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De AK, Sawhney S, Sunder J, Muthiyan R, Ponraj P, Sujatha T, Malakar D, Mondal S, Bera AK, Kumar A, Chakurkar EB, Bhattacharya D. Peeping into Mitochondrial Diversity of Andaman Goats: Unveils Possibility of Maritime Transport with Diversified Geographic Signaling. Genes (Basel) 2023; 14:genes14040784. [PMID: 37107542 PMCID: PMC10138289 DOI: 10.3390/genes14040784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/22/2023] [Accepted: 03/14/2023] [Indexed: 04/29/2023] Open
Abstract
Andaman and Nicobar Islands, a part of South-East Asia, is enriched with the presence of native breeds of livestock (cattle, pig, goat) and poultry. There are two native goat breeds, viz., Andaman local goat and Teressa goat in Andaman and Nicobar Islands. However, to date, the origin and genetic makeup of these two breeds have not been detailed. Therefore, the present study describes the genetic makeup of Andaman goats through analysis of mitochondrial D-loop sequence for sequence polymorphism, phylogeographical signaling and population expansion events. The genetic diversity of the Teressa goat was less compared to the Andaman local goat due to its sole presence on Teressa Island. Out of 38 well-defined haplotypes of Andaman goats, the majority of haplotypes belonged to haplogroup A followed by haplogroup B and haplogroup D. The result of mismatch distribution and neutrality tests indicated no population expansion event of haplogroup A and B. Finally, based on poor geographical signaling, we hypothesize that Andaman goats have been imported to these Islands either through multidirectional diffusion or unidirectional diffusion. We justify our hypothesis of multidirectional diffusion on the basis of observation of the haplotype and nucleotide diversity of Andaman goats. Simultaneously, the probability of unidirectional diffusion of goats in these islands from the Indian subcontinent in different spells of domestication events through maritime routes cannot be ignored.
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Affiliation(s)
- Arun Kumar De
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
| | - Sneha Sawhney
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
| | - Jai Sunder
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
| | - Ramachandran Muthiyan
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
| | - Perumal Ponraj
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
| | - Tamilvanan Sujatha
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
| | - Dhruba Malakar
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Samiran Mondal
- Department of Veterinary Pathology, West Bengal University of Animal and Fishery Sciences, Kolkata 700037, West Bengal, India
| | - Asit Kumar Bera
- Reservoir and Wetland Fisheries Division, ICAR-Central Inland Fishery Research Institute, Barrackpore 700120, West Bengal, India
| | - Ashish Kumar
- Centre for Technology Alternatives for Rural Areas, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Eaknath Bhanudasrao Chakurkar
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
| | - Debasis Bhattacharya
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
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Baenyi Simon P, Owino Junga J, Tarekegn GM, Machuka E, Tiambo CK, Kabange D, Musale M Dieudinné K, Vumilia Kizungu R, Ochieng JW, Pelle R. Haplotype analysis of the mitochondrial DNA d-loop region reveals the maternal origin and historical dynamics among the indigenous goat populations in east and west of the Democratic Republic of Congo. Ecol Evol 2022; 12:e8713. [PMID: 35342608 PMCID: PMC8928878 DOI: 10.1002/ece3.8713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 12/10/2021] [Accepted: 02/18/2022] [Indexed: 12/03/2022] Open
Abstract
This study aimed at assessing haplotype diversity and population dynamics of three Congolese indigenous goat populations that included Kasai goat (KG), small goat (SG), and dwarf goat (DG) of the Democratic Republic of Congo (DRC). The 1169 bp d‐loop region of mitochondrial DNA (mtDNA) was sequenced for 339 Congolese indigenous goats. The total length of sequences was used to generate the haplotypes and evaluate their diversities, whereas the hypervariable region (HVI, 453 bp) was analyzed to define the maternal variation and the demographic dynamic. A total of 568 segregating sites that generated 192 haplotypes were observed from the entire d‐loop region (1169 bp d‐loop). Phylogenetic analyses using reference haplotypes from the six globally defined goat mtDNA haplogroups showed that all the three Congolese indigenous goat populations studied clustered into the dominant haplogroup A, as revealed by the neighbor‐joining (NJ) tree and median‐joining (MJ) network. Nine haplotypes were shared between the studied goats and goat populations from Pakistan (1 haplotype), Kenya, Ethiopia and Algeria (1 haplotype), Zimbabwe (1 haplotype), Cameroon (3 haplotypes), and Mozambique (3 haplotypes). The population pairwise analysis (FST) indicated a weak differentiation between the Congolese indigenous goat populations. Negative and significant (p‐value <.05) values for Fu's Fs (−20.418) and Tajima's (−2.189) tests showed the expansion in the history of the three Congolese indigenous goat populations. These results suggest a weak differentiation and a single maternal origin for the studied goats. This information will contribute to the improvement of the management strategies and long‐term conservation of indigenous goats in DRC.
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Affiliation(s)
- Patrick Baenyi Simon
- Department of Animal Production Université Evangélique en Afrique Bukavu Democratic Republic of Congo.,Department of Animal Production University of Nairobi Nairobi Kenya.,Institut National d'Etudes et des Recherches Agronomiques INERA Mulungu Bukavu Democratic Republic of Congo
| | | | - Getinet Mekuriaw Tarekegn
- Bioscience Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub Nairobi Kenya.,Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Uppsala Sweden.,Department of Animal Production and Technology Bahir Dar University Bahir Dar Ethiopia
| | - Eunice Machuka
- Bioscience Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub Nairobi Kenya
| | | | - Dorine Kabange
- Department of Veterinary Medicine Université de Lubumbashi Lubumbashi Democratic Republic of Congo
| | - Katunga Musale M Dieudinné
- Institut National d'Etudes et des Recherches Agronomiques INERA Mulungu Bukavu Democratic Republic of Congo
| | - Roger Vumilia Kizungu
- Institut National d'Etudes et des Recherches Agronomiques INERA, Gombe Kinshasa Kinshasa Democratic Republic of Congo
| | | | - Roger Pelle
- Bioscience Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub Nairobi Kenya
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Ressaissi Y, Amills M, Noce A, Ben Hamouda M. Characterizing the Mitochondrial Diversity of Arbi Goats from Tunisia. Biochem Genet 2021; 59:1225-1232. [PMID: 33743097 DOI: 10.1007/s10528-021-10058-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 03/08/2021] [Indexed: 10/21/2022]
Abstract
Arbi is one of the main local goat breeds in Tunisia, representing an important economic resource in arid and hot areas where cattle and sheep cannot thrive successfully. In the current work, we have characterized the mitochondrial diversity of 26 Arbi goats by partially sequencing the mitochondrial D-loop region. These sequences plus 10 retrieved from GenBank were analyzed with the DnaSP v.5.10.1, evidencing the existence of 12 different haplotypes. Nucleotide and haplotype diversities were 0.02 and 0.96. Moreover, median-joining network analysis showed that all D-loop sequences from Arbi goats correspond to haplogroup A and that in general they do not cluster with sequences from other goat breeds. The high diversity that has been observed in North African goats is compatible with the maritime diffusion of the Neolithic package 10,000-7000 YBP. Moreover, there are evidences that local Tunisian breeds have been extensively crossed with highly productive transboundary breeds in order to improve meat and milk yields. These uncontrolled crossing practices may lead to the loss of alleles that play key roles in the adaptation of Tunisian local breeds to a harsh environment.
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Affiliation(s)
- Yosra Ressaissi
- Institut National Agronomique de La Tunisie (INAT), 43 Avenue Charles Nicolle, 1082, Tunis, Tunisia.
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Antonia Noce
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Mohamed Ben Hamouda
- Institut National de La Recherche Agronomique de Tunisie (INRAT), Rue Hédi Karray, 2049, Ariana, Tunisie
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Dettori ML, Petretto E, Pazzola M, Vidal O, Amills M, Vacca GM. Assessing the Diversity and Population Substructure of Sarda Breed Bucks by Using Mtdna and Y-Chromosome Markers. Animals (Basel) 2020; 10:E2194. [PMID: 33255190 PMCID: PMC7761473 DOI: 10.3390/ani10122194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/21/2020] [Accepted: 11/22/2020] [Indexed: 11/16/2022] Open
Abstract
A sample of 146 Sarda bucks from eight subregions of Sardinia, Italy (Nuorese, Barbagia, Baronia, Ogliastra, Sarrabus, Guspinese, Iglesiente, Sulcis) were characterized for Y-chromosome and mtDNA markers to assess the levels of population substructure. Five polymorphic loci (SRY, AMELY, ZFY, and DDX3Y) on the Y-chromosome were genotyped. The control region of mtDNA was sequenced as a source of complementary information. Analysis of Y-chromosome data revealed the segregation of 5 haplotypes: Y1A (66.43%), Y2 (28.57%), Y1C (3.57%), Y1B1 (0.71%), and Y1B2 (0.71%). High levels of Y-chromosome diversity were observed in populations from Southwest Sardinia. The FST values based on Y-chromosome and mtDNA data were low, although a paternal genetic differentiation was observed when comparing the Nuorese and Barbagia populations (Central Sardinia) with the Sulcis, Iglesiente, and Sarrabus populations (Southern Sardinia). AMOVA analysis supported the lack of population substructure. These results suggest the occurrence of a historical and extensive gene flow between Sarda goat populations from different locations of Sardinia, despite the fact that this island is covered by several large mountain ranges. Introgression with foreign caprine breeds in order to improve milk production might have also contributed to avoiding the genetic differentiation amongst Sarda populations.
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Affiliation(s)
- Maria Luisa Dettori
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100 Sassari, Italy; (E.P.); (M.P.); (G.M.V.)
| | - Elena Petretto
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100 Sassari, Italy; (E.P.); (M.P.); (G.M.V.)
| | - Michele Pazzola
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100 Sassari, Italy; (E.P.); (M.P.); (G.M.V.)
| | - Oriol Vidal
- Departament de Biologia, Universitat de Girona, 17003 Girona, Spain;
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Department of Animal Genetics, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Giuseppe Massimo Vacca
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100 Sassari, Italy; (E.P.); (M.P.); (G.M.V.)
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Escudeiro A, Ferreira D, Mendes-da-Silva A, Heslop-Harrison JS, Adega F, Chaves R. Bovine satellite DNAs – a history of the evolution of complexity and its impact in the Bovidae family. THE EUROPEAN ZOOLOGICAL JOURNAL 2019. [DOI: 10.1080/24750263.2018.1558294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- A. Escudeiro
- Department of Genetics and Biotechnology (DGB), CAG – Laboratory of Cytogenomics and Animal Genomics (CAG), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - D. Ferreira
- Department of Genetics and Biotechnology (DGB), CAG – Laboratory of Cytogenomics and Animal Genomics (CAG), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - A. Mendes-da-Silva
- Department of Genetics and Biotechnology (DGB), CAG – Laboratory of Cytogenomics and Animal Genomics (CAG), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | | | - F. Adega
- Department of Genetics and Biotechnology (DGB), CAG – Laboratory of Cytogenomics and Animal Genomics (CAG), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - R. Chaves
- Department of Genetics and Biotechnology (DGB), CAG – Laboratory of Cytogenomics and Animal Genomics (CAG), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
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Kamalakkannan R, Jose J, Thomas S, Prabhu VR, Nagarajan M. Genetic diversity and maternal lineages of south Indian goats. Mol Biol Rep 2018; 45:2741-2748. [PMID: 30145642 DOI: 10.1007/s11033-018-4322-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 08/20/2018] [Indexed: 10/28/2022]
Abstract
In India, goats are considered to be one of the important livestock species that reinforce the rural economy. Even though India has 23 well-recognized goat breeds, the knowledge about their genetic diversity and domestication history is limited. In this study, we have analyzed the genetic diversity of 104 goats representing five different south Indian breeds using mtDNA D-loop region. The haplotype diversity of the breeds ranged from 0.9524 ± 0.0403 (Malabari) to 0.9921 ± 0.0154 (Kanni aadu). Analysis of molecular variance showed only 1.05% variation among breeds. On other hand, the variation within breed was remarkably high (98.95%) which suggested the weak phylogeographic structure of south Indian goats. The phylogenetic analysis revealed three haplogroups representing maternal lineages namely A, B and D. The analysis of 466 Indian goat sequences showed an additional lineage C. As reported in the previous studies, a major fraction of analyzed goats fell into haplogroup A. Our study confirms the presence of three maternal lineages for south Indian domestic goats.
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Affiliation(s)
- Ranganathan Kamalakkannan
- Department of Genomic Science, School of Biological Science, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Jesna Jose
- Department of Genomic Science, School of Biological Science, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Subhash Thomas
- Department of Genomic Science, School of Biological Science, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Vandana R Prabhu
- Department of Genomic Science, School of Biological Science, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Muniyandi Nagarajan
- Department of Genomic Science, School of Biological Science, Central University of Kerala, Kasaragod, Kerala, 671316, India.
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Vacca GM, Paschino P, Dettori ML, Bergamaschi M, Cipolat-Gotet C, Bittante G, Pazzola M. Environmental, morphological, and productive characterization of Sardinian goats and use of latent explanatory factors for population analysis. J Anim Sci 2017; 94:3947-3957. [PMID: 27898896 DOI: 10.2527/jas.2016-0542] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Dairy goat farming is practiced worldwide, within a range of different farming systems. Here we investigated the effects of environmental factors and morphology on milk traits of the Sardinian goat population. Sardinian goats are currently reared in Sardinia (Italy) in a low-input context, similar to many goat farming systems, especially in developing countries. Milk and morphological traits from 1,050 Sardinian goats from 42 farms were recorded. We observed a high variability regarding morphological traits, such as coat color, ear length and direction, horn presence, and udder shape. Such variability derived partly from the unplanned repeated crossbreeding of the native Sardinian goats with exotic breeds, especially Maltese goats. The farms located in the mountains were characterized by the traditional farming system and the lowest percentage of crossbred goats. Explanatory factors analysis was used to summarize the interrelated measured milk variables. The explanatory factor related to fat, protein, and energy content of milk (the "Quality" latent variable) explained about 30% of the variance of the whole data set of measured milk traits followed by the "Hygiene" (19%), "Production" (19%), and "Acidity" (11%) factors. The "Quality" and "Hygiene" factors were not affected by any of the farm classification items, whereas "Production" and "Acidity" were affected only by altitude and size of herds, respectively, indicating the adaptation of the local goat population to different environmental conditions. The use of latent explanatory factor analysis allowed us to clearly explain the large variability of milk traits, revealing that the Sardinian goat population cannot be divided into subpopulations based on milk attitude The factors, properly integrated with genetic data, may be useful tools in future selection programs.
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Ahmed S, Grobler P, Madisha T, Kotze A. Mitochondrial D-loop sequences reveal a mixture of endemism and immigration in Egyptian goat populations. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:711-716. [PMID: 27159728 DOI: 10.3109/24701394.2016.1174225] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The mitochondrial D-loop region was used to investigate genetic diversity within and between populations of Egyptian goats, to elucidate processes that explain present patterns of diversity and differentiation and to characterize Egyptian goats relative to international breeds. A total of 120 animals from six populations were sampled. Results confirm the main trend from previous studies of mtDNA diversity in goats, with high levels of diversity within populations, but with a comparative lack of genetic structure supporting geographic distribution. Haplotype diversity varied in a narrow range whereas nucleotide diversity values were more informative in showing differences between populations. The majority of goats analyzed (93.2%) displayed haplotypes that group with Haplogroup A, the most common type found in global goat populations. The remaining animals grouped with the less common Haplogroup G. Population differentiation analysis showed some uniqueness in the Aswan and Sharkawi populations from the South and East of Egypt. Overall, the structure of the Egyptian goat population is characterized by a high degree of homogeneity among populations from the north-western coastal region, the Nile Delta and the upper and middle regions of the Nile valley, but with possible introgression of rarer haplotypes into populations at the southern and eastern extremities of the country.
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Affiliation(s)
- Sahar Ahmed
- a Department of Cell Biology, Genetic Engineering and Biotechnology Division , National Research Centre , Giza , Egypt
| | - Paul Grobler
- b Department of Genetics , University of the Free State , Bloemfontein , South Africa
| | - Thabang Madisha
- c National Zoological Gardens of South Africa , Pretoria , South Africa
| | - Antionette Kotze
- b Department of Genetics , University of the Free State , Bloemfontein , South Africa.,c National Zoological Gardens of South Africa , Pretoria , South Africa
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Nieddu M, Mezzanotte R, Pichiri G, Coni PP, Dedola GL, Dettori ML, Pazzola M, Vacca GM, Robledo R. Evolution of satellite DNA sequences in two tribes of Bovidae: A cautionary tale. Genet Mol Biol 2015; 38:513-8. [PMID: 26692159 PMCID: PMC4763316 DOI: 10.1590/s1415-475738420150094] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 07/17/2015] [Indexed: 01/13/2023] Open
Abstract
Two clones, Bt1 from Bos taurus and Om1 from Ovis orientalis
musimon, were used as probes for hybridization on genomic DNA and on
metaphase chromosomes in members of Bovini and Caprini tribes. Bt1 and Om1 are
sequences respectively belonging to the 1.715 and 1.714 DNA satellite I families.
Southern blots and fluorescence in situ hybridization experiments
showed completely coherent results: the Bovini probe Bt1 hybridized only to members
of the Bovini tribe and not to members of Caprini. Likewise, the Caprini probe Om1
hybridized only to members of the Caprini tribe and not to members of Bovini.
Hybridization signals were detected in the heterochromatic regions of every
acrocentric autosome, except for two pairs of autosomes from Capra
hircus that did not show hybridization to probe Om1. No signal was
detected on X and Y chromosomes or on bi-armed autosomes. Remarkably, probe Om1
showed almost 100% homology with a bacterial sequence reported in
Helicobacter pylori.
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Affiliation(s)
- Mariella Nieddu
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Roberto Mezzanotte
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Giuseppina Pichiri
- Department of Surgical Sciences, University of Cagliari, Cagliari, Italy
| | - Pier Paolo Coni
- Department of Surgical Sciences, University of Cagliari, Cagliari, Italy
| | - Gian Luca Dedola
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | | | - Michele Pazzola
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | | | - Renato Robledo
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
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Variability of the caprine whey protein genes and their association with milk yield, composition and renneting properties in the Sarda breed: 2. The BLG gene. J DAIRY RES 2015; 82:442-8. [PMID: 26373476 DOI: 10.1017/s0022029915000473] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The variability of the promoter region and the 3'UTR (exon-7) of the BLG gene, encoding the β-lactoglobulin, was investigated by sequencing in 263 lactating Sarda goats in order to assess its association with milk traits. Milk traits included: milk yield, fat, total protein and lactose content, pH, daily fat and protein yield (DFPY), freezing point, milk energy, somatic cell count, total microbial mesophilic count, rennet coagulation time (RCT), curd firming rate (k20) and curd firmness (a30). A total of 7 polymorphic sites were detected and the sequence analysed was given accession number KM817769. Only three SNPs (c.-381C>T, c.-323C>T and c.*420C>A) had minor allele frequency higher than 0.05. The effects of farm, stage of lactation and the interaction farm × stage of lactation significantly influenced all the milk traits (P T and c.*420C>A (P T (P < 0.001). The c.-381TT homozygous goats showed lower pH, RCT and k20 than c.-381CT (P < 0.05). In conclusion the polymorphism of the goat BLG gene did not affect the total protein content of the Sarda goat milk, and only weakly influenced RCT and k20. On the other hand, an interesting effect on milk yields and DFPY emerged in two SNPs. This information might be useful in dairy goat breeding programs.
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Variability of the caprine whey protein genes and their association with milk yield, composition and renneting properties in the Sarda breed. 1. The LALBA gene. J DAIRY RES 2015; 82:434-41. [PMID: 26304038 DOI: 10.1017/s0022029915000461] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The 5' flanking region and 3' UTR of the caprine LALBA gene were analysed by SSCP and sequencing. A total of nine SNPs were detected: three in the promoter region, two were synonymous coding SNPs at exon-1, and four SNPs were in exon-4, within the 3'UTR. The nucleotide changes located in the promoter region (c.-358T>C, c.-163G>A, c.-121T>G) were genotyped by SSCP in 263 Sarda goats to evaluate their possible effect on milk yield, composition and renneting properties. We observed an effect of the three SNPs on milk yield and lactose content. Genotypes TT and CT at c.-358T>C (P A (P C and c.-121T>G were part of transcription factors binding sites, potentially involved in modulating the LALBA gene expression. The LALBA genotype affected renneting properties (P < 0.001), as heterozygotes c.-358CT and c.-163GA were characterised by delayed rennet coagulation time and curd firming time and the lowest value of curd firmness. The present investigation increases the panel of SNPs and adds new information about the effects of the caprine LALBA gene polymorphism.
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The effect of cold acidified milk replacer on productive performance of suckling kids reared in an extensive farming system. Small Rumin Res 2014. [DOI: 10.1016/j.smallrumres.2014.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Vacca GM, Dettori ML, Piras G, Manca F, Paschino P, Pazzola M. Goat casein genotypes are associated with milk production traits in the Sarda breed. Anim Genet 2014; 45:723-31. [PMID: 24990661 DOI: 10.1111/age.12188] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2014] [Indexed: 11/26/2022]
Abstract
The aim of the current work was to analyze, in the Sarda breed goat, genetic polymorphism within the casein genes and to assess their influence on milk traits. Genetic variants at the CSN1S1, CSN2, CSN1S2 and CSN3 gene loci were investigated using PCR-based methods, cloning and sequencing. Strong alleles prevailed at the CSN1S1 gene locus and defective alleles also were revealed. Null alleles were evidenced at each calcium-sensitive gene locus. At the CSN3 gene locus, we observed a prevalence of the CSN3 A and B alleles; the occurrence of rare alleles such as CSN3 B'', C, C', D, E and M; and the CSN3 S allele (GenBank KF644565) described here for the first time in Capra hircus. Statistical analysis showed that all genes, except CSN3, significantly influenced milk traits. The CSN1S1 BB and AB genotypes were associated with the highest percentages of protein (4.41 and 4.40 respectively) and fat (5.26 and 5.34 respectively) (P < 0.001). A relevant finding was that CSN2 and CSN1S2 genotypes affected milk protein content and yield. The polymorphism of the CSN2 gene affected milk protein percentage with the highest values recorded in the CSN2 AA goats (4.35, at P < 0.001). The CSN1S2 AC goats provided the highest fat (51.02 g/day) and protein (41.42 g/day) (P < 0.01) production. This information can be incorporated into selection schemes for the Sarda breed goat.
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Affiliation(s)
- G M Vacca
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, via Vienna 2, Sassari, 07100, Italy; Centro di Competenza Biodiversità Animale, viale Adua 2C, Sassari, 07100, Italy
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14
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Doro MG, Piras D, Leoni GG, Casu G, Vaccargiu S, Parracciani D, Naitana S, Pirastu M, Novelletto A. Phylogeny and patterns of diversity of goat mtDNA haplogroup A revealed by resequencing complete mitogenomes. PLoS One 2014; 9:e95969. [PMID: 24763315 PMCID: PMC3999278 DOI: 10.1371/journal.pone.0095969] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 04/01/2014] [Indexed: 11/18/2022] Open
Abstract
We sequenced to near completion the entire mtDNA of 28 Sardinian goats, selected to represent the widest possible diversity of the most widespread mitochondrial evolutionary lineage, haplogroup (Hg) A. These specimens were reporters of the diversity in the island but also elsewhere, as inferred from their affiliation to each of 11 clades defined by D-loop variation. Two reference sequences completed the dataset. Overall, 206 variations were found in the full set of 30 sequences, of which 23 were protein-coding non-synonymous single nucleotide substitutions. Many polymorphic sites within Hg A were informative for the reconstruction of its internal phylogeny. Bayesian and network clustering revealed a general similarity over the entire molecule of sequences previously assigned to the same D-loop clade, indicating evolutionarily meaningful lineages. Two major sister groupings emerged within Hg A, which parallel distinct geographical distributions of D-loop clades in extant stocks. The pattern of variation in protein-coding genes revealed an overwhelming role of purifying selection, with the quota of surviving variants approaching neutrality. However, a simple model of relaxation of selection for the bulk of variants here reported should be rejected. Non-synonymous diversity of Hg's A, B and C denoted that a proportion of variants not greater than that allowed in the wild was given the opportunity to spread into domesticated stocks. Our results also confirmed that a remarkable proportion of pre-existing Hg A diversity became incorporated into domestic stocks. Our results confirm clade A11 as a well differentiated and ancient lineage peculiar of Sardinia.
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Affiliation(s)
- Maria Grazia Doro
- Institute of Population Genetics, National Research Council (CNR), Sassari, Italy
| | - Daniela Piras
- Institute of Population Genetics, National Research Council (CNR), Sassari, Italy
- Experimental Zoo-prophylactic Institute of Sardinia, Sassari, Italy
| | | | - Giuseppina Casu
- Institute of Population Genetics, National Research Council (CNR), Sassari, Italy
| | - Simona Vaccargiu
- Institute of Population Genetics, National Research Council (CNR), Sassari, Italy
| | | | - Salvatore Naitana
- Faculty of Veterinary Sciences, University of Sassari, Sassari, Italy
| | - Mario Pirastu
- Institute of Population Genetics, National Research Council (CNR), Sassari, Italy
- Genetic Park of Ogliastra, Perdasdefogu, Italy
| | - Andrea Novelletto
- Department of Biology, University “Tor Vergata”, Rome, Italy
- * E-mail:
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15
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Pazzola M, Dettori M, Pira E, Noce A, Paschino P, Vacca G. Effect of polymorphisms at the casein gene cluster on milk renneting properties of the Sarda goat. Small Rumin Res 2014. [DOI: 10.1016/j.smallrumres.2013.12.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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16
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Cornale P, Renna M, Lussiana C, Bigi D, Chessa S, Mimosi A. The Grey Goat of Lanzo Valleys (Fiurinà): Breed characteristics, genetic diversity, and quantitative-qualitative milk traits. Small Rumin Res 2014. [DOI: 10.1016/j.smallrumres.2013.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Genetic diversity analysis of the mitochondrial D-loop of Nigerian indigenous sheep. ACTA ACUST UNITED AC 2012. [DOI: 10.1017/s2078633612000070] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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18
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Piras D, Doro MG, Casu G, Melis PM, Vaccargiu S, Piras I, Parracciani D, Stradoni R, Frongia B, Lai G, Sale S, Cattari W, Piras R, Querci O, Demuro P, Cui S, Atzori F, Mancosu M, Marchiori F, Cammelli R, Spiga A, Loddo PP, Pili G, Boi R, Argiolas G, Mereu P, Leoni GG, Naitana S, Pirastu M, Novelletto A. Haplotype affinities resolve a major component of goat (Capra hircus) MtDNA D-loop diversity and reveal specific features of the Sardinian stock. PLoS One 2012; 7:e30785. [PMID: 22363488 PMCID: PMC3281868 DOI: 10.1371/journal.pone.0030785] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 12/28/2011] [Indexed: 11/18/2022] Open
Abstract
Goat mtDNA haplogroup A is a poorly resolved lineage absorbing most of the overall diversity and is found in locations as distant as Eastern Asia and Southern Africa. Its phylogenetic dissection would cast light on an important portion of the spread of goat breeding. The aims of this work were 1) to provide an operational definition of meaningful mtDNA units within haplogroup A, 2) to investigate the mechanisms underlying the maintenance of diversity by considering the modes of selection operated by breeders and 3) to identify the peculiarities of Sardinian mtDNA types. We sequenced the mtDNA D-loop in a large sample of animals (1,591) which represents a non-trivial quota of the entire goat population of Sardinia. We found that Sardinia mirrors a large quota of mtDNA diversity of Western Eurasia in the number of variable sites, their mutational pattern and allele frequency. By using bayesian analysis, a distance-based tree and a network analysis, we recognized demographically coherent groups of sequences identified by particular subsets of the variable positions. The results showed that this assignment system could be reproduced in other studies, capturing the greatest part of haplotype diversity.We identified haplotype groups overrepresented in Sardinian goats as a result of founder effects. We found that breeders maintain diversity of matrilines most likely through equalization of the reproductive potential. Moreover, the relevant amount of inter-farm mtDNA diversity found does not increase proportionally with distance. Our results illustrate the effects of breeding practices on the composition of maternal gene pool and identify mtDNA types that may be considered in projects aimed at retrieving the maternal component of the oldest breeds of Sardinia.
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Affiliation(s)
- Daniela Piras
- Institute of Population Genetics, National Research Council, Sassari, Italy
| | - Maria Grazia Doro
- Institute of Population Genetics, National Research Council, Sassari, Italy
| | - Giuseppina Casu
- Institute of Population Genetics, National Research Council, Sassari, Italy
| | - Paola Maria Melis
- Institute of Population Genetics, National Research Council, Sassari, Italy
| | - Simona Vaccargiu
- Institute of Population Genetics, National Research Council, Sassari, Italy
| | | | | | | | | | | | - Salvatore Sale
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | - Walter Cattari
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | - Roberto Piras
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | - Ombretta Querci
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | | | - Sandro Cui
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | - Franco Atzori
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | - Marco Mancosu
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | | | - Rossana Cammelli
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | - Alessandra Spiga
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | - Pier Paolo Loddo
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | - Gianfranco Pili
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | - Roberto Boi
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | | | - Paolo Mereu
- Department of Physiological, Biochemical and Cell Sciences, University of Sassari, Sassari, Italy
| | | | - Salvatore Naitana
- Faculty of Veterinary Sciences, University of Sassari, Sassari, Italy
| | - Mario Pirastu
- Institute of Population Genetics, National Research Council, Sassari, Italy
- Genetic Park of Ogliastra, Perdasdefogu, Italy
| | - Andrea Novelletto
- Department of Biology, University “Tor Vergata”, Rome, Italy
- * E-mail:
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Hughes S, Fernández H, Cucchi T, Duffraisse M, Casabianca F, Istria D, Pompanon F, Vigne JD, Hänni C, Taberlet P. A dig into the past mitochondrial diversity of Corsican goats reveals the influence of secular herding practices. PLoS One 2012; 7:e30272. [PMID: 22299033 PMCID: PMC3267719 DOI: 10.1371/journal.pone.0030272] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 12/14/2011] [Indexed: 12/02/2022] Open
Abstract
The goat (Capra hircus) is one of the earliest domesticated species ca. 10,500 years ago in the Middle-East where its wild ancestor, the bezoar (Capra aegagrus), still occurs. During the Neolithic dispersal, the domestic goat was then introduced in Europe, including the main Mediterranean islands. Islands are interesting models as they maintain traces of ancient colonization, historical exchanges or of peculiar systems of husbandry. Here, we compare the mitochondrial genetic diversity of both medieval and extant goats in the Island of Corsica that presents an original and ancient model of breeding with free-ranging animals. We amplified a fragment of the Control Region for 21 medieval and 28 current goats. Most of them belonged to the A haplogroup, the most worldwide spread and frequent today, but the C haplogroup is also detected at low frequency in the current population. Present Corsican goats appeared more similar to medieval goats than to other European goat populations. Moreover, 16 out of the 26 haplotypes observed were endemic to Corsica and the inferred demographic history suggests that the population has remained constant since the Middle Ages. Implications of these results on management and conservation of endangered Corsican goats currently decimated by a disease are addressed.
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Affiliation(s)
- Sandrine Hughes
- Paléogénomique et Evolution Moléculaire, Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS UMR 5242, INRA, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France.
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