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Safaa H, Khaled R, Isaac S, Mostafa R, Ragab M, Elsayed DAA, Helal M. Genome-wide in silico characterization, validation, and cross-species transferability of microsatellite markers in Mallard and Muscovy ducks. J Genet Eng Biotechnol 2023; 21:105. [PMID: 37856056 PMCID: PMC10587045 DOI: 10.1186/s43141-023-00556-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/08/2023] [Indexed: 10/20/2023]
Abstract
BACKGROUND Microsatellites are important markers for livestock including ducks. The development of microsatellites is expensive and labor-intensive. Meanwhile, the in silico approach for mining for microsatellites became a practicable alternative. Therefore, the current study aimed at comparing whole-genome and chromosome-wise microsatellite mining approaches in Muscovy and Mallard ducks and testing the transferability of markers between them. The GMATA software was used for the in silico study, and validation was performed using 26 primers. RESULTS The total number of the detected microsatellites using chromosome-wise was 250,053 and 226,417 loci compared to 260,059 and 238,462 loci using whole genome in Mallards and Muscovies. The frequencies of different motifs had similar patterns using the two approaches. Dinucleotide motifs were predominant (> 50%) in both Mallards and Muscovies. The amplification of the genomes revealed an average number of alleles of 5.08 and 4.96 in Mallards and Muscovies. One locus was monographic in Mallards, and two were monomorphic in Muscovies. The average expected heterozygosity was higher in Muscovy than in Mallards (0.45 vs. 0.43) with no significant difference between the two primer sets, which indicated the usefulness of cross-species amplification of different primers. CONCLUSION The current study developed a whole-genome SSR panel for ducks for the first time, and the results could prove that using chromosome-wise mining did not generate different results compared to the whole-genome approach.
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Affiliation(s)
- Hosam Safaa
- Department of Biology, College of Science, University of Bisha, P.O. Box 551, 61922, Bisha, Saudi Arabia.
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt.
| | - Rawan Khaled
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Suzy Isaac
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Rofida Mostafa
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Mohamed Ragab
- Poultry Production Department, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh, Egypt
- Animal Breeding and Genetics Department, National Institute for Agricultural and Food Research and Technology (INIA), 28040, Madrid, Spain
| | - Dalia A A Elsayed
- Department of Poultry Breeding, Agriculture Research Center, Animal Production Research Institute, Dokki, Giza, Egypt
| | - Mostafa Helal
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt.
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The whole mitochondrial genome signature of Teressa goat, an indigenous goat germplasm of Andaman and Nicobar Islands, India. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Genetic structure, population diversity and ancestry of Nicobari fowl based on mtDNA complete D-loop sequences. J Genet 2022. [DOI: 10.1007/s12041-022-01372-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Sai Satyanarayana D, Ahlawat S, Sharma R, Arora R, Sharma A, Tantia MS, Vijh RK. Mitochondrial DNA diversity divulges high levels of haplotype diversity and lack of genetic structure in the Indian camels. Gene X 2022; 820:146279. [PMID: 35143947 DOI: 10.1016/j.gene.2022.146279] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 01/08/2022] [Accepted: 02/03/2022] [Indexed: 11/04/2022] Open
Abstract
Camels represent an important genetic resource of the desert ecosystems of India, with the dromedary and Bactrian camels inhabiting the hot and cold deserts, respectively. This study is the first attempt to investigate mitochondrial DNA based genetic diversity in the Indian camel populations and explores their relationship in the context of global genetic diversity of all the three large camel species (Camelus ferus, Camelus bactrianus and Camelus dromedaries). A mitochondrial DNA fragment encompassing part of cytochrome b gene, tRNAThr, tRNAPro and the beginning of the control region was amplified and analyzed in 72 dromedary and 8 Bactrian camels of India. Sequence analysis revealed that the haplotype and nucleotide diversity (Hd: 0.937 and π: 0.00431) in the Indian dromedaries was higher than the indices reported so far for the dromedary or Bactrian camels across the globe. The corresponding values in the Indian Bactrian camels were 1.000 and 0.00393, respectively. Signals of population expansion were evident in the dromedaries of India on the basis of mismatch analysis and Fu's Fs values. The analysis of molecular variance attributed most of the genetic variance (92.15%) between the dromedary, wild Bactrian and domestic Bactrian camels indicating separate maternal origins. The existence of three mitochondrial lineages in the old world camels (C. bactrianus: Lineage A; C. ferus: Lineage B and C. dromedarius: Lineage C) was also substantiated by the topology of the Median-Joining network.
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Affiliation(s)
- D Sai Satyanarayana
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India; ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India.
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Annu Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - M S Tantia
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - R K Vijh
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
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Adeola AC, Sola-Ojo FE, Opeyemi YA, Oguntunji AO, Nneji LM, Ewuola MK, Bello SF, Olaniyi WA, Adesoji AT, Karuno AP, Sanke OJ, Daniel EL. Genetic diversity and population structure of muscovy duck ( Cairina moschata) from Nigeria. PeerJ 2022; 10:e13236. [PMID: 35444865 PMCID: PMC9014852 DOI: 10.7717/peerj.13236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/17/2022] [Indexed: 01/15/2023] Open
Abstract
The domestic Muscovy duck (Cairina moschata) provide unique genetic resources patterned by both tropical environmental conditions and human activities, the evaluation of their genetic diversity and population structure will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the variation in mtDNA cytochrome b and nuclear DNA CYP2U1 sequences of 378 Nigerian Muscovy ducks (comprising of 287 de novo and 91 downloaded) plus 80 published sequences of Muscovy ducks from India. The results showed high haplotype diversity (0.800 ± 0.023) among Nigerian Muscovy duck populations with 91 distinct haplotypes for the nuclear DNA CYP2U1 gene but low (0.266 ± 0.033) for cytochrome b with 31 haplotypes. The median-joining networks of both markers grouped Nigerian Muscovy ducks into two; the first group consisting of only Nigerian Muscovy duck populations, and the second group Nigerian with Indian populations. Neutrality test results indicated that Nigerian populations experienced recent population expansion and/or genetic hitchhiking. A geographic signal was absent in line with previously studied poultry species in Nigeria. The most prominent haplotype dominated across all regions in Nigeria, which may be due to extensive genetic intermixing except for the Indian population (F ST = 0.02550, P = 0.01075). This indicated low genetic differentiation between and within Nigerian Muscovy duck as revealed by the suitability of the nuclear DNA CYP2U1 gene.
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Affiliation(s)
- Adeniyi C. Adeola
- Molecular Evolution and Genome Diversity, State Key Laboratory of Genetic Resources & Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, Yunnan, China,Centre for Biotechnology Research, Bayero University, Kano, Nigeria
| | - Foluke E. Sola-Ojo
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, Kwara, Nigeria
| | - Yusuf A. Opeyemi
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, Kwara, Nigeria
| | - Abel O. Oguntunji
- Department of Animal Science and Fisheries Management, Bowen University, Iwo, Osun, Nigeria
| | - Lotanna Micah Nneji
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States
| | - Muslim K. Ewuola
- Animal Breeding and Genetics Unit/Department of Animal Science, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Semiu F. Bello
- Department of Animal Genetics/Breeding and Reproduction/College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Wasiu A. Olaniyi
- Department of Animal Science, Faculty of Agriculture, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Adeosun T. Adesoji
- Department of Agricultural Education, Federal College of Education, Bichi, Kano, Nigeria
| | - Alex P. Karuno
- Molecular Evolution and Genome Diversity, State Key Laboratory of Genetic Resources & Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Oscar J. Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Taraba, Nigeria
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