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Jain K, Panigrahi M, Nayak SS, Rajawat D, Sharma A, Sahoo SP, Bhushan B, Dutt T. The evolution of contemporary livestock species: Insights from mitochondrial genome. Gene 2024; 927:148728. [PMID: 38944163 DOI: 10.1016/j.gene.2024.148728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/05/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024]
Abstract
The domestication of animals marks a pivotal moment in human history, profoundly influencing our demographic and cultural progress. This process has led to significant genetic, behavioral, and physical changes in livestock species compared to their wild ancestors. Understanding the evolutionary history and genetic diversity of livestock species is crucial, and mitochondrial DNA (mtDNA) has emerged as a robust marker for investigating molecular diversity in animals. Its highly conserved gene content across animal species, minimal duplications, absence of introns, and short intergenic regions make mtDNA analysis ideal for such studies. Mitochondrial DNA analysis has uncovered distinct cattle domestication events dating back to 8000 years BC in Southwestern Asia. The sequencing of water buffalo mtDNA in 2004 provided important insights into their domestication history. Caprine mtDNA analysis identified three haplogroups, indicating varied maternal origins. Sheep, domesticated 12,000 years ago, exhibit diverse mtDNA lineages, suggesting multiple domestication events. Ovine mtDNA studies revealed clades A, B, C, and a fourth lineage, group D. The origins of domestic pigs were traced to separate European and Asian events followed by interbreeding. In camels, mtDNA elucidated the phylogeographic structure and genetic differentiation between wild and domesticated species. Horses, domesticated around 3500 BC, show significant mtDNA variability, highlighting their diverse origins. Yaks exhibit unique adaptations for high-altitude environments, with mtDNA analysis providing insights into their adaptation. Chicken mtDNA studies supported a monophyletic origin from Southeast Asia's red jungle fowl, with evidence of multiple origins. This review explores livestock evolution and diversity through mtDNA studies, focusing on cattle, water buffalo, goat, sheep, pig, camel, horse, yak and chicken. It highlights mtDNA's significance in unraveling maternal lineages, genetic diversity, and domestication histories, concluding with insights into its potential application in improving livestock production and reproduction dynamics.
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Affiliation(s)
- Karan Jain
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | | | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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Cabrera VM. New Canary Islands Roman mediated settlement hypothesis deduced from coalescence ages of curated maternal indigenous lineages. Sci Rep 2024; 14:11150. [PMID: 38750053 PMCID: PMC11096394 DOI: 10.1038/s41598-024-61731-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 05/09/2024] [Indexed: 05/18/2024] Open
Abstract
Numerous genetic studies have contributed to reconstructing the human history of the Canary Islands population. The recent use of new ancient DNA targeted enrichment and next-generation sequencing techniques on new Canary Islands samples have greatly improved these molecular results. However, the bulk of the available data is still provided by the classic mitochondrial DNA phylogenetic and phylogeographic studies carried out on the indigenous, historical, and extant human populations of the Canary Islands. In the present study, making use of all the accumulated mitochondrial information, the existence of DNA contamination and archaeological sample misidentification in those samples is evidenced. Following a thorough review of these cases, the new phylogeographic analysis revealed the existence of a heterogeneous indigenous Canarian population, asymmetrically distributed across the various islands, which most likely descended from a unique mainland settlement. These new results and new proposed coalescent ages are compatible with a Roman-mediated arrival driven by the exploitation of the purple dye manufacture in the Canary Islands.
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Affiliation(s)
- Vicente M Cabrera
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, 38200, San Cristobal de La Laguna, Spain.
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Senczuk G, Macrì M, Di Civita M, Mastrangelo S, Del Rosario Fresno M, Capote J, Pilla F, Delgado JV, Amills M, Martínez A. The demographic history and adaptation of Canarian goat breeds to environmental conditions through the use of genome-wide SNP data. Genet Sel Evol 2024; 56:2. [PMID: 38172652 PMCID: PMC10763158 DOI: 10.1186/s12711-023-00869-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND The presence of goats in the Canary Islands dates back to the late 1st millennium BC, which coincides with the colonization by the Amazigh settlers. However, the exact geographic origin of Canarian goats is uncertain since the Amazigh peoples were distributed over a wide spatial range. Nowadays, three Canarian breeds (Palmera, Majorera and Tinerfeña) are officially recognized, along with two distinct South and North Tinerfeña ecotypes, with the South Tinerfeña and Majorera goats thriving in arid and dry semi-desertic environments and the Palmera and North Tinerfeña goats are adapted to humid and temperate areas that are influenced by trade winds. Genotypes for 224 Canarian goats were generated using the Illumina Goat single nucleotide polymorphism (SNP)50 BeadChip. By merging these data with the genotypes from 1007 individuals of African and Southern European ancestry, our aim was to ascertain the geographic origin of the Canarian goats and identify genes associated with adaptation to diverse environmental conditions. RESULTS The diversity indices of the Canarian breeds align with most of those of the analyzed local breeds from Africa and Europe, except for the Palmera goats that showed lower levels of genetic variation. The Canarian breeds demonstrate a significant genetic differentiation compared to other populations, which indicates a history of prolonged geographic isolation. Moreover, the phylogenetic reconstruction indicated that the ancestry of the Canarian goats is fundamentally North African rather than West African. The ADMIXTURE and the TreeMix analyses showed no evidence of gene flow between Canarian goats and other continental breeds. The analysis of runs of homozygosity (ROH) identified 13 ROH islands while the window-based FST method detected 25 genomic regions under selection. Major signals of selection were found on Capra hircus (CHI) chromosomes 6, 7, and 10 using various comparisons and methods. CONCLUSIONS This genome-wide analysis sheds new light on the evolutionary history of the four breeds that inhabit the Canary Islands. Our findings suggest a North African origin of the Canarian goats. In addition, within the genomic regions highlighted by the ROH and FST approaches, several genes related to body size and heat tolerance were identified.
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Affiliation(s)
- Gabriele Senczuk
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy.
| | - Martina Macrì
- Animal Breeding Consulting S.L., 14014, Córdoba, Spain
- Universidad de Córdoba, 14071, Córdoba, Spain
| | - Marika Di Civita
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
| | - Salvatore Mastrangelo
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128, Palermo, Italy
| | | | - Juan Capote
- Instituto Canario de Investigaciones Científicas, 38260, Tenerife, Spain
| | - Fabio Pilla
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
| | | | - Marcel Amills
- CRAG, CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
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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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Forcina G, Woutersen K, Sánchez-Ramírez S, Angelone S, Crampe JP, Pérez JM, Fandos P, Granados JE, Jowers MJ. Demography reveals populational expansion of a recently extinct Iberian ungulate. ZOOSYST EVOL 2021. [DOI: 10.3897/zse.97.61854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Reconstructing the demographic history of endangered taxa is paramount to predict future fluctuations and disentangle the contributing factors. Extinct taxa or populations might also provide key insights in this respect by means of the DNA extracted from museum specimens. Nevertheless, the degraded status of biological material and the limited number of records may pose some constraints. For this reason, identifying all available sources, including private and public biological collections, is a crucial step forward. In this study, we reconstructed the demographic history based on cytochrome-b sequence data of the Pyrenean ibex (Capra pyrenaica pyrenaica), a charismatic taxon of the European wildlife that became extinct in the year 2000. Moreover, we built a database of the museum specimens available in public biological collections worldwide and genotyped a privately owned 140-year-old trophy from the Spanish Pyrenees to confirm its origin. We found that the population of the Pyrenean ibex underwent a recent expansion approximately 20,000 years ago, after which trophy hunting and epizootics triggered a relentless population decline. Our interpretations, based on the genetic information currently available in public repositories, provide a solid basis for more exhaustive analyses relying on all the new sources identified. In particular, the adoption of a genome-wide approach appears a fundamental prerequisite to disentangle the multiple contributing factors associated with low genetic diversity, including inbreeding depression, acting as extinction drivers.
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Saleh AA, Rashad AMA, Hassanine NNAM, Sharaby MA, Zhao Y. Evaluation of morphological traits and physiological variables of several Chinese goat breeds and their crosses. Trop Anim Health Prod 2021; 53:74. [PMID: 33400045 DOI: 10.1007/s11250-020-02549-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/22/2020] [Indexed: 10/22/2022]
Abstract
The current study was undertaken to evaluate some morphological traits of the goat breeds raised in Southwest China. The field experimentation and data collection were from 434 animals presenting seven breeds of the Dazu black goat (DBG; n = 203), Saanen milk goat (SMG; n = 50), Black Boer × Dazu black goat (BXC; n = 28), Hechuan white goat (HWG; n = 49), Inner Mongolia Cashmere goat (IMCG; n = 25), IMCG × DBG (F1; n = 57) and F1 × F1 (F2; n = 22). All studied animals were adult and selected to be at the same age (36.50 ± 0.75 months). After editing, more than 20 morphological and production traits like body condition score (BCS), testicle measurements, coat colour, fibre traits, skin colour, horn colour, horn shape, horn orientation, wattles, front hair, beard, ear shape, ear size, rump angle, hind leg angulation and physiological variables were analysed. BXC and DBG had dark coat colour, whilst SMG, HWG and IMCG had light colour, whilst F1 and F2 ranged from light to dark coat colour. Concerning BCS, the breeds BXC and DBG were characterized as fat goats, whilst SMG, HWG, F1 and F2 were average, whilst IMCG was thin. The maximum values for testis measurements were recorded for BXC, SMG and DBG. For fibre traits, IMCG, F1 and F2 were the most superior. BXC and DBG males have good fertility parameters. The highest values for rectal temperature, skin temperature and breath rate were recorded for SMG. These findings revealed the presence of a wide range of morphological differences among studied goat breeds. Such diversity in the performance of goat breeds raised in Southwest China is crucial to implement reliable selection strategies for breeding goats in this area.
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Affiliation(s)
- Ahmed A Saleh
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, 400715, People's Republic of China.,Animal and Fish Production Department, Faculty of Agriculture (Alshatby), Alexandria University, Alexandria, 11865, Egypt
| | - Amr M A Rashad
- Animal and Fish Production Department, Faculty of Agriculture (Alshatby), Alexandria University, Alexandria, 11865, Egypt
| | - Nada N A M Hassanine
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, 400715, People's Republic of China
| | - Mahmoud A Sharaby
- Animal and Fish Production Department, Faculty of Agriculture (Alshatby), Alexandria University, Alexandria, 11865, Egypt
| | - Yongju Zhao
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, 400715, People's Republic of China.
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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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Parreira JR, Hernández-Castellano LE, Argüello A, Capote J, Castro N, de Sousa Araújo S, de Almeida AM. Understanding seasonal weight loss tolerance in dairy goats: a transcriptomics approach. BMC Genomics 2020; 21:629. [PMID: 32928114 PMCID: PMC7489022 DOI: 10.1186/s12864-020-06968-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 08/03/2020] [Indexed: 02/07/2023] Open
Abstract
Background Seasonal weight loss (SWL) is a very important limitation to the production of ruminants in the Mediterranean and Tropical regions. In these areas, long dry seasons lead to poor pastures with low nutritional value. During the dry season, ruminants, particularly those raised in extensive production systems, lose around 30% of their body weight. Seasonal weight loss has important consequences on animal productive performance and health. In this study, RNA sequencing was used to characterize feed restriction effects in dairy goat of 2 breeds with different SWL tolerance: Majorera (tolerant) and Palmera (susceptible). Nine Majorera and ten Palmera goats were randomly distributed in a control and a restricted group: Majorera Control (adequately fed; MC; n = 4), Palmera Control (adequately fed; PC; n = 6), Majorera Restricted (feed restricted; ME; n = 5) and Palmera Restricted (feed restricted; PE; n = 4). On day 22 of the trial, mammary gland biopsies were collected for transcriptomics analysis. Results From these samples, 24,260 unique transcripts were identified. From those, 82 transcripts were differentially expressed between MC and ME, 99 between PC and PE, twelve between both control groups and twenty-nine between both restricted groups. Conclusions Feed restriction affected several biochemical pathways in both breeds such as: carbohydrate and lipid transport; intracellular trafficking, RNA processing and signal transduction. This research also highlights the importance or involvement of the genes in tolerance (ENPP1, S-LZ, MT2A and GPNB) and susceptibility (GPD1, CTPS1, ELOVL6 and NR4A1) to SWL with respectively higher expression in the Majorera restriced group and the Palmera restricted group in comparison to the control groups. In addition, results from the study may be extrapolated to other dairy ruminant species.
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Affiliation(s)
- José Ricardo Parreira
- IBET - Instituto de Biologia Experimental e Tecnológica, Av. da República, 2780-157, Oeiras, Portugal.,ITQB NOVA - Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | | | - Anastasio Argüello
- Animal Production and Biotechnology group, Institute of Animal Health and Food Safety, Universidad de Las Palmas de Gran Canaria, 35413, Arucas, Spain
| | - Juan Capote
- Unit of Animal Production, Pasture, and Forage in Arid and Subtropical Areas, Canary Islands Institute for Agricultural Research, 38270, La Laguna, Spain
| | - Noemí Castro
- Animal Production and Biotechnology group, Institute of Animal Health and Food Safety, Universidad de Las Palmas de Gran Canaria, 35413, Arucas, Spain
| | - Susana de Sousa Araújo
- ITQB NOVA - Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - André Martinho de Almeida
- LEAF - Linking Landscape, Environment, Agriculture And Food, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 13409-017, Lisbon, Portugal.
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Diwedi J, Singh AW, Ahlawat S, Sharma R, Arora R, Sharma H, Raja KN, Verma NK, Tantia MS. Comprehensive analysis of mitochondrial DNA based genetic diversity in Indian goats. Gene 2020; 756:144910. [PMID: 32574758 DOI: 10.1016/j.gene.2020.144910] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/01/2020] [Accepted: 06/17/2020] [Indexed: 11/18/2022]
Abstract
Thirty four distinct breeds and many non-descript populations represent the caprine diversity of India. Genetic characterization of breeds is an essential element in designing breeding strategies and preserving genetic diversity. Considering the popularity of mitochondrial DNA for phylogeographical studies, this study involved an extensive analysis of population structure and genetic diversity of 28 defined breeds and 5 lesser known populations representing all four major agro-climatic zones of India using mitochondrial DNA markers. Analysis of hypervariable region 1 of mtDNA control region in 443 goats together with 22 reference sequences, delineated 341 distinct haplotypes belonging to four maternal haplogroups; A, B, C and D, with haplogroup A representing 90% of the individuals. The haplotype and nucleotide diversity indices of Indian goats were 0.998 ± 0.001 and 0.028 ± 0.001, respectively indicating abundant genetic variability. Estimates of population demographic parameters from mismatch analysis suggested a relatively good fit to the model of either spatial or demographic expansion of Indian goats. AMOVA analysis and topology of MJ network suggested lack of phylogeographic structure in domestic goats, which can be attributed to unstructured animal breeding, dwindling pastures and nomadic pastoralism. Genetic differentiation between goats from different agro-ecological regions was in accordance with their geographical propinquity.
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Affiliation(s)
- Jyotsana Diwedi
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | | | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India.
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Himani Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - K N Raja
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - N K Verma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - M S Tantia
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
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Mammary gland and milk fatty acid composition of two dairy goat breeds under feed-restriction. J DAIRY RES 2018; 84:264-271. [PMID: 28831968 DOI: 10.1017/s0022029917000371] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Goat dairy products are an important source of animal protein in the tropics. During the dry season, pasture scarcity leads animals to lose up to 40% of their body weight, a condition known as Seasonal Weight Loss (SWL) that is one of the major constraints in ruminant production. Breeds with high tolerance to SWL are relevant to understand the physiological responses to pasture scarcity so they could be used in programs for animal breeding. In the Canary Islands there are two dairy goat breeds with different levels of tolerance to SWL: the Palmera, susceptible to SWL; and the Majorera, tolerant to SWL. Fat is one of the milk components most affected by environmental and physiological conditions. This study hypothesises that feed-restriction affects Majorera and Palmera breeds differently, leading to different fatty acid profiles in the mammary gland and milk. An interaction between breed and feed-restriction was observed in the mammary gland. Feed-restriction was associated with an increase in oleic acid and a decrease in palmitic acid percentage in the Palmera breed whereas no differences were observed in the Majorera breed. Palmitic and oleic acids together constituted around 60% of the total fatty acids identified, which suggests that Palmera breed is more susceptible to SWL. In milk, feed-restriction affected both breeds similarly. Regarding the interaction of the breed with the treatment, we also observed similar responses in both breeds, but this influence affects only around 2% of the total fatty acids. In general, Majorera breed is more tolerant to feed-restriction.
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11
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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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12
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Palma M, Hernández-Castellano LE, Castro N, Arguëllo A, Capote J, Matzapetakis M, de Almeida AM. NMR-metabolomics profiling of mammary gland secretory tissue and milk serum in two goat breeds with different levels of tolerance to seasonal weight loss. MOLECULAR BIOSYSTEMS 2017; 12:2094-107. [PMID: 27001028 DOI: 10.1039/c5mb00851d] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Goats are of special importance in the Mediterranean and tropical regions for producing a variety of dairy products. The scarcity of pastures during the dry season leads to seasonal weight loss (SWL), which affects milk production. In this work, we studied the effect of feed-restriction on two dairy goat breeds, with different tolerance levels to SWL: the Majorera breed (tolerant) and the Palmera breed (susceptible). Nuclear magnetic resonance (NMR) was used to compare the metabolome of an aqueous fraction of the mammary gland and milk serum from both breeds. Goats in mid-lactation were divided by breed, and each in two feed-regime groups: the control group and the restricted-fed group (to achieve 15-20% reduction of body weight at the end of the experiment). Milk and mammary gland samples were collected at the end of the experimental period (23rd day). (1)H NMR spectra were collected from the aqueous extract of the mammary gland biopsies and the milk serum. Profiling analysis has led to the identification of 46 metabolites in the aqueous extract of the mammary gland. Lactose, glutamate, glycine and lactate were found to be the most abundant. Analysis of milk serum allowed the identification of 50 metabolites, the most abundant being lactose, citrate and creatine. Significant differences were observed, in mammary gland biopsies and milk serum, between control and restricted-fed groups in both breeds, albeit with no differences between the breeds. Variations seem to be related to metabolism adaptation to the low-energy diet and are indicative of breed-specific microflora. Milk serum showed more metabolites varying between control and restricted groups, than the mammary gland. The Majorera breed also showed more variations than the Palmera breed in milk samples, which could be an indication of a prompt adaptation to SWL by the Majorera breed.
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Affiliation(s)
- Mariana Palma
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | | | - Noemí Castro
- Department of Animal Science, Universidad de Las Palmas de Gran Canaria, Arucas, Gran Canaria, Spain
| | - Anastasio Arguëllo
- Department of Animal Science, Universidad de Las Palmas de Gran Canaria, Arucas, Gran Canaria, Spain
| | - Juan Capote
- ICIA - Instituto Canario de Investigaciones Agrarias, Valle Guerra, Tenerife, Spain
| | - Manolis Matzapetakis
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - André Martinho de Almeida
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal. and Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal and Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
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Manunza A, Noce A, Serradilla JM, Goyache F, Martínez A, Capote J, Delgado JV, Jordana J, Muñoz E, Molina A, Landi V, Pons A, Balteanu V, Traoré A, Vidilla M, Sánchez-Rodríguez M, Sànchez A, Cardoso TF, Amills M. A genome-wide perspective about the diversity and demographic history of seven Spanish goat breeds. Genet Sel Evol 2016; 48:52. [PMID: 27455838 PMCID: PMC4960707 DOI: 10.1186/s12711-016-0229-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 06/29/2016] [Indexed: 12/19/2022] Open
Abstract
Background The main goal of the current work was to infer the demographic history of seven Spanish goat breeds (Malagueña, Murciano-Granadina, Florida, Palmera, Mallorquina, Bermeya and Blanca de Rasquera) based on genome-wide diversity data generated with the Illumina Goat SNP50 BeadChip (population size, N = 176). Five additional populations from Europe (Saanen and Carpathian) and Africa (Tunisian, Djallonké and Sahel) were also included in this analysis (N = 80) for comparative purposes. Results Our results show that the genetic background of Spanish goats traces back mainly to European breeds although signs of North African admixture were detected in two Andalusian breeds (Malagueña and Murciano-Granadina). In general, observed and expected heterozygosities were quite similar across the seven Spanish goat breeds under analysis irrespective of their population size and conservation status. For the Mallorquina and Blanca de Rasquera breeds, which have suffered strong population declines during the past decades, we observed increased frequencies of large-sized (ROH), a finding that is consistent with recent inbreeding. In contrast, a substantial part of the genome of the Palmera goat breed comprised short ROH, which suggests a strong and ancient founder effect. Conclusions Admixture with African goats, genetic drift and inbreeding have had different effects across the seven Spanish goat breeds analysed in the current work. This has generated distinct patterns of genome-wide diversity that provide new clues about the demographic history of these populations. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0229-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Arianna Manunza
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Antonia Noce
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | | | - Félix Goyache
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, Gijón, 33394, Spain
| | - Amparo Martínez
- Departamento de Genética, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Juan Capote
- Instituto Canario de Investigaciones Agrarias, 38108, La Laguna, Tenerife, Spain
| | | | - Jordi Jordana
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Eva Muñoz
- Departamento de Genética, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Antonio Molina
- Departamento de Genética, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Vincenzo Landi
- Departamento de Genética, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Agueda Pons
- Unitat de Races Autòctones, Servei de Millora Agrària i Pesquera (SEMILLA), 07198, Son Ferriol, Spain
| | - Valentin Balteanu
- Faculty of Animal Science and Biotechnologies and Institute of Life Sciences, University of Agricultural Sciences and Veterinary Medicine, 400372, Cluj-Napoca, Romania
| | - Amadou Traoré
- Institut de l'Environnement et Recherches Agricoles, 04 BP 8645, Ouagadougou 04, Burkina Faso
| | - Montse Vidilla
- Associació de Ramaders de Cabra Blanca de Rasquera, Rasquera, 43513, Spain
| | | | - Armand Sànchez
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Tainã Figueiredo Cardoso
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Marcel Amills
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain. .,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
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14
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Cugno G, Parreira JR, Ferlizza E, Hernández-Castellano LE, Carneiro M, Renaut J, Castro N, Arguello A, Capote J, Campos AMO, Almeida AM. The Goat (Capra hircus) Mammary Gland Mitochondrial Proteome: A Study on the Effect of Weight Loss Using Blue-Native PAGE and Two-Dimensional Gel Electrophoresis. PLoS One 2016; 11:e0151599. [PMID: 27031334 PMCID: PMC4816393 DOI: 10.1371/journal.pone.0151599] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/01/2016] [Indexed: 12/23/2022] Open
Abstract
Seasonal weight loss (SWL) is the most important limitation to animal production in the Tropical and Mediterranean regions, conditioning producer’s incomes and the nutritional status of rural communities. It is of importance to produce strategies to oppose adverse effects of SWL. Breeds that have evolved in harsh climates have acquired tolerance to SWL through selection. Most of the factors determining such ability are related to changes in biochemical pathways as affected by SWL. In this study, a gel based proteomics strategy (BN: Blue-Native Page and 2DE: Two-dimensional gel electrophoresis) was used to characterize the mitochondrial proteome of the secretory tissue of the goat mammary gland. In addition, we have conducted an investigation of the effects of weight loss in two goat breeds with different levels of adaptation to nutritional stress: Majorera (tolerant) and Palmera (susceptible). The study used Majorera and Palmera dairy goats, divided in 4 sets, 2 for each breed: underfed group fed on wheat straw (restricted diet, so their body weight would be 15–20% reduced by the end of experiment), and a control group fed with an energy-balanced diet. At the end of the experimental period (22 days), mammary gland biopsies were obtained for all experimental groups. The proteomic analysis of the mitochondria enabled the resolution of a total of 277 proteins, and 148 (53%) were identified by MALDI-TOF/TOF mass spectrometry. Some of the proteins were identified as subunits of the glutamate dehydrogenase complex and the respiratory complexes I, II, IV, V from mitochondria, as well as numerous other proteins with functions in: metabolism, development, localization, cellular organization and biogenesis, biological regulation, response to stimulus, among others, that were mapped in both BN and 2DE gels. The comparative proteomics analysis enabled the identification of several proteins: NADH-ubiquinone oxidoreductase 75 kDa subunit and lamin B1 mitochondrial (up-regulated in the Palmera breed), Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2 (up-regulated in the Majorera breed) and cytochrome b-c1 complex subunit 1, mitochondrial and Chain D, Bovine F1-C8 Sub-Complex Of Atp Synthase (down-regulated in the Majorera breed) as a consequence of weight loss.
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Affiliation(s)
- Graziano Cugno
- CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal
- Animal Science Department, Universidad de Las Palmas de Gran Canaria, Arucas, Gran Canaria, Spain
| | - José R. Parreira
- IBET – Instituto de Biologia Experimental e Tecnologica, Oeiras, Portugal
- ITQB/UNL – Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Enea Ferlizza
- CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Lorenzo E. Hernández-Castellano
- Animal Science Department, Universidad de Las Palmas de Gran Canaria, Arucas, Gran Canaria, Spain
- Veterinary Physiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Mariana Carneiro
- CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal
| | - Jenny Renaut
- LIST – Luxemburg Institute of Science and Technology, Belvaux, Luxemburg
| | - Noemí Castro
- Animal Science Department, Universidad de Las Palmas de Gran Canaria, Arucas, Gran Canaria, Spain
| | - Anastasio Arguello
- Animal Science Department, Universidad de Las Palmas de Gran Canaria, Arucas, Gran Canaria, Spain
| | - Juan Capote
- Instituto Canario de Investigaciones Agrarias, Valle Guerra, Tenerife, Spain
| | - Alexandre M. O. Campos
- CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal
| | - André M. Almeida
- IBET – Instituto de Biologia Experimental e Tecnologica, Oeiras, Portugal
- ITQB/UNL – Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- CIISA-Centro Interdisciplinar de Investigação em Sanidade Animal, Lisboa, Portugal
- * E-mail:
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15
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Martínez AM, Gama LT, Delgado JV, Cañón J, Amills M, de Sousa CB, Ginja C, Zaragoza P, Manunza A, Landi V, Sevane N. The Southwestern fringe of Europe as an important reservoir of caprine biodiversity. Genet Sel Evol 2015; 47:86. [PMID: 26542127 PMCID: PMC4635977 DOI: 10.1186/s12711-015-0167-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 10/28/2015] [Indexed: 11/18/2022] Open
Abstract
Background Portugal and Spain, with six and 22 officially recognized caprine breeds, encompass 25 % of the European Union goat census. Many of these populations have suffered strong demographic declines because of competition with exotic breeds and the phasing-out of low income rural activities. In this study, we have investigated the consequences of these and other demographic processes on the genetic diversity, population structure and inbreeding levels of Iberian and Atlantic goats. Methods A sample of 975 individuals representing 25 officially recognized breeds from Portugal and Spain, two small populations not officially recognized (Formentera and Ajuí goats) and two ecotypes of the Tinerfeña and Blanca Celtibérica breeds were genotyped with a panel of 20 microsatellite markers. A wide array of population genetics methods was applied to make inferences about the genetic relationships and demography of these caprine populations. Results Genetic differentiation among Portuguese and Spanish breeds was weak but significant (FST = 0.07; P < 0.001), which is probably the consequence of their short splitting times and extensive gene flow due to transhumance. In contrast, Canarian goats were strongly differentiated because of prolonged geographic isolation. Most populations displayed considerable levels of diversity (mean He = 0.65). Conclusions High diversity levels and weak population structures are distinctive features of Portuguese and Spanish breeds. In general, these local breeds have a reduced census, but are still important reservoirs of genetic diversity. These findings reinforce the need for the implementation of management and breeding programs based on genetic data in order to minimize inbreeding, maintain overall genetic and allelic diversities and breed identities, while at the same time taking into account the within-breed genetic structure. Electronic supplementary material The online version of this article (doi:10.1186/s12711-015-0167-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Luis T Gama
- CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisbon, Portugal.
| | - Juan V Delgado
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain.
| | - Javier Cañón
- Departamento de Producción Animal, Universidad Complutense de Madrid, Madrid, Spain.
| | - Marcel Amills
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UABUB), Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.
| | - Carolina Bruno de Sousa
- Centro de Ciências do Mar, Universidade do Algarve, Instituto de Higiene e Medicina Tropical (UPMM), UNL, Lisbon, Portugal.
| | - Catarina Ginja
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal.
| | - Pilar Zaragoza
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain.
| | - Arianna Manunza
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UABUB), Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.
| | - Vincenzo Landi
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain.
| | - Natalia Sevane
- Departamento de Producción Animal, Universidad Complutense de Madrid, Madrid, Spain.
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16
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Establishment of the biochemical and endocrine blood profiles in the Majorera and Palmera dairy goat breeds: the effect of feed restriction. J DAIRY RES 2015; 82:416-25. [DOI: 10.1017/s0022029915000412] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Feed restriction, and seasonal weight loss (SWL), are major setbacks for animal production in the tropics and the Mediterranean. They may be solved through the use of autochthonous breeds particularly well adapted to SWL. It is therefore of major importance to determine markers of tolerance to feed restriction of putative use in animal selection. Two indigenous breeds from the Canary Islands, Palmera and Majorera, are commonly used by dairy goat farmers and, interestingly, have different phenotype characteristics albeit with a common ancestry. Indeed, Majorera is well adapted to feed restriction whereas the Palmera is susceptible to feed restriction. In addition, regardless of their importance in dairy production, there are only a limited number of reports relating to these breeds and, to the best of our knowledge, there is no description of their blood metabolite standard values under control conditions or as affected by feed restriction. In this study we analysed the blood metabolite profiles in Majorera and Palmera goats aiming to establish the differential responses to feed restriction between the two breeds and to characterise their metabolite standard values under control conditions. We observed significant differences in creatinine, urea, non-esterified fatty acids (NEFAs), cholesterol, IGF-1 and T3 due to underfeeding. Furthermore, a PCA analysis, revealed that animals submitted to undernutrition could be distinguished from the control groups, with the formation of three separate clusters (Palmera individuals after 22 d of subnutrition (PE22); Majorera individuals after 22 d of subnutrition (ME22) and animals assigned to control conditions (MC0, MC22, PC0 and PC22)), highlighting different responses of the two breeds to undernutrition.
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17
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Ferrando A, Manunza A, Jordana J, Capote J, Pons A, Pais J, Delgado T, Atoche P, Cabrera B, Martínez A, Landi V, Delgado JV, Argüello A, Vidal O, Lalueza-Fox C, Ramírez O, Amills M. A mitochondrial analysis reveals distinct founder effect signatures in Canarian and Balearic goats. Anim Genet 2015; 46:452-6. [DOI: 10.1111/age.12302] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2015] [Indexed: 11/28/2022]
Affiliation(s)
- A. Ferrando
- Departament de Ciència Animal i dels Aliments; Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
| | - A. Manunza
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Campus Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
| | - J. Jordana
- Departament de Ciència Animal i dels Aliments; Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
| | - J. Capote
- Instituto Canario de Investigaciones Agrarias; La Laguna 38108 Tenerife Spain
| | - A. Pons
- Àrea Tècnica Agrària; Servei de Millora Agrària i Pesquera (SEMILLA); Son Ferriol 07198 Spain
| | - J. Pais
- Museo Arqueológico Benahorita; Camino de Las Adelfas; 38760 Los Llanos de Aridane La Palma Spain
| | - T. Delgado
- Museo Canario; Doctor Verneau; 2, 35001 Las Palmas de Gran Canaria Spain
| | - P. Atoche
- Departamento de Ciencias Históricas; Universidad de Las Palmas de Gran Canaria; 35001 Las Palmas de Gran Canaria
| | - B. Cabrera
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Campus Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
| | - A. Martínez
- Departamento de Genética; Universidad de Córdoba; Córdoba 14071 Spain
| | - V. Landi
- Departamento de Genética; Universidad de Córdoba; Córdoba 14071 Spain
| | - J. V. Delgado
- Departamento de Genética; Universidad de Córdoba; Córdoba 14071 Spain
| | - A. Argüello
- Department of Animal Science; Universidad de Las Palmas de Gran Canaria; Arucas 35413 Spain
| | - O. Vidal
- Departament de Biologia; Universitat de Girona; Girona 17071 Spain
| | - C. Lalueza-Fox
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra); Barcelona 08003 Spain
| | - O. Ramírez
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra); Barcelona 08003 Spain
| | - M. Amills
- Departament de Ciència Animal i dels Aliments; Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Campus Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
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18
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Badaoui B, Manunza A, Castelló A, D'Andrea M, Pilla F, Capote J, Jordana J, Ferrando A, Martínez A, Cabrera B, Delgado JV, Landi V, Gómez M, Pons A, El Ouni M, Vidal O, Amills M. Technical note: Advantages and limitations of authenticating Palmera goat dairy products by pyrosequencing the melanocortin 1 receptor (MC1R) gene. J Dairy Sci 2014; 97:7293-7. [PMID: 25200789 DOI: 10.3168/jds.2014-8316] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 07/23/2014] [Indexed: 11/19/2022]
Abstract
Inferring the breed of origin of dairy products can be achieved through molecular analysis of genetic markers with a population-specific pattern of segregation. The goal of the current work was to generate such markers in goats by resequencing several pigmentation genes [melanocortin 1 receptor (MC1R), v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (KIT), tyrosinase (TYR), and tyrosinase-related protein 2 (TYRP2)]. This experiment revealed 10 single nucleotide polymorphisms (SNP), including 5 missense mutations and 1 nonsense mutation. These markers were genotyped in 560 goats from 18 breeds originally from Italy, the Iberian Peninsula, the Canary Islands, and North Africa. Although the majority of SNP segregated at moderate frequencies in all populations (including 2 additional markers that were used as a source of information), we identified a c.764G>A SNP in MC1R that displayed highly divergent allelic frequencies in the Palmera breed compared with the Majorera and Tinerfeña breeds from the Canary Islands. Thus, we optimized a pyrosequencing-based technique that allowed us to estimate, very accurately, the allele frequencies of this marker in complex DNA mixtures from different individuals. Once validated, we applied this method to generating breed-specific DNA profiles that made it possible to detect fraudulent cheeses in which Palmero cheese was manufactured with milk from Majorera goats. One limitation of this approach, however, is that it cannot be used to detect illegal manufacturing where Palmero dairy products are produced by mixing milk from Palmera and Majorera goats, because the c.764G>A SNP segregates in both breeds.
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Affiliation(s)
- B Badaoui
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - A Manunza
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - A Castelló
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - M D'Andrea
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Via de Sanctis, 86100 Campobasso, Italy
| | - F Pilla
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Via de Sanctis, 86100 Campobasso, Italy
| | - J Capote
- Instituto Canario de Investigaciones Agrarias, La Laguna 38108, Tenerife, Spain
| | - J Jordana
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - A Ferrando
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - A Martínez
- Departamento de Genética, Universidad de Córdoba, Córdoba 14071, Spain
| | - B Cabrera
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - J V Delgado
- Departamento de Genética, Universidad de Córdoba, Córdoba 14071, Spain
| | - V Landi
- Departamento de Genética, Universidad de Córdoba, Córdoba 14071, Spain
| | - M Gómez
- Servicio de Ganadería, Diputación Foral de Bizkaia, 48014 Bilbao, Spain
| | - A Pons
- Unitat de Races Autòctones, Servei de Millora Agrària, (SEMILLA-SAU), Son Ferriol 07198, Spain
| | - M El Ouni
- Livestock & Wildlife Laboratory, Arid Land Institute Medenine, 4119 Médenine, Tunisia
| | - O Vidal
- Departament de Biologia, Universitat de Girona, Girona 17071, Spain
| | - M Amills
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
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Lérias JR, Hernández-Castellano LE, Morales-delaNuez A, Araújo SS, Castro N, Argüello A, Capote J, Almeida AM. Body live weight and milk production parameters in the Majorera and Palmera goat breeds from the Canary Islands: influence of weight loss. Trop Anim Health Prod 2013; 45:1731-6. [DOI: 10.1007/s11250-013-0423-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2013] [Indexed: 11/22/2022]
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20
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Acín C, Martín-Burriel I, Monleón E, Lyahyai J, Pitarch JL, Serrano C, Monzón M, Zaragoza P, Badiola JJ. Prion protein gene variability in Spanish goats. Inference through susceptibility to classical scrapie strains and pathogenic distribution of peripheral PrP(sc.). PLoS One 2013; 8:e61118. [PMID: 23580248 PMCID: PMC3620333 DOI: 10.1371/journal.pone.0061118] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 03/06/2013] [Indexed: 02/02/2023] Open
Abstract
Classical scrapie is a neurological disorder of the central nervous system (CNS) characterized by the accumulation of an abnormal, partially protease resistant prion protein (PrP(sc)) in the CNS and in some peripheral tissues in domestic small ruminants. Whereas the pathological changes and genetic susceptibility of ovine scrapie are well known, caprine scrapie has been less well studied. We report here a pathological study of 13 scrapie-affected goats diagnosed in Spain during the last 9 years. We used immunohistochemical and biochemical techniques to discriminate between classical and atypical scrapie and bovine spongiform encephalopathy (BSE). All the animals displayed PrP(sc) distribution patterns and western blot characteristics compatible with classical scrapie. In addition, we determined the complete open reading frame sequence of the PRNP in these scrapie-affected animals. The polymorphisms observed were compared with those of the herd mates (n = 665) and with the frequencies of healthy herds (n = 581) of native Spanish goats (Retinta, Pirenaica and Moncaina) and other worldwide breeds reared in Spain (Saanen, Alpine and crossbreed). In total, sixteen polymorphic sites were identified, including the known amino acid substitutions at codons G37V, G127S, M137I, I142M, H143R, R151H, R154H, R211Q, Q222K, G232W, and P240S, and new polymorphisms at codons G74D, M112T, R139S, L141F and Q215R. In addition, the known 42, 138 and 179 silent mutations were detected, and one new one is reported at codon 122. The genetic differences observed in the population studied have been attributed to breed and most of the novel polymorphic codons show frequencies lower than 5%. This work provides the first basis of polymorphic distribution of PRNP in native and worldwide goat breeds reared in Spain.
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Affiliation(s)
- Cristina Acín
- Centro de Investigación en Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain.
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Morales-delaNuez A, Rodríguez C, Santana M, Hernandez-Castellano L, Niño T, Reyes-Chacon R, Moreno-Indias I, Castro N, Capote J. Morphological measurements and indexes as a tool to support molecular genetic studies: an example in Canary Islands. JOURNAL OF APPLIED ANIMAL RESEARCH 2012. [DOI: 10.1080/09712119.2012.658062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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22
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Kim JH, Byun MJ, Ko YG, Kim SW, Kim SW, Do YJ, Kim MJ, Yoon SH, Choi SB. Phylogenetic Analysis of Korean Native Goats Based on the Mitochondrial Cytochrome b Gene. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2012. [DOI: 10.5187/jast.2012.54.4.241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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23
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Martínez A, Ferrando A, Manunza A, Gómez M, Landi V, Jordana J, Capote J, Badaoui B, Vidal O, Delgado J, Amills M. Inferring the demographic history of a highly endangered goat breed through the analysis of nuclear and mitochondrial genetic signatures. Small Rumin Res 2012. [DOI: 10.1016/j.smallrumres.2011.11.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Arévalo J, de Nascimento L, Fernández-Lugo S, Mata J, Bermejo L. Grazing effects on species composition in different vegetation types (La Palma, Canary Islands). ACTA OECOLOGICA 2011. [DOI: 10.1016/j.actao.2011.02.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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25
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Polymorphism of the goat agouti signaling protein gene and its relationship with coat color in Italian and Spanish breeds. Biochem Genet 2011; 49:523-32. [PMID: 21373989 DOI: 10.1007/s10528-011-9427-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 12/15/2010] [Indexed: 10/18/2022]
Abstract
Agouti signaling protein (ASIP) is one of the key players in the modulation of hair pigmentation in mammals. Binding to the melanocortin 1 receptor, ASIP induces the synthesis of phaeomelanin, associated with reddish brown, red, tan, and yellow coats. We have sequenced 2.8 kb of the goat ASIP gene in 48 individuals and identified two missense (Cys126Gly and Val128Gly) and two intronic polymorphisms. In silico analysis revealed that the Cys126Gly substitution may cause a structural change by disrupting a highly conserved disulfide bond. We studied its segregation in 12 Spanish and Italian goat breeds (N = 360) with different pigmentation patterns and found striking differences in the frequency of the putative loss-of-function Gly(126) allele (Italian 0.43, Spanish Peninsular 0.08), but we did not observe a clear association with coat color. This suggests that the frequency of this putative loss-of-function allele has evolved under the influence of demographic rather than selection factors in goats from these two geographical areas.
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Martínez A, Vega-Pla J, León J, Camacho M, Delgado J, Ribeiro M. Is the Murciano-Granadina a single goat breed? A molecular genetics approach. ARQ BRAS MED VET ZOO 2010. [DOI: 10.1590/s0102-09352010000500023] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The population structure of the Murciano-Granadina breed was determined using 25 microsatellites from 266 goats of seven populations. The results of the genetic differentiation analysis showed that it is possible to differentiate the Murciana and Granadina populations even though a low F ST value (0.0432) had been obtained. Individuals could be assigned to their populations with a success rate of more than 80%. Bayesian-based clustering analysis of allele frequencies and multivariate analysis revealed that Murciana and Granadina populations were grouped in different clusters since K=3. The results demonstrate that Murciana and Granadina are still two different genetic groups included into Murciano-Granadina denomination. There is the opportunity to the genetically manage these populations, under a single herd-book but adding the necessary modifications to respect the conservation of the genetic diversity based on the use of multibreed models of genetic evaluation.
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Vacca GM, Daga C, Pazzola M, Carcangiu V, Dettori ML, Cozzi MC. D-loop sequence mitochondrial DNA variability of Sarda goat and other goat breeds and populations reared in the Mediterranean area. J Anim Breed Genet 2010; 127:352-60. [PMID: 20831559 DOI: 10.1111/j.1439-0388.2010.00863.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- G M Vacca
- Department of Animal Biology, University of Sassari, Sassari, Italy Department of Animal Science, University of Milano, Milano, Italy
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Groeneveld LF, Lenstra JA, Eding H, Toro MA, Scherf B, Pilling D, Negrini R, Finlay EK, Jianlin H, Groeneveld E, Weigend S. Genetic diversity in farm animals--a review. Anim Genet 2010; 41 Suppl 1:6-31. [PMID: 20500753 DOI: 10.1111/j.1365-2052.2010.02038.x] [Citation(s) in RCA: 293] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, molecular genetic studies allow a comparison of genetic diversity within and across breeds and a reconstruction of the history of breeds and ancestral populations. This has been summarized for cattle, yak, water buffalo, sheep, goats, camelids, pigs, horses, and chickens. Further progress is expected to benefit from advances in molecular technology.
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Affiliation(s)
- L F Groeneveld
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Hoeltystr. 10, 31535 Neustadt, Germany
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Pereira F, Queirós S, Gusmão L, Nijman IJ, Cuppen E, Lenstra JA, Davis SJM, Nejmeddine F, Amorim A. Tracing the History of Goat Pastoralism: New Clues from Mitochondrial and Y Chromosome DNA in North Africa. Mol Biol Evol 2009; 26:2765-73. [PMID: 19729424 DOI: 10.1093/molbev/msp200] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Filipe Pereira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.
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Pariset L, Cuteri A, Ligda C, Ajmone-Marsan P, Valentini A. Geographical patterning of sixteen goat breeds from Italy, Albania and Greece assessed by Single Nucleotide Polymorphisms. BMC Ecol 2009; 9:20. [PMID: 19725964 PMCID: PMC2754418 DOI: 10.1186/1472-6785-9-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Accepted: 09/02/2009] [Indexed: 12/01/2022] Open
Abstract
Background SNP data of goats of three Mediterranean countries were used for population studies and reconstruction of geographical patterning. 496 individuals belonging to Italian, Albanian and Greek breeds were genotyped to assess the basic population parameters. Results A total of 26 SNPs were used, for a total of 12,896 genotypes assayed. Statistical analysis revealed that breeds are not so similar in terms of genetic variability, as reported in studies performed using different markers. The Mantel test showed a strongly significant correlation between genetic and geographic distance. Also, PCA analysis revealed that breeds are grouped according to geographical origin, with the exception of the Greek Skopelos breed. Conclusion Our data point out that the use of SNP markers to analyze a wider breed sample could help in understanding the recent evolutionary history of domestic goats. We found correlation between genetic diversity and geographic distance. Also PCA analysis shows that the breeds are well differentiated, with good correspondence to geographical locations, thus confirming the correlation between geographical and genetic distances. This suggests that migration history of the species played a pivotal role in the present-day structure of the breeds and a scenario in which coastal routes were easier for migrating in comparison with inland routes. A westward coastal route to Italy through Greece could have led to gene flow along the Northern Mediterranean.
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Affiliation(s)
- Lorraine Pariset
- Dipartimento di Produzioni Animali, Università degli Studi della Tuscia, Viterbo, Italy.
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31
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Amills M, Ramírez O, Tomàs A, Badaoui B, Marmi J, Acosta J, Sànchez A, Capote J. Mitochondrial DNA diversity and origins of South and Central American goats. Anim Genet 2009; 40:315-22. [DOI: 10.1111/j.1365-2052.2008.01837.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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32
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Royo LJ, Traoré A, Tambourá HH, Álvarez I, Kaboré A, Fernández I, Ouédraogo-Sanou G, Toguyeni A, Sawadogo L, Goyache F. Analysis of mitochondrial DNA diversity in Burkina Faso populations confirms the maternal genetic homogeneity of the West African goat. Anim Genet 2009; 40:344-7. [DOI: 10.1111/j.1365-2052.2008.01828.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Folch J, Cocero M, Chesné P, Alabart J, Domínguez V, Cognié Y, Roche A, Fernández-Árias A, Martí J, Sánchez P, Echegoyen E, Beckers J, Bonastre AS, Vignon X. First birth of an animal from an extinct subspecies (Capra pyrenaica pyrenaica) by cloning. Theriogenology 2009; 71:1026-34. [DOI: 10.1016/j.theriogenology.2008.11.005] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 11/14/2008] [Accepted: 11/19/2008] [Indexed: 11/17/2022]
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Hammer SE, Schwammer HM, Suchentrunk F. Evidence for introgressive hybridization of captive markhor (Capra falconeri) with domestic goat: cautions for reintroduction. Biochem Genet 2008; 46:216-26. [PMID: 18228130 DOI: 10.1007/s10528-008-9145-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Accepted: 11/02/2007] [Indexed: 11/27/2022]
Abstract
Markhors (Capra falconeri) are among the most endangered mammal species, and several conservation measures, including ex situ breeding, are implemented to prevent their extinction. We studied sequence diversity and differentiation of the first hypervariable segment of the mitochondrial DNA control region among C. f. heptneri and C. f. megaceros kept in four zoos in relationship to lineages of other wild and domestic goats, to assess for the first time the level of molecular distinctness and variability among those subspecies, and to check for possible introgression by related Capra taxa, such as domestic goats. Levels of differentiation between some Capra falconeri lineages and modern domestic goats were similar to levels between other wild goat species (i.e., Capra aegagrus, Capra ibex) and domestic goats. Among pure markhor lineages, paraphyly was observed for C. f. heptneri, suggesting occurrence of shared ancestral polymorphism among markhor subspecies and/or ancient or recent gene exchange between subspecies. Interestingly, 35.7% of all studied markhors from three zoos are introgressed by the domestic goat. Furthermore, despite relatively small breeding group sizes, markhors have maintained a relatively high proportion of mtDNA variation within zoo groups. In any case, the existence of markhors introgressed with domestic goat DNA in zoos should be considered when selecting markhors for ex situ breeding programs with the aim of building up a stock for later reintroduction into the wild.
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Affiliation(s)
- Sabine E Hammer
- Clinical Immunology, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210, Vienna, Austria.
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35
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Fan B, Chen SL, Kijas JH, Liu B, Yu M, Zhao SH, Zhu MJ, Xiong TA, Li K. Phylogenetic relationships among Chinese indigenous goat breeds inferred from mitochondrial control region sequence. Small Rumin Res 2007. [DOI: 10.1016/j.smallrumres.2006.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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36
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Naderi S, Rezaei HR, Taberlet P, Zundel S, Rafat SA, Naghash HR, El-Barody MAA, Ertugrul O, Pompanon F. Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity. PLoS One 2007; 2:e1012. [PMID: 17925860 PMCID: PMC1995761 DOI: 10.1371/journal.pone.0001012] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2007] [Accepted: 09/17/2007] [Indexed: 11/29/2022] Open
Abstract
Background From the beginning of domestication, the transportation of domestic animals resulted in genetic and demographic processes that explain their present distribution and genetic structure. Thus studying the present genetic diversity helps to better understand the history of domestic species. Methodology/Principal Findings The genetic diversity of domestic goats has been characterized with 2430 individuals from all over the old world, including 946 new individuals from regions poorly studied until now (mainly the Fertile Crescent). These individuals represented 1540 haplotypes for the HVI segment of the mitochondrial DNA (mtDNA) control region. This large-scale study allowed the establishment of a clear nomenclature of the goat maternal haplogroups. Only five of the six previously defined groups of haplotypes were divergent enough to be considered as different haplogroups. Moreover a new mitochondrial group has been localized around the Fertile Crescent. All groups showed very high haplotype diversity. Most of this diversity was distributed among groups and within geographic regions. The weak geographic structure may result from the worldwide distribution of the dominant A haplogroup (more than 90% of the individuals). The large-scale distribution of other haplogroups (except one), may be related to human migration. The recent fragmentation of local goat populations into discrete breeds is not detectable with mitochondrial markers. The estimation of demographic parameters from mismatch analyses showed that all groups had a recent demographic expansion corresponding roughly to the period when domestication took place. But even with a large data set it remains difficult to give relative dates of expansion for different haplogroups because of large confidence intervals. Conclusions/Significance We propose standard criteria for the definition of the different haplogroups based on the result of mismatch analysis and on the use of sequences of reference. Such a method could be also applied for clarifying the nomenclature of mitochondrial haplogroups in other domestic species.
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Affiliation(s)
- Saeid Naderi
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble, France
- Natural Resources Faculty, University of Guilan, Guilan, Iran
| | - Hamid-Reza Rezaei
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble, France
- Environmental Sciences Department, Gorgan University of Agriculture and Natural Resources, Gorgan, Iran
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble, France
| | - Stéphanie Zundel
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble, France
| | - Seyed-Abbas Rafat
- Animal Science Department, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Hamid-Reza Naghash
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble, France
| | | | - Okan Ertugrul
- Department of Genetics, Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey
| | - François Pompanon
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble, France
- * To whom correspondence should be addressed. E-mail:
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Badaoui B, Serradilla JM, Tomàs A, Urrutia B, Ares JL, Carrizosa J, Sànchez A, Jordana J, Amills M. Short communication: Identification of two polymorphisms in the goat lipoprotein lipase gene and their association with milk production traits. J Dairy Sci 2007; 90:3012-7. [PMID: 17517743 DOI: 10.3168/jds.2006-409] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Lipoprotein lipase (LPL) is a glycoprotein that plays a central role in plasma triglyceride metabolism by hydrolyzing triglyceride-rich chylomicrons and very low density lipoproteins. The activity of milk LPL has been shown to differ among several goat breeds, suggesting the existence of a genetic polymorphism influencing the functional properties of this enzyme. We have characterized the complete coding sequence of the goat LPL gene in 18 individuals belonging to 3 breeds. The coding region of the goat LPL cDNA was 1,437 bp long and encoded a protein of 478 amino acids. Moreover, we have identified 2 single nucleotide polymorphisms (SNP) including a G50C missense mutation, which involved a Ser-->Thr amino acid replacement at position 17 of the signal peptide, and a C2094T substitution in the 3' untranslated region. A univariate mixed model was used to evaluate the association between LPL genotypes and milk production and composition in 130 Murciano-Granadina goats. The G50C SNP was suggestively associated with milk fat content and tended to affect the milk dry weight basis. The C2094T SNP was not associated with any of the measured traits.
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Affiliation(s)
- B Badaoui
- Departament de Ciència Animal, Facultat de Veterinària, Universitat Autónoma de Barcelona, Bellaterra 08193, Spain
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Sardina MT, Ballester M, Marmi J, Finocchiaro R, van Kaam JBCHM, Portolano B, Folch JM. Phylogenetic analysis of Sicilian goats reveals a new mtDNA lineage. Anim Genet 2006; 37:376-8. [PMID: 16879350 DOI: 10.1111/j.1365-2052.2006.01451.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The mitochondrial hypervariable region 1 (HVR1) sequence of 67 goats belonging to the Girgentana, Maltese and Derivata di Siria breeds was partially sequenced in order to present the first phylogenetic characterization of Sicilian goat breeds. These sequences were compared with published sequences of Indian and Pakistani domestic goats and wild goats. Mitochondrial lineage A was observed in most of the Sicilian goats. However, three Girgentana haplotypes were highly divergent from the Capra hircus clade, indicating that a new mtDNA lineage in domestic goats was found.
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Affiliation(s)
- M T Sardina
- Dipartimento S.En.Fi.Mi.Zo.-Sezione Produzioni Animali, Facoltà di Agraria, Università degli Studi di Palermo, Viale delle Scienze, Palermo 90128, Italy
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39
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Martínez AM, Acosta J, Vega-Pla JL, Delgado JV. Analysis of the genetic structure of the canary goat populations using microsatellites. Livest Sci 2006. [DOI: 10.1016/j.livsci.2005.12.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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40
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Azor PJ, Monteagudo LV, Luque M, Tejedor MT, Rodero E, Sierra I, Herrera M, Rodero A, Arruga MV. Phylogenetic relationships among Spanish goats breeds. Anim Genet 2006; 36:423-5. [PMID: 16167986 DOI: 10.1111/j.1365-2052.2005.01327.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We partially sequenced the mitochondrial hypervariable region 1 (HVR1) in 60 goats belonging to six Spanish breeds. The analysis of these and previously published sequences reveals a weak phylogeographical structure in the Iberian Peninsula breeds. Individuals from a single breed did not group into a single cluster. Furthermore, individuals from different breeds often shared single phylogenetic tree branches after UPGMA analysis. This could reflect the non-existence of breed isolation because of traditional seasonal pastoralism and annual long-distance migrations. Three goats belonging to the C maternal lineage were found, demonstrating a wider than previously thought distribution for this lineage.
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Affiliation(s)
- P J Azor
- Department of Genetics, University of Córdoba, Córdoba, Spain
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41
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Pereira F, Pereira L, Van Asch B, Bradley DG, Amorim A. The mtDNA catalogue of all Portuguese autochthonous goat (Capra hircus) breeds: high diversity of female lineages at the western fringe of European distribution. Mol Ecol 2005; 14:2313-8. [PMID: 15969716 DOI: 10.1111/j.1365-294x.2005.02594.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Goat is believed to be the first true livestock domesticated and, apart from its historical importance, keeps playing an essential economic role in very diverse human societies. We have analysed the female gene pool of all Portuguese autochthonous breeds (Bravia, Serrana, Charnequeira, Serpentina and Algarvia) through the mtDNA HVI sequencing of 288 unrelated animals sampled throughout the country. All breeds proved to be extremely diverse (average haplotype diversity of 0.977), in contrast with the Portuguese peripheral geographic situation in the distribution range of the species. Moreover, observed genetic distances between breeds do not correlate with microgeography inside Portugal. These observations are consistent with recurrent refreshment of the breeding stock through the introduction of exotic animals. Fitting the new data into the still loosely defined female genetic pool landscape of goats, all Portuguese animals, one sample excepted (belonging to Bravia), are classified into haplogroup A and haplotype sharing is geographically very sparse, including a Far East match. Our results confirm that goats stand out among most of domesticates as exceptionally diverse and showing an unparalleled degree of mobility of animals (at least females) used for reproductive purposes.
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Affiliation(s)
- F Pereira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), R. Dr. Roberto Frias s/n, 4200-465 Porto, Portugal.
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