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Qi Z, Shi J, Yu Y, Yin G, Zhou X, Yu Y. Paternal Mitochondrial DNA Leakage in Natural Populations of Large-Scale Loach, Paramisgurnus dabryanus. BIOLOGY 2024; 13:604. [PMID: 39194542 DOI: 10.3390/biology13080604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 08/02/2024] [Accepted: 08/08/2024] [Indexed: 08/29/2024]
Abstract
Animal mitochondrial DNA is usually considered to comply with strict maternal inheritance, and only one mitochondrial DNA haplotype exists in an individual. However, mitochondrial heteroplasmy, the occurrence of more than one mitochondrial haplotype, has recently been reported in some animals, such as mice, mussels, and birds. This study conducted extensive field surveys to obtain representative samples to investigate the existence of paternal inheritance of mitochondrial DNA (mtDNA) in natural fish populations. Evidence of paternal mitochondrial DNA leakage of P. dabryanus was discovered using high-throughput sequencing and bioinformatics methods. Two distinct mitochondrial haplotypes (16,569 bp for haplotype I and 16,646 bp for haplotype II) were observed, differing by 18.83% in nucleotide sequence. Phylogenetic analysis suggests divergence between these haplotypes and potential interspecific hybridization with M. anguillicaudatus, leading to paternal leakage. In natural populations of P. dabryanus along the Yangtze River, both haplotypes are present, with Type I being dominant (75% copy number). Expression analysis shows that Type I has higher expression levels of ND3 and ND6 genes compared to Type II, suggesting Type I's primary role. This discovery of a species with two mitochondrial types provides a model for studying paternal leakage heterogeneity and insights into mitochondrial genome evolution and inheritance.
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Affiliation(s)
- Zixin Qi
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiaoxu Shi
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Agronomy and Life Science Department, Zhaotong University, Zhaotong 657000, China
| | - Yue Yu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangmei Yin
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoyun Zhou
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongyao Yu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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Árnadóttir ER, Moore KHS, Guðmundsdóttir VB, Ebenesersdóttir SS, Guity K, Jónsson H, Stefánsson K, Helgason A. The rate and nature of mitochondrial DNA mutations in human pedigrees. Cell 2024; 187:3904-3918.e8. [PMID: 38851187 DOI: 10.1016/j.cell.2024.05.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 03/06/2024] [Accepted: 05/13/2024] [Indexed: 06/10/2024]
Abstract
We examined the rate and nature of mitochondrial DNA (mtDNA) mutations in humans using sequence data from 64,806 contemporary Icelanders from 2,548 matrilines. Based on 116,663 mother-child transmissions, 8,199 mutations were detected, providing robust rate estimates by nucleotide type, functional impact, position, and different alleles at the same position. We thoroughly document the true extent of hypermutability in mtDNA, mainly affecting the control region but also some coding-region variants. The results reveal the impact of negative selection on viable deleterious mutations, including rapidly mutating disease-associated 3243A>G and 1555A>G and pre-natal selection that most likely occurs during the development of oocytes. Finally, we show that the fate of new mutations is determined by a drastic germline bottleneck, amounting to an average of 3 mtDNA units effectively transmitted from mother to child.
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Affiliation(s)
| | | | - Valdís B Guðmundsdóttir
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | | | - Kamran Guity
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Kári Stefánsson
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
| | - Agnar Helgason
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Department of Anthropology, University of Iceland, Reykjavik, Iceland.
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Yonezawa T, Mannen H, Honma K, Matsunaga M, Rakotondraparany F, Ratsoavina FM, Wu J, Nishibori M, Yamamoto Y. Origin and spatial population structure of Malagasy native chickens based on mitochondrial DNA. Sci Rep 2024; 14:569. [PMID: 38177203 PMCID: PMC10766636 DOI: 10.1038/s41598-023-50708-x] [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] [Received: 08/03/2023] [Accepted: 12/23/2023] [Indexed: 01/06/2024] Open
Abstract
Since Malagasy human culture became established in a multi-layered way by genetic admixture of Austronesian (Indonesia), Bantu (East Africa) and West Asian populations, the Malagasy native livestock should also have originated from these regions. While recent genetic studies revealed that Malagasy native dogs and goats were propagated from Africa, the origin of Malagasy native chickens is still controversial. Here, we conducted a phylogeographic analysis of the native chickens, focusing on the historical relationships among the Indian Ocean rim countries and based on mitochondrial D-loop sequences. Although previous work suggested that the rare Haplogroup D occurs with high frequencies in Island Southeast Asia-Pacific, East Africa and Madagascar, the major mitochondrial lineage in Malagasy populations is actually not Haplogroup D but the Sub-haplogroup C2, which is also observed in East Africa, North Africa, India and West Asia. We demonstrate that the Malagasy native chickens were propagated directly from West Asia (including India and North Africa), and not via East Africa. Furthermore, they display clear genetic differentiation within Madagascar, separated into the Highland and Lowland regions as seen in the human genomic landscape on this island. Our findings provide new insights for better understanding the intercommunion of material/non-material cultures within and around Madagascar.
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Affiliation(s)
- Takahiro Yonezawa
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan.
- Faculty of Agriculture, Tokyo University of Agriculture, 1737 Funako, Atsugi, Kanagawa, 243-0034, Japan.
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Nada, Kobe, 657-8501, Japan
| | - Kaho Honma
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
- Chubu Regional Office, Agriculture and Forestry Bureau, Tottori, 682-0802, Japan
| | - Megumi Matsunaga
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
| | - Felix Rakotondraparany
- Department of Zoology and Animal Biodiversity, Faculty of Science, University of Antananarivo, BP 906, 101, Antananarivo, Madagascar
| | - Fanomezana Mihaja Ratsoavina
- Department of Zoology and Animal Biodiversity, Faculty of Science, University of Antananarivo, BP 906, 101, Antananarivo, Madagascar
| | - Jiaqi Wu
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
- Department of Molecular Life Science, Tokai University School of Medicine, 143 Shimo-Kasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Masahide Nishibori
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan.
| | - Yoshio Yamamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan.
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4
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Population structure and hybridisation in a population of Hawaiian feral chickens. Heredity (Edinb) 2023; 130:154-162. [PMID: 36725960 PMCID: PMC9981564 DOI: 10.1038/s41437-022-00589-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 02/03/2023] Open
Abstract
Chickens are believed to have inhabited the Hawaiian island of Kauai since the first human migrations around 1200AD, but numbers have peaked since the tropical storms Iniki and Iwa in the 1980s and 1990s that destroyed almost all the chicken coops on the island and released large numbers of domestic chickens into the wild. Previous studies have shown these now feral chickens are an admixed population between Red Junglefowl (RJF) and domestic chickens. Here, using genetic haplotypic data, we estimate the time of the admixture event between the feral population on the island and the RJF to 1981 (1976-1995), coinciding with the timings of storm Iwa and Iniki. Analysis of genetic structure reveals a greater similarity between individuals inhabiting the northern and western part of the island to RJF than individuals from the eastern part of the island. These results point to the possibility of introgression events between feral chickens and the wild chickens in areas surrounding the Koke'e State Park and the Alaka'i plateau, posited as two of the major RJF reservoirs in the island. Furthermore, we have inferred haplotype blocks from pooled data to determine the most plausible source of the feral population. We identify a clear contribution from RJF and layer chickens of the White Leghorn (WL) breed. This work provides independent confirmation of the traditional hypothesis surrounding the origin of the feral populations and draws attention to the possibility of introgression of domestic alleles into the wild reservoir.
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Godinez CJP, Layos JKN, Yamamoto Y, Kunieda T, Duangjinda M, Liao LM, Huang XH, Nishibori M. Unveiling new perspective of phylogeography, genetic diversity, and population dynamics of Southeast Asian and Pacific chickens. Sci Rep 2022; 12:14609. [PMID: 36028749 PMCID: PMC9418149 DOI: 10.1038/s41598-022-18904-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 08/22/2022] [Indexed: 11/10/2022] Open
Abstract
The complex geographic and temporal origins of chicken domestication have attracted wide interest in molecular phylogeny and phylogeographic studies as they continue to be debated up to this day. In particular, the population dynamics and lineage-specific divergence time estimates of chickens in Southeast Asia (SEA) and the Pacific region are not well studied. Here, we analyzed 519 complete mitochondrial DNA control region sequences and identified 133 haplotypes with 70 variable sites. We documented 82.7% geographically unique haplotypes distributed across major haplogroups except for haplogroup C, suggesting high polymorphism among studied individuals. Mainland SEA (MSEA) chickens have higher overall genetic diversity than island SEA (ISEA) chickens. Phylogenetic trees and median-joining network revealed evidence of a new divergent matrilineage (i.e., haplogroup V) as a sister-clade of haplogroup C. The maximum clade credibility tree estimated the earlier coalescence age of ancestral D-lineage (i.e., sub-haplogroup D2) of continental chickens (3.7 kya; 95% HPD 1985-4835 years) while island populations diverged later at 2.1 kya (95% HPD 1467-2815 years). This evidence of earlier coalescence age of haplogroup D ancestral matriline exemplified dispersal patterns to the ISEA, and thereafter the island clade diversified as a distinct group.
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Affiliation(s)
- Cyrill John P Godinez
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan.
- Department of Animal Science, College of Agriculture and Food Science, Visayas State University, Visca, Baybay City, Leyte, 6521, Philippines.
| | - John King N Layos
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
- College of Agriculture and Forestry, Capiz State University, Burias, Mambusao, Capiz, 5807, Philippines
| | - Yoshio Yamamoto
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
| | - Tetsuo Kunieda
- Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Ehime, 794-8555, Japan
| | - Monchai Duangjinda
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Lawrence M Liao
- Laboratory of Aquatic Botany, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
| | - Xun-He Huang
- School of Life Sciences, Jiaying University, Meizhou, 514015, China
| | - Masahide Nishibori
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan.
- Department of Animal Science, College of Agriculture and Food Science, Visayas State University, Visca, Baybay City, Leyte, 6521, Philippines.
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Pei Y, Forstmeier W, Ruiz-Ruano FJ, Mueller JC, Cabrero J, Camacho JPM, Alché JD, Franke A, Hoeppner M, Börno S, Gessara I, Hertel M, Teltscher K, Knief U, Suh A, Kempenaers B. Occasional paternal inheritance of the germline-restricted chromosome in songbirds. Proc Natl Acad Sci U S A 2022; 119:e2103960119. [PMID: 35058355 PMCID: PMC8794876 DOI: 10.1073/pnas.2103960119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 11/06/2021] [Indexed: 11/29/2022] Open
Abstract
Songbirds have one special accessory chromosome, the so-called germline-restricted chromosome (GRC), which is only present in germline cells and absent from all somatic tissues. Earlier work on the zebra finch (Taeniopygia guttata castanotis) showed that the GRC is inherited only through the female line-like the mitochondria-and is eliminated from the sperm during spermatogenesis. Here, we show that the GRC has the potential to be paternally inherited. Confocal microscopy using GRC-specific fluorescent in situ hybridization probes indicated that a considerable fraction of sperm heads (1 to 19%) in zebra finch ejaculates still contained the GRC. In line with these cytogenetic data, sequencing of ejaculates revealed that individual males from two families differed strongly and consistently in the number of GRCs in their ejaculates. Examining a captive-bred male hybrid of the two zebra finch subspecies (T. g. guttata and T. g. castanotis) revealed that the mitochondria originated from a castanotis mother, whereas the GRC came from a guttata father. Moreover, analyzing GRC haplotypes across nine castanotis matrilines, estimated to have diverged for up to 250,000 y, showed surprisingly little variability among GRCs. This suggests that a single GRC haplotype has spread relatively recently across all examined matrilines. A few diagnostic GRC mutations that arose since this inferred spreading suggest that the GRC has continued to jump across matriline boundaries. Our findings raise the possibility that certain GRC haplotypes could selfishly spread through the population via occasional paternal transmission, thereby outcompeting other GRC haplotypes that were limited to strict maternal inheritance, even if this was partly detrimental to organismal fitness.
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Affiliation(s)
- Yifan Pei
- Department of Behavioral Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology 82319 Seewiesen, Germany;
| | - Wolfgang Forstmeier
- Department of Behavioral Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology 82319 Seewiesen, Germany;
| | - Francisco J Ruiz-Ruano
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TU, United Kingdom;
- Department of Organismal Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University SE-752 36 Uppsala, Sweden
| | - Jakob C Mueller
- Department of Behavioral Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology 82319 Seewiesen, Germany
| | - Josefa Cabrero
- Department of Genetics, University of Granada E-18071 Granada, Spain
| | | | - Juan D Alché
- Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Spanish National Research Council E-18008 Granada, Spain
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel 24118 Kiel, Germany
| | - Marc Hoeppner
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel 24118 Kiel, Germany
| | - Stefan Börno
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics 14195 Berlin, Germany
| | - Ivana Gessara
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology 82319 Seewiesen, Germany
| | - Moritz Hertel
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology 82319 Seewiesen, Germany
| | - Kim Teltscher
- Department of Behavioral Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology 82319 Seewiesen, Germany
| | - Ulrich Knief
- Division of Evolutionary Biology, Faculty of Biology, Ludwig Maximilian University of Munich D-82152 Planegg-Martinsried, Germany
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TU, United Kingdom;
- Department of Organismal Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University SE-752 36 Uppsala, Sweden
| | - Bart Kempenaers
- Department of Behavioral Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology 82319 Seewiesen, Germany
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Al-Jumaili AS, Hanotte O. The usefulness of maternally inherited genetic markers for phylogeographic studies in village chicken. Anim Biotechnol 2022:1-19. [PMID: 35073494 DOI: 10.1080/10495398.2021.2000429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Phylogeography plays a major role in understanding micro and macroevolutionary processes dealing with evolutionary interpretations of geographical distribution. This field integrates information from molecular genetics, population genetics, demography, and phylogeny for the interpretation of the geographical distribution of lineages. The full mtDNA sequence and W chromosome polymorphisms were exploited to assess the usefulness of two maternally-inherited genetic markers for phylogeographic studies of village chickens. We studied 243 full mtDNA sequences from three countries (Iraq, n = 27; Ethiopia, n = 211; and Saudi Arabia, n = 5) and a 13-kb fragment of the W chromosome from 20 Iraqi and 137 Ethiopian female chickens. The results show a high level of genetic diversity for the mtDNA within and among countries as well as within populations. On the other hand, sequence analysis of the W chromosome shows low genetic diversity both within and among populations. Six full mtDNA haplogroups (A, B, C1, C2, D1, and E1) were observed and 25 distinct W haplotypes. The results support the effectiveness of full mtDNA sequences but not the W chromosome in tracing the maternal historical genome background with, however, weak within a country phylogeographic signal.
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Affiliation(s)
- Ahmed S. Al-Jumaili
- Medical Laboratory Techniques Department, Al-Maarif University College, Anbar, Iraq
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
| | - Olivier Hanotte
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
- LiveGene–CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
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Mon SLY, Lwin M, Maw AA, Htun LL, Bawm S, Kawabe K, Wada Y, Okamoto S, Shimogiri T. Phylogenetic analysis of Myanmar indigenous chickens using mitochondrial D-loop sequence reveals their characteristics as a genetic resource. Anim Sci J 2021; 92:e13647. [PMID: 34647390 DOI: 10.1111/asj.13647] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 09/15/2021] [Accepted: 09/23/2021] [Indexed: 01/16/2023]
Abstract
Myanmar indigenous chickens play important roles in food, entertainment, and farm business for the people of Myanmar. In this study, complete mitochondrial D-loop sequences (1232 bp) were analyzed using 176 chickens, including three indigenous breeds, two fighting cock populations, and three indigenous populations to elucidate genetic diversity and accomplish a phylogenetic analysis of Myanmar indigenous chickens. The average haplotype and nucleotide diversities were 0.948 ± 0.009 and 0.00814 ± 0.00024, respectively, exhibiting high genetic diversity of Myanmar indigenous chickens. Sixty-four haplotypes were classified as seven haplogroups, with the majority being haplogroup F. The breeds and populations except Inbinwa had multiple maternal haplogroups, suggesting that they experienced no recent purifying selection and bottleneck events. All breeds and populations examined shared haplogroup F. When 232 sequences belonging to haplogroup F (79 from Myanmar and 153 deposited sequences from other Asian countries/region) were analyzed together, the highest genetic diversity was observed in Myanmar indigenous chickens. Furthermore, Myanmar indigenous chickens and red junglefowls were observed in the center of the star-like median-joining network of 37 F-haplotypes, suggesting that Myanmar is one of the origins of haplogroup F. These findings revealed the unique genetic characteristic of Myanmar indigenous chickens as important genetic resources.
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Affiliation(s)
- Su Lai Yee Mon
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | - Moe Lwin
- Research and Development Division, Livestock Breeding and Veterinary Department, Yangon, Myanmar
| | - Aye Aye Maw
- Department of Genetics and Animal Breeding, University of Veterinary Science, Nay Pyi Taw, Myanmar
| | - Lat Lat Htun
- Department of Pharmacology and Parasitology, University of Veterinary Science, Nay Pyi Taw, Myanmar
| | - Saw Bawm
- Department of International Relations and Information Technology, University of Veterinary Science, Nay Pyi Taw, Myanmar
| | - Kotaro Kawabe
- Education Center, Kagoshima University, Kagoshima, Japan
| | - Yasuhiko Wada
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.,Faculty of Agriculture, Saga University, Saga, Japan
| | - Shin Okamoto
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | - Takeshi Shimogiri
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
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Godinez CJP, Dadios PJD, Espina DM, Matsunaga M, Nishibori M. Population Genetic Structure and Contribution of Philippine Chickens to the Pacific Chicken Diversity Inferred From Mitochondrial DNA. Front Genet 2021; 12:698401. [PMID: 34367257 PMCID: PMC8340678 DOI: 10.3389/fgene.2021.698401] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/17/2021] [Indexed: 11/20/2022] Open
Abstract
The Philippines is considered one of the biodiversity hotspots for animal genetic resources. In spite of this, population genetic structure, genetic diversity, and past population history of Philippine chickens are not well studied. In this study, phylogeny reconstruction and estimation of population genetic structure were based on 107 newly generated mitochondrial DNA (mtDNA) complete D-loop sequences and 37 previously published sequences of Philippine chickens, consisting of 34 haplotypes. Philippine chickens showed high haplotypic diversity (Hd = 0.915 ± 0.011) across Southeast Asia and Oceania. The phylogenetic analysis and median-joining (MJ) network revealed predominant maternal lineage haplogroup D classified throughout the population, while support for Philippine-Pacific subclade was evident, suggesting a Philippine origin of Pacific chickens. Here, we observed Philippine red junglefowls (RJFs) at the basal position of the tree within haplogroup D indicating an earlier introduction into the Philippines potentially via mainland Southeast Asia (MSEA). Another observation was the significantly low genetic differentiation and high rate of gene flow of Philippine chickens into Pacific chicken population. The negative Tajima's D and Fu's Fs neutrality tests revealed that Philippine chickens exhibited an expansion signal. The analyses of mismatch distribution and neutrality tests were consistent with the presence of weak phylogeographic structuring and evident population growth of Philippine chickens (haplogroup D) in the islands of Southeast Asia (ISEA). Furthermore, the Bayesian skyline plot (BSP) analysis showed an increase in the effective population size of Philippine chickens, relating with human settlement, and expansion events. The high level of genetic variability of Philippine chickens demonstrates conservation significance, thus, must be explored in the future.
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Affiliation(s)
- Cyrill John P. Godinez
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
- Department of Animal Science, College of Agriculture and Food Science, Visayas State University, Baybay City, Philippines
| | - Peter June D. Dadios
- College of Aquatic and Applied Life Sciences, Southern Leyte State University, Southern Leyte, Philippines
| | - Dinah M. Espina
- Department of Animal Science, College of Agriculture and Food Science, Visayas State University, Baybay City, Philippines
| | - Megumi Matsunaga
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Masahide Nishibori
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
- Department of Animal Science, College of Agriculture and Food Science, Visayas State University, Baybay City, Philippines
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Insights into the Mitochondrial and Nuclear Genome Diversity of Two High Yielding Strains of Laying Hens. Animals (Basel) 2021; 11:ani11030825. [PMID: 33804055 PMCID: PMC8001891 DOI: 10.3390/ani11030825] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/05/2021] [Accepted: 03/10/2021] [Indexed: 12/06/2022] Open
Abstract
Simple Summary Mitochondria are commonly known as “the powerhouse of the cell”, influencing the fitness, lifespan and metabolism of eukaryotic organisms. In our study we examined mitochondrial and nuclear genomic diversity in two high yielding strains of laying hens. We tested if the mitochondrial genome affects functional traits such as body weight and phosphorus utilization. We discovered a surprisingly low mitochondrial genetic diversity and an unequal distribution of the haplotypes among both strains, leading to limitations of robust links to phenotypic traits. In contrast, we found similar levels of nuclear genome diversity in both strains. Our study explores the potential influence of the mitochondrial genome on phenotypic traits and thus contributes to a better understanding of the function of this organelle in laying hens. Further, we focus on its usefulness as a genetic marker, which is often underestimated in breeding approaches, given the different inheritance mechanism compared to the nuclear genome. Abstract Mitochondria are essential components of eukaryotes as they are involved in several organismic key processes such as energy production, apoptosis and cell growth. Despite their importance for the metabolism and physiology of all eukaryotic organisms, the impact of mitochondrial haplotype variation has only been studied for very few species. In this study we sequenced the mitochondrial genome of 180 individuals from two different strains of laying hens. The resulting haplotypes were combined with performance data such as body weight, feed intake and phosphorus utilization to assess their influence on the hens in five different life stages. After detecting a surprisingly low level of genetic diversity, we investigated the nuclear genetic background to estimate whether the low mitochondrial diversity is representative for the whole genetic background of the strains. Our results highlight the need for more in-depth investigation of the genetic compositions and mito-nuclear interaction in individuals to elucidate the basis of phenotypic performance differences. In addition, we raise the question of how the lack of mitochondrial variation developed, since the mitochondrial genome represents genetic information usually not considered in breeding approaches.
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Alves JS, Diaz IDPS, da Cruz VAR, Bastos MS, de Oliveira LSM, de Albuquerque LG, de Camargo GMF, Costa RB. The effect of mitochondrial DNA polymorphisms on cattle reproduction. Mol Biol Rep 2021; 48:1005-1008. [PMID: 33393009 DOI: 10.1007/s11033-020-06068-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/03/2020] [Indexed: 11/25/2022]
Abstract
The aim of this study was to identify SNPs located in mitochondrial DNA that are associated with reproductive traits in beef cows. A total of 1999 Nelore females genotyped with the high-density Illumina BovineHD BeadChip (Illumina Inc., San Diego, CA, USA) were used to study the association of mitochondrial DNA variants with reproductive traits using a single-step procedure. In a preliminary analysis, the present results indicate a small participation of the mitogenome in the expression of reproductive traits in beef cattle. However, possible difficulties related to the biological characteristics of mitochondrial DNA and its inheritance, genotyping, and annotation of the phenotypes studied may also explain the results.
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Affiliation(s)
- Jackeline Santos Alves
- Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia (UFBA), Salvador, Bahia, Brazil
| | - Iara Del Pilar Solar Diaz
- Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia (UFBA), Salvador, Bahia, Brazil
| | | | - Marisa Silva Bastos
- Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia (UFBA), Salvador, Bahia, Brazil
| | | | - Lucia Galvão de Albuquerque
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo, Brazil
| | | | - Raphael Bermal Costa
- Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia (UFBA), Salvador, Bahia, Brazil.
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12
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Mrowiec P, Bugno-Poniewierska M, Młodawska W. The perspective of the incompatible of nucleus and mitochondria in interspecies somatic cell nuclear transfer for endangered species. Reprod Domest Anim 2020; 56:199-207. [PMID: 33190359 DOI: 10.1111/rda.13864] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/19/2020] [Accepted: 11/11/2020] [Indexed: 01/02/2023]
Abstract
Taking into account the latest Red List of the International Union for Conservation of Nature in which 25% of all mammals are threatened with extinction, somatic cell nuclear transfer (SCNT) could be a beneficial tool and holds a lot of potential for aiding the conservation of endangered, exotic or even extinct animal species if somatic cells of such animals are available. In the case of shortage and sparse amount of wild animal oocytes, interspecies somatic cell nuclear transfer (iSCNT), where the recipient ooplasm and donor nucleus are derived from different species, is the alternative SCNT technique. The successful application of iSCNT, resulting in the production of live offspring, was confirmed in several combination of closely related species. When nucleus donor cells and recipient oocytes have been used in many other combinations, very often with a very distant taxonomical relation iSCNT resulted only in the very early stages of cloned embryo development. Problems encountered during iSCNT related to mitochondrial DNA (mtDNA)/genomic DNA incompatibility, mtDNA heteroplasmy, embryonic genome activation of the donor nucleus by the recipient oocyte and availability of suitable foster mothers for iSCNT embryos. Implementing assisted reproductive technologies, including iSCNT, to conservation programmes also raises concerns that the production of genetically identical populations might cause problems with inbreeding. The article aims at presenting achievements, limitations and perspectives of iSCNT in maintaining animal biodiversity.
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Affiliation(s)
- Patrycja Mrowiec
- Department of Animal Reproduction, Anatomy and Genomics, Faculty of Animal Science, University of Agriculture in Krakow, Kraków, Poland
| | - Monika Bugno-Poniewierska
- Department of Animal Reproduction, Anatomy and Genomics, Faculty of Animal Science, University of Agriculture in Krakow, Kraków, Poland
| | - Wiesława Młodawska
- Department of Animal Reproduction, Anatomy and Genomics, Faculty of Animal Science, University of Agriculture in Krakow, Kraków, Poland
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Khan S, Nisar A, Ahmad H, Mehmood SA, Hameed M, Zhao X, Yang X, Feng X. Analyses of mitogenomic markers shed light on the divergence, population dynamics, and demographic history of Pakistani chickens. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 32:34-42. [PMID: 33179562 DOI: 10.1080/24701394.2020.1845323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Pakistan is one of a few sites, associated with the earliest known independent domestication event in the evolutionary history of chicken, which is socio-economically and historically the most important poultry bird in the country. However, the divergence, past population dynamics, and demographic history of Pakistani chickens have not been addressed so far. Therefore, we herein investigated the indigenous Pakistani chickens using mitogenomic markers. We first prepared individual DNA samples from the chicken feathers, and generated nucleotide sequence data, which was then subjected to various population genetics analyses. In molecular phylogenetic analysis, the Pakistani chickens were clustered under nine different clades. Among the wild fowls, the Indian red jungle fowl (IRJF) shared very close affinities to Pakistani chickens. The Bayesian skyline plot showed an increase in the effective population size of Pakistani chickens during the last 50 years. Finally, a time-calibrated phylogeny inferred molecular divergence of the Pakistani chickens. A molecular rate of 3.6 × 10-6 mutations/site/year (95% HPD interval: 2.28 × 10-8 to 9.32 × 10-6) was estimated for the data set. In a rooted tree with root-age of 12058 years (95% HPD interval: 1161-38411), the Pakistani chicken haplotypes showed divergence from IRJF haplotypes around 6987 years (95% HPD interval: 1132-20746) ago, and they shared their most recent common ancestor with Gallus gallus spadiceus, and G. g. jabouillei at the root of the tree. Overall, these results suggest that Pakistani chicken haplotypes share their ancestral gene pool with the IRJF as compared to other red jungle fowl subspecies.
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Affiliation(s)
- Sawar Khan
- 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
| | - Ayesha Nisar
- 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
| | - Habib Ahmad
- Department of Genetics, Hazara University, Mansehra, Pakistan
| | | | - Muddassar Hameed
- 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
| | - Xiaochao Zhao
- 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
| | - Xiangshu Yang
- 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
- 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
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14
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Rodríguez-Pena E, Verísimo P, Fernández L, González-Tizón A, Bárcena C, Martínez-Lage A. High incidence of heteroplasmy in the mtDNA of a natural population of the spider crab Maja brachydactyla. PLoS One 2020; 15:e0230243. [PMID: 32191743 PMCID: PMC7082002 DOI: 10.1371/journal.pone.0230243] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 02/26/2020] [Indexed: 12/19/2022] Open
Abstract
Mitochondria are mostly inherited by maternal via, that is, only mitochondria from eggs are retained in the embryos. However, this general assumption of uniparentally transmitted, homoplasmic and non-recombining mitochondrial genomes is becoming more and more controversial. The presence of different sequences of mtDNA within a cell or individual, known as heteroplasmy, is increasingly reported in several taxon of animals, such as molluscs, arthropods and vertebrates. In this work, a considerable frequency of heteroplasmy were detected in the COI and 16S genes of the spider crab Maja brachydactyla, possibly associated to hybridisation with the congeneric species Maja squinado. This finding is a fact to keep in mind before addressing molecular analyses based on mitochondrial markers, since the assumption of maternal inheritance could lead to erroneous results. As M. brachydactyla is a commercial species, heteroplasmy is an important aspect to take into account for the fisheries management of this resource, since effective population size could be overestimated.
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Affiliation(s)
- Elba Rodríguez-Pena
- Dpto. de Biología, Facultad de Ciencias, Centro de Investigaciones Científicas Avazadas, Universidade da Coruña, A Coruña, Spain
| | - Patricia Verísimo
- Dpto. de Biología, Facultad de Ciencias, Centro de Investigaciones Científicas Avazadas, Universidade da Coruña, A Coruña, Spain
| | - Luis Fernández
- Dpto. de Biología, Facultad de Ciencias, Centro de Investigaciones Científicas Avazadas, Universidade da Coruña, A Coruña, Spain
| | - Ana González-Tizón
- Dpto. de Biología, Facultad de Ciencias, Centro de Investigaciones Científicas Avazadas, Universidade da Coruña, A Coruña, Spain
| | - Covadonga Bárcena
- Dpto. de Biología, Facultad de Ciencias, Centro de Investigaciones Científicas Avazadas, Universidade da Coruña, A Coruña, Spain
| | - Andrés Martínez-Lage
- Dpto. de Biología, Facultad de Ciencias, Centro de Investigaciones Científicas Avazadas, Universidade da Coruña, A Coruña, Spain
- * E-mail:
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15
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Al-Jumaili AS, Boudali SF, Kebede A, Al-Bayatti SA, Essa AA, Ahbara A, Aljumaah RS, Alatiyat RM, Mwacharo JM, Bjørnstad G, Naqvi AN, Gaouar SBS, Hanotte O. The maternal origin of indigenous domestic chicken from the Middle East, the north and the horn of Africa. BMC Genet 2020; 21:30. [PMID: 32171253 PMCID: PMC7071775 DOI: 10.1186/s12863-020-0830-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 02/25/2020] [Indexed: 12/18/2022] Open
Abstract
Background Indigenous domestic chicken represents a major source of protein for agricultural communities around the world. In the Middle East and Africa, they are adapted to hot dry and semi-dry areas, in contrast to their wild ancestor, the Red junglefowl, which lives in humid and sub-humid tropical areas. Indigenous populations are declining following increased demand for poultry meat and eggs, favouring the more productive exotic commercial breeds. In this paper, using the D-loop of mitochondrial DNA as a maternally inherited genetic marker, we address the question of the origin and dispersal routes of domestic chicken of the Middle East (Iraq and Saudi Arabia), the northern part of the African continent (Algeria and Libya) and the Horn of Africa (Ethiopia). Results The analysis of the mtDNA D-loop of 706 chicken samples from Iraq (n = 107), Saudi Arabia (n = 185), Algeria (n = 88), Libya (n = 23), Ethiopia (n = 211) and Pakistan (n = 92) show the presence of five haplogroups (A, B, C, D and E), suggesting more than one maternal origin for the studied populations. Haplogroup E, which occurred in 625 samples, was the most frequent in all countries. This haplogroup most likely originates from the Indian subcontinent and probably migrated following a terrestrial route to these different countries. Haplotypes belonging to haplogroup D were present in all countries except Algeria and Libya, it is likely a legacy of the Indian Ocean maritime trading network. Haplogroup A was present in all countries and may be of commercial origin. Haplogroup B was found only in Ethiopia. Haplogroup C was only detected in the South-Western region of Saudi Arabia and in Ethiopia. Conclusion The results support a major influence of the Indian subcontinent on the maternal diversity of the today’s chicken populations examined here. Most of the diversity occurs within rather than between populations. This lack of phylogeographic signal agrees with both ancient and more recent trading networks having shaped the modern-day diversity of indigenous chicken across populations and countries.
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Affiliation(s)
- Ahmed S Al-Jumaili
- School of Life Sciences, the University of Nottingham, University Park, Nottingham, NG7 2RD, UK. .,University of Anbar, Ministry of Higher Education and Scientific Research, Anbar, Iraq.
| | - Selma Farah Boudali
- Laboratoire de Génétique Moléculaire et Cellulaire, Université des Sciences et de la Technologie d'Oran Mohamed Boudiaf, USTO-MB, BP 1505, El M'naouer, Oran, 31000, Algérie
| | - Adebabay Kebede
- Amhara Regional Agricultural Research Institute (ARARI), P.O. Box:527 Code 100, Bahir Dar, Ethiopia.,LiveGene, International Livestock Research Institute (ILRI), P. O. 5689, Addis Ababa, Ethiopia
| | - Sahar A Al-Bayatti
- Animal Sources Department, Directorate of Animal Resources, Ministry of Agriculture, Baghdad, Iraq
| | - Abdulamir A Essa
- Animal Sources Department, Directorate of Animal Resources, Ministry of Agriculture, Baghdad, Iraq
| | - Abulgasim Ahbara
- School of Life Sciences, the University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Riyadh S Aljumaah
- Animal Biotechnology, Animal Science Department, College of Food and Agriculture, King Saud University, P.O.Box 246, Riyadh, 11451, Kingdom of Saudi Arabia
| | - Raed M Alatiyat
- Genetics and Biotechnology, Animal Science Department, Agriculture Faculty, Mutah University, Karak, Jordan
| | - Joram M Mwacharo
- Small Ruminant Genetics and Genomics Group, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, ILRI-Ethiopia Campus, Addis Ababa, Ethiopia
| | - Gro Bjørnstad
- Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway
| | - Arifa N Naqvi
- Faculty of Life Sciences, Karakorum International University, Gilgit Baltistan, Pakistan
| | | | - Olivier Hanotte
- School of Life Sciences, the University of Nottingham, University Park, Nottingham, NG7 2RD, UK. .,LiveGene, International Livestock Research Institute (ILRI), P. O. 5689, Addis Ababa, Ethiopia.
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16
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Abstract
Mitochondria, a nearly ubiquitous feature of eukaryotes, are derived from an ancient symbiosis. Despite billions of years of cooperative coevolution - in what is arguably the most important mutualism in the history of life - the persistence of mitochondrial genomes also creates conditions for genetic conflict with the nucleus. Because mitochondrial genomes are present in numerous copies per cell, they are subject to both within- and among-organism levels of selection. Accordingly, 'selfish' genotypes that increase their own proliferation can rise to high frequencies even if they decrease organismal fitness. It has been argued that uniparental (often maternal) inheritance of cytoplasmic genomes evolved to curtail such selfish replication by minimizing within-individual variation and, hence, within-individual selection. However, uniparental inheritance creates conditions for cytonuclear conflict over sex determination and sex ratio, as well as conditions for sexual antagonism when mitochondrial variants increase transmission by enhancing maternal fitness but have the side-effect of being harmful to males (i.e., 'mother's curse'). Here, we review recent advances in understanding selfish replication and sexual antagonism in the evolution of mitochondrial genomes and the mechanisms that suppress selfish interactions, drawing parallels and contrasts with other organelles (plastids) and bacterial endosymbionts that arose more recently. Although cytonuclear conflict is widespread across eukaryotes, it can be cryptic due to nuclear suppression, highly variable, and lineage-specific, reflecting the diverse biology of eukaryotes and the varying architectures of their cytoplasmic genomes.
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Affiliation(s)
- Justin C Havird
- Department of Integrative Biology, The University of Texas, Austin, TX 78712, USA.
| | - Evan S Forsythe
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Alissa M Williams
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
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17
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Ågren JA, Munasinghe M, Clark AG. Sexual conflict through mother's curse and father's curse. Theor Popul Biol 2019; 129:9-17. [PMID: 31054851 DOI: 10.1016/j.tpb.2018.12.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 11/15/2018] [Accepted: 12/27/2018] [Indexed: 12/31/2022]
Abstract
In contrast with autosomes, lineages of sex chromosomes reside for different amounts of time in males and females, and this transmission asymmetry makes them hotspots for sexual conflict. Similarly, the maternal inheritance of the mitochondrial genome (mtDNA) means that mutations that are beneficial in females can spread in a population even if they are deleterious in males, a form of sexual conflict known as Mother's Curse. While both Mother's Curse and sex chromosome induced sexual conflict have been well studied on their own, the interaction between mitochondrial genes and genes on sex chromosomes is poorly understood. Here, we use analytical models and computer simulations to perform a comprehensive examination of how transmission asymmetries of nuclear, mitochondrial, and sex chromosome-linked genes may both cause and resolve sexual conflicts. For example, the accumulation of male-biased Mother's Curse mtDNA mutations will lead to selection in males for compensatory nuclear modifier loci that alleviate the effect. We show how the Y chromosome, being strictly paternally transmitted provides a particularly safe harbor for such modifiers. This analytical framework also allows us to discover a novel kind of sexual conflict, by which Y chromosome-autosome epistasis may result in the spread of male beneficial but female deleterious mutations in a population. We christen this phenomenon Father's Curse. Extending this analytical framework to ZW sex chromosome systems, where males are the heterogametic sex, we also show how W-autosome epistasis can lead to a novel kind of nuclear Mother's Curse. Overall, this study provides a comprehensive framework to understand how genetic transmission asymmetries may both cause and resolve sexual conflicts.
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Affiliation(s)
- J Arvid Ågren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14583, USA
| | - Manisha Munasinghe
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14583, USA; Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853, USA.
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18
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Paternal Leakage of Mitochondrial DNA in the Raccoon Dog (Nyctereutes Procyonoides Gray 1834). ANNALS OF ANIMAL SCIENCE 2019. [DOI: 10.2478/aoas-2018-0049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The aim of the study was to describe the mechanism of mitochondrial DNA inheritance in a group of farmed raccoon dogs. The study involved 354 individuals. Whole peripheral blood was the research material. DNA was isolated and PCR was performed for two fragments of mitochondrial genes: COX1 (cytochrome oxidase subunit 1 gene) and COX2 (cytochrome oxidase subunit 2 gene). The PCR products were sequenced and subjected to bioinformatics analyses. Three mitochondrial haplotypes were identified in the COX1 gene fragment and two in the COX2 gene fragment. The analysis of mtDNA inheritance in the paternal line confirmed the three cases of paternal mtDNA inheritance, i.e. the so-called “paternal leakage” in the analysed population. In two families, all offspring inherited paternal mitochondrial DNA, whereas in one family one descendant inherited paternal mtDNA and another one inherited maternal mtDNA. The lineage data indicated that one female which inherited maternal mitochondrial DNA transferred it onto the next generation. To sum up, the results of the study for the first time demonstrated the phenomenon of “paternal leakage” in farmed raccoon dogs, which facilitated description of mitochondrial DNA inheritance in the paternal line.
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19
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20
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Huang XH, Wu YJ, Miao YW, Peng MS, Chen X, He DL, Suwannapoom C, Du BW, Li XY, Weng ZX, Jin SH, Song JJ, Wang MS, Chen JB, Li WN, Otecko NO, Geng ZY, Qu XY, Wu YP, Yang XR, Jin JQ, Han JL, Zhong FS, Zhang XQ, Zhang YP. Was chicken domesticated in northern China? New evidence from mitochondrial genomes. Sci Bull (Beijing) 2018; 63:743-746. [PMID: 36658946 DOI: 10.1016/j.scib.2017.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/14/2017] [Accepted: 11/16/2017] [Indexed: 01/21/2023]
Affiliation(s)
- Xun-He Huang
- School of Life Sciences, Jiaying University, Meizhou 514015, China
| | - Ya-Jiang Wu
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Yong-Wang Miao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, 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; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Xing Chen
- 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
| | - Dan-Lin He
- College of Animal Sciences, South China Agricultural University, Guangzhou 510642, China
| | | | - Bing-Wang Du
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524088, China
| | - Xian-Yao Li
- College of Animal Science and Technology, Shandong Agricultural University, Taian 271018, China
| | - Zhuo-Xian Weng
- School of Life Sciences, Jiaying University, Meizhou 514015, China; College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Si-Hua Jin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Jiao-Jiao Song
- 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
| | - Ming-Shan 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, Kunming 650223, China
| | - Jie-Bo Chen
- School of Life Sciences, Jiaying University, Meizhou 514015, China
| | - Wei-Na Li
- School of Life Sciences, Jiaying University, Meizhou 514015, China
| | - Newton Otieno Otecko
- 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; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Zhao-Yu Geng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Xiang-Yong Qu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Yan-Ping Wu
- Institute of Animal Science, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Xiu-Rong Yang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Jie-Qiong Jin
- 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; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences (CAS-SEABRI), Yezin 05282, Myanmar
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | - Fu-Sheng Zhong
- School of Life Sciences, Jiaying University, Meizhou 514015, China.
| | - Xi-Quan Zhang
- College of Animal Sciences, South China Agricultural University, Guangzhou 510642, China.
| | - Ya-Ping Zhang
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming 650091, China; 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; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China.
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21
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The sperm factor: paternal impact beyond genes. Heredity (Edinb) 2018; 121:239-247. [PMID: 29959427 DOI: 10.1038/s41437-018-0111-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 06/12/2018] [Accepted: 06/16/2018] [Indexed: 12/20/2022] Open
Abstract
The fact that sperm carry more than the paternal DNA has only been discovered just over a decade ago. With this discovery, the idea that the paternal condition may have direct implications for the fitness of the offspring had to be revisited. While this idea is still highly debated, empirical evidence for paternal effects is accumulating. Male condition not only affects male fertility but also offspring early development and performance later in life. Several factors have been identified as possible carriers of non-genetic information, but we still know little about their origin and function and even less about their causation. I consider four possible non-mutually exclusive adaptive and non-adaptive explanations for the existence of paternal effects in an evolutionary context. In addition, I provide a brief overview of the main non-genetic components found in sperm including DNA methylation, chromatin modifications, RNAs and proteins. I discuss their putative functions and present currently available examples for their role in transferring non-genetic information from the father to the offspring. Finally, I identify some of the most important open questions and present possible future research avenues.
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22
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Jambui M, Honaker CF, Siegel PB. Correlated responses to long-term divergent selection for 8-week body weight in female White Plymouth Rock chickens: Sexual maturity. Poult Sci 2018; 96:3844-3851. [PMID: 29050442 DOI: 10.3382/ps/pex224] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 08/04/2017] [Indexed: 02/03/2023] Open
Abstract
Reported here are correlated responses for reproductive traits to long-term divergent selection (54 generations) for 8-week body weight (BW8). Comparisons involved both selected and relaxed lines. Traits measured were age at first egg (AFE), body weight at first egg (WFE), and ratio of body weight and age at first egg (WAFE). Although sexual maturity was delayed in the selected lines, the effect was more pronounced in the low than high selected and relaxed lines. Selection for low BW resulted in decreases in WFE and WAFE. Correlated responses to selection for high BW were increased WFE and WAFE. Minimum AFE, WFE, and WAFE in relation to sexual maturity were line specific and influenced by selection for BW8. WAFE provided a "yardstick" for target body weights that were optimum for successful attainment of sexual maturity and higher reproductive rates. Such may be line specific. There was opposition between relaxed and artificial selection, resulting in a higher reproductive performance and fitness for the former.
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Affiliation(s)
- M Jambui
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061-0306
| | - C F Honaker
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061-0306
| | - P B Siegel
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061-0306
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23
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Gadek CR, Newsome SD, Beckman EJ, Chavez AN, Galen SC, Bautista E, Witt CC. Why are tropical mountain passes “low” for some species? Genetic and stable-isotope tests for differentiation, migration and expansion in elevational generalist songbirds. J Anim Ecol 2017; 87:741-753. [DOI: 10.1111/1365-2656.12779] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/23/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Chauncey R. Gadek
- Department of Biology; University of New Mexico; Albuquerque NM USA
- Museum of Southwestern Biology; University of New Mexico; Albuquerque NM USA
| | - Seth D. Newsome
- Department of Biology; University of New Mexico; Albuquerque NM USA
| | - Elizabeth J. Beckman
- Department of Biology; University of New Mexico; Albuquerque NM USA
- Museum of Southwestern Biology; University of New Mexico; Albuquerque NM USA
- Division of Biological Sciences; University of Montana; Missoula MT USA
| | - Andrea N. Chavez
- Department of Biology; University of New Mexico; Albuquerque NM USA
- Museum of Southwestern Biology; University of New Mexico; Albuquerque NM USA
- Bureau of Land Management; Rio Puerco District Office; Albuquerque NM USA
| | - Spencer C. Galen
- Sackler Institute for Comparative Genomics; American Museum of Natural History; New York NY USA
| | - Emil Bautista
- Centro de Ornitología y Biodiversidad (CORBIDI); Urbanización Huertos de San Antonio; Surco Lima Perú
| | - Christopher C. Witt
- Department of Biology; University of New Mexico; Albuquerque NM USA
- Museum of Southwestern Biology; University of New Mexico; Albuquerque NM USA
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Jambui M, Honaker C, Siegel P. Selection for juvenile body weight in chickens: Standardizing for scaling. Poult Sci 2017; 96:2562-2568. [DOI: 10.3382/ps/pex080] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 03/21/2017] [Indexed: 11/20/2022] Open
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Lillie M, Sheng Z, Honaker CF, Dorshorst BJ, Ashwell CM, Siegel PB, Carlborg Ö. Genome-wide standing variation facilitates long-term response to bidirectional selection for antibody response in chickens. BMC Genomics 2017; 18:99. [PMID: 28100171 PMCID: PMC5244587 DOI: 10.1186/s12864-016-3414-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/12/2016] [Indexed: 12/13/2022] Open
Abstract
Background Long-term selection experiments provide a powerful approach to gain empirical insights into adaptation, allowing researchers to uncover the targets of selection and infer their contributions to the mode and tempo of adaptation. Here we implement a pooled genome re-sequencing approach to investigate the consequences of 39 generations of bidirectional selection in White Leghorn chickens on a humoral immune trait: antibody response to sheep red blood cells. Results We observed wide genome involvement in response to this selection regime. Many genomic regions were highly differentiated resulting from this experimental selection regime, an involvement of up to 20% of the chicken genome (208.8 Mb). While genetic drift has certainly contributed to this, we implement gene ontology, association analysis and population simulations to increase our confidence in candidate selective sweeps. Three strong candidate genes, MHC, SEMA5A and TGFBR2, are also presented. Conclusions The extensive genomic changes highlight the polygenic genetic architecture of antibody response in these chicken populations, which are derived from a common founder population, demonstrating the extent of standing immunogenetic variation available at the onset of selection. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3414-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mette Lillie
- Department of Medical Biochemistry and Microbiology, Genomics, Uppsala University, Uppsala, 75123, Sweden.
| | - Zheya Sheng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Christa F Honaker
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Ben J Dorshorst
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Christopher M Ashwell
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Paul B Siegel
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Örjan Carlborg
- Department of Medical Biochemistry and Microbiology, Genomics, Uppsala University, Uppsala, 75123, Sweden
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Ristov S, Brajkovic V, Cubric-Curik V, Michieli I, Curik I. MaGelLAn 1.0: a software to facilitate quantitative and population genetic analysis of maternal inheritance by combination of molecular and pedigree information. Genet Sel Evol 2016; 48:65. [PMID: 27613390 PMCID: PMC5018160 DOI: 10.1186/s12711-016-0242-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 08/29/2016] [Indexed: 11/23/2022] Open
Abstract
Background Identification of genes or even nucleotides that are responsible for quantitative and adaptive trait variation is a difficult task due to the complex interdependence between a large number of genetic and environmental factors. The polymorphism of the mitogenome is one of the factors that can contribute to quantitative trait variation. However, the effects of the mitogenome have not been comprehensively studied, since large numbers of mitogenome sequences and recorded phenotypes are required to reach the adequate power of analysis. Current research in our group focuses on acquiring the necessary mitochondria sequence information and analysing its influence on the phenotype of a quantitative trait. To facilitate these tasks we have produced software for processing pedigrees that is optimised for maternal lineage analysis. Results We present MaGelLAn 1.0 (maternal genealogy lineage analyser), a suite of four Python scripts (modules) that is designed to facilitate the analysis of the impact of mitogenome polymorphism on quantitative trait variation by combining molecular and pedigree information. MaGelLAn 1.0 is primarily used to: (1) optimise the sampling strategy for molecular analyses; (2) identify and correct pedigree inconsistencies; and (3) identify maternal lineages and assign the corresponding mitogenome sequences to all individuals in the pedigree, this information being used as input to any of the standard software for quantitative genetic (association) analysis. In addition, MaGelLAn 1.0 allows computing the mitogenome (maternal) effective population sizes and probability of mitogenome (maternal) identity that are useful for conservation management of small populations. Conclusions MaGelLAn is the first tool for pedigree analysis that focuses on quantitative genetic analyses of mitogenome data. It is conceived with the purpose to significantly reduce the effort in handling and preparing large pedigrees for processing the information linked to maternal lines. The software source code, along with the manual and the example files can be downloaded at http://lissp.irb.hr/software/magellan-1-0/ and https://github.com/sristov/magellan. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0242-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Strahil Ristov
- Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia.
| | - Vladimir Brajkovic
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000, Zagreb, Croatia
| | - Vlatka Cubric-Curik
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000, Zagreb, Croatia
| | - Ivan Michieli
- Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia
| | - Ino Curik
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000, Zagreb, Croatia
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Buzala M, Janicki B. Review: Effects of different growth rates in broiler breeder and layer hens on some productive traits. Poult Sci 2016; 95:2151-9. [PMID: 27194733 DOI: 10.3382/ps/pew173] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2016] [Indexed: 12/26/2022] Open
Abstract
Genetic selection that has been carried out for several dozen years has led to significant progress in poultry production by improving productive traits and increasing the profitability of broiler breeder and layer hen production. After hatching, broilers and layers differ mainly in feed intake, growth rate, efficiency of nutrient utilization, and development of muscles and adipose tissue. A key role can be played by hormonal mechanisms of appetite control in broilers and layers. The paper discusses the consequences of different growth rates resulting from long-term genetic selection on feed intake, efficiency of nutrient utilization, and development of muscles and adipose tissue, with particular consideration of the hormonal mechanisms of appetite control in broilers and layers. The information presented in this review paper shows that it would be worth comparing these issues in a meta-analysis.
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Affiliation(s)
- M Buzala
- Department of Animal Biochemistry and Biotechnology, UTP University of Science and Technology, Mazowiecka 28, 85-084 Bydgoszcz, Poland
| | - B Janicki
- Department of Animal Biochemistry and Biotechnology, UTP University of Science and Technology, Mazowiecka 28, 85-084 Bydgoszcz, Poland
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