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Gáspárdy A, Berger B, Zabavnik-Piano J, Kovács E, Annus K, Zenke P, Sáfár L, Maróti-Agóts Á. Comparison of mtDNA control region among descendant breeds of the extinct Zaupel sheep revealed haplogroup C and D in Central Europe. Vet Med Sci 2021; 7:2330-2338. [PMID: 34291885 PMCID: PMC8604133 DOI: 10.1002/vms3.585] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The consideration of the descendance is indispensable in the preservation of endangered animal breeds. The authors compared mitochondrial DNA (mtDNA) control region sequence in three descendant breeds of the extinct Zaupel sheep, firstly. Their investigation was carried out in order to prove the common origin of Waldschaf (Austria), Bovec sheep (Slovenia) and Cikta (Hungary). A total of 118 biological samples were taken from non-related representatives of the three breeds between 2015 and 2017. A newly designed primer pair was also used to amplify the segment (1180 bp) to be tested. The total number of haplotypes in the whole study population was 49. The majority of which fell into haplogroup B. The significant negative value of the Fu's Fs statistic (Fs statistic = -3.296, p = 0.013) based on haplotype frequencies demonstrated a moderate foreign gene flow. As a novel observation haplogroups C and D appeared in Cikta and Bovec sheep, respectively. The Tajima D-test value in the entire study population was -0.914 (p > 0.10), meaning that the separation of the three descendant breeds did not cause genetic drift, these are collectively in genetic equilibrium. The genetic information confirmed the common origin of the breeds known from the breed history.
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Affiliation(s)
- András Gáspárdy
- Department of Animal Breeding, Nutrition and Laboratory Animal Science, University of Veterinary Medicine, Budapest, Hungary
| | - Beate Berger
- Federal Ministry of Agriculture, Forestry, Environment and Water Management, Institute for Organic Agriculture and Biodiversity, Wels-Thalheim, Austria
| | - Jelka Zabavnik-Piano
- Veterinary Faculty, Department of Biochemistry, Molecular Biology and Genetics, University of Ljubljana, Ljubljana, Slovenia
| | - Endre Kovács
- Department of Animal Breeding, Nutrition and Laboratory Animal Science, University of Veterinary Medicine, Budapest, Hungary
| | - Kata Annus
- Department of Animal Breeding, Nutrition and Laboratory Animal Science, University of Veterinary Medicine, Budapest, Hungary
| | - Petra Zenke
- Department of Animal Breeding, Nutrition and Laboratory Animal Science, University of Veterinary Medicine, Budapest, Hungary
| | - László Sáfár
- Hungarian Sheep and Goat Breeders' Association, Budapest, Hungary
| | - Ákos Maróti-Agóts
- Department of Animal Breeding, Nutrition and Laboratory Animal Science, University of Veterinary Medicine, Budapest, Hungary
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Engel L, Becker D, Nissen T, Russ I, Thaller G, Krattenmacher N. Exploring the Origin and Relatedness of Maternal Lineages Through Analysis of Mitochondrial DNA in the Holstein Horse. Front Genet 2021; 12:632500. [PMID: 34335677 PMCID: PMC8320364 DOI: 10.3389/fgene.2021.632500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 06/18/2021] [Indexed: 11/26/2022] Open
Abstract
Maternal lineages are important for the breeding decision in the Holstein horse breed. To investigate the genetic diversity of the maternal lineages and the relationships between founder mares, the maternal inherited mitochondrial genome (except the repetitive part of the non-coding region) of 271 mares representing 75 lineages was sequenced. The sequencing predominantly revealed complete homology in the nucleotide sequences between mares from one lineage with exceptions in 13 lineages, where differences in one to three positions are probably caused by de novo mutations or alternate fixation of heteroplasmy. We found 78 distinct haplotypes that have not yet been described in other breeds. Six of these occurred in two or three different lineages indicating a common ancestry. Haplotypes can be divided into eight clusters with all mares from one lineage belonging to the same cluster. Within a cluster, the average number of pairwise differences ranged from zero to 16.49 suggesting close maternal relationships between these mares. The results showed that the current breeding population originated from at least eight ancestral founder mares.
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Affiliation(s)
- Laura Engel
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, Kiel, Germany
| | - Doreen Becker
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Thomas Nissen
- Verband der Züchter des Holsteiner Pferdes e.V., Kiel, Germany
| | - Ingolf Russ
- Tierzuchtforschung e.V. München, Grub, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, Kiel, Germany
| | - Nina Krattenmacher
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, Kiel, Germany
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Riahi L, Snoussi M, Romdhane MB, Zoghlami N. New insights into the intraspecific cytoplasmic DNA diversity, maternal lineages classification and conservation issues of Tunisian pearl millet landraces. Plant Biotechnol (Tokyo) 2021; 38:17-22. [PMID: 34177320 PMCID: PMC8215465 DOI: 10.5511/plantbiotechnology.20.0831a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/31/2020] [Indexed: 06/13/2023]
Abstract
Tunisian pearl millet (Pennisetum glaucum L.) landraces are still growing in contrasting agro-ecological environments and are considered potentially useful for national and international breeders. Despite its genetic potential, the cropping areas of this species are still limited and scattered which increases the risk of genetic erosion. The chloroplast DNA polymorphism and maternal lineages classification of forty nine pearl millet landraces representing seven populations covering the main distribution area of this crop in Tunisia were undertaken based on informative cpSSR molecular markers. A total of 21 alleles combining to 9 haplotypes were detected with a mean value of 3.5 alleles per locus and a haplotype genetic diversity (Hd) of 0.82. The number of chloroplast haplotypes per population ranged from 1 to 4 with an average of 1.28. The haplotypes median-joining network and UPGMA analyses revealed two probable ancestral maternal lineages with a differential pearl millet seed-exchange rate between the investigated areas. Northern and Central populations presented unique genetic backgrounds while historical farmers' practices in the South-East area resulted in the isolation of their own local landraces. The genetic evidences strongly support at least two introduction origins of pearl millet in Tunisia, one in the North and the other in the South followed by distinct local dispersal histories. Complementary in-situ and ex-situ conservation strategies taking into account the conservation of the maternal lineage cytoplasmic diversity are required. The investigated chloroplast SSRs provide useful molecular markers which could be used in further genetic studies and breeding surveys of pearl millet genetic resources.
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Affiliation(s)
- Leila Riahi
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, BP 901, 2050 Hammam-Lif, Tunisia
- Laboratory of Biotechnology and Bio-Geo Resources Valorization BVBGR-LR11ES31, University of Manouba, Higher Institute of Biotechnology of Sidi Thabet, Higher Institute of Biotechnology of Sidi Thabet, 2020 Ariana, Tunisia
| | - Marwa Snoussi
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, BP 901, 2050 Hammam-Lif, Tunisia
| | - Mériam Ben Romdhane
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, BP 901, 2050 Hammam-Lif, Tunisia
| | - Nejia Zoghlami
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, BP 901, 2050 Hammam-Lif, Tunisia
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Crespo CM, Cardozo DG, Tessone A, Vázquez M, Kisielinski C, Arencibia V, Tackney J, Zangrando AF, Dejean CB. Distribution of maternal lineages in hunter-gatherer societies of the southern coast of Tierra del Fuego, Argentina. Am J Phys Anthropol 2020; 173:709-720. [PMID: 32808278 DOI: 10.1002/ajpa.24107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/18/2020] [Accepted: 06/09/2020] [Indexed: 11/07/2022]
Abstract
OBJECTIVES The aim of this work is to explore the maternal genetic diversity of hunter-gatherers of the southern Tierra del Fuego, specifically the north coast of Beagle Channel, the Península Mitre, and Isla de los Estados through ancient mitochondrial DNA analysis. MATERIALS AND METHODS The hypervariable regions 1 and 2 of the mitochondrial genome of five individuals from the north coast of Beagle Channel, six individuals from Península Mitre, and one individual from Isla de los Estados were analyzed. Through diversity statistics, Analysis of Molecular Variance (AMOVA), and Median Joining networks analyses, maternal relationships in the region were evaluated and phylogenetic similarities between ancient and contemporary populations of Tierra del Fuego were determined. RESULTS The mitochondrial DNA lineages from the ancient individuals analyzed reveals the presence of subclades C1b and D1g. Pattern of decreasing genetic diversity toward the South is observed. The AMOVAs performed found no statistically significant differences between individuals of the north coast of Beagle Channel and Península Mitre-Isla de los Estados, and modern Yámana populations. Median joining network of haplotypes of clades C1 and D1g, show the same results. DISCUSSION Ethnohistoric and ethnographic records of Península Mitre show that this region was occupied during the 19th century by Haush or Manekenk populations, although their biological, cultural, and subsistence characterization is unclear. We explore their maternal lineages and encounter low levels of genetic diversity and the absence of population differentiation with modern Yámana groups. We suggest that Península Mitre-Isla de los Estado was part of the same hunting and gathering populations as those of the Beagle Channel.
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Affiliation(s)
- Cristian M Crespo
- Departamento de Cs. Naturales y Antropológicas, CEBBAD, Universidad Maimónides, CONICET, Equipo de Antropología Biológica, Buenos Aires, Argentina
| | - Darío G Cardozo
- Departamento de Cs. Naturales y Antropológicas, CEBBAD, Universidad Maimónides, CONICET, Equipo de Antropología Biológica, Buenos Aires, Argentina
| | - Augusto Tessone
- Instituto de Geocronología y Geología Isotópica (INGEIS-CONICET), Pabellón INGEIS, Ciudad Universitaria, Buenos Aires, Argentina
| | - Martín Vázquez
- Centro Austral de Investigaciones Científicas (CADIC-CONICET), Ushuaia, Argentina
| | | | - Valeria Arencibia
- Departamento de Cs. Naturales y Antropológicas, CEBBAD, Universidad Maimónides, CONICET, Equipo de Antropología Biológica, Buenos Aires, Argentina
| | - Justin Tackney
- Department of Anthropology, University of Kansas, Lawrence, Kansas, USA
| | | | - Cristina B Dejean
- Departamento de Cs. Naturales y Antropológicas, CEBBAD, Universidad Maimónides, Equipo de Antropología Biológica, Buenos Aires, Argentina.,UBA, Sección de Antropología Biológica, ICA, FFyL, Buenos Aires, Argentina
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Li R, Sun J, Zhao Y, Xiao H, Chen S. Maternal origins, population structure and demographic history of ten Chinese indigenous goat breeds from Yunnan. J Anim Breed Genet 2020; 138:108-121. [PMID: 32658371 DOI: 10.1111/jbg.12492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 04/13/2020] [Accepted: 06/09/2020] [Indexed: 11/30/2022]
Abstract
Yunnan as a frontier zone that connects China with South and Southeast Asia, has 11 well-recognized goat breeds. However, the knowledge about maternal origins, population structure and demographic history of Chinese indigenous goats from Yunnan is limited. In this study, we analysed a 481-bp fragment of first hypervariable segment (HVSI) of the mitochondrial DNA (mtDNA) control region sequences of 749 individuals from 10 Yunnan indigenous goat breeds, of which 556 sequences were newly determined. There were 110 polymorphic sites that defined 158 haplotypes among all sequences. The haplotype and nucleotide diversity of these breeds ranged from 0.782 ± 0.079 to 0.982 ± 0.015 and from 0.028 ± 0.003 to 0.043 ± 0.005, respectively. Phylogenetic analysis identified two lineages A and B, of which the lineage A had higher frequency (68.1%) and distributed in all Yunnan breeds. We combined previously reported sequences with our sequences belonging to the lineage B and detected two subclades B1 and B2, in which the B1 subclade shared individuals from Eastern Asia, Southeast Asia and Southern Asia. Given higher level of diversity and more unique haplotypes, the B2 subclade probably originated from Southwestern China. The haplotype network, analysis of molecular variance (AMOVA) and a Mantel test revealed no significant phylogeographic structuring among Yunnan goat breeds. This can be explained by high gene flow and genetic admixture among these breeds from different geographic regions in Yunnan. Additionally, both the lineages A and B reflected different demographic histories. This study will provide a scientific basis for the conservation and utilization of Yunnan indigenous goats.
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Affiliation(s)
- Rong Li
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China
| | - Jianshu Sun
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, China
| | - Yincheng Zhao
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, China
| | - Heng Xiao
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, China
| | - Shanyuan Chen
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, China
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Chen SG, Li J, Zhang F, Xiao B, Hu JM, Cui YQ, Hofreiter M, Hou XD, Sheng GL, Lai XL, Yuan JX. Different maternal lineages revealed by ancient mitochondrial genome of Camelus bactrianus from China. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:786-793. [PMID: 31542986 DOI: 10.1080/24701394.2019.1659250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Domestic Bactrian camel (Camelus bactrianus) used to be one of the most important livestock species in Chinese history, as well as the major transport carrier on the ancient Silk Road. However, archeological studies on Chinese C. bactrianus are still limited, and molecular biology research on this species is mainly focused on modern specimens. In this study, we retrieved the complete mitochondrial genome from a C. bactrianus specimen, which was excavated from northwestern China and dated at 1290-1180 cal. years before present (yBP). Phylogenetic analyses using 18 mitochondrial genomes indicated that the C. bactrianus clade was divided into two maternal lineages. The majority of samples originating from Iran to Japan and Mongolia belong to subclade A1, while our sample together with two Mongolian individuals formed the much smaller subclade A2. Furthermore, the divergence time of these two maternal lineages was estimated as 165 Kya (95% credibility interval 117-222 Kya), this might indicate that several different evolutionary lineages were incorporated into the domestic gene pool during the initial domestication process. Bayesian skyline plot (BSP) analysis suggest a slow increase in female effective population size of C. bactrianus from 5000 years ago, which corresponds to the beginning of domestication of C. bactrianus. The present study also revealed that there were extensive exchanges of genetic information among C. bactrianus populations in regions along the Silk Road.
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Affiliation(s)
- Shun-Gang Chen
- Faculty of Materials Science and Chemistry, China University of Geosciences , Wuhan , China.,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Ji Li
- Insitute of Silk Road Studies, Northwest University , Xi'an , China
| | - Fan Zhang
- Ancient DNA Lab, School of Life Science, Jilin University , Changchun , China
| | - Bo Xiao
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Jia-Ming Hu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Yin-Qiu Cui
- Ancient DNA Lab, School of Life Science, Jilin University , Changchun , China
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse , Potsdam , Germany
| | - Xin-Dong Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Gui-Lian Sheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Xu-Long Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
| | - Jun-Xia Yuan
- Faculty of Materials Science and Chemistry, China University of Geosciences , Wuhan , China.,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan , China
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