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Dettori ML, Pazzola M, Noce A, Landi V, Vacca GM. Variations in Casein Genes Are Associated with Milk Protein and Fat Contents in Sarda Goats ( Capra hircus), with an Important Role of CSN1S2 for Milk Yield. Animals (Basel) 2023; 14:56. [PMID: 38200787 PMCID: PMC10778555 DOI: 10.3390/ani14010056] [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: 10/03/2023] [Revised: 11/18/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
This work aimed to assess the variability of casein genes in a population of 153 bucks and 825 lactating does of the Sarda breed, and to perform association analysis between polymorphic sites and milk yield and composition traits. To genotype the casein genes, we chose an SNP panel including 44 SNPs mapping to the four casein genes CSN1S1, CSN2, CSN1S2, and CSN3. Genotyping (made by KASP™ genotyping assay, based on competitive allele-specific PCR) revealed the high variability of the Sarda goat, and haplotype analysis revealed linkage disequilibrium (LD) between CSN1S1 and CSN2 genes, in addition to two LD blocks within the CSN1S2 and two LD blocks within the CSN3 gene, in bucks and does. Association analysis revealed that variability at all four casein genes was associated with milk protein content, total solids, and milk energy. The three Ca-sensitive casein genes were associated with lipid content, and CSN1S2 showed a unique pattern, with intron variants associated with milk yield, in addition to milk pH, NaCl, and SCS (Somatic Cell Score). This information might prove useful in selection schemes and in future investigations aiming to better understand the biology of lactation, and the direct link between genotype and phenotype.
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Affiliation(s)
- Maria Luisa Dettori
- Dipartimento Medicina Veterinaria, Università degli Studi di Sassari, 07100 Sassari, Italy; (M.P.); (G.M.V.)
| | - Michele Pazzola
- Dipartimento Medicina Veterinaria, Università degli Studi di Sassari, 07100 Sassari, Italy; (M.P.); (G.M.V.)
| | - Antonia Noce
- Centre de Recerca Agrigenòmica (CRAG), Campus Universitat Autònoma de Barcelona, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
| | - Vincenzo Landi
- Dipartimento Medicina Veterinaria, Università degli Studi di Bari Aldo Moro, 70121 Bari, Italy;
| | - Giuseppe Massimo Vacca
- Dipartimento Medicina Veterinaria, Università degli Studi di Sassari, 07100 Sassari, Italy; (M.P.); (G.M.V.)
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Qin W, Chen D, Guo P, Hu L, Zheng X, Cheng J, Chen H. Ecogroups and maternal haplogroups reveal the ancestral origin of native Chinese goat populations based on the variation of mtDNA D-loop sequences. Ecol Evol 2023; 13:e10382. [PMID: 37554396 PMCID: PMC10405232 DOI: 10.1002/ece3.10382] [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: 01/31/2023] [Revised: 06/22/2023] [Accepted: 07/18/2023] [Indexed: 08/10/2023] Open
Abstract
China is rich in goat breeding resources. Officially recognized local goat breeds are mainly distributed in agro-ecological regions. The population structure and matrilineal origin of native Chinese goats can be used to formulate protection and utilization strategies for these genetic resources. In this study, the genetic structure and maternal origin of native Chinese goats were investigated using mtDNA D-loop sequences. A total of 329 goat samples from 25 Chinese indigenous goat populations and five introduced goat breeds from abroad were collected; these populations were distributed in four ecogroups designated as Southwest, South-central, the North China Plain, and Foreign-ecogroup. A larger average number of nucleotide differences and richer nucleotide diversity were observed in South-central and Foreign-ecogroup, whereas these were lower in Southwest. The 216 haplotypes divided into several haplogroups, of which HapA contained 99 haplotypes distributed in Southwest, the North China Plain, and Foreign-ecogroup with high frequency (0.53-0.77), whereas the frequency of HapA in South-central was <0.09. HapB was mostly found in South-central (0.5538) and was distributed to the North China Plain (0.2667), while it was rare in Southwest (<0.08) and Foreign-ecogroup (<0.07). According to the estimation of kinship and ancestry, HapA had five ancestors (A2, A3, A5, A10, and A12), HapB had a single maternal ancestor (A8), and HapC had two maternal ancestors (A1 and A4). This study showed that native Chinese goat breeds were mainly divided into three haplogroups (HapA, HapB, and HapC) and goat populations have expanded in the ecological regions.
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Affiliation(s)
- Wenjuan Qin
- School of Animal Science and TechnologyAnhui Agricultural UniversityHefeiChina
- Key Laboratory of Anhui Local Livestock and Poultry Genetic Resources Conservation and Biobreeding of Anhui ProvinceHefeiChina
- Animal Molecular Immunization Center of Anhui Agricultural UniversityHefeiChina
| | - Daosong Chen
- School of Animal Science and TechnologyAnhui Agricultural UniversityHefeiChina
- Animal Molecular Immunization Center of Anhui Agricultural UniversityHefeiChina
| | - Panpan Guo
- School of Animal Science and TechnologyAnhui Agricultural UniversityHefeiChina
- Hefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina
| | - Lixing Hu
- School of Animal Science and TechnologyAnhui Agricultural UniversityHefeiChina
| | - Xiaodong Zheng
- Department of DermatologyThe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
| | - Jin Cheng
- College of Biological and Pharmaceutical EngineeringWest Anhui UniversityLuanChina
| | - Hongquan Chen
- School of Animal Science and TechnologyAnhui Agricultural UniversityHefeiChina
- Key Laboratory of Anhui Local Livestock and Poultry Genetic Resources Conservation and Biobreeding of Anhui ProvinceHefeiChina
- Animal Molecular Immunization Center of Anhui Agricultural UniversityHefeiChina
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Andaman local goat: mitochondrial genome characterization and lineage analysis. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01234-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Deniskova TE, Dotsev AV, Selionova MI, Upadhyay M, Medugorac I, Zinovieva NA. Characteristics of Dagestan Local Goat Subpopulations (Capra hircus) Based on the Analysis of the Complete Mitogenome Polymorphism. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422050040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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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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Maternal Origins and Haplotype Diversity of Seven Russian Goat Populations Based on the D-loop Sequence Variability. Animals (Basel) 2020; 10:ani10091603. [PMID: 32916903 PMCID: PMC7552281 DOI: 10.3390/ani10091603] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 12/27/2022] Open
Abstract
Simple Summary Russia has diverse specifically selected and multipurpose goat resources. However, the origin of the local goats is still enigmatic. In this study, we sequenced and analyzed mitochondrial DNA (mtDNA) fragments of seven Russian local goat populations to provide the first insight into their maternal lineage. Abstract The territory of modern Russia lies on the crossroads of East and West and covers various geographical environments where diverse groups of local goats originated. In this work, we present the first study on the maternal origin of Russian local goats, including Altai Mountain (n = 9), Dagestan Downy (n = 18), Dagestan Local (n = 12), Dagestan Milk (n = 15), Karachaev (n = 21), Orenburg (n = 10), and Soviet Mohair (n = 7) breeds, based on 715 bp D-loop mitochondrial DNA (mtDNA) sequences. Saanen goats (n = 5) were used for comparison. Our findings reveal a high haplotype (HD = 0.843–1.000) and nucleotide diversity (π = 0.0112–0.0261). A total of 59 haplotypes were determined in the Russian goat breeds, in which all differed from the haplotypes of the Saanen goats. The haplotypes identified in Altai Mountain, Orenburg, Soviet Mohair, and Saanen goats were breed specific. Most haplotypes (56 of 59) were clustered together with samples belonging to haplogroup A, which was in accordance with the global genetic pattern of maternal origin seen in most goats worldwide. The haplotypes that were grouped together with rare haplogroups D and G were found in the Altai Mountain breed and haplogroup C was detected in the Soviet Mohair breed. Thus, our findings revealed that local goats might have been brought to Russia via various migration routes. In addition, haplotype sharing was found in aboriginal goat populations from overlapping regions, which might be useful information for their official recognition status.
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Abdoli R, Zamani P, Ghasemi M. Genetic similarities and phylogenetic analysis of human and farm animal species based on mitogenomic nucleotide sequences. Meta Gene 2018. [DOI: 10.1016/j.mgene.2017.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Al-Araimi NA, Al-Atiyat RM, Gaafar OM, Vasconcelos R, Luzuriaga-Neira A, Eisa MO, Amir N, Benaissa MH, Alfaris AA, Aljumaah RS, Elnakhla SM, Salem MM, Ishag IA, El Khasmi M, Beja-Pereira A. Maternal genetic diversity and phylogeography of native Arabian goats. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.09.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Deng J, Feng J, Li L, Zhong T, Wang L, Guo J, Ba G, Song T, Zhang H. Polymorphisms, differentiation, and phylogeny of 10 Tibetan goat populations inferred from mitochondrial D-loop sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:439-445. [PMID: 28358643 DOI: 10.1080/24701394.2017.1303491] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
China has abundant population of Tibetan goats, but available information regarding genetic structure and phylogenetic status remains limited. Here, 130 mitochondrial D-loop sequences of individuals from 10 Tibetan goat populations located in distinct plateau areas were analyzed. Eighty-six haplotypes were defined, among which 97.7% were group-specific haplotypes. Haplotype and nucleotide diversity indices were 0.990 ± 0.003 and 0.0145 ± 0.0013, respectively. The pairwise Wright's F-statistics ranged from -0.028 to 0.385, and over half of them were greater than 0.05, indicating apparent genetic differentiation among the populations. AMOVA analysis (FST = 0.0858) manifested that the genetic structure has become weak. Phylogenetic trees revealed four haplogroups (A, B, C, and D), suggesting that Tibetan goats had four origins. Mismatch distribution analyses and neutrality tests indicated that at least one population expansion event occurred during the demographic history of Tibetan goat. These results will provide a more complete understanding of Tibetan goat genetic resources.
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Affiliation(s)
- Juan Deng
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province , Sichuan Agricultural University , Chengdu , Sichuan , P. R. China
| | - Jing Feng
- b Institute of Animal Science , Tibet Academy of Agricultural & Animal Husbandry Science , Lhasa , P. R. China
| | - Li Li
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province , Sichuan Agricultural University , Chengdu , Sichuan , P. R. China
| | - Tao Zhong
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province , Sichuan Agricultural University , Chengdu , Sichuan , P. R. China
| | - Linjie Wang
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province , Sichuan Agricultural University , Chengdu , Sichuan , P. R. China
| | - Jiazhong Guo
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province , Sichuan Agricultural University , Chengdu , Sichuan , P. R. China
| | - Gui Ba
- b Institute of Animal Science , Tibet Academy of Agricultural & Animal Husbandry Science , Lhasa , P. R. China
| | - Tianzeng Song
- b Institute of Animal Science , Tibet Academy of Agricultural & Animal Husbandry Science , Lhasa , P. R. China
| | - Hongping Zhang
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province , Sichuan Agricultural University , Chengdu , Sichuan , P. R. China
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Doro MG, Casu G, Leoni GG, Naitana S, Pirastu M, Novelletto A, Fraticelli F. The complete mitochondrial DNA sequence of the Montecristo goat. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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11
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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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Colli L, Lancioni H, Cardinali I, Olivieri A, Capodiferro MR, Pellecchia M, Rzepus M, Zamani W, Naderi S, Gandini F, Vahidi SMF, Agha S, Randi E, Battaglia V, Sardina MT, Portolano B, Rezaei HR, Lymberakis P, Boyer F, Coissac E, Pompanon F, Taberlet P, Ajmone Marsan P, Achilli A. Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability. BMC Genomics 2015; 16:1115. [PMID: 26714643 PMCID: PMC4696231 DOI: 10.1186/s12864-015-2342-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 12/22/2015] [Indexed: 01/31/2023] Open
Abstract
Background The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA). Results We present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aegagrus) from Iran. Our phylogenetic analyses dated the most recent common ancestor of C. hircus to ~460,000 years (ka) ago and identified five distinctive domestic haplogroups (A, B1, C1a, D1 and G). More than 90 % of goats examined were in haplogroup A. These domestic lineages are predominantly nested within C. aegagrus branches, diverged concomitantly at the interface between the Epipaleolithic and early Neolithic periods, and underwent a dramatic expansion starting from ~12–10 ka ago. Conclusions Domestic goat mitogenomes descended from a small number of founding haplotypes that underwent domestication after surviving the last glacial maximum in the Near Eastern refuges. All modern haplotypes A probably descended from a single (or at most a few closely related) female C. aegagrus. Zooarchaelogical data indicate that domestication first occurred in Southeastern Anatolia. Goats accompanying the first Neolithic migration waves into the Mediterranean were already characterized by two ancestral A and C variants. The ancient separation of the C branch (~130 ka ago) suggests a genetically distinct population that could have been involved in a second event of domestication. The novel diagnostic mutational motifs defined here, which distinguish wild and domestic haplogroups, could be used to understand phylogenetic relationships among modern breeds and ancient remains and to evaluate whether selection differentially affected mitochondrial genome variants during the development of economically important breeds. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2342-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Licia Colli
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. .,Research Center on Biodiversity and Ancient DNA - BioDNA, Università Cattolica del S. Cuore, Piacenza, 29122, Italy.
| | - Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy.
| | - Irene Cardinali
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy.
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy.
| | - Marco Rosario Capodiferro
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy. .,Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy.
| | - Marco Pellecchia
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy.
| | - Marcin Rzepus
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. .,Institute of Food Science and Nutrition - ISAN, Università Cattolica del S. Cuore, Piacenza, 29122, Italy.
| | - Wahid Zamani
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France. .,Department of Environmental Sciences, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Noor, Mazandaran, 46414-356, Iran.
| | - Saeid Naderi
- Natural Resources Faculty, University of Guilan, Guilan, 41335-1914, Iran.
| | - Francesca Gandini
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy. .,School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, UK.
| | | | - Saif Agha
- Department of Animal Production, Faculty of Agriculture, Ain Shams University, Cairo, 11241, Egypt.
| | - Ettore Randi
- Laboratorio di Genetica, Istituto per la Protezione e la Ricerca Ambientale (ISPRA), Bologna, 40064, Italy. .,Department 18/Section of Environmental Engineering, Aalborg University, Aalborg, DK-9000, Denmark.
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy.
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Palermo, 90128, Italy.
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Palermo, 90128, Italy.
| | - Hamid Reza Rezaei
- Environmental Sciences Department, Gorgan University of Agriculture and Natural Resources, Gorgan, 49138-15739, Iran.
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Iraklio, Crete, 71409, Greece.
| | - Frédéric Boyer
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France.
| | - Eric Coissac
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France.
| | - François Pompanon
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France.
| | - Pierre Taberlet
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France.
| | - Paolo Ajmone Marsan
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. .,Research Center on Biodiversity and Ancient DNA - BioDNA, Università Cattolica del S. Cuore, Piacenza, 29122, Italy.
| | - Alessandro Achilli
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy. .,Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy.
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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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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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