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Abstract
Cattle, sheep and goats were domesticated about 10,000 years ago, spread out of the domestication centers in Europe, Asia, and Africa during the next few thousands years, and gave many populations locally adapted. After a very long period of soft selection, the situation changed dramatically 200 years ago with the emergence of the breed concept. The selection pressure strongly increased, and the reproduction among breeds was seriously reduced, leading to the fragmentation of the initial gene pool. More recently, the selection pressure was increased again via the use of artificial insemination, leading to a few industrial breeds with very high performances, but with low effective population sizes. Beside this performance improvement of industrial breeds, genetic resources are being lost, because of the replacement of traditional breeds by high performance industrial breeds at the worldwide level, and because of the loss of genetic diversity in these industrial breeds. Many breeds are already extinct, and genetic resources in cattle, sheep, and goats are thus highly endangered, particularly in developed countries. The recent development of next generation sequencing technologies opens new avenues for properly characterizing the genetic resources, not only in the very diverse domestic breeds, but also in their wild relatives. Based on sound genetic characterization, urgent conservation measures must be taken to avoid an irremediable loss of farm animal genetic resources, integrating economical, sociological, and political parameters.
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Edwards CJ, Ginja C, Kantanen J, Pérez-Pardal L, Tresset A, Stock F, Gama LT, Penedo MCT, Bradley DG, Lenstra JA, Nijman IJ. Dual origins of dairy cattle farming--evidence from a comprehensive survey of European Y-chromosomal variation. PLoS One 2011; 6:e15922. [PMID: 21253012 PMCID: PMC3016991 DOI: 10.1371/journal.pone.0015922] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Accepted: 11/29/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Diversity patterns of livestock species are informative to the history of agriculture and indicate uniqueness of breeds as relevant for conservation. So far, most studies on cattle have focused on mitochondrial and autosomal DNA variation. Previous studies of Y-chromosomal variation, with limited breed panels, identified two Bos taurus (taurine) haplogroups (Y1 and Y2; both composed of several haplotypes) and one Bos indicus (indicine/zebu) haplogroup (Y3), as well as a strong phylogeographic structuring of paternal lineages. METHODOLOGY AND PRINCIPAL FINDINGS Haplogroup data were collected for 2087 animals from 138 breeds. For 111 breeds, these were resolved further by genotyping microsatellites INRA189 (10 alleles) and BM861 (2 alleles). European cattle carry exclusively taurine haplotypes, with the zebu Y-chromosomes having appreciable frequencies in Southwest Asian populations. Y1 is predominant in northern and north-western Europe, but is also observed in several Iberian breeds, as well as in Southwest Asia. A single Y1 haplotype is predominant in north-central Europe and a single Y2 haplotype in central Europe. In contrast, we found both Y1 and Y2 haplotypes in Britain, the Nordic region and Russia, with the highest Y-chromosomal diversity seen in the Iberian Peninsula. CONCLUSIONS We propose that the homogeneous Y1 and Y2 regions reflect founder effects associated with the development and expansion of two groups of dairy cattle, the pied or red breeds from the North Sea and Baltic coasts and the spotted, yellow or brown breeds from Switzerland, respectively. The present Y1-Y2 contrast in central Europe coincides with historic, linguistic, religious and cultural boundaries.
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Affiliation(s)
- Ceiridwen J. Edwards
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- Research Laboratory for Archaeology, University of Oxford, Oxford, United Kingdom
| | - Catarina Ginja
- Veterinary Genetics Laboratory, University of California Davis, Davis, California, United States of America
- Departamento de Genética, Melhoramento Animal e Reprodução, Instituto Nacional dos Recursos Biológicos, Fonte Boa, Vale de Santarém, Portugal
| | - Juha Kantanen
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland
| | | | - Anne Tresset
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, CNRS Muséum National d'Histoire Naturelle, Paris, France
| | - Frauke Stock
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | | | - Luis T. Gama
- Departamento de Genética, Melhoramento Animal e Reprodução, Instituto Nacional dos Recursos Biológicos, Fonte Boa, Vale de Santarém, Portugal
| | - M. Cecilia T. Penedo
- Veterinary Genetics Laboratory, University of California Davis, Davis, California, United States of America
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Johannes A. Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Isaäc J. Nijman
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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The enigmatic origin of bovine mtDNA haplogroup R: sporadic interbreeding or an independent event of Bos primigenius domestication in Italy? PLoS One 2010; 5:e15760. [PMID: 21209945 PMCID: PMC3011016 DOI: 10.1371/journal.pone.0015760] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 11/23/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND When domestic taurine cattle diffused from the Fertile Crescent, local wild aurochsen (Bos primigenius) were still numerous. Moreover, aurochsen and introduced cattle often coexisted for millennia, thus providing potential conditions not only for spontaneous interbreeding, but also for pastoralists to create secondary domestication centers involving local aurochs populations. Recent mitochondrial genomes analyses revealed that not all modern taurine mtDNAs belong to the shallow macro-haplogroup T of Near Eastern origin, as demonstrated by the detection of three branches (P, Q and R) radiating prior to the T node in the bovine phylogeny. These uncommon haplogroups represent excellent tools to evaluate if sporadic interbreeding or even additional events of cattle domestication occurred. METHODOLOGY The survey of the mitochondrial DNA (mtDNA) control-region variation of 1,747 bovine samples (1,128 new and 619 from previous studies) belonging to 37 European breeds allowed the identification of 16 novel non-T mtDNAs, which after complete genome sequencing were confirmed as members of haplogroups Q and R. These mtDNAs were then integrated in a phylogenetic tree encompassing all available P, Q and R complete mtDNA sequences. CONCLUSIONS Phylogenetic analyses of 28 mitochondrial genomes belonging to haplogroups P (N = 2), Q (N = 16) and R (N = 10) together with an extensive survey of all previously published mtDNA datasets revealed major similarities between haplogroups Q and T. Therefore, Q most likely represents an additional minor lineage domesticated in the Near East together with the founders of the T subhaplogroups. Whereas, haplogroup R is found, at least for the moment, only in Italy and nowhere else, either in modern or ancient samples, thus supporting an origin from European aurochsen. Haplogroup R could have been acquired through sporadic interbreeding of wild and domestic animals, but our data do not rule out the possibility of a local and secondary event of B. primigenius domestication in Italy.
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Genetic signals of origin, spread, and introgression in a large sample of maize landraces. Proc Natl Acad Sci U S A 2010; 108:1088-92. [PMID: 21189301 DOI: 10.1073/pnas.1013011108] [Citation(s) in RCA: 215] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The last two decades have seen important advances in our knowledge of maize domestication, thanks in part to the contributions of genetic data. Genetic studies have provided firm evidence that maize was domesticated from Balsas teosinte (Zea mays subspecies parviglumis), a wild relative that is endemic to the mid- to lowland regions of southwestern Mexico. An interesting paradox remains, however: Maize cultivars that are most closely related to Balsas teosinte are found mainly in the Mexican highlands where subspecies parviglumis does not grow. Genetic data thus point to primary diffusion of domesticated maize from the highlands rather than from the region of initial domestication. Recent archeological evidence for early lowland cultivation has been consistent with the genetics of domestication, leaving the issue of the ancestral position of highland maize unresolved. We used a new SNP dataset scored in a large number of accessions of both teosinte and maize to take a second look at the geography of the earliest cultivated maize. We found that gene flow between maize and its wild relatives meaningfully impacts our inference of geographic origins. By analyzing differentiation from inferred ancestral gene frequencies, we obtained results that are fully consistent with current ecological, archeological, and genetic data concerning the geography of early maize cultivation.
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105
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Muller MH, Latreille M, Tollon C. The origin and evolution of a recent agricultural weed: population genetic diversity of weedy populations of sunflower (Helianthus annuus L.) in Spain and France. Evol Appl 2010; 4:499-514. [PMID: 25567998 PMCID: PMC3352525 DOI: 10.1111/j.1752-4571.2010.00163.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Accepted: 09/19/2010] [Indexed: 12/02/2022] Open
Abstract
The recurrent evolution of crop-related weeds during agricultural history raises serious economic problems and challenging scientific questions. Weedy forms of sunflower, a species native from America, have been reported in European sunflower fields for a few decades. In order to understand their origin, we analysed the genetic diversity of a sample of weedy populations from France and Spain, and of conventional and ornamental varieties. A crop-specific maternally inherited marker was present in all weeds. At 16 microsatellite loci, the weedy populations shared most of their diversity with the conventional varieties. But they showed a large number of additional alleles absent from the cultivated pool. European weedy populations thus most probably originated from the unintentional pollination of maternal lines in seed production fields by wild plants growing nearby, resulting in the introduction of crop-wild hybrids into the farmers’ fields. The wide diversity and the low population structure detected were indicative of a multiplicity of introductions events rather than of field-to-field propagation. Further studies are required to understand the local evolutionary dynamics of a weedy population, and especially the respective roles of crop-to-weed gene flow and selection in the fate of an initial source of crop-wild hybrids.
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Arrigo N, Felber F, Parisod C, Buerki S, Alvarez N, David J, Guadagnuolo R. Origin and expansion of the allotetraploid Aegilops geniculata, a wild relative of wheat. THE NEW PHYTOLOGIST 2010; 187:1170-1180. [PMID: 20561204 DOI: 10.1111/j.1469-8137.2010.03328.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
*This study reconstructs the phylogeography of Aegilops geniculata, an allotetraploid relative of wheat, to discuss the impact of past climate changes and recent human activities (e.g. the early expansion of agriculture) on the genetic diversity of ruderal plant species. *We combined chloroplast DNA (cpDNA) sequencing, analysed using statistical parsimony network, with nonhierarchical K-means clustering of amplified fragment length polymorphism (AFLP) genotyping, to unravel patterns of genetic structure across the native range of Ae. geniculata. The AFLP dataset was further explored by measurement of the regional genetic diversity and the detection of isolation by distance patterns. *Both cpDNA and AFLP suggest an eastern Mediterranean origin of Ae. geniculata. Two lineages have spread independently over northern and southern Mediterranean areas. Northern populations show low genetic diversity but strong phylogeographical structure among the main peninsulas, indicating a major influence of glacial cycles. By contrast, low genetic structuring and a high genetic diversity are detected in southern Mediterranean populations. Finally, we highlight human-mediated dispersal resulting in substantial introgression between resident and migrant populations. *We have shown that the evolutionary trajectories of ruderal plants can be similar to those of wild species, but are interfered by human activities, promoting range expansions through increased long-distance dispersal and the creation of suitable habitats.
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Affiliation(s)
- Nils Arrigo
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, 11 rue Emile-Argand, 2009 Neuchâtel, Switzerland
| | - François Felber
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, 11 rue Emile-Argand, 2009 Neuchâtel, Switzerland
| | - Christian Parisod
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, 11 rue Emile-Argand, 2009 Neuchâtel, Switzerland
| | - Sven Buerki
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, 11 rue Emile-Argand, 2009 Neuchâtel, Switzerland
| | - Nadir Alvarez
- Department of Ecology and Evolution, University of Lausanne - UNIL Sorge, Biophore Building, 1015 Lausanne, Switzerland
| | - Jacques David
- UMR Diversité et Adaptation des Plantes Cultivées, SupAgro, 2 Place P. Viala, Domaine de Melgueil, 34130 Mauguio, France
| | - Roberto Guadagnuolo
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, 11 rue Emile-Argand, 2009 Neuchâtel, Switzerland
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Van Tassel DL, DeHaan LR, Cox TS. Missing domesticated plant forms: can artificial selection fill the gap? Evol Appl 2010; 3:434-52. [PMID: 25567937 PMCID: PMC3352511 DOI: 10.1111/j.1752-4571.2010.00132.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Accepted: 04/12/2010] [Indexed: 11/26/2022] Open
Abstract
In the course of their evolution, the angiosperms have radiated into most known plant forms and life histories. Their adaptation to a recently created habitat, the crop field, produced a novel form: the plant that allocates an unprecedented 30-60% of its net productivity to sexual structures. Long-lived trees, shrubs and vines of this form evolved, as did annual herbs. Perennial herb forms with increased allocation to asexual reproduction evolved, but there are no examples of perennial herbs with high sexual effort. We suggest that sowing seed into annually tilled fields favored shorter-lived herbs because of trade-offs between first-year seed production and relative growth rate and/or persistence. By propagating cuttings, people quickly domesticated tuber crops and large woody plants. Perennial herbs were too small to be efficiently propagated by cuttings, and the association between longevity, allogamy and genetic load made rapid domestication by sexual cycles unlikely. Perennial grain crops do not exist because they could not have evolved under the original set of conditions; however, they can be deliberately developed today through artificial phenotypic and genotypic selection.
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108
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Ajmone-Marsan P, Garcia JF, Lenstra JA. On the origin of cattle: How aurochs became cattle and colonized the world. Evol Anthropol 2010. [DOI: 10.1002/evan.20267] [Citation(s) in RCA: 148] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA. Proc Natl Acad Sci U S A 2010; 107:7686-91. [PMID: 20404179 DOI: 10.1073/pnas.0912264107] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The establishment of agricultural economies based upon domestic animals began independently in many parts of the world and led to both increases in human population size and the migration of people carrying domestic plants and animals. The precise circumstances of the earliest phases of these events remain mysterious given their antiquity and the fact that subsequent waves of migrants have often replaced the first. Through the use of more than 1,500 modern (including 151 previously uncharacterized specimens) and 18 ancient (representing six East Asian archeological sites) pig (Sus scrofa) DNA sequences sampled across East Asia, we provide evidence for the long-term genetic continuity between modern and ancient Chinese domestic pigs. Although the Chinese case for independent pig domestication is supported by both genetic and archaeological evidence, we discuss five additional (and possibly) independent domestications of indigenous wild boar populations: one in India, three in peninsular Southeast Asia, and one off the coast of Taiwan. Collectively, we refer to these instances as "cryptic domestication," given the current lack of corroborating archaeological evidence. In addition, we demonstrate the existence of numerous populations of genetically distinct and widespread wild boar populations that have not contributed maternal genetic material to modern domestic stocks. The overall findings provide the most complete picture yet of pig evolution and domestication in East Asia, and generate testable hypotheses regarding the development and spread of early farmers in the Far East.
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Abstract
The increased battery of molecular markers, derived from comparative genomics, is aiding our understanding of the genetics of domestication. The recent BMC Biology article pertaining to the evolution of small size in dogs is an example of how such methods can be used to study the origin and diversification of the domestic dog. We are still challenged, however, to appreciate the genetic mechanisms responsible for the phenotypic diversity seen in 'our best friend'.
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Affiliation(s)
- Rodney L Honeycutt
- Department of Biology, National Science Division, Pepperdine University, 24255 Pacific Coast Highway, Malibu, California 90263-4321, USA.
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112
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Ancient mitochondrial DNA analysis reveals complexity of indigenous North American turkey domestication. Proc Natl Acad Sci U S A 2010; 107:2807-12. [PMID: 20133614 DOI: 10.1073/pnas.0909724107] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although the cultural and nutritive importance of the turkey (Meleagris gallopavo) to precontact Native Americans and contemporary people worldwide is clear, little is known about the domestication of this bird compared to other domesticates. Mitochondrial DNA analysis of 149 turkey bones and 29 coprolites from 38 archaeological sites (200 BC-AD 1800) reveals a unique domesticated breed in the precontact Southwestern United States. Phylogeographic analyses indicate that this domestic breed originated from outside the region, but rules out the South Mexican domestic turkey (Meleagris gallopavo gallopavo) as a progenitor. A strong genetic bottleneck within the Southwest turkeys also reflects intensive human selection and breeding. This study points to at least two occurrences of turkey domestication in precontact North America and illuminates the intensity and sophistication of New World animal breeding practices.
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Haseneyer G, Stracke S, Piepho HP, Sauer S, Geiger HH, Graner A. DNA polymorphisms and haplotype patterns of transcription factors involved in barley endosperm development are associated with key agronomic traits. BMC PLANT BIOLOGY 2010; 10:5. [PMID: 20064201 PMCID: PMC2822787 DOI: 10.1186/1471-2229-10-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2009] [Accepted: 01/08/2010] [Indexed: 05/04/2023]
Abstract
BACKGROUND Association mapping is receiving considerable attention in plant genetics for its potential to fine map quantitative trait loci (QTL), validate candidate genes, and identify alleles of interest. In the present study association mapping in barley (Hordeum vulgare L.) is investigated by associating DNA polymorphisms with variation in grain quality traits, plant height, and flowering time to gain further understanding of gene functions involved in the control of these traits. We focused on the four loci BLZ1, BLZ2, BPBF and HvGAMYB that play a role in the regulation of B-hordein expression, the major fraction of the barley storage protein. The association was tested in a collection of 224 spring barley accessions using a two-stage mixed model approach. RESULTS Within the sequenced fragments of four candidate genes we observed different levels of nucleotide diversity. The effect of selection on the candidate genes was tested by Tajima's D which revealed significant values for BLZ1, BLZ2, and BPBF in the subset of two-rowed barleys. Pair-wise LD estimates between the detected SNPs within each candidate gene revealed different intra-genic linkage patterns. On the basis of a more extensive examination of genomic regions surrounding the four candidate genes we found a sharp decrease of LD (r2<0.2 within 1 cM) in all but one flanking regions.Significant marker-trait associations between SNP sites within BLZ1 and flowering time, BPBF and crude protein content and BPBF and starch content were detected. Most haplotypes occurred at frequencies <0.05 and therefore were rejected from the association analysis. Based on haplotype information, BPBF was associated to crude protein content and starch content, BLZ2 showed association to thousand-grain weight and BLZ1 was found to be associated with flowering time and plant height. CONCLUSIONS Differences in nucleotide diversity and LD pattern within the candidate genes BLZ1, BLZ2, BPBF, and HvGAMYB reflect the impact of selection on the nucleotide sequence of the four candidate loci.Despite significant associations, the analysed candidate genes only explained a minor part of the total genetic variation although they are known to be important factors influencing the expression of seed quality traits. Therefore, we assume that grain quality as well as plant height and flowering time are influenced by many factors each contributing a small part to the expression of the phenotype. A genome-wide association analysis could provide a more comprehensive picture of loci involved in the regulation of grain quality, thousand grain weight and the other agronomic traits that were analyzed in this study. However, despite available high-throughput genotyping arrays the marker density along the barely genome is still insufficient to cover all associations in a whole genome scan. Therefore, the candidate gene-based approach will further play an important role in barley association studies.
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Affiliation(s)
- Grit Haseneyer
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
- University of Hohenheim, Institute for Plant Breeding, Seed Science and Population Genetics (350), 70593 Stuttgart, Germany
- Plant Breeding, Centre of Life and Food Sciences Weihenstephan, Technische Universitaet Muenchen, Am Hochanger 4, 85350 Freising, Germany
| | - Silke Stracke
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
- Department of Crop Sciences, Quality of Plant Products, University of Goettingen, Carl-Sprengel-Weg 1, 37075 Goettingen, Germany
| | - Hans-Peter Piepho
- University of Hohenheim, Institute for Crop Production and Grassland Research (340), Bioinformatics, 70593 Stuttgart, Germany
| | - Sascha Sauer
- Max-Planck Institute for Molecular Genetics, Ihnestr. 73, D-14195 Berlin, Germany
| | - Hartwig H Geiger
- University of Hohenheim, Institute for Plant Breeding, Seed Science and Population Genetics (350), 70593 Stuttgart, Germany
| | - Andreas Graner
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
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Breton C, Terral JF, Pinatel C, Médail F, Bonhomme F, Bervillé A. The origins of the domestication of the olive tree. C R Biol 2009; 332:1059-64. [DOI: 10.1016/j.crvi.2009.08.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Revised: 08/12/2009] [Accepted: 08/14/2009] [Indexed: 11/29/2022]
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Emshwiller E, Theim T, Grau A, Nina V, Terrazas F. Origins of domestication and polyploidy in oca (Oxalis tuberosa; Oxalidaceae). 3. AFLP data of oca and four wild, tuber-bearing taxa. AMERICAN JOURNAL OF BOTANY 2009; 96:1839-1848. [PMID: 21622305 DOI: 10.3732/ajb.0800359] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Many crops are polyploids, and it can be challenging to untangle the often complicated history of their origins of domestication and origins of polyploidy. To complement other studies of the origins of polyploidy of the octoploid tuber crop oca (Oxalis tuberosa) that used DNA sequence data and phylogenetic methods, we here compared AFLP data for oca with four wild, tuber-bearing Oxalis taxa found in different regions of the central Andes. Results confirmed the divergence of two use-categories of cultivated oca that indigenous farmers use for different purposes, suggesting the possibility that they might have had separate origins of domestication. Despite previous results with nuclear-encoded, chloroplast-expressed glutamine synthetase suggesting that O. picchensis might be a progenitor of oca, AFLP data of this species, as well as different populations of wild, tuber-bearing Oxalis found in Lima Department, Peru, were relatively divergent from O. tuberosa. Results from all analytical methods suggested that the unnamed wild, tuber-bearing Oxalis found in Bolivia and O. chicligastensis in NW Argentina are the best candidates as the genome donors for polyploid O. tuberosa, but the results were somewhat equivocal about which of these two taxa is the more strongly supported as oca's progenitor.
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Affiliation(s)
- Eve Emshwiller
- University of Wisconsin-Madison, Botany Department/Birge Hall, 430 Lincoln Drive, Madison, Wisconsin 53706-1381 USA
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Pang JF, Kluetsch C, Zou XJ, Zhang AB, Luo LY, Angleby H, Ardalan A, Ekström C, Sköllermo A, Lundeberg J, Matsumura S, Leitner T, Zhang YP, Savolainen P. mtDNA data indicate a single origin for dogs south of Yangtze River, less than 16,300 years ago, from numerous wolves. Mol Biol Evol 2009; 26:2849-64. [PMID: 19723671 PMCID: PMC2775109 DOI: 10.1093/molbev/msp195] [Citation(s) in RCA: 207] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
There is no generally accepted picture of where, when, and how the domestic dog originated. Previous studies of mitochondrial DNA (mtDNA) have failed to establish the time and precise place of origin because of lack of phylogenetic resolution in the so far studied control region (CR), and inadequate sampling. We therefore analyzed entire mitochondrial genomes for 169 dogs to obtain maximal phylogenetic resolution and the CR for 1,543 dogs across the Old World for a comprehensive picture of geographical diversity. Hereby, a detailed picture of the origins of the dog can for the first time be suggested. We obtained evidence that the dog has a single origin in time and space and an estimation of the time of origin, number of founders, and approximate region, which also gives potential clues about the human culture involved. The analyses showed that dogs universally share a common homogenous gene pool containing 10 major haplogroups. However, the full range of genetic diversity, all 10 haplogroups, was found only in southeastern Asia south of Yangtze River, and diversity decreased following a gradient across Eurasia, through seven haplogroups in Central China and five in North China and Southwest (SW)Asia, down to only four haplogroups in Europe. The mean sequence distance to ancestral haplotypes indicates an origin 5,400–16,300 years ago (ya) from at least 51 female wolf founders. These results indicate that the domestic dog originated in southern China less than 16,300 ya, from several hundred wolves. The place and time coincide approximately with the origin of rice agriculture, suggesting that the dogs may have originated among sedentary hunter-gatherers or early farmers, and the numerous founders indicate that wolf taming was an important culture trait.
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Affiliation(s)
- Jun-Feng Pang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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Iso-Touru T, Kantanen J, Li MH, Gizejewski Z, Vilkki J. Divergent evolution in the cytoplasmic domains of PRLR and GHR genes in Artiodactyla. BMC Evol Biol 2009; 9:172. [PMID: 19622175 PMCID: PMC2720954 DOI: 10.1186/1471-2148-9-172] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Accepted: 07/22/2009] [Indexed: 11/10/2022] Open
Abstract
Background Prolactin receptor (PRLR) and growth hormone receptor (GHR) belong to the large superfamily of class 1 cytokine receptors. Both of them have been identified as candidate genes affecting key quantitative traits, like growth and reproduction in livestock. We have previously studied the molecular anatomy of the cytoplasmic domain of GHR in different cattle breeds and artiodactyl species. In this study we have analysed the corresponding cytoplasmic signalling region of PRLR. Results We sequenced PRLR gene exon 10, coding for the major part of the cytoplasmic domain, from cattle, American bison, European bison, yak, sheep, pig and wild boar individuals. We found different patterns of variation in the two receptors within and between ruminants and pigs. Pigs and bison species have no variation within GHR exon 10, but show high haplotype diversity for the PRLR exon 10. In cattle, PRLR shows lower diversity than GHR. The Bovinae PRLR haplotype network fits better the known phylogenetic relationships between the species than that of the GHR, where differences within cattle breeds are larger than between the different species in the subfamily. By comparison with the wild boar haplotypes, a high number of subsequent nonsynonymous substitutions seem to have accumulated in the pig PRLR exon 10 after domestication. Conclusion Both genes affect a multitude of traits that have been targets of selection after domestication. The genes seem to have responded differently to different selection pressures imposed by human artificial selection. The results suggest possible effects of selective sweeps in GHR before domestication in the pig lineage or species divergence in the Bison lineage. The PRLR results may be explained by strong directional selection in pigs or functional switching.
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Affiliation(s)
- Terhi Iso-Touru
- Biotechnology and Food Research, MTT Agrifood Research Finland,Jokioinen, Finland.
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From wild animals to domestic pets, an evolutionary view of domestication. Proc Natl Acad Sci U S A 2009; 106 Suppl 1:9971-8. [PMID: 19528637 DOI: 10.1073/pnas.0901586106] [Citation(s) in RCA: 264] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Artificial selection is the selection of advantageous natural variation for human ends and is the mechanism by which most domestic species evolved. Most domesticates have their origin in one of a few historic centers of domestication as farm animals. Two notable exceptions are cats and dogs. Wolf domestication was initiated late in the Mesolithic when humans were nomadic hunter-gatherers. Those wolves less afraid of humans scavenged nomadic hunting camps and over time developed utility, initially as guards warning of approaching animals or other nomadic bands and soon thereafter as hunters, an attribute tuned by artificial selection. The first domestic cats had limited utility and initiated their domestication among the earliest agricultural Neolithic settlements in the Near East. Wildcat domestication occurred through a self-selective process in which behavioral reproductive isolation evolved as a correlated character of assortative mating coupled to habitat choice for urban environments. Eurasian wildcats initiated domestication and their evolution to companion animals was initially a process of natural, rather than artificial, selection over time driven during their sympatry with forbear wildcats.
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120
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Initial formation of an indigenous crop complex in eastern North America at 3800 B.P. Proc Natl Acad Sci U S A 2009; 106:6561-6. [PMID: 19366669 DOI: 10.1073/pnas.0901846106] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although geneticists and archaeologists continue to make progress world-wide in documenting the time and place of the initial domestication of a growing number of plants and animals, far less is known regarding the critically important context of coalescence of various species into distinctive sets or complexes of domesticates in each of the world's 10 or more independent centers of agricultural origin. In this article, the initial emergence of a crop complex is described for one of the best-documented of these independent centers, eastern North America (ENA). Before 4000 B.P. there is no indication of a crop complex in ENA, only isolated evidence for single indigenous domesticate species. By 3800 B.P., however, at least 5 domesticated seed-bearing plants formed a coherent complex in the river valley corridors of ENA. Accelerator mass spectrometer radiocarbon dates and reanalysis of archaeobotanical assemblages from a short occupation of the Riverton Site in Illinois documents the contemporary cultivation at 3800 B.P. of domesticated bottle gourd (Lagenaria siceraria), marshelder (Iva annua var. macrocarpa), sunflower (Helianthus annuus var. macrocarpus), and 2 cultivated varieties of chenopod (Chenopodium berlandieri), as well as the possible cultivation of Cucurbita pepo squash and little barley (Hordeum pusillum). Rather than marking either an abrupt developmental break or a necessary response to population-packing or compressed resource catchments, the coalescence of an initial crop complex in ENA appears to reflect an integrated expansion and enhancement of preexisting hunting and gathering economies that took place within a context of stable long-term adaptation to resource-rich river valley settings.
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Abbo S, Saranga Y, Peleg Z. Reconsidering Domestication Of Legumes Versus Cereals In The Ancient Near East. QUARTERLY REVIEW OF BIOLOGY 2009; 84:29-50. [DOI: 10.1086/596462] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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122
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Wang L, Hao L, Li X, Hu S, Ge S, Yu J. SNP deserts of Asian cultivated rice: genomic regions under domestication. J Evol Biol 2009; 22:751-61. [PMID: 19243488 DOI: 10.1111/j.1420-9101.2009.01698.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
When performing a genome-wide comparison between indica (93-11) and japonica (Nipponbare), we find 8% of the genome, which have an extremely low SNP rate (< 1 SNP/kb). Inside these 'SNP deserts', experimentally confirmed genes show increased K(a)/K(s) that indicate adaptive selection. To further elucidate this connection, we survey the level and pattern of genetic variation in both cultivated and wild rice groups, using 155 noncoding regions located within SNP deserts. The results suggest that cultivated rice has greatly reduced genetic variation within SNP deserts as compared to either the nondesert or corresponding genomic regions in wild rice. Consistent with this reduction in genetic variation, we find a biased distribution of derived allele frequency in the cultivated group, indicative of positive selection. Furthermore, over half of the confirmed, domestication-related genes are found within SNP deserts, also suggesting that SNP deserts are strongly related to domestication, and might be the key sites in the process of domestication.
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Affiliation(s)
- L Wang
- CAS Key Laboratory of Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
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123
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Abstract
Plant domestication is an outstanding example of plant-animal co-evolution and is a far richer model for studying evolution than is generally appreciated. There have been numerous studies to identify genes associated with domestication, and archaeological work has provided a clear understanding of the dynamics of human cultivation practices during the Neolithic period. Together, these have provided a better understanding of the selective pressures that accompany crop domestication, and they demonstrate that a synthesis from the twin vantage points of genetics and archaeology can expand our understanding of the nature of evolutionary selection that accompanies domestication.
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Affiliation(s)
- Michael D Purugganan
- Department of Biology and Centre for Genomics and Systems Biology, 100 Washington Square East, New York University, New York 10003, USA.
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124
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Masseti M. Mammals of the Mediterranean islands: homogenisation and the loss of biodiversity. MAMMALIA 2009. [DOI: 10.1515/mamm.2009.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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125
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Wang JX, Gao TG, Knapp S. Ancient Chinese literature reveals pathways of eggplant domestication. ANNALS OF BOTANY 2008; 102:891-7. [PMID: 18819950 PMCID: PMC2712397 DOI: 10.1093/aob/mcn179] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Revised: 06/09/2008] [Accepted: 08/07/2008] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Changes in key traits occurring during the processes of plant domestication have long been subjects of debate. Only in the case of genetic analysis or with extensive plant remains can specific sets of changes be documented. Historical details of the plant domestication processes are rare and other evidence of morphological change can be difficult to obtain, especially for those vegetables that lack a substantial body of archaeological data. Botanical records chronicled in the ancient literature of established ancient civilizations, such as that of China, are invaluable resources for the study and understanding of the process of plant domestication. Here, the considerable body of ancient Chinese literature is used to explore the domestication process that has occurred with the eggplant (Solanum melongena), an important vegetable in Old World. METHODS Information about eggplant domestication in the ancient Chinese literature was retrieved using a variety of methods. The information obtained was then sorted by taxon, examined and taxonomic identifications verified. KEY RESULTS It was found that the earliest record of the eggplant documented in ancient Chinese literature was in a work from 59 bc. As far as is known, this is the earliest reliable and accurately dated record of eggplant in cultivation. The analysis reveals that the process of domestication of the eggplant in China involved three principal aspects of fruit quality: size, shape and taste. These traits were actively and gradually selected; fruit size changed from small to large, taste changed from not palatable to what was termed at the time sweetish, and that over time, a wider variety of fruit shapes was cultivated. CONCLUSIONS The results indicate that, in addition to data gleaned from archaeology and genetics, evidence as to changes in key traits occurring during the process of plant domestication and selective forces responsible for these changes can be traced through the ancient literature in some civilizations.
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Affiliation(s)
- Jin-Xiu Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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126
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The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals. Proc Natl Acad Sci U S A 2008; 105:17659-64. [PMID: 19004765 DOI: 10.1073/pnas.0804782105] [Citation(s) in RCA: 166] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The emergence of farming during the Neolithic transition, including the domestication of livestock, was a critical point in the evolution of human kind. The goat (Capra hircus) was one of the first domesticated ungulates. In this study, we compared the genetic diversity of domestic goats to that of the modern representatives of their wild ancestor, the bezoar, by analyzing 473 samples collected over the whole distribution range of the latter species. This partly confirms and significantly clarifies the goat domestication scenario already proposed by archaeological evidence. All of the mitochondrial DNA haplogroups found in current domestic goats have also been found in the bezoar. The geographic distribution of these haplogroups in the wild ancestor allowed the localization of the main domestication centers. We found no haplotype that could have been domesticated in the eastern half of the Iranian Plateau, nor further to the east. A signature of population expansion in bezoars of the C haplogroup suggests an early domestication center on the Central Iranian Plateau (Yazd and Kerman Provinces) and in the Southern Zagros (Fars Province), possibly corresponding to the management of wild flocks. However, the contribution of this center to the current domestic goat population is rather low (1.4%). We also found a second domestication center covering a large area in Eastern Anatolia, and possibly in Northern and Central Zagros. This last domestication center is the likely origin of almost all domestic goats today. This finding is consistent with archaeological data identifying Eastern Anatolia as an important domestication center.
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127
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Macé M, Crouau-Roy B. A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla. BMC Genet 2008; 9:64. [PMID: 18925953 PMCID: PMC2580767 DOI: 10.1186/1471-2156-9-64] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Accepted: 10/16/2008] [Indexed: 11/24/2022] Open
Abstract
Background The early radiation of the Cetartiodactyla is complex, and unambiguous molecular characters are needed to clarify the positions of hippotamuses, camels and pigs relative to the remaining taxa (Cetacea and Ruminantia). There is also a need for informative genealogic markers for Y-chromosome population genetics as well as a sexing method applicable to all species from this group. We therefore studied the sequence variation of a partial sequence of the evolutionary conserved amelogenin gene to assess its potential use in each of these fields. Results and discussion We report a large interstitial insertion in the Y amelogenin locus in most of the Cetartiodactyla lineages (cetaceans and ruminants). This sex-linked size polymorphism is the result of a 460–465 bp inserted element in intron 4 of the amelogenin gene of Ruminants and Cetaceans. Therefore, this polymorphism can easily be used in a sexing assay for these species. When taking into account this shared character in addition to nucleotide sequence, gene genealogy follows sex-chromosome divergence in Cetartiodactyla whereas it is more congruent with zoological history when ignoring these characters. This could be related to a loss of homology between chromosomal copies given the old age of the insertion. The 1 kbp Amel-Y amplified fragment is also characterized by high nucleotide diversity (64 polymorphic sites spanning over 1 kbp in seven haplotypes) which is greater than for other Y-chromosome sequence markers studied so far but less than the mitochondrial control region. Conclusion The gender-dependent polymorphism we have identified is relevant not only for phylogenic inference within the Cetartiodactyla but also for Y-chromosome based population genetics and gender determination in cetaceans and ruminants. One single protocol can therefore be used for studies in population and evolutionary genetics, reproductive biotechnologies, and forensic science.
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Affiliation(s)
- Matthias Macé
- UMR 5174 UPS/CNRS EDB Evolution et Diversité biologique, Bât 4R3b2, Université Paul Sabatier, 118 route de Narbonne, 31062 TOULOUSE cedex 9, France.
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128
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Freeman AR, Lynn DJ, Murray C, Bradley DG. Detecting the effects of selection at the population level in six bovine immune genes. BMC Genet 2008; 9:62. [PMID: 18838007 PMCID: PMC2576349 DOI: 10.1186/1471-2156-9-62] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Accepted: 10/06/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The capacity of a species or population to respond to and survive novel infectious disease challenge is one of the most significant selective forces shaping genetic diversity and the period following animal domestication was likely one of the most important in terms of newly emerging diseases. Inter-specific genome-wide comparison has suggested that genes, including cluster of differentiation 2 (CD2), ADP-ribosyltransferase 4 (ART4), tyrosine kinase binding protein (TYROBP) and interleukins IL2, IL5, IL13, may have undergone positive selection during the evolution of the bovine lineage. Past adaptive change implies that more recent variation may have also been subject to selective forces. RESULTS In this paper, we re-sequence each of these genes in cattle cohorts from Europe, Africa and Asia to investigate patterns of polymorphism at the population level. Patterns of diversity are higher within Bos indicus suggesting different demographic history to that of Bos taurus. Significant coding polymorphism was observed within each of the cell-surface receptors. In particular, CD2 shows two divergent haplotypes defined by a series of six derived nonsynonymous substitutions that are significantly clustered on the extracellular surface of the protein and give significant values for Fay and Wu's H, strongly suggesting a recent adaptive history. In contrast, the signaling molecules (especially IL13) display outlying allele frequency spectra which are consistent with the effects of selection, but display negligible coding polymorphism. CONCLUSION We present evidence suggestive of recent adaptive history in bovine immune genes; implying some correspondence between intra- and inter-specific signals of selection. Interestingly, three signaling molecules have negligible nonsynonymous variation but show outlying test statistics in contrast to three receptors, where it is protein sequence diversity that suggests selective history.
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129
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Røed KH, Flagstad O, Nieminen M, Holand O, Dwyer MJ, Røv N, Vilà C. Genetic analyses reveal independent domestication origins of Eurasian reindeer. Proc Biol Sci 2008; 275:1849-55. [PMID: 18460427 DOI: 10.1098/rspb.2008.0332] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although there is little doubt that the domestication of mammals was instrumental for the modernization of human societies, even basic features of the path towards domestication remain largely unresolved for many species. Reindeer are considered to be in the early phase of domestication with wild and domestic herds still coexisting widely across Eurasia. This provides a unique model system for understanding how the early domestication process may have taken place. We analysed mitochondrial sequences and nuclear microsatellites in domestic and wild herds throughout Eurasia to address the origin of reindeer herding and domestication history. Our data demonstrate independent origins of domestic reindeer in Russia and Fennoscandia. This implies that the Saami people of Fennoscandia domesticated their own reindeer independently of the indigenous cultures in western Russia. We also found that augmentation of local reindeer herds by crossing with wild animals has been common. However, some wild reindeer populations have not contributed to the domestic gene pool, suggesting variation in domestication potential among populations. These differences may explain why geographically isolated indigenous groups have been able to make the technological shift from mobile hunting to large-scale reindeer pastoralism independently.
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Affiliation(s)
- Knut H Røed
- Department of Basic Sciences and Aquatic Medicine, Norwegian School of Veterinary Science, PO Box 8146, Departmental Division, 0033 Oslo, Norway.
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130
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Cruz F, Vila C, Webster MT. The Legacy of Domestication: Accumulation of Deleterious Mutations in the Dog Genome. Mol Biol Evol 2008; 25:2331-6. [DOI: 10.1093/molbev/msn177] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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131
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Shi W, Yang CF, Chen JM, Guo YH. Genetic variation among wild and cultivated populations of the Chinese medicinal plant Coptis chinensis (Ranunculaceae). PLANT BIOLOGY (STUTTGART, GERMANY) 2008; 10:485-491. [PMID: 18557908 DOI: 10.1111/j.1438-8677.2008.00035.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
To examine if the cultivation process has reduced the genetic variation of modern cultivars of the traditional Chinese medicinal plant, Coptis chinensis, the levels and distribution of genetic variation was investigated using ISSR markers. A total of 214 C. chinensis individuals from seven wild and three cultivated populations were included in the study. Seven ISSR primers were used and a total of 91 DNA fragments were scored. The levels of genetic diversity in cultivated populations were similar as those in wild populations (mean PPL = 65.2% versus PPL = 52.4%, mean H = 0.159 versus H = 0.153 and mean I = 0.255 versus I = 0.237), suggesting that cultivation did not seriously influence genetic variation of present-day cultivated populations. Neighbour-joining cluster analysis showed that wild populations and cultivated populations were not separated into two groups. The coefficient of genetic differentiation between a cultivar and its wild progenitor was 0.066 (G(st)), which was in good accordance with the result by amova analysis (10.9% of total genetic variation resided on the two groups), indicating that cultivated populations were not genetically differentiated from wild progenitors. For the seven wild populations, a significant genetic differentiation among populations was found using amova analysis (45.9% of total genetic variation resided among populations). A number of causes, including genetic drift and inbreeding in the small and isolated wild populations, the relative limited gene flow between wild populations (N(m) = 0.590), and high gene flow between cultivars and their wild progenitors (N(m) = 7.116), might have led to the observed genetic profiles of C. chinensis.
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Affiliation(s)
- W Shi
- Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
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132
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Trapezov OV, Trapezova LI, Sergeev EG. Effect of coat color mutations on behavioral polymorphism in farm populations of American minks (Mustela vison Schreber, 1777) and sables (Martes zibellina Linnaeus, 1758). RUSS J GENET+ 2008. [DOI: 10.1134/s1022795408040108] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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133
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Fénart S, Arnaud JF, De Cauwer I, Cuguen J. Nuclear and cytoplasmic genetic diversity in weed beet and sugar beet accessions compared to wild relatives: new insights into the genetic relationships within the Beta vulgaris complex species. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 116:1063-77. [PMID: 18335202 DOI: 10.1007/s00122-008-0735-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Accepted: 02/18/2008] [Indexed: 05/12/2023]
Abstract
Hybridization between cultivated species and their wild relatives is now widely considered to be common. In the Beta vulgaris complex, the sugar beet seed multiplication areas have been the scene of inadvertent pollination of sugar beet seed bearers by wild ruderal pollen donors, generating a weedy form of beet which infests sugar beet fields in European countries. Up to now, investigations of evolutionary dynamics of genetic diversity within the B. vulgaris complex were addressed using few genetical markers and few accessions. In this study, we tackled this issue using a panel of complementary markers: five nuclear microsatellite loci, four mitochondrial minisatellite loci and one chloroplastic PCR-RFLP marker. We sampled 1,640 individuals that illustrate the actual distribution of inland ruderal beets of South Western France, weed beets and wild sea beets of northern France as well as the diversity of 35 contemporary European diploid cultivars. Nuclear genetic diversity in weed beets appeared to be as high as those of ruderal beets and sea beets, whereas the narrowness of cultivar accessions was confirmed. This genetic bottleneck in cultivars is even more important in the cytoplasmic genome as only one haplotype was found among all sugar beet cultivars. The large majority of weed beet populations also presented this unique cytoplasmic haplotype, as expected owing to their maternal cultivated origin. Nonetheless, various cytoplasmic haplotypes were found within three populations of weed beets, implying wild-to-weed seed flows. Finally, our findings gave new insights into the genetical relationships between the components of the B. vulgaris complex: (1) we found a very strong genetic divergence between wild sea beet and other relatives, which was unexpected given the recent evolutionary history and the full cross-compatibility of all taxa and (2) we definitely confirmed that the classification into cultivated, wild, ruderal and weed forms according to their geographical location, phenotype or their domesticated status is clearly in accordance with genetic clustering despite the very recent domestication process of sugar beet.
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Affiliation(s)
- Stéphane Fénart
- Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8016, Université des Sciences et Technologies de Lille, Lille 1, Bâtiment SN2, 59655 Villeneuve d'Ascq Cedex, France
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134
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MASSETI MARCO, PECCHIOLI ELENA, VERNESI CRISTIANO. Phylogeography of the last surviving populations of Rhodian and Anatolian fallow deer (Dama dama dama L., 1758). Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.2007.00951.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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135
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Abstract
Domestication of the donkey from the African wild ass transformed ancient transport systems in Africa and Asia and the organization of early cities and pastoral societies. Genetic research suggests an African origin for the donkey, but pinpointing the timing and location of domestication has been challenging because donkeys are uncommon in the archaeological record and markers for early phases of animal domestication are hard to determine. We present previously undescribed evidence for the earliest transport use of the donkey and new paleopathological indicators for early phases of donkey domestication. Findings are based on skeletal data from 10 approximately 5,000-year-old ass skeletons recently discovered entombed in an early pharaonic mortuary complex at Abydos, Middle Egypt, and a concurrent study of 53 modern donkey and African wild ass skeletons. Morphometric studies showed that Abydos metacarpals were similar in overall proportions to those of wild ass, but individual measurements varied. Midshaft breadths resembled wild ass, but midshaft depths and distal breadths were intermediate between wild ass and domestic donkey. Despite this, all of the Abydos skeletons exhibited a range of osteopathologies consistent with load carrying. Morphological similarities to wild ass show that, despite their use as beasts of burden, donkeys were still undergoing considerable phenotypic change during the early Dynastic period in Egypt. This pattern is consistent with recent studies of other domestic animals that suggest that the process of domestication is slower and less linear than previously thought.
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136
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Nagamine Y, Nirasawa K, Takahashi H, Sasaki O, Ishii K, Minezawa M, Oda S, Visscher PM, Furukawa T. Estimation of the Time of Divergence between Japanese Mishima Island Cattle and Other Cattle Populations Using Microsatellite DNA Markers. J Hered 2008; 99:202-7. [DOI: 10.1093/jhered/esm129] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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137
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Virányi Z, Gácsi M, Kubinyi E, Topál J, Belényi B, Ujfalussy D, Miklósi A. Comprehension of human pointing gestures in young human-reared wolves (Canis lupus) and dogs (Canis familiaris). Anim Cogn 2008; 11:373-87. [PMID: 18183437 DOI: 10.1007/s10071-007-0127-y] [Citation(s) in RCA: 146] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2005] [Revised: 12/11/2007] [Accepted: 12/13/2007] [Indexed: 10/22/2022]
Abstract
Dogs have a remarkable skill to use human-given cues in object-choice tasks, but little is known to what extent their closest wild-living relative, the wolf can achieve this performance. In Study 1, we compared wolf and dog pups hand-reared individually and pet dogs of the same age in their readiness to form eye-contact with a human experimenter in an object-choice task and to follow her pointing gesture. The results showed that dogs already at 4 months of age use momentary distal pointing to find hidden food even without intensive early socialization. Wolf pups, on the contrary, do not attend to this subtle pointing. Accordingly in Studies 2 and 3, these wolves were tested longitudinally with this and four other (easier) human-given cues. This revealed that wolves socialized at a comparable level to dogs are able to use simple human-given cues spontaneously if the human's hand is close to the baited container (e.g. touching, proximal pointing). Study 4 showed that wolves can follow also momentary distal pointing similarly to dogs if they have received extensive formal training. Comparing the wolves to naïve pet dogs of the same age revealed that during several months of formal training wolves can reach the level of dogs in their success of following momentary distal pointing in parallel with improving their readiness to form eye-contact with a human experimenter. We assume that the high variability in the wolves' communicative behaviour might have provided a basis for selection during the course of domestication of the dog.
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Affiliation(s)
- Zsófia Virányi
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary.
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138
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Taberlet P, Valentini A, Rezaei HR, Naderi S, Pompanon F, Negrini R, Ajmone-Marsan P. Are cattle, sheep, and goats endangered species? Mol Ecol 2008; 17:275-84. [PMID: 17927711 DOI: 10.1111/j.1365-294x.2007.03475.x] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- P Taberlet
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble cedex 09, France.
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139
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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: 125] [Impact Index Per Article: 7.4] [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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Abstract
Ten thousand years ago human societies around the globe began to transition from hunting and gathering to agriculture. By 4000 years ago, ancient peoples had completed the domestication of all major crop species upon which human survival is dependent, including rice, wheat, and maize. Recent research has begun to reveal the genes responsible for this agricultural revolution. The list of genes to date tentatively suggests that diverse plant developmental pathways were the targets of Neolithic "genetic tinkering," and we are now closer to understanding how plant development was redirected to meet the needs of a hungry world.
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Affiliation(s)
- John F Doebley
- Department of Genetics, University of Wisconsin, Madison, WI 53706, USA.
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Zhu Q, Zheng X, Luo J, Gaut BS, Ge S. Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Mol Biol Evol 2007; 24:875-88. [PMID: 17218640 DOI: 10.1093/molbev/msm005] [Citation(s) in RCA: 276] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Varying degrees of reduction of genetic diversity in crops relative to their wild progenitors occurred during the process of domestication. Such information, however, has not been available for the Asian cultivated rice (Oryza sativa) despite its importance as a staple food and a model organism. To reveal levels and patterns of nucleotide diversity and to elucidate the genetic relationship and demographic history of O. sativa and its close relatives (Oryza rufipogon and Oryza nivara), we investigated nucleotide diversity data from 10 unlinked nuclear loci in species-wide samples of these species. The results indicated that O. rufipogon and O. nivara possessed comparable levels of nucleotide variation ((sil) = 0.0077 approximately 0.0095) compared with the relatives of other crops. In contrast, nucleotide diversity of O. sativa was as low as (sil) = 0.0024 and even lower ((sil) = 0.0021 for indica and 0.0011 for japonica), if we consider the 2 subspecies separately. Overall, only 20-10% of the diversity in the wild species was retained in 2 subspecies of the cultivated rice (indica and japonica), respectively. Because statistic tests did not reject the assumption of neutrality for all 10 loci, we further used coalescent to simulate bottlenecks under various lengths and population sizes to better understand the domestication process. Consistent with the dramatic reduction in nucleotide diversity, we detected a severe domestication bottleneck and demonstrated that the sequence diversity currently found in the rice genome could be explained by a founding population of 1,500 individuals if the initial domestication event occurred over a 3,000-year period. Phylogenetic analyses revealed close genetic relationships and ambiguous species boundary of O. rufipogon and O. nivara, providing additional evidence to treat them as 2 ecotypes of a single species. Lowest linkage disequilibrium (LD) was found in the perennial O. rufipogon where the r(2) value dropped to a negligible level within 400 bp, and the highest in the japonica rice where LD extended to the entirely sequenced region ( approximately 900 bp), implying that LD mapping by genome scans may not be feasible in wild rice due to the high density of markers needed.
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Affiliation(s)
- Qihui Zhu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Tapio M, Marzanov N, Ozerov M, Cinkulov M, Gonzarenko G, Kiselyova T, Murawski M, Viinalass H, Kantanen J. Sheep Mitochondrial DNA Variation in European, Caucasian, and Central Asian Areas. Mol Biol Evol 2006; 23:1776-83. [PMID: 16782761 DOI: 10.1093/molbev/msl043] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Three distinct mitochondrial maternal lineages (haplotype Groups A, B, and C) have been found in the domestic sheep. Group B has been observed primarily in European domestic sheep. The European mouflon carries this haplotype group. This could suggest that European mouflon was independently domesticated in Europe, although archaeological evidence supports sheep domestication in the central part of the Fertile Crescent. To investigate this question, we sequenced a highly variable segment of mitochondrial DNA (mtDNA) in 406 unrelated animals from 48 breeds or local varieties. They originated from a wide area spanning northern Europe and the Balkans to the Altay Mountains in south Siberia. The sample included a representative cross-section of sheep breeds from areas close to the postulated Near Eastern domestication center and breeds from more distant northern areas. Four (A, B, C, and D) highly diverged sheep lineages were observed in Caucasus, 3 (A, B and C) in Central Asia, and 2 (A and B) in the eastern fringe of Europe, which included the area north and west of the Black Sea and the Ural Mountains. Only one example of Group D was detected. The other haplotype groups demonstrated signs of population expansion. Sequence variation within the lineages implied Group A to have expanded first. This group was the most frequent type only in Caucasian and Central Asian breeds. Expansion of Group C appeared most recently. The expansion of Group B involving Caucasian sheep took place at nearly the same time as the expansion of Group A. Group B expansion for the eastern European area started approximately 3,000 years after the earliest inferred expansion. An independent European domestication of sheep is unlikely. The distribution of Group A variation as well as other results are compatible with the Near East being the domestication site. Groups C and D may have been introgressed later into a domestic stock, but larger samples are needed to infer their geographical origin. The results suggest that some mitochondrial lineages arrived in northern Europe from the Near East across Russia.
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Affiliation(s)
- Miika Tapio
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland
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