1
|
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]
|
2
|
Yang X, E GX, Yang BG, Liu CL, Guo Y, Gong Y, Chen BE, Zhang DP, Li MH. Genetic Diversity and Phylogeny Pattern across Chongqing (China) Chicken Populations Using mtDNA D-Loop Sequences. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422080117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
3
|
Dave AR, Chaudhary DF, Mankad PM, Koringa PG, Rank DN. Genetic diversity among two native Indian chicken populations using cytochrome c oxidase subunit I and cytochrome b DNA barcodes. Vet World 2021; 14:1389-1397. [PMID: 34220145 PMCID: PMC8243695 DOI: 10.14202/vetworld.2021.1389-1397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/15/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND AND AIM India has large varieties (recognized, unrecognized) of native chickens (Desi) scattered throughout the country, managed under scavenging system different from commercial chicken breeds. However, they are less investigated for genetic diversity they harbor. The present study was planned to evaluate genetic diversity among two native chicken populations of North Gujarat (proposed Aravali breed) and South Gujarat (Ankleshwar breed). Aravali chicken, a distinct population with unique characters different from the registered chicken breeds of India is under process to be registered as a new chicken breed of Gujarat, India. MATERIALS AND METHODS Two mitochondrial markers, namely, cytochrome oxidase c subunit I (COX I) and cytochrome b (Cyt b) genes were studied across 10 birds from each population. Methodology included sample collection (blood), DNA isolation (manual), polymerase chain reaction amplification of mitochondrial genes, Sanger sequencing, and purification followed by data analysis using various softwares. RESULTS Haplotype analysis of the COX I gene unveiled a total eight and three haplotypes from the Aravali and Ankleshwar populations, respectively, with haplotype diversity (Hd) of 92.70 % for the Aravali and 34.50% for the Ankleshwar breed. Haplotype analysis of the Cyt b gene revealed a total of four haplotypes from the Aravali population with 60% Hd and no polymorphism in Ankleshwar breed. The phylogenetic analysis uncovered Red Jungle Fowl and Gray Jungle Fowl as prime roots for both populations and all domestic chicken breeds. CONCLUSION Study findings indicated high genetic variability in Aravali chicken populations with COX I mitochondrial marker being more informative for evaluating genetic diversity in chickens.
Collapse
Affiliation(s)
- Ankit R. Dave
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand, Anand Agricultural University, Gujarat, India
| | - Dhaval F. Chaudhary
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand, Anand Agricultural University, Gujarat, India
| | - Pooja M. Mankad
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand, Anand Agricultural University, Gujarat, India
| | - Prakash G. Koringa
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand, Anand Agricultural University, Gujarat, India
| | - D. N. Rank
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand, Anand Agricultural University, Gujarat, India
| |
Collapse
|
4
|
Zang H, Wang Y, Yang HH, He PL, Pan SQ, Geng ZY, Jin SH. Characterisation of the complete mitochondrial genome, genetic diversity and maternal origin of Huainan Partridge chicken. Br Poult Sci 2021; 62:320-327. [PMID: 33263413 DOI: 10.1080/00071668.2020.1855628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
1. The objectives of the present study were to investigate the complete mitochondrial genome, genetic diversity and maternal origin of Huainan Partridge chicken (HPC).2. One complete mitochondrial genome and 37 complete D-loop regions of HPC were sequenced. Moreover, 400 mitochondrial genome D-loop sequences of Chinese native chicken were downloaded from the National Centre for Biotechnology Information database.3. The complete HPC genome was 16,785 bp in size, including 22 tRNA genes, two rRNA genes, 13 protein-coding genes and one non-coding control region. The haplotype diversity and nucleotide diversity of HPC were 0.964, and 0.00615, respectively. Twenty-three variable sites defining 22 haplotypes were identified, and the 22 haplotypes were distributed into three haplogroups (A, B, and C).4. In conclusion, HPC has a typical vertebrate mitochondrial genome, relatively high haplotype diversity, relatively low nucleotide diversity, and potentially three maternal lineages. HPC showed considerable genetic information exchange with Southwest Chinese chicken populations and had not admixed with European commercial breeds in the course of domestication.
Collapse
Affiliation(s)
- H Zang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Department of Poultry Genetics and Breeding, Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding, Hefei, China
| | - Y Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Department of Poultry Genetics and Breeding, Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding, Hefei, China
| | - H H Yang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - P L He
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - S Q Pan
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Z Y Geng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Department of Poultry Genetics and Breeding, Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding, Hefei, China
| | - S H Jin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Department of Poultry Genetics and Breeding, Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding, Hefei, China
| |
Collapse
|
5
|
Nisar A, Waheed A, Khan S, Feng X, Shah AH. Population structure, genetic diversity and phylogenetic analysis of different rural and commercial chickens of Pakistan using complete sequence of mtDNA D-loop. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:273-280. [PMID: 30231799 DOI: 10.1080/24701394.2018.1484118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Chicken is the most important poultry bird in Pakistan that not only provides nutrition but also contributes to country's economy. The Pakistani chicken and its germplasm resources are not genetically characterized and explored. Here, we focused at rural and commercial chickens of Pakistan and explored genetic diversity, population structure and phylogeny. We first collected feather samples from Rural and Broiler populations of Pakistani chickens, isolated DNA and sequenced complete D-loop of mtDNA. The length of complete D-loop ranged from 1231 to 1234 bp in Pakistani chickens. The GC content was 39%. Hotspots of mutations were three hypervariable sites (HVS). Most of the variations (77%) were in HVS1. In a total, 26 polymorphic sites defined 12 haplotypes and all major haplogroups (A-I) in genetic structure of Pakistani chickens. Genetic diversity remained relatively very low in Broiler (Pi = 0.00212 ± 0.00136). There was a low sharing of matrilineages between the two populations (Fst = 0.170). With high Hd value (0.825 ± 0.051) and presence of all nine major haplogroups the rural chicken population showed relatively rich genepool. Finally we did molecular phylogenetic analysis and inferred phylogeny. Presence of subcontinent specific haplogroups E3 and I and clustering of Indian red junglefowl closely with Pakistani chickens in Bayesian inference tree, provide further evidence for an independent domestication event of chicken in subcontinent.
Collapse
Affiliation(s)
- Ayesha Nisar
- a Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Key Laboratory of Animal Parasitology, Ministry of Agriculture of China , Shanghai , People's Republic of China.,b Department of Zoology , Government Post Graduate College , Mansehra , Pakistan
| | - Abdul Waheed
- b Department of Zoology , Government Post Graduate College , Mansehra , Pakistan
| | - Sawar Khan
- a Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Key Laboratory of Animal Parasitology, Ministry of Agriculture of China , Shanghai , People's Republic of China
| | - Xingang Feng
- a Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Key Laboratory of Animal Parasitology, Ministry of Agriculture of China , Shanghai , People's Republic of China
| | - Abbas Hussain Shah
- c Department of Botany , Government Post Graduate College , Mansehra , Pakistan
| |
Collapse
|
6
|
Zhang M, Han W, Tang H, Li G, Zhang M, Xu R, Liu Y, Yang T, Li W, Zou J, Wu K. Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs. BMC Genomics 2018; 19:598. [PMID: 30092770 PMCID: PMC6085637 DOI: 10.1186/s12864-018-4973-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 07/31/2018] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Maintaining maximum genetic diversity and preserving breed viability in conserved populations necessitates the rigorous evaluation of conservation schemes. Three chicken breeds (Baier Yellow Chicken (BEC), Beijing You Chicken (BYC) and Langshan Chicken (LSC)) are currently in conservation programs in China. Changes in genetic diversity were measured by heterozygosity, genomic inbreeding coefficients, and autozygosity, using estimates derived from runs of homozygosity (ROH) that were identified using SNPs. RESULTS Ninety DNA samples were collected from three generations for each breed. In the most recent generation, the highest genetic diversity was observed in LSC, followed by BEC and BYC. Inbreeding coefficients based on ROH for the three breeds declined slightly between the first and middle generations, and then rapidly increased. No inbreeding coefficients exceeded 0.1. Population structure assessments using neighbor-joining tree analysis, principal components analysis, and STRUCTURE analysis indicated that no genetic differentiation existed within breeds. LD decay and ROH at different cut-off lengths were used to identify traces left by recent or ancient inbreeding. Few long ROH were identified, indicating that inbreeding has been largely avoided with the current conservation strategy. The observed losses in genetic diversity and occurrences of inbreeding might be consequences of sub-optimal effective population sizes. CONCLUSIONS The conserved Chinese chicken populations have high genomic diversity under the current conservation program (R: F). Furthermore, this study highlights the need to monitor dynamic changes in genetic diversity in conserved breeds over successive generations. Our research provides new insights into genetic diversity dynamics in conserved populations, and lays a solid foundation for improving conservation schemes.
Collapse
Affiliation(s)
- Mengmeng Zhang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Wei Han
- National Chickens Genetic Resources, Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou, 225125 People’s Republic of China
| | - Hui Tang
- College of Animal Science and Technology, Shandong Agricultural University, Tai’an, 271018 People’s Republic of China
| | - Guohui Li
- National Chickens Genetic Resources, Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou, 225125 People’s Republic of China
| | - Minjie Zhang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 People’s Republic of China
- Beijing Key Laboratory for Animal Genetic Improvement, Beijing, 100193 People’s Republic of China
| | - Ran Xu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Yijun Liu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 People’s Republic of China
- College of Animal Science, Southwest University, Chongqing, 402460 People’s Republic of China
| | - Tao Yang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Wenting Li
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 People’s Republic of China
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002 People’s Republic of China
| | - Jianmin Zou
- National Chickens Genetic Resources, Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou, 225125 People’s Republic of China
| | - Keliang Wu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 People’s Republic of China
| |
Collapse
|