yaxi Xu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Animal Nutrition; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Simeng Yu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Animal Nutrition; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Wenjing Liu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Animal Nutrition; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, PR China.,College of Animal Science, Qingdao Agricultural University, Qingdao, PR China
| | - Zhanbao Guo
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Animal Nutrition; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Wei Huang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Animal Nutrition; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Zhengkui Zhou
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Animal Nutrition; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, PR China.
| | - Shuisheng Hou
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Animal Nutrition; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, PR China.
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16
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Guo X, He XX, Chen H, Wang ZC, Li HF, Wang JX, Wang MS, Jiang RS. Revisiting the evolutionary history of domestic and wild ducks based on genomic analyses. Zool Res 2021; 42:43-50. [PMID: 33269825 PMCID: PMC7840458 DOI: 10.24272/j.issn.2095-8137.2020.133] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Although domestic ducks have been important poultry species throughout human history, their origin remains enigmatic, with mallards and/or Chinese spot-billed ducks being proposed as the direct wild ancestor(s) of domestic ducks. Here, we analyzed 118 whole genomes from mallard, Chinese spot-billed, and domestic ducks to reconstruct their evolutionary history. We found pervasive introgression patterns among these duck populations. Furthermore, we showed that domestic ducks separated from mallard and Chinese spot-billed ducks nearly 38 thousand years ago (kya) and 54 kya, respectively, which is considerably outside the time period of presumed duck domestication. Thus, our results suggest that domestic ducks may have originated from another wild duck population that is currently undefined or unsampled, rather than from present-day mallard and/or Chinese spot-billed ducks, as previously thought. Overall, this study provides new insight into the complex evolution of ducks.
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Affiliation(s)
- Xing Guo
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xin-Xin He
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Hong Chen
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Zhi-Cheng Wang
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Hui-Fang Li
- Jiangsu Institute of Poultry Science, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Jiang-Xian Wang
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Ming-Shan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, CA 95064, USA. E-mail:
| | - Run-Shen Jiang
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China. E-mail:
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17
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Gu H, Zhu T, Li X, Chen Y, Wang L, Lv X, Yang W, Jia Y, Jiang Z, Qu L. A joint analysis strategy reveals genetic changes associated with artificial selection between egg-type and meat-type ducks. Anim Genet 2020; 51:890-898. [PMID: 33058234 DOI: 10.1111/age.13014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2020] [Indexed: 12/16/2022]
Abstract
Egg-type ducks and meat-type ducks are predominantly commercial or indigenous and have been subjected to artificial directional selection. These two duck types differ substantially in body shape, production performance and reproductivity. However, the genetic changes associated with phenotypic differences remain unclear. Here, we compared the two duck types at the genomic and transcriptomic levels. We identified a large number of SNPs and genes in genomic divergent regions in terms of FST and θπ values. The corresponding genes were mainly enriched in embryonic development function and metabolic pathway. RNA-seq analysis also revealed differential gene expression in the liver and gonads. The differentially expressed genes were functionally associated with signal transmission and substance metabolism respectively. Furthermore, we found that seven genes were related to differentiation between the two types by both g genome and transcriptome analysis and were plausible candidate genes. These genes were annotated to GO categories of cell development and disease immunity. These findings will enable a better understanding of the artificial selection history of meat and egg ducks and provide a valuable resource for future research on the breeding of these two lineages.
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Affiliation(s)
- H Gu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Yuanmingyuan West Road 2#, Beijing, 100193, China
| | - T Zhu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Yuanmingyuan West Road 2#, Beijing, 100193, China
| | - X Li
- College of Animal Science and Technology, Shandong Agricultural University, Daizong Street #61, Tai'an, Shandong, 271018, China
| | - Y Chen
- Beijing Municipal General Station of Animal Science, Beiyuan Road 15A#, Beijing, 100107, China
| | - L Wang
- Beijing Municipal General Station of Animal Science, Beiyuan Road 15A#, Beijing, 100107, China
| | - X Lv
- Beijing Municipal General Station of Animal Science, Beiyuan Road 15A#, Beijing, 100107, China
| | - W Yang
- Beijing Municipal General Station of Animal Science, Beiyuan Road 15A#, Beijing, 100107, China
| | - Y Jia
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Beijing, 100193, China
| | - Z Jiang
- Department of Animal Sciences, center for Reproductive Biology, Veterinary and Biomedical Research Building, Washington State University, Pullman, Washington, 647010, USA
| | - L Qu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Yuanmingyuan West Road 2#, Beijing, 100193, China
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18
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Guo X, Wang ZC, Wang S, Li HF, Suwannapoom C, Wang JX, Zhang C, Shao Y, Wang MS, Jiang RS. Genetic signature of hybridization between Chinese spot-billed ducks and domesticated ducks. Anim Genet 2020; 51:866-875. [PMID: 33020910 DOI: 10.1111/age.13002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 08/17/2020] [Accepted: 08/24/2020] [Indexed: 12/27/2022]
Abstract
In this study, we analyzed 93 whole genomes from Chinese spot-billed ducks (CSB), meat-type ducks (MET), and egg and dual purpose-type ducks (EDT) to characterize the genetic material flowing between the CSB and modern ducks. Using a frequency of shared identical-by-descent method, approximately 10.9 Mb introgression segments containing 140 genes were identified showing the signatures of introgression between CSB and EDT. Meanwhile, nearly 10.6 M introgression regions containing 149 genes were identified between CSB and MET. Based on the haplotypes tree of each segment, we found that the introgression between CSB and domesticated ducks was asymmetric with a high level of gene flow from domestic to CSB and a low level of migration in the opposite direction. Moreover, we identified several genes that were introgressions from CSB and showed the signature of positive selection, which may contribute to the breeding of modern ducks. Our results provide new insight into the evolution and breeding history of domestic ducks and may be useful for the future management of wild and domestic duck populations.
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Affiliation(s)
- X Guo
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Z-C Wang
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - S Wang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Dong Road, Kunming, Yunnan, 650223, China
| | - H-F Li
- Jiangsu Institute of Poultry Science, Chinese Academy of Agriculture Science, 58 cangjie Rode, Yangzhou, Jiangsu, 225125, China
| | - C Suwannapoom
- School of Agriculture and Natural Resources, University of Phayao, 19 Moo 2 Tambon Maeka, Amphur Muang, Phayao, 56000, Thailand
| | - J-X Wang
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - C Zhang
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Y Shao
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Dong Road, Kunming, Yunnan, 650223, China
| | - M-S Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, 1156 High St, Santa Cruz, CA, 95064, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High St, Santa Cruz, CA, 95064, USA
| | - R-S Jiang
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
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19
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Hopken MW, Piaggio AJ, Pabilonia KL, Pierce J, Anderson T, Pierce C, Abdo Z. Population genomic transformations induced by isolation of wild bird avian influenza viruses (Orthomyxoviridae) in embryonated chicken eggs. INFECTION GENETICS AND EVOLUTION 2020; 90:104505. [PMID: 32827730 DOI: 10.1016/j.meegid.2020.104505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/09/2020] [Accepted: 08/13/2020] [Indexed: 12/21/2022]
Abstract
Isolation and cultivation of wild-type viruses in model organism cells or tissues is standard practice in virology. Oftentimes, the virus host species is distantly related to the species from which the culture system was developed. Thus, virus culture in these tissues and cells basically constitutes a host jump, which can lead to genomic changes through genetic drift and/or adaptation to the culture system. We directly sequenced 70 avian influenza virus (Orthomyxoviridae) genomes from oropharyngeal/cloacal swabs collected from wild bird species and paired virus isolates propagated from the same samples following isolation in specific-pathogen-free embryonated chicken eggs. The data were analyzed using population genetic approaches including evaluation of single nucleotide polymorphism (SNP) frequencies and divergence with pooled-sequencing analyses, consensus sequence placement in neighbor-joining trees, and haplotype reconstruction and networks. We found that propagation of virus in eggs leads to skewed SNP mutation spectra with some SNPs going to fixation. Both synonymous and nonsynonmous SNP frequencies shifted. We found multiple consensus sequences that differed between the swabs and the isolates, with some sequences from the same sample falling into divergent genetic clusters. Twenty of 23 coinfections detected had different dominant subtypes following virus isolation, thus sequences from both the swab and isolate were needed to obtain full subtype data. Haplotype networks revealed haplotype frequency shifts and the appearance or loss of low-frequency haplotypes following isolation. The results from this study revealed that isolation of wild bird avian influenza viruses in chicken eggs leads to skewed populations that are different than the input populations. Consensus sequence changes from virus isolation can lead to flawed phylogenetic inferences, and subtype detection is biased. These results suggest that for genomic studies of wild bird influenza viruses the biological field should move away from chicken egg isolation towards directly sequencing the virus from host samples.
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Affiliation(s)
- Matthew W Hopken
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO 80521, USA.
| | - Antoinette J Piaggio
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO 80521, USA
| | - Kristy L Pabilonia
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; Veterinary Diagnostics Laboratories, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO 80526, USA
| | - James Pierce
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Theodore Anderson
- Veterinary Diagnostics Laboratories, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO 80526, USA
| | - Courtney Pierce
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO 80521, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
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20
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Wang L, Guo J, Xi Y, Ma S, Li Y, He H, Wang J, Han C, Bai L, Mustafa A, Liu H, Li L. Understanding the Genetic Domestication History of the Jianchang Duck by Genotyping and Sequencing of Genomic Genes Under Selection. G3 (BETHESDA, MD.) 2020; 10:1469-1476. [PMID: 32165372 PMCID: PMC7202016 DOI: 10.1534/g3.119.400893] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/01/2020] [Indexed: 12/11/2022]
Abstract
The Jianchang duck is mainly distributed in Southwest China, and has the characteristics of fast growth rate and strong abilities in lipid deposition in the liver. In order to investigate the effects of domestication process on formation of the unique characteristics of Jianchang duck, the whole genome of sixteen individuals and three pooling of Jianchang duck were re-sequenced, and genome data of 70 mallards and 83 domestic ducks from thirteen different places in China were obtained from NCBI. The population stratification and evolution analysis showed gene exchanges existed between the Jianchang and other domestic duck populations, as well as Jianchang ducks and mallards. Genomic comparison between mallards and Jianchang ducks showed genes, including CNTN1, CHRNA9, and SHANK2, which is involved in brain and nerve development, experienced strong positive selection in the process of Jianchang duck domestication. The genomic comparison between Jianchang and domestic duck populations showed that HSD17B12 and ESM1, which affect lipid metabolism, experienced strong positive selection during the domestication process. FST analysis among populations of Jianchang duck with different plumage colors indicated that MITF was related to the phenotype of a white feather, while MC1R was related to the phenotype of hemp feather. Our results provided a base for the domestication process of Jianchang duck and the genomic genes for unique traits.
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Affiliation(s)
- Lei Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P.R. China
| | - Jiazhong Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P.R. China
| | - Yang Xi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P.R. China
| | - Shengchao Ma
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P.R. China
| | - Yanying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P.R. China
| | - Hua He
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P.R. China
| | - Jiwen Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P.R. China
| | - Chunchun Han
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P.R. China
| | - Lili Bai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P.R. China
| | - Ahsan Mustafa
- Institute of Animal Nutrition, Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Sichuan Agricultural University, Chengdu, P.R. China
| | - Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P.R. China
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P.R. China
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21
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Adeola AC, Ewuola MK, Nneji LM, Oguntunji AO, Bello SF, Sola-Ojo FE, Ayoola AO, Adesoji AT, Sanke OJ, Ebiakpo DL, Jonah KN, Jia X, Wu RN, Peng MS, Zhang YP. Mitochondrial DNA variation of Nigerian Muscovy duck (Cairina moschata). Anim Genet 2020; 51:485-486. [PMID: 32100314 DOI: 10.1111/age.12924] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, 650223, China
| | - Muslim K Ewuola
- Animal Breeding and Genetics Unit, Department of Animal Science, University of Ibadan, Ibadan, 200284, Nigeria
| | - Lotanna M Nneji
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, 650223, China
| | - Abel O Oguntunji
- Department of Animal Science and Fisheries Management, Bowen University, Iwo, 232102, Nigeria
| | - Semiu F Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Foluke E Sola-Ojo
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, 240213, Nigeria
| | - Adeola O Ayoola
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Adeosun T Adesoji
- Department of Agricultural Education, Federal College of Education, Bichi, 703101, Nigeria
| | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, 660221, Nigeria
| | - Daniel L Ebiakpo
- Department of Animal Science, University of Benin, Benin City, 300283, Nigeria
| | | | - Xinzheng Jia
- School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Ru-Nian Wu
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
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22
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Gu L, Wang F, Lin Z, Xu T, Lin D, Xing M, Yang S, Chao Z, Ye B, Lin P, Hui C, Lu L, Hou S. Genetic characteristics of Jiaji Duck by whole genome re-sequencing. PLoS One 2020; 15:e0228964. [PMID: 32049997 PMCID: PMC7015413 DOI: 10.1371/journal.pone.0228964] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 01/27/2020] [Indexed: 12/30/2022] Open
Abstract
Jiaji Duck (JJ) is a Muscovy duck species that possesses many superior characteristics, and it has become an important genetic resource in China. However, to date, its genetic characteristics and genetic relationship with other duck breeds have not been explored yet, which greatly limits the utilization of JJ. In the present study, we investigated the genome sequences of 15 individual ducks representing five different duck populations, including JJ, French Muscovy duck (FF), mallard (YD), hong duck (HD) and Beijing duck (BD). Moreover, we investigated the characteristics of JJ-specific single nucleotide polymorphisms (SNPs) and compared the genome sequences of JJ vs. YD and JJ vs. BD using integrated strategies, including mutation detection, selective screening, and Gene Ontology (GO) analysis. More than 40 Gb of clean data were obtained for each population (mean coverage of 13.46 Gb per individual). A total number of 22,481,367 SNPs and 4,156,829 small insertion-deletions (Indels) were identified for the five duck populations, which could be used as molecular markers in breeding and utilization of JJ. Moreover, we identified 1,447,932 JJ-specific SNPs, and found that genes covering at least one JJ-specific SNP mainly involved in protein phosphorylation and dephosphorylation, as well as DNA modification. Phylogenetic tree and principal components analysis (PCA) revealed that the genetic relationship of JJ was closest to FF, while it was farthest to BD. A total of 120 and 111 genes were identified as positive selection genes for JJ vs. BD and JJ vs. YD, respectively. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the positive selection genes for JJ vs. BD ducks mainly involved in pigmentation, muscle contraction and stretch, gland secretion, and immunology, while the positive selection genes obtained from JJ vs. YD ducks mainly involved in embryo development, muscle contraction and stretch, and gland secretion. Taken together, our findings enabled us to better understand the characteristics of JJ and provided a molecular basis for the breeding and hybrid utilization of JJ in the future.
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Affiliation(s)
- Lihong Gu
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Feng Wang
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Zhemin Lin
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Tieshan Xu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, P. R. China
| | - Dajie Lin
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Manping Xing
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Shaoxiong Yang
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Zhe Chao
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Baoguo Ye
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Peng Lin
- Hainan Chuanwei Muscovy Duck Breeding Co., Ltd, Wenchang, P. R. China
| | - Chunhui Hui
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Lizhi Lu
- Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Shuisheng Hou
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
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23
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Analysis of Anasplatyrhynchos genome resequencing data reveals genetic signatures of artificial selection. PLoS One 2019; 14:e0211908. [PMID: 30735526 PMCID: PMC6368380 DOI: 10.1371/journal.pone.0211908] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 01/22/2019] [Indexed: 02/05/2023] Open
Abstract
Three artificially selected duck populations (AS), higher lean meat ratios (LTPD), higher fat ratios (FTPD) and higher quality meat (CMD), have been developed in China, providing excellent populations for investigation of artificial selection effects. However, the genetic signatures of artificial selection are unclear. In this study, we sequenced the genome sequences of these three artificially selected populations and their ancestral population (mallard, M). We then compared the genome sequences between AS and M and between LTPD and FTPD using integrated strategies such as anchoring scaffolds to pseudo-chromosomes, mutation detection, selective screening, GO analysis, qRT-PCR, and protein multiple sequences alignment to uncover genetic signatures of selection. We anchored duck scaffolds to pseudo-chromosomes and obtained 28 pseudo-chromosomes, accounting for 84% of duck genome in length. Totally 78 and 99 genes were found to be under selection between AS and M and between LTPD and FTPD. Genes under selection between AS and M mainly involved in pigmentation and heart rates, while genes under selection between LTPD and FTPD involved in muscle development and fat deposition. A heart rate regulator (HCN1), the strongest selected gene between AS and M, harbored a GC deletion in AS and displayed higher mRNA expression level in M than in AS. IGF2R, a regulator of skeletal muscle mass, was found to be under selection between FTPD and LTPD. We also found two nonsynonymous substitutions in IGF2R, which might lead to higher IGF2R mRNA expression level in FTPD than LTPD, indicating the two nonsynonymous substitutions might play a key role for the regulation of duck skeletal muscle mass. Taken together, these results of this study provide valuable insight for the genetic basis of duck artificial selection.
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24
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Liu G, Li Q, Gong Z, Wang C. The complete mitochondrial genome of Mallard Shengjin Lake Anas platyrhynchos. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1617059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Gang Liu
- School of Life Sciences, Anhui Medical University, Hefei, P. R. China
| | - Qingyue Li
- School of Life Sciences, Anhui Medical University, Hefei, P. R. China
| | - Zhizong Gong
- School of Life Sciences, Anhui Medical University, Hefei, P. R. China
| | - Chong Wang
- School of Life Sciences, Anhui Medical University, Hefei, P. R. China
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25
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Yu C, Qiu M, Jiang X, Zhang Z, Du H, Li Q, Xia B, Song X, Hu C, Xiong X, Yang L, Peng H, Chen J, Wang Y, Yang C. Genetic Diversity and Phyletic Evolution of Eleven Chinese Indigenous and Three Commercial Chicken Breeds by mtDNA Sequences. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2019. [DOI: 10.1590/1806-9061-2018-0807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- C Yu
- Sichuan Animal Science Academy, China
| | - M Qiu
- Sichuan Animal Science Academy, China
| | - X Jiang
- Sichuan Animal Science Academy, China
| | - Z Zhang
- Sichuan Animal Science Academy, China
| | - H Du
- Sichuan Animal Science Academy, China
| | - Q Li
- Sichuan Animal Science Academy, China
| | - B Xia
- Sichuan Animal Science Academy, China
| | - X Song
- Sichuan Animal Science Academy, China
| | - C Hu
- Sichuan Animal Science Academy, China
| | - X Xiong
- Sichuan Animal Science Academy, China
| | - L Yang
- Sichuan Animal Science Academy, China
| | - H Peng
- Sichuan Animal Science Academy, China
| | - J Chen
- Sichuan Animal Science Academy, China
| | - Y Wang
- Sichuan Agricultural University, China
| | - C Yang
- Sichuan Animal Science Academy, China
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26
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An intercross population study reveals genes associated with body size and plumage color in ducks. Nat Commun 2018; 9:2648. [PMID: 30018292 PMCID: PMC6050300 DOI: 10.1038/s41467-018-04868-4] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 05/31/2018] [Indexed: 12/15/2022] Open
Abstract
Comparative population genomics offers an opportunity to discover the signatures of artificial selection during animal domestication, however, their function cannot be directly revealed. We discover the selection signatures using genome-wide comparisons among 40 mallards, 36 indigenous-breed ducks, and 30 Pekin ducks. Then, the phenotypes are fine-mapped based on resequencing of 1026 ducks from an F2 segregating population generated by wild × domestic crosses. Interestingly, the two key economic traits of Pekin duck are associated with two selective sweeps with fixed mutations. A novel intronic insertion most possibly leads to a splicing change in MITF accounted for white duck down feathers. And a putative long-distance regulatory mutation causes continuous expression of the IGF2BP1 gene after birth which increases body size by 15% and feed efficiency by 6%. This study provides new insights into genotype-phenotype associations in animal research and constitutes a promising resource on economically important genes in fowl.
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27
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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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28
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Gao YS, Jia XX, Tang XJ, Fan YF, Lu JX, Huang SH, Tang MJ. The genetic diversity of chicken breeds from Jiangxi, assessed with BCDO2 and the complete mitochondrial DNA D-loop region. PLoS One 2017; 12:e0173192. [PMID: 28257510 PMCID: PMC5336267 DOI: 10.1371/journal.pone.0173192] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 02/16/2017] [Indexed: 12/31/2022] Open
Abstract
The Jiangxi Province of China has numerous native domestic chicken breeds, including some black skin breeds. The genetic diversity of Jiangxi native chickens is largely unknown, and specifically, the genetic contribution of the grey junglefowl to black skin chickens is not well understood. To address these questions, the complete D-loop region of the mitochondrial DNA (mtDNA) and beta-carotene dioxygenase 2(BCDO2)gene was sequenced in a total of 209 chickens representing seven Jiangxi native breeds. Thirty-one polymorphic sites were identified across the complete mtDNA D-loop region sequence. Twenty-three haplotypes were observed in the seven breeds, which belonged to four distinct mitochondrial clades (A, B, C and E). Clade A and B were dominant in the chickens with a frequency of approximately 67.9%. There were five SNPs that defined two haplotypes, W and Y in BCDO2. Four breeds had one haplotype and three breeds had two. We conclude that Jiangxi native chicken breeds have relatively low genetic diversity and likely share four common maternal lineages from two different maternal ancestors of junglefowl. Furthermore, some Jiangxi chicken populations may have been mixed with chickens with exotic lineage. Further research should be established to protect these domestic chicken resources.
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Affiliation(s)
- Yu-shi Gao
- Jiangsu institute of Poultry Science, Yangzhou, China
- * E-mail: (XXJ); (YSG)
| | - Xiao-xu Jia
- Jiangsu institute of Poultry Science, Yangzhou, China
- * E-mail: (XXJ); (YSG)
| | - Xiu-jun Tang
- Jiangsu institute of Poultry Science, Yangzhou, China
| | - Yan-feng Fan
- Jiangsu institute of Poultry Science, Yangzhou, China
| | - Jun-xian Lu
- Jiangsu institute of Poultry Science, Yangzhou, China
| | | | - Meng-jun Tang
- Jiangsu institute of Poultry Science, Yangzhou, China
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29
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Chen L, Zeng T, Li GQ, Liu R, Tian Y, Li QH, Lu LZ. PCK1 expression is correlated with the plasma glucose level in the duck. Anim Genet 2017; 48:358-361. [PMID: 28198082 DOI: 10.1111/age.12540] [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] [Accepted: 12/22/2016] [Indexed: 11/30/2022]
Abstract
Phosphoenolpyruvate carboxykinase 1 (soluble) (PCK1) is a key gene in gluconeogenesis and glyceroneogenesis. Although its functions have been extensively studied in mice, bats and humans, little is known in ducks. Here, PCK1 functions were studied using a duck domestication model and a 48-h fasting experiment. We found PCK1 expression significantly decreased in two breeds of domestic ducks (Jinyun Pockmark ducks and Cherry Valley ducks) as compared with wild ducks (Anas platyrhynchos). Simultaneously, plasma levels of glucose, triglycerides and free fatty acid in domestic ducks were lower than in wild ducks. When compared with fed ducks, the plasma triglyceride level was observed to be significantly decreased, while the glucose and free fatty acid levels remained constant in 48-h fasting ducks. The expression analysis of gluconeogenic genes revealed that fructose-1,6-bisphosphatase genes (FBP1 and FBP2) and the glucose-6-phosphatase gene (G6PC2) were not changed, whereas PCK1 was significantly upregulated. In addition, the reported regulators of PCK1, including forkhead box A2 (FOXA2) gene and orphan nuclear receptor NR4A family genes (NR4A1, NR4A2 and NR4A3), exhibited similar expression levels between 48-h fasting ducks and fed ducks, suggesting that PCK1 is not regulated by these genes in the duck under fasting conditions. In conclusion, PCK1 expression may affect plasma levels of glucose, triglycerides and free fatty acid during the duck domestication process. This work demonstrates for the first time in duck that PCK1 is a key gene in maintaining plasma glucose homeostasis during fasting and that the upregulated expression of PCK1 may be responsible for constant plasma free fatty acid level by the glyceroneogenesis process.
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Affiliation(s)
- L Chen
- Institute of Animal Sciences and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - T Zeng
- Institute of Animal Sciences and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - G Q Li
- Institute of Animal Sciences and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - R Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Y Tian
- Institute of Animal Sciences and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Q H Li
- State Key Laboratory for Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - L Z Lu
- Institute of Animal Sciences and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
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30
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Zhu F, Cui QQ, Hou ZC. SNP discovery and genotyping using Genotyping-by-Sequencing in Pekin ducks. Sci Rep 2016; 6:36223. [PMID: 27845353 PMCID: PMC5109183 DOI: 10.1038/srep36223] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/11/2016] [Indexed: 11/09/2022] Open
Abstract
Genomic selection and genome-wide association studies need thousands to millions of SNPs. However, many non-model species do not have reference chips for detecting variation. Our goal was to develop and validate an inexpensive but effective method for detecting SNP variation. Genotyping by sequencing (GBS) can be a highly efficient strategy for genome-wide SNP detection, as an alternative to microarray chips. Here, we developed a GBS protocol for ducks and tested it to genotype 49 Pekin ducks. A total of 169,209 SNPs were identified from all animals, with a mean of 55,920 SNPs per individual. The average SNP density reached 1156 SNPs/MB. In this study, the first application of GBS to ducks, we demonstrate the power and simplicity of this method. GBS can be used for genetic studies in to provide an effective method for genome-wide SNP discovery.
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Affiliation(s)
- Feng Zhu
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Qian-Qian Cui
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Zhuo-Cheng Hou
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China
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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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Jia XX, Tang XJ, Lu JX, Fan YF, Chen DW, Tang MJ, Gu R, Gao YS. The investigation of genetic diversity and evolution of Daweishan Mini chicken based on the complete mitochondrial (mt)DNA D-loop region sequence. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3001-4. [PMID: 26153755 DOI: 10.3109/19401736.2015.1060478] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
This study evaluated the genetic diversity and origin of Daweishan Mini chickens using mtDNA sequence polymorphism. Blood samples from 30 Daweishan Mini chickens were collected. The complete D-loop was PCR amplified, sequenced and compared with the DNA data of five Red Junglefowl (Gallus gallus) subspecies. Eighteen variable sites that defined six haplotypes were observed. The six haplotypes were clustered into four clades (A, B, D and E), of which clade A and B were dominant. Clades Aand B were clustered with G.g. spadiceus, indicating these two clades may have originated from this subspecies. These results show there is diversity in the middle of the mtDNA D-loop, and indicate there are multiple maternal origins for Daweishan Mini chickens. It appears that G.g. spadiceus contributed more to the evolution of the Daweishan Mini chickens breed than the other four subspecies tested here.
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Affiliation(s)
- Xiao-Xu Jia
- a Jiangsu Institute of Poultry Science , Yangzhou , Jiangsu Province , People's Republic of China
| | - Xiu-Jun Tang
- a Jiangsu Institute of Poultry Science , Yangzhou , Jiangsu Province , People's Republic of China
| | - Jun-Xian Lu
- a Jiangsu Institute of Poultry Science , Yangzhou , Jiangsu Province , People's Republic of China
| | - Yan-Feng Fan
- a Jiangsu Institute of Poultry Science , Yangzhou , Jiangsu Province , People's Republic of China
| | - Da-Wei Chen
- a Jiangsu Institute of Poultry Science , Yangzhou , Jiangsu Province , People's Republic of China
| | - Meng-Jun Tang
- a Jiangsu Institute of Poultry Science , Yangzhou , Jiangsu Province , People's Republic of China
| | - Rong Gu
- a Jiangsu Institute of Poultry Science , Yangzhou , Jiangsu Province , People's Republic of China
| | - Yu-Shi Gao
- a Jiangsu Institute of Poultry Science , Yangzhou , Jiangsu Province , People's Republic of China
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Phylogenetic analysis between domestic and wild duck species in Korea using mtDNA D-loop sequences. Mol Biol Rep 2014; 41:1645-52. [PMID: 24415297 DOI: 10.1007/s11033-013-3012-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 12/30/2013] [Indexed: 10/25/2022]
Abstract
Recently, the consumption of duck meat has increased; therefore, we need to reveal the origin and gene flow of domestic ducks in Korea. In order to discriminate between duck species, D-loop variations in mitochondrial DNA (mtDNA) have been investigated. In this study, 45 individuals from seven species of wild and domestic ducks in Korea were considered for the D-loop region sequences. With the participation of all the sequences, a phylogenetic neighbor-joining tree was constructed to differentiate between the wild and domestic duck species. In consideration of these sequences, a total 66 haplotypes were obtained (indel included) with an average haplotype of 76.9%, and a haplotype and nucleotide diversity of 0.91 and 0.01, respectively. Also, an estimation of the sequence divergence within and between species was measured in 0.045 and 0.013-0.095, respectively. Meanwhile, the lowest distances of 0.024, 0.013 and 0.018 were observed in three species, including the Mallard, Spot-billed and domestic duck, respectively, which have relatively close genetic relationships. All haplotypes were used for the median-joining network analysis to differentiate all duck species, while three duck species were closely related. Moreover, 26 indel polymorphisms were identified which could be used for the discrimination among the duck species. Based on our results, duck species were effectively discriminated in a D-loop region, which could then be used for an appropriate genetic conservation program for the wild duck and domestic duck breeds in Korea.
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Phylogenetic Relationships among Dabbling Duck Species in Korea using <i>COI </i>Gene Variations in mtDNA. J Poult Sci 2012. [DOI: 10.2141/jpsa.011102] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Genetic Variation in the Growth Hormone Promoter Region of Anas platyrhynchos, a Duck Native to Myanmar. J Poult Sci 2012. [DOI: 10.2141/jpsa.011062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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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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