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Manunza A, Ramírez-Díaz J, Rincón Flórez JC, Almeida de Oliveira T. Editorial: Environmental and genomic strategies for conservation and selection in small ruminants. Front Vet Sci 2024; 11:1396289. [PMID: 38628938 PMCID: PMC11018938 DOI: 10.3389/fvets.2024.1396289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 03/12/2024] [Indexed: 04/19/2024] Open
Affiliation(s)
- Arianna Manunza
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Milan, Italy
| | - Johanna Ramírez-Díaz
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Milan, Italy
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2
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He Y, Zhang K, Shi Y, Lin H, Huang X, Lu X, Wang Z, Li W, Feng X, Shi T, Chen Q, Wang J, Tang Y, Chapman MA, Germ M, Luthar Z, Kreft I, Janovská D, Meglič V, Woo SH, Quinet M, Fernie AR, Liu X, Zhou M. Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheat. Genome Biol 2024; 25:61. [PMID: 38414075 PMCID: PMC10898187 DOI: 10.1186/s13059-024-03203-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 02/21/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Tartary buckwheat, Fagopyrum tataricum, is a pseudocereal crop with worldwide distribution and high nutritional value. However, the origin and domestication history of this crop remain to be elucidated. RESULTS Here, by analyzing the population genomics of 567 accessions collected worldwide and reviewing historical documents, we find that Tartary buckwheat originated in the Himalayan region and then spread southwest possibly along with the migration of the Yi people, a minority in Southwestern China that has a long history of planting Tartary buckwheat. Along with the expansion of the Mongol Empire, Tartary buckwheat dispersed to Europe and ultimately to the rest of the world. The different natural growth environments resulted in adaptation, especially significant differences in salt tolerance between northern and southern Chinese Tartary buckwheat populations. By scanning for selective sweeps and using a genome-wide association study, we identify genes responsible for Tartary buckwheat domestication and differentiation, which we then experimentally validate. Comparative genomics and QTL analysis further shed light on the genetic foundation of the easily dehulled trait in a particular variety that was artificially selected by the Wa people, a minority group in Southwestern China known for cultivating Tartary buckwheat specifically for steaming as a staple food to prevent lysine deficiency. CONCLUSIONS This study provides both comprehensive insights into the origin and domestication of, and a foundation for molecular breeding for, Tartary buckwheat.
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Affiliation(s)
- Yuqi He
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Kaixuan Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yaliang Shi
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hao Lin
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xu Huang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiang Lu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhirong Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xibo Feng
- Tibet Key Experiments of Crop Cultivation and Farming/College of Plant Science, Tibet Agriculture and Animal Husbandry University, Linzhi, 860000, China
| | - Taoxiong Shi
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, China
| | - Qingfu Chen
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, China
| | - Junzhen Wang
- Xichang Institute of Agricultural Science, Liangshan Yi People Autonomous Prefecture, Liangshan, Sichuan, 615000, China
| | - Yu Tang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Mateja Germ
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Zlata Luthar
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Ivan Kreft
- Nutrition Institute, Koprska Ulica 98, SI-1000, Ljubljana, Slovenia
| | - Dagmar Janovská
- Gene Bank, Crop Research Institute, Drnovská 507, Prague 6, Czech Republic
| | - Vladimir Meglič
- Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000, Ljubljana, Slovenia
| | - Sun-Hee Woo
- Department of Crop Science, Chungbuk National University, Cheong-ju, Republic of Korea
| | - Muriel Quinet
- Groupe de Recherche en Physiologie Végétale (GRPV), Earth and Life Institute-Agronomy (ELI-A), Université catholique de Louvain, Croix du Sud 45, boîte L7.07.13, B-1348, Louvain-la-Neuve, Belgium
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Xu Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Meiliang Zhou
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Benjelloun B, Leempoel K, Boyer F, Stucki S, Streeter I, Orozco-terWengel P, Alberto FJ, Servin B, Biscarini F, Alberti A, Engelen S, Stella A, Colli L, Coissac E, Bruford MW, Ajmone-Marsan P, Negrini R, Clarke L, Flicek P, Chikhi A, Joost S, Taberlet P, Pompanon F. Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints. Mol Ecol 2023:e17257. [PMID: 38149334 DOI: 10.1111/mec.17257] [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: 09/15/2022] [Revised: 08/18/2023] [Accepted: 12/05/2023] [Indexed: 12/28/2023]
Abstract
The question of how local adaptation takes place remains a fundamental question in evolutionary biology. The variation of allele frequencies in genes under selection over environmental gradients remains mainly theoretical and its empirical assessment would help understanding how adaptation happens over environmental clines. To bring new insights to this issue we set up a broad framework which aimed to compare the adaptive trajectories over environmental clines in two domesticated mammal species co-distributed in diversified landscapes. We sequenced the genomes of 160 sheep and 161 goats extensively managed along environmental gradients, including temperature, rainfall, seasonality and altitude, to identify genes and biological processes shaping local adaptation. Allele frequencies at putatively adaptive loci were rarely found to vary gradually along environmental gradients, but rather displayed a discontinuous shift at the extremities of environmental clines. Of the 430 candidate adaptive genes identified, only 6 were orthologous between sheep and goats and those responded differently to environmental pressures, suggesting different putative mechanisms involved in local adaptation in these two closely related species. Interestingly, the genomes of the 2 species were impacted differently by the environment, genes related to signatures of selection were most related to altitude, slope and rainfall seasonality for sheep, and summer temperature and spring rainfall for goats. The diversity of candidate adaptive pathways may result from a high number of biological functions involved in the adaptations to multiple eco-climatic gradients, and a differential role of climatic drivers on the two species, despite their co-distribution along the same environmental gradients. This study describes empirical examples of clinal variation in putatively adaptive alleles with different patterns in allele frequency distributions over continuous environmental gradients, thus showing the diversity of genetic responses in adaptive landscapes and opening new horizons for understanding genomics of adaptation in mammalian species and beyond.
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Affiliation(s)
- Badr Benjelloun
- Livestock Genomics Laboratory, Regional Center of Agricultural Research Tadla, National Institute of Agricultural Research INRA, Rabat, Morocco
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Kevin Leempoel
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Frédéric Boyer
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Sylvie Stucki
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Pablo Orozco-terWengel
- School of Biosciences, Cardiff University, Wales, UK
- Sustainable Places Research Institute, Cardiff University, Cardiff, UK
| | - Florian J Alberto
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, Castanet-Tolosan, France
| | - Filippo Biscarini
- Institute of Agricultural Biology and Biotechnology, Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, Evry, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Stefan Engelen
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique CEA, Université Paris-Saclay, Evry, France
| | - Alessandra Stella
- Institute of Agricultural Biology and Biotechnology, Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | - Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
- BioDNA - Centro di Ricerca sulla Biodiversità e sul DNA Antico, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Eric Coissac
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Wales, UK
- Sustainable Places Research Institute, Cardiff University, Cardiff, UK
| | - Paolo Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
- BioDNA - Centro di Ricerca sulla Biodiversità e sul DNA Antico, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Riccardo Negrini
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
- AIA Associazione Italiana Allevatori, Roma, Italy
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Abdelkader Chikhi
- Livestock Genomics Laboratory, Regional Center of Agricultural Research Tadla, National Institute of Agricultural Research INRA, Rabat, Morocco
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Pierre Taberlet
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - François Pompanon
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
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Zhang M, Wang S, Xu R, Liu Y, Zhang H, Sun M, Wang J, Liu Z, Wu K. Managing genomic diversity in conservation programs of Chinese domestic chickens. Genet Sel Evol 2023; 55:92. [PMID: 38097971 PMCID: PMC10722821 DOI: 10.1186/s12711-023-00866-3] [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: 01/25/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Effective conservation and utilization of farm animals are fundamental for realizing sustainable increases in food production. In situ and ex situ conservation are the two main strategies that are currently used to protect the genetic integrity of Chinese domestic chicken breeds. However, genomic diversity and population structure have not been compared in these conserved populations. RESULTS Three hundred and sixty-one individuals from three Chinese domestic chicken breeds were collected from populations conserved in situ and ex situ and genotyped using genotyping-by-sequencing (GBS). First, we used different parameters based on heterozygosity, genomic inbreeding, and linkage disequilibrium to estimate the genomic diversity of these populations, and applied principal component analysis (PCA), neighbor-joining tree, and ADMIXTURE to analyze population structure. We found that the small ex situ conserved populations, which have been maintained in controlled environments, retained less genetic diversity than the in situ conserved populations. In addition, genetic differentiation was detected between the in situ and ex situ conserved populations of the same breed. Next, we analyzed signatures of selection using three statistical methods (fixation index (FST), nucleotide diversity (Pi), and cross-population extended haplotype homozygosity (XP-EHH) to study the genetic footprints that underlie the differentiation between in situ and ex situ conserved populations. We concluded that, in these small populations, differentiation might be caused by genetic drift or by mutations from the original populations. The differentiation observed in the population of Beijing You chicken probably reflects adaptation to environmental changes in temperature and humidity that the animals faced when they were moved from their place of origin to the new site for ex situ conservation. CONCLUSIONS Conservation programs of three Chinese domestic chicken breeds have maintained their genomic diversity to a sustainable degree. The small ex situ conserved populations, which are maintained in controlled environments, retain less genetic diversity than populations conserved in situ. In addition, the transfer of populations from their place of origin to another site for conservation purposes results in genetic differentiation, which may be caused by genetic drift or adaptation. This study provides a basis for further optimization of in situ and ex situ conservation programs for domestic chicken breeds in China.
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Affiliation(s)
- Mengmeng Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
- Beijing Capital Agribusiness Future Biotechnology Co., Ltd., No. 75 Bingjiaokou Hutong, Beijing, 100088, People's Republic of China
| | - Shiwei Wang
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Ran Xu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yijun Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
- College of Animal Science, Southwest University, Chongqing, 402460, People's Republic of China
| | - Han Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Mengxia Sun
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Junyan Wang
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Zhexi Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Keliang Wu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
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Demir E, Moravčíková N, Kaya S, Kasarda R, Doğru H, Bilginer Ü, Balcioğlu MS, Karsli T. Genome-wide genetic variation and population structure of native and cosmopolitan cattle breeds reared in Türkiye. Anim Biotechnol 2023; 34:3877-3886. [PMID: 37471206 DOI: 10.1080/10495398.2023.2235600] [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] [Indexed: 07/22/2023]
Abstract
This is the first comprehensive study to reveal genetic variation and population structure at genome level in six Anatolian (Anatolian Black, East Anatolian Red, South Anatolian Red, South Anatolian Yellow, Turkish Grey Steppe, and Zavot) and two cosmopolitan (Brown Swiss and Holstein Friesian) cattle breeds reared in Türkiye. Being 20 samples from each population, a total of 160 blood samples retrieved from representative herds were utilized to generate genomic libraries by ddRADseq method. Genomic libraries sequenced by Illumina HiSeq X Ten instrument revealed a total of 211,119 bi-allelic SNPs with high call rate. Compared to cosmopolitan cattle breeds, a higher genetic variation was observed in native Turkish cattle with an average of 0.380 observed heterozygosity. Genetic distances were comparatively low between native cattle breeds, whereas the highest genetic distance (0.064) was detected between South Anatolian Yellow and Brown Swiss. Population structure analyses showed that the native Turkish and cosmopolitan cattle breeds were clearly different from each other according to their phylogenetic origin. Besides, a high level of genetic admixture was detected among Anatolian Black, Turkish Grey Steppe, South Anatolian Red, and South Anatolian Yellow, whereas East Anatolian Red and Zavot were distinct from the other native and cosmopolitan cattle breeds. TreeMix algorithm under the assumption of one and two migration events revealed a migration route from Anatolian clade to Anatolian Black, while a second migration edge was drawn from Brown Swiss to East Anatolian Red. This study demonstrates the importance of national conservation studies in the native breeds whose population size has dramatically decreased. In addition, SNP arrays and next-generation sequencing platforms are recommended for future studies to reveal the genetic variation of other local Turkish livestock species to arrange effective conservation programs.
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Affiliation(s)
- Eymen Demir
- Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, Republic of Türkiye
| | - Nina Moravčíková
- Institute of Nutrition and Genomics, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Slovak Republic
| | - Sarp Kaya
- Department of Medical Services and Techniques, Vocational School of Burdur Health Services, Burdur Mehmet Akif Ersoy University, Burdur, Republic of Türkiye
| | - Radovan Kasarda
- Institute of Nutrition and Genomics, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Slovak Republic
| | - Huriye Doğru
- Department of Medical Services and Techniques, Vocational School of Burdur Health Services, Burdur Mehmet Akif Ersoy University, Burdur, Republic of Türkiye
| | - Ümit Bilginer
- Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, Republic of Türkiye
| | - Murat Soner Balcioğlu
- Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, Republic of Türkiye
| | - Taki Karsli
- Department of Animal Science, Faculty of Agriculture, Eskisehir Osmangazi University, Eskisehir, Republic of Türkiye
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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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The whole mitochondrial genome signature of Teressa goat, an indigenous goat germplasm of Andaman and Nicobar Islands, India. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Ben Sassi-Zaidy Y, Mohamed-Brahmi A, Chaouch M, Maretto F, Cendron F, Charfi-Cheikhrouha F, Ben Abderrazak S, Djemali M, Cassandro M. Historical Westward Migration Phases of Ovis aries Inferred from the Population Structure and the Phylogeography of Occidental Mediterranean Native Sheep Breeds. Genes (Basel) 2022; 13:genes13081421. [PMID: 36011332 PMCID: PMC9408117 DOI: 10.3390/genes13081421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/22/2022] [Accepted: 08/04/2022] [Indexed: 01/18/2023] Open
Abstract
In this study, the genetic relationship and the population structure of western Mediterranean basin native sheep breeds are investigated, analyzing Maghrebian, Central Italian, and Venetian sheep with a highly informative microsatellite markers panel. The phylogeographical analysis, between breeds’ differentiation level (Wright’s fixation index), gene flow, ancestral relatedness measured by molecular coancestry, genetic distances, divergence times estimates and structure analyses, were revealed based on the assessment of 975 genotyped animals. The results unveiled the past introduction and migration history of sheep in the occidental Mediterranean basin since the early Neolithic. Our findings provided a scenario of three westward sheep migration phases fitting properly to the westward Neolithic expansion argued by zooarcheological, historical and human genetic studies.
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Affiliation(s)
- Yousra Ben Sassi-Zaidy
- Laboratory of Diversity, Management and Conservation of Biological Systems, LR18ES06, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 2092, Tunisia
- Department of Agronomy, Animal, Food, Natural Resources and Environment, University of Padova, 35020 Legnaro Padova, Italy
- Laboratory of Animal Genetic and Feed Resources Research, Department of Animal Science, Institut National Agronomique de Tunis (INAT), University of Carthage, Tunis-Mahragène Tunis 2078, Tunisia
- Correspondence: (Y.B.S.-Z.); (F.C.); Tel.: +39-049-8272871 (F.C.); Fax: +39-049-8272633 (F.C.)
| | - Aziza Mohamed-Brahmi
- Laboratory of Agricultural Production Systems Sustainability in the North Western Region of Tunisia, Department of Animal Production, Ecole Supérieure d’Agriculture du Kef Boulifa, University of Jendouba, Le Kef 7119, Tunisia
| | - Melek Chaouch
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules (LR11IPT06), Institut Pasteur de Tunis, Tunis 1002, Tunisia
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Fabio Maretto
- Department of Agronomy, Animal, Food, Natural Resources and Environment, University of Padova, 35020 Legnaro Padova, Italy
| | - Filippo Cendron
- Department of Agronomy, Animal, Food, Natural Resources and Environment, University of Padova, 35020 Legnaro Padova, Italy
- Correspondence: (Y.B.S.-Z.); (F.C.); Tel.: +39-049-8272871 (F.C.); Fax: +39-049-8272633 (F.C.)
| | - Faouzia Charfi-Cheikhrouha
- Laboratory of Diversity, Management and Conservation of Biological Systems, LR18ES06, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 2092, Tunisia
| | - Souha Ben Abderrazak
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules (LR11IPT06), Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Mnaour Djemali
- Laboratory of Animal Genetic and Feed Resources Research, Department of Animal Science, Institut National Agronomique de Tunis (INAT), University of Carthage, Tunis-Mahragène Tunis 2078, Tunisia
| | - Martino Cassandro
- Department of Agronomy, Animal, Food, Natural Resources and Environment, University of Padova, 35020 Legnaro Padova, Italy
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Pangenomics and Crop Genome Adaptation in a Changing Climate. PLANTS 2022; 11:plants11151949. [PMID: 35956427 PMCID: PMC9370458 DOI: 10.3390/plants11151949] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 12/15/2022]
Abstract
During crop domestication and breeding, wild plant species have been shaped into modern high-yield crops and adapted to the main agro-ecological regions. However, climate change will impact crop productivity in these regions, and agriculture needs to adapt to support future food production. On a global scale, crop wild relatives grow in more diverse environments than crop species, and so may host genes that could support the adaptation of crops to new and variable environments. Through identification of individuals with increased climate resilience we may gain a greater understanding of the genomic basis for this resilience and transfer this to crops. Pangenome analysis can help to identify the genes underlying stress responses in individuals harbouring untapped genomic diversity in crop wild relatives. The information gained from the analysis of these pangenomes can then be applied towards breeding climate resilience into existing crops or to re-domesticating crops, combining environmental adaptation traits with crop productivity.
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Bednarik RG, Saniotis A, Henneberg M. Auto-domestication hypothesis and the rise in mental disorders in modern humans. Med Hypotheses 2022. [DOI: 10.1016/j.mehy.2022.110874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Monzani PS, Adona PR, Long SA, Wheeler MB. Cows as Bioreactors for the Production of Nutritionally and Biomedically Significant Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1354:299-314. [PMID: 34807448 DOI: 10.1007/978-3-030-85686-1_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Dairy and beef cattle make a vital contribution to global nutrition, and since their domestication, they have been continuously exposed to natural and artificial selection to improve production characteristics. The technologies of transgenesis and gene editing used in cattle are responsible for generating news characteristics in bovine breeding, such as alteration of nutritional components of milk and meat enhancing human health benefits, disease resistance decreasing production costs and offering safe products for human food, as well as the recombinant protein production of biomedical significance. Different methodologies have been used to generate transgenic cattle as bioreactors. These methods include the microinjection of vectors in pronuclear, oocyte or zygote, sperm-mediate transgenesis, and somatic cell nuclear transfer. Gene editing has been applied to eliminate unwanted genes related to human and animal health, such as allergy, infection, or disease, and to insert transgenes into specific sites in the host genome. Methodologies for the generation of genetically modified cattle are laborious and not very efficient. However, in the last 30 years, transgenic animals were produced using many biotechnological tools. The result of these modifications includes (1) the change of nutritional components, including proteins, amino acids and lipids for human nutrition; (2) the removal allergic proteins milk; (3) the production of cows resistant to disease; or (4) the production of essential proteins used in biomedicine (biomedical proteins) in milk and blood plasma. The genetic modification of cattle is a powerful tool for biotechnology. It allows for the generation of new or modified products and functionality that are not currently available in this species.
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Affiliation(s)
- P S Monzani
- Instituto Chico Mendes de Conservação da Biodiversidade/Centro Nacional de Pesquisa e Conservação da Biodiversidade Aquática Continental, Pirassununga, SP, Brasil.
| | - P R Adona
- Saúde e Produção de Ruminantes, Universidade Norte do Paraná, Arapongas, PR, Brasil
| | - S A Long
- Departments of Animal Sciences and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - M B Wheeler
- Departments of Animal Sciences and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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12
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An etiology of human modernity. ANTHROPOLOGICAL REVIEW 2021. [DOI: 10.2478/anre-2021-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Following the refutation of the replacement hypothesis, which had proposed that a ‘superior’ hominin species arose in Africa and replaced all other humans existing at the time, the auto-domestication hypothesis remains the only viable explanation for the relatively abrupt change from robust to gracile humans in the Late Pleistocene. It invokes the incidental institution of the domestication syndrome in humans, most probably by newly introduced cultural practices. It also postulates that the induction of exograms compensated for the atrophy of the brain caused by domestication. This new explanation of the origins of modernity in humans elucidates practically all its many aspects, in stark contrast to the superseded replacement hypothesis, which explained virtually nothing. The first results of the domestication syndrome’s genetic exploration have become available in recent years, and they endorse the human self-domestication hypothesis.
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13
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Ancient Faunal History Revealed by Interdisciplinary Biomolecular Approaches. DIVERSITY 2021. [DOI: 10.3390/d13080370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Starting four decades ago, studies have examined the ecology and evolutionary dynamics of populations and species using short mitochondrial DNA fragments and stable isotopes. Through technological and analytical advances, the methods and biomolecules at our disposal have increased significantly to now include lipids, whole genomes, proteomes, and even epigenomes. At an unprecedented resolution, the study of ancient biomolecules has made it possible for us to disentangle the complex processes that shaped the ancient faunal diversity across millennia, with the potential to aid in implicating probable causes of species extinction and how humans impacted the genetics and ecology of wild and domestic species. However, even now, few studies explore interdisciplinary biomolecular approaches to reveal ancient faunal diversity dynamics in relation to environmental and anthropogenic impact. This review will approach how biomolecules have been implemented in a broad variety of topics and species, from the extinct Pleistocene megafauna to ancient wild and domestic stocks, as well as how their future use has the potential to offer an enhanced understanding of drivers of past faunal diversity on Earth.
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Fernandez AR, Sáez A, Quintero C, Gleiser G, Aizen MA. Intentional and unintentional selection during plant domestication: herbivore damage, plant defensive traits and nutritional quality of fruit and seed crops. THE NEW PHYTOLOGIST 2021; 231:1586-1598. [PMID: 33977519 DOI: 10.1111/nph.17452] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/23/2021] [Indexed: 05/19/2023]
Abstract
Greater susceptibility to herbivory can arise as an effect of crop domestication. One proposed explanation is that defenses decreased intentionally or unintentionally during the domestication process, but evidence for this remains elusive. An alternative but nonexclusive explanation is presumed selection for higher nutritional quality. We used a metaanalytical approach to examine susceptibility to herbivores in fruit and seed crops and their wild relatives. Our analyses provide novel insights into the mechanisms of increased susceptibility by evaluating whether it can be attributed to either a reduction in herbivore defensive traits, including direct/indirect and constitutive/inducible defenses, or an increase in the nutritional content of crops. The results confirm higher herbivory and lower levels of all types of defenses in crops compared to wild relatives, although indirect defenses were more affected than direct ones. Contrary to expectations, nutritional quality was lower in crops than in wild relatives, which may enhance biomass loss to herbivores if they increase consumption to meet nutritional requirements. Our findings represent an important advance in our understanding of how changes in defensive and nutritional traits following domestication could influence, in combination or individually, crop susceptibility to herbivore attacks.
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Affiliation(s)
- Anahí R Fernandez
- Laboratorio Ecotono, INIBIOMA, CONICET, Universidad Nacional del Comahue, Quintral 1250, Bariloche, 8400, Argentina
- IRNAD, CONICET, Universidad Nacional de Río Negro, Mitre 630, Bariloche, 8400, Argentina
| | - Agustín Sáez
- Laboratorio Ecotono, INIBIOMA, CONICET, Universidad Nacional del Comahue, Quintral 1250, Bariloche, 8400, Argentina
| | - Carolina Quintero
- Laboratorio Ecotono, INIBIOMA, CONICET, Universidad Nacional del Comahue, Quintral 1250, Bariloche, 8400, Argentina
| | - Gabriela Gleiser
- Laboratorio Ecotono, INIBIOMA, CONICET, Universidad Nacional del Comahue, Quintral 1250, Bariloche, 8400, Argentina
| | - Marcelo A Aizen
- Laboratorio Ecotono, INIBIOMA, CONICET, Universidad Nacional del Comahue, Quintral 1250, Bariloche, 8400, Argentina
- Wissenschaftskolleg zu Berlin, Berlin, 14193, Germany
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15
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Cultivar-Groups in Cucurbita maxima Duchesne: Diversity and Possible Domestication Pathways. DIVERSITY 2021. [DOI: 10.3390/d13080354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Domesticated Cucurbita has been remarked as one of the plant genera with the highest diversity in color, shape and fruit dimensions. Their economic and cultural values are related to the consumption of the mature or immature fruits, seeds, flowers, and to the use as decoration. The wild ancestor of C. maxima, the ssp. andreana has an actual scattered and disjointed distribution, associated with megafauna seed disperser syndrome. It was domesticated in South America around 9000–7000 years BP. The cultivar-group is a subspecific category for assembling cultivars on the basis of defined similarity. The work describes and pictures nine cultivar-groups for the species, Banana, Turban, Hubbard, Show, Buttercup, Zapallito, Plomo, Zipinka and Nugget. The molecular and a morphological join data analysis scatter biplot showed Turban and Buttercup in a central position, suggesting a first step in the domestication pathway associated with seed and immature fruit consumption; afterward, bigger bearing fruits groups were selected for their mature fruit flesh quality on one hand, and bush type, short day induction and temperate climate adaptation on the other hand. The striking domesticated Brazilian accession MAX24 intermediate between cultigens and ssp. andreana strengthens, in concordance with archeological remains, the possible domestication place of the species more easternward than previously believed.
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16
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Al-Atiyat RM, Tabbaa MJ, Barakeh FS, Awawdeh FT, Baghdadi SH. Power of phenotypes in discriminating Awassi sheep to pure strains and from other breeds. Trop Anim Health Prod 2021; 53:139. [PMID: 33495970 DOI: 10.1007/s11250-021-02578-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/15/2020] [Indexed: 11/26/2022]
Abstract
The phenotypic description is the oldest method for animal taxonomic studies. In this study, we report phenotypic traits of discriminant power to assign sheep individuals into Awassi breed or other exotic breeds found in Jordan. Twenty-two and 19 phenotype traits for ewes and rams, respectively, were utilized using multivariate and discriminant analyses. Seven traits, out of them, for ewes and five for rams were qualitative traits: body color, nose shape, horn presence, ear shape, wattles presence, udder shape, and teat placement. The other 15 traits were quantitative traits: body weight, head width, head length, chest depth, chest girth, shoulder width, withers height, foreleg height, shin circumference, body length, rump width, rump length, rump height, rear leg height, and udder height. The traits were taken on 1697 and 652 adult ewes and rams of different breeds, respectively. The breeds were predefined as Awassi and three exotic breeds: Chios, Assaf, and improved Awassi sheep. The results indicated a significant relationship of the 21 and 16 studied traits in assigning and discriminating individual's sheep into their correct breed. The analysis revealed the clustering of the three strains of Awassi sheep in Jordan as the Baladi, the Naemi, and the Saqri. The genetic distances have also confirmed the findings. However, the potential of gene flow between Awassi strains and the exotic breed was reported. The phenotypic traits with discriminant power would be utilized in a guideline for sheep taxonomy in general and for Awassi sheep in particular.
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Affiliation(s)
- Raed M Al-Atiyat
- Department of Animal Production, Faculty of Agriculture, Mutah University, Mu'tah, Jordan.
| | - Mohammad J Tabbaa
- Department of Animal Production, School of Agriculture, The University of Jordan, Amman, Jordan
| | - Faisal S Barakeh
- Small-Ruminants Investment and Graduating Household in Transition (SIGHT) project, Amman, Jordan
| | - Faisal T Awawdeh
- International Fund for Agriculture Development (IFAD), Amman, Jordan
| | - Savinaz H Baghdadi
- Management Unit of SIGHT project, Ministry of Agriculture, Amman, Jordan
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17
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Hessenauer P, Feau N, Gill U, Schwessinger B, Brar GS, Hamelin RC. Evolution and Adaptation of Forest and Crop Pathogens in the Anthropocene. PHYTOPATHOLOGY 2021; 111:49-67. [PMID: 33200962 DOI: 10.1094/phyto-08-20-0358-fi] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Anthropocene marks the era when human activity is making a significant impact on earth, its ecological and biogeographical systems. The domestication and intensification of agricultural and forest production systems have had a large impact on plant and tree health. Some pathogens benefitted from these human activities and have evolved and adapted in response to the expansion of crop and forest systems, resulting in global outbreaks. Global pathogen genomics data including population genomics and high-quality reference assemblies are crucial for understanding the evolution and adaptation of pathogens. Crops and forest trees have remarkably different characteristics, such as reproductive time and the level of domestication. They also have different production systems for disease management with more intensive management in crops than forest trees. By comparing and contrasting results from pathogen population genomic studies done on widely different agricultural and forest production systems, we can improve our understanding of pathogen evolution and adaptation to different selection pressures. We find that in spite of these differences, similar processes such as hybridization, host jumps, selection, specialization, and clonal expansion are shaping the pathogen populations in both crops and forest trees. We propose some solutions to reduce these impacts and lower the probability of global pathogen outbreaks so that we can envision better management strategies to sustain global food production as well as ecosystem services.
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Affiliation(s)
- Pauline Hessenauer
- Faculty of Forestry, Geography and Geomatics, Laval University, Quebec City, QC, G1V 0A6 Canada
| | - Nicolas Feau
- Faculty of Forestry, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Upinder Gill
- College of Agriculture, Food Systems, and Natural Resources, North Dakota State University, Fargo, ND 58102, U.S.A
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Acton, ACT 2601 Australia
| | - Gurcharn S Brar
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Richard C Hamelin
- Faculty of Forestry, Geography and Geomatics, Laval University, Quebec City, QC, G1V 0A6 Canada
- Faculty of Forestry, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
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18
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Li H, Sun H, Jiang J, Sun X, Tan L, Sun C. TAC4 controls tiller angle by regulating the endogenous auxin content and distribution in rice. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:64-73. [PMID: 32628357 PMCID: PMC7769243 DOI: 10.1111/pbi.13440] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 04/29/2020] [Accepted: 06/18/2020] [Indexed: 05/17/2023]
Abstract
Tiller angle, an important component of plant architecture, greatly influences the grain yield of rice (Oryza sativa L.). Here, we identified Tiller Angle Control 4 (TAC4) as a novel regulator of rice tiller angle. TAC4 encodes a plant-specific, highly conserved nuclear protein. The loss of TAC4 function leads to a significant increase in the tiller angle. TAC4 can regulate rice shoot gravitropism by increasing the indole acetic acid content and affecting the auxin distribution. A sequence analysis revealed that TAC4 has undergone a bottleneck and become fixed in indica cultivars during domestication and improvement. Our findings facilitate an increased understanding of the regulatory mechanisms of tiller angle and also provide a potential gene resource for the improvement of rice plant architecture.
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Affiliation(s)
- Hua Li
- State Key Laboratory of Plant Physiology and BiochemistryChina Agricultural UniversityBeijingChina
- National Center for Evaluation of Agricultural Wild Plants (Rice)Beijing Key Laboratory of Crop Genetic ImprovementLaboratory of Crop Heterosis and UtilizationMOEDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Hongying Sun
- State Key Laboratory of Plant Physiology and BiochemistryChina Agricultural UniversityBeijingChina
- National Center for Evaluation of Agricultural Wild Plants (Rice)Beijing Key Laboratory of Crop Genetic ImprovementLaboratory of Crop Heterosis and UtilizationMOEDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Jiahuang Jiang
- National Center for Evaluation of Agricultural Wild Plants (Rice)Beijing Key Laboratory of Crop Genetic ImprovementLaboratory of Crop Heterosis and UtilizationMOEDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Xianyou Sun
- National Center for Evaluation of Agricultural Wild Plants (Rice)Beijing Key Laboratory of Crop Genetic ImprovementLaboratory of Crop Heterosis and UtilizationMOEDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Lubin Tan
- National Center for Evaluation of Agricultural Wild Plants (Rice)Beijing Key Laboratory of Crop Genetic ImprovementLaboratory of Crop Heterosis and UtilizationMOEDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Chuanqing Sun
- State Key Laboratory of Plant Physiology and BiochemistryChina Agricultural UniversityBeijingChina
- National Center for Evaluation of Agricultural Wild Plants (Rice)Beijing Key Laboratory of Crop Genetic ImprovementLaboratory of Crop Heterosis and UtilizationMOEDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
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19
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Feurtey A, Guitton E, De Gracia Coquerel M, Duvaux L, Shiller J, Bellanger MN, Expert P, Sannier M, Caffier V, Giraud T, Le Cam B, Lemaire C. Threat to Asian wild apple trees posed by gene flow from domesticated apple trees and their "pestified" pathogens. Mol Ecol 2020; 29:4925-4941. [PMID: 33031644 DOI: 10.1111/mec.15677] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 11/28/2022]
Abstract
Secondary contact between crops and their wild relatives poses a threat to wild species, not only through gene flow between plants, but also through the dispersal of crop pathogens and genetic exchanges involving these pathogens, particularly those that have become more virulent by indirect selection on resistant crops, a phenomenon known as "pestification." Joint analyses of wild and domesticated hosts and their pathogens are essential to address this issue, but such analyses remain rare. We used population genetics approaches, demographic inference and pathogenicity tests on host-pathogen pairs of wild or domesticated apple trees from Central Asia and their main fungal pathogen, Venturia inaequalis, which itself has differentiated agricultural and wild-type populations. We confirmed the occurrence of gene flow from cultivated (Malus domestica) to wild (Malus sieversii) apple trees in Asian forests, potentially threatening the persistence of Asian wild apple trees. Pathogenicity tests demonstrated the pestification of V. inaequalis, the agricultural-type population being more virulent on both wild and domesticated trees. Single nucleotide polymorphism (SNP) markers and the demographic modelling of pathogen populations revealed hybridization following secondary contact between agricultural and wild-type fungal populations, and dispersal of the agricultural-type pathogen population in wild forests, increasing the threat of disease in the wild apple species. We detected an SNP potentially involved in pathogen pestification, generating an early stop codon in a gene encoding a small secreted protein in the agricultural-type fungal population. Our findings, based on joint analyses of paired host and pathogen data sets, highlight the threat posed by cultivating a crop near its centre of origin, in terms of pestified pathogen invasions in wild plant populations and introgression in the wild-type pathogen population.
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Affiliation(s)
- Alice Feurtey
- Ecologie Systématique Evolution, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France.,Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Ellen Guitton
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, Beaucouzé, France
| | | | - Ludovic Duvaux
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, Beaucouzé, France.,BIOGECO, INRAE, Université de Bordeaux, Cestas, France
| | - Jason Shiller
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, Beaucouzé, France.,Noble Research Institute, Ardmore, OK, USA
| | | | - Pascale Expert
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, Beaucouzé, France
| | - Mélanie Sannier
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, Beaucouzé, France
| | - Valérie Caffier
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, Beaucouzé, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Bruno Le Cam
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, Beaucouzé, France
| | - Christophe Lemaire
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, Beaucouzé, France
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Vilela B, Fristoe T, Tuff T, Kavanagh PH, Haynie HJ, Gray RD, Gavin MC, Botero CA. Cultural transmission and ecological opportunity jointly shaped global patterns of reliance on agriculture. EVOLUTIONARY HUMAN SCIENCES 2020; 2:e53. [PMID: 37588375 PMCID: PMC10427461 DOI: 10.1017/ehs.2020.55] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The evolution of agriculture improved food security and enabled significant increases in the size and complexity of human groups. Despite these positive effects, some societies never adopted these practices, became only partially reliant on them, or even reverted to foraging after temporarily adopting them. Given the critical importance of climate and biotic interactions for modern agriculture, it seems likely that ecological conditions could have played a major role in determining the degree to which different societies adopted farming. However, this seemingly simple proposition has been surprisingly difficult to prove and is currently controversial. Here, we investigate how recent agricultural practices relate both to contemporary ecological opportunities and the suitability of local environments for the first species domesticated by humans. Leveraging a globally distributed dataset on 1,291 traditional societies, we show that after accounting for the effects of cultural transmission and more current ecological opportunities, levels of reliance on farming continue to be predicted by the opportunities local ecologies provided to the first human domesticates even after centuries of cultural evolution. Based on the details of our models, we conclude that ecology probably helped shape the geography of agriculture by biasing both human movement and the human-assisted dispersal of domesticates.
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Affiliation(s)
- Bruno Vilela
- Department of Biology, Washington University in Saint Louis, St Louis, MO, USA
- Instituto de Biologia, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Trevor Fristoe
- Department of Biology, Washington University in Saint Louis, St Louis, MO, USA
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Ty Tuff
- Department of Biology, Washington University in Saint Louis, St Louis, MO, USA
- Department of Biology, McGill University, Quebec, Canada
| | - Patrick H. Kavanagh
- Department of Human Dimensions of Natural Resources, Colorado State University, Fort Collins, CO, USA
| | - Hannah J. Haynie
- Department of Human Dimensions of Natural Resources, Colorado State University, Fort Collins, CO, USA
- Department of Linguistics, University of Colorado at Boulder, Boulder, CO, USA
| | - Russell D. Gray
- Department of Linguistic and Cultural Evolution, Max Planck Institute for The Science of Human History, Jena, Germany
| | - Michael C. Gavin
- Department of Human Dimensions of Natural Resources, Colorado State University, Fort Collins, CO, USA
- Department of Linguistic and Cultural Evolution, Max Planck Institute for The Science of Human History, Jena, Germany
| | - Carlos A. Botero
- Department of Biology, Washington University in Saint Louis, St Louis, MO, USA
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Barrera-Redondo J, Piñero D, Eguiarte LE. Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners. Front Genet 2020; 11:742. [PMID: 32760427 PMCID: PMC7373799 DOI: 10.3389/fgene.2020.00742] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/22/2020] [Indexed: 01/07/2023] Open
Abstract
In the last decade, genomics and the related fields of transcriptomics and epigenomics have revolutionized the study of the domestication process in plants and animals, leading to new discoveries and new unresolved questions. Given that some domesticated taxa have been more studied than others, the extent of genomic data can range from vast to nonexistent, depending on the domesticated taxon of interest. This review is meant as a rough guide for students and academics that want to start a domestication research project using modern genomic tools, as well as for researchers already conducting domestication studies that are interested in following a genomic approach and looking for alternate strategies (cheaper or more efficient) and future directions. We summarize the theoretical and technical background needed to carry out domestication genomics, starting from the acquisition of a reference genome and genome assembly, to the sampling design for population genomics, paleogenomics, transcriptomics, epigenomics and experimental validation of domestication-related genes. We also describe some examples of the aforementioned approaches and the relevant discoveries they made to understand the domestication of the studied taxa.
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Affiliation(s)
| | | | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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22
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Van Tassel DL, Tesdell O, Schlautman B, Rubin MJ, DeHaan LR, Crews TE, Streit Krug A. New Food Crop Domestication in the Age of Gene Editing: Genetic, Agronomic and Cultural Change Remain Co-evolutionarily Entangled. FRONTIERS IN PLANT SCIENCE 2020; 11:789. [PMID: 32595676 PMCID: PMC7300247 DOI: 10.3389/fpls.2020.00789] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 05/18/2020] [Indexed: 05/24/2023]
Abstract
The classic domestication scenario for grains and fruits has been portrayed as the lucky fixation of major-effect "domestication genes." Characterization of these genes plus recent improvements in generating novel alleles (e.g., by gene editing) have created great interest in de novo domestication of new crops from wild species. While new gene editing technologies may accelerate some genetic aspects of domestication, we caution that de novo domestication should be understood as an iterative process rather than a singular event. Changes in human social preferences and relationships and ongoing agronomic innovation, along with broad genetic changes, may be foundational. Allele frequency changes at many loci controlling quantitative traits not normally included in the domestication syndrome may be required to achieve sufficient yield, quality, defense, and broad adaptation. The environments, practices and tools developed and maintained by farmers and researchers over generations contribute to crop yield and success, yet those may not be appropriate for new crops without a history of agronomy. New crops must compete with crops that benefit from long-standing participation in human cultural evolution; adoption of new crops may require accelerating the evolution of new crops' culinary and cultural significance, the emergence of markets and trade, and the formation and support of agricultural and scholarly institutions. We provide a practical framework that highlights and integrates these genetic, agronomic, and cultural drivers of change to conceptualize de novo domestication for communities of new crop domesticators, growers and consumers. Major gene-focused domestication may be valuable in creating allele variants that are critical to domestication but will not alone result in widespread and ongoing cultivation of new crops. Gene editing does not bypass or diminish the need for classical breeding, ethnobotanical and horticultural knowledge, local agronomy and crop protection research and extension, farmer participation, and social and cultural research and outreach. To realize the ecological and social benefits that a new era of de novo domestication could offer, we call on funding agencies, proposal reviewers and authors, and research communities to value and support these disciplines and approaches as essential to the success of the breakthroughs that are expected from gene editing techniques.
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Affiliation(s)
| | - Omar Tesdell
- Department of Geography, Birzeit University, Birzeit, Palestine
| | | | - Matthew J. Rubin
- Donald Danforth Plant Science Center, St. Louis, MO, United States
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Ahmad HI, Ahmad MJ, Jabbir F, Ahmar S, Ahmad N, Elokil AA, Chen J. The Domestication Makeup: Evolution, Survival, and Challenges. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Hlongwane NL, Hadebe K, Soma P, Dzomba EF, Muchadeyi FC. Genome Wide Assessment of Genetic Variation and Population Distinctiveness of the Pig Family in South Africa. Front Genet 2020; 11:344. [PMID: 32457791 PMCID: PMC7221027 DOI: 10.3389/fgene.2020.00344] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 03/23/2020] [Indexed: 12/12/2022] Open
Abstract
Genetic diversity is of great importance and a prerequisite for genetic improvement and conservation programs in pigs and other livestock populations. The present study provides a genome wide analysis of the genetic variability and population structure of pig populations from different production systems in South Africa relative to global populations. A total of 234 pigs sampled in South Africa and consisting of village (n = 91), commercial (n = 60), indigenous (n = 40), Asian (n = 5) and wild (n = 38) populations were genotyped using Porcine SNP60K BeadChip. In addition, 389 genotypes representing village and commercial pigs from America, Europe, and Asia were accessed from a previous study and used to compare population clustering and relationships of South African pigs with global populations. Moderate heterozygosity levels, ranging from 0.204 for Warthogs to 0.371 for village pigs sampled from Capricorn municipality in Eastern Cape province of South Africa were observed. Principal Component Analysis of the South African pigs resulted in four distinct clusters of (i) Duroc; (ii) Vietnamese; (iii) Bush pig and Warthog and (iv) a cluster with the rest of the commercial (SA Large White and Landrace), village, Wild Boar and indigenous breeds of Koelbroek and Windsnyer. The clustering demonstrated alignment with genetic similarities, geographic location and production systems. The PCA with the global populations also resulted in four clusters that where populated with (i) all the village populations, wild boars, SA indigenous and the large white and landraces; (ii) Durocs (iii) Chinese and Vietnamese pigs and (iv) Warthog and Bush pig. K = 10 (The number of population units) was the most probable ADMIXTURE based clustering, which grouped animals according to their populations with the exception of the village pigs that showed presence of admixture. AMOVA reported 19.92%-98.62% of the genetic variation to be within populations. Sub structuring was observed between South African commercial populations as well as between Indigenous and commercial breeds. Population pairwise F ST analysis showed genetic differentiation (P ≤ 0.05) between the village, commercial and wild populations. A per marker per population pairwise F ST analysis revealed SNPs associated with QTLs for traits such as meat quality, cytoskeletal and muscle development, glucose metabolism processes and growth factors between both domestic populations as well as between wild and domestic breeds. Overall, the study provided a baseline understanding of porcine diversity and an important foundation for porcine genomics of South African populations.
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Affiliation(s)
- Nompilo Lucia Hlongwane
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Pietermartizburg, South Africa
| | - Khanyisile Hadebe
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
| | - Pranisha Soma
- Animal Production Institute, Agricultural Research Council, Irene, South Africa
| | - Edgar Farai Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Pietermartizburg, South Africa
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Lee HY, Ro NY, Patil A, Lee JH, Kwon JK, Kang BC. Uncovering Candidate Genes Controlling Major Fruit-Related Traits in Pepper via Genotype-by-Sequencing Based QTL Mapping and Genome-Wide Association Study. FRONTIERS IN PLANT SCIENCE 2020; 11:1100. [PMID: 32793261 PMCID: PMC7390901 DOI: 10.3389/fpls.2020.01100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 07/03/2020] [Indexed: 05/09/2023]
Abstract
All modern pepper accessions are products of the domestication of wild Capsicum species. However, due to the limited availability of genome-wide association study (GWAS) data and selection signatures for various traits, domestication-related genes have not been identified in pepper. Here, to address this problem, we obtained data for major fruit-related domestication traits (fruit length, width, weight, pericarp thickness, and fruit position) using a highly diverse panel of 351 pepper accessions representing the worldwide Capsicum germplasm. Using a genotype-by-sequencing (GBS) method, we developed 187,966 genome-wide high-quality SNP markers across 230 C. annuum accessions. Linkage disequilibrium (LD) analysis revealed that the average length of the LD blocks was 149 kb. Using GWAS, we identified 111 genes that were linked to 64 significant LD blocks. We cross-validated the GWAS results using 17 fruit-related QTLs and identified 16 causal genes thought to be associated with fruit morphology-related domestication traits, with molecular functions such as cell division and expansion. The significant LD blocks and candidate genes identified in this study provide unique molecular footprints for deciphering the domestication history of Capsicum. Further functional validation of these candidate genes should accelerate the cloning of genes for major fruit-related traits in pepper.
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Affiliation(s)
- Hea-Young Lee
- Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Na-Young Ro
- National Academy of Agricultural Science, National Agrobiodiversity Center, Rural Development Administration, Jeonju, South Korea
| | - Abhinandan Patil
- Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Joung-Ho Lee
- Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jin-Kyung Kwon
- Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- *Correspondence: Byoung-Cheorl Kang,
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Lauri PÉ. Corner's rules as a framework for plant morphology, architecture and functioning - issues and steps forward. THE NEW PHYTOLOGIST 2019; 221:1679-1684. [PMID: 30276821 DOI: 10.1111/nph.15503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 09/24/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Pierre-Éric Lauri
- SYSTEM, Univ Montpellier, INRA, Cirad, Montpellier SupAgro, CIHEAM-IAMM, 2 Place Pierre Viala, Montpellier, 34060, France
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Dong Z, Alexander M, Chuck G. Understanding Grass Domestication through Maize Mutants. Trends Genet 2019; 35:118-128. [DOI: 10.1016/j.tig.2018.10.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/17/2018] [Accepted: 10/29/2018] [Indexed: 11/28/2022]
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Zhao Y, Song Z, Zhong L, Li Q, Chen J, Rong J. Inferring the Origin of Cultivated Zizania latifolia, an Aquatic Vegetable of a Plant-Fungus Complex in the Yangtze River Basin. FRONTIERS IN PLANT SCIENCE 2019; 10:1406. [PMID: 31787995 PMCID: PMC6856052 DOI: 10.3389/fpls.2019.01406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/10/2019] [Indexed: 05/10/2023]
Abstract
Crop domestication is one of the essential topics in evolutionary biology. Cultivated Zizania latifolia, domesticated as the special form of a plant-fungus (the host Zizania latifolia and the endophyte Ustilago esculenta) complex, is a popular aquatic vegetable endemic in East Asia. The rapid domestication of cultivated Z. latifolia can be traced in the historical literature but still need more evidence. This study focused on deciphering the genetic relationship between wild and cultivated Z. latifolia, as well as the corresponding parasitic U. esculenta. Twelve microsatellites markers were used to study the genetic variations of 32 wild populations and 135 landraces of Z. latifolia. Model simulations based on approximate Bayesian computation (ABC) were then performed to hierarchically infer the population history. We also analyzed the ITS sequences of the smut fungus U. esculenta to reveal its genetic structure. Our results indicated a significant genetic divergence between cultivated Z. latifolia and its wild ancestors. The wild Z. latifolia populations showed significant hierarchical genetic subdivisions, which may be attributed to the joint effect of isolation by distance and hydrological unconnectedness between watersheds. Cultivated Z. latifolia was supposedly domesticated once in the low reaches of the Yangtze River. The genetic structure of U. esculenta also indicated a single domestication event, and the genetic variations in this fungus might be associated with the diversification of cultivars. These findings provided molecular evidence in accordance with the historical literature that addressed the domestication of cultivated Z. latifolia involved adaptive evolution driven by artificial selection in both the plant and fungus.
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Affiliation(s)
- Yao Zhao
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Zhiping Song
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Lan Zhong
- Institute of Vegetable, Wuhan Academy of Agriculture Science and Technology, Wuhan, China
| | - Qin Li
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Jiakuan Chen
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Jun Rong
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
- *Correspondence: Jun Rong,
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Winkel T, Aguirre MG, Arizio CM, Aschero CA, Babot MDP, Benoit L, Burgarella C, Costa-Tártara S, Dubois MP, Gay L, Hocsman S, Jullien M, López-Campeny SML, Manifesto MM, Navascués M, Oliszewski N, Pintar E, Zenboudji S, Bertero HD, Joffre R. Discontinuities in quinoa biodiversity in the dry Andes: An 18-century perspective based on allelic genotyping. PLoS One 2018; 13:e0207519. [PMID: 30517116 PMCID: PMC6281180 DOI: 10.1371/journal.pone.0207519] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 10/30/2018] [Indexed: 11/18/2022] Open
Abstract
History and environment shape crop biodiversity, particularly in areas with vulnerable human communities and ecosystems. Tracing crop biodiversity over time helps understand how rural societies cope with anthropogenic or climatic changes. Exceptionally well preserved ancient DNA of quinoa (Chenopodium quinoa Willd.) from the cold and arid Andes of Argentina has allowed us to track changes and continuities in quinoa diversity over 18 centuries, by coupling genotyping of 157 ancient and modern seeds by 24 SSR markers with cluster and coalescence analyses. Cluster analyses revealed clear population patterns separating modern and ancient quinoas. Coalescence-based analyses revealed that genetic drift within a single population cannot explain genetic differentiation among ancient and modern quinoas. The hypothesis of a genetic bottleneck related to the Spanish Conquest also does not seem to apply at a local scale. Instead, the most likely scenario is the replacement of preexisting quinoa gene pools with new ones of lower genetic diversity. This process occurred at least twice in the last 18 centuries: first, between the 6th and 12th centuries—a time of agricultural intensification well before the Inka and Spanish conquests—and then between the 13th century and today—a period marked by farming marginalization in the late 19th century likely due to a severe multidecadal drought. While these processes of local gene pool replacement do not imply losses of genetic diversity at the metapopulation scale, they support the view that gene pool replacement linked to social and environmental changes can result from opposite agricultural trajectories.
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Affiliation(s)
- Thierry Winkel
- Centre d'Écologie Fonctionnelle et Évolutive CEFE, Institut de Recherche pour le Développement IRD, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier UPVM3, École Pratique des Hautes Études EPHE, Montpellier, France
- * E-mail:
| | - María Gabriela Aguirre
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán (FCN e IML, UNT), San Miguel de Tucumán, Argentina
| | | | - Carlos Alberto Aschero
- Instituto Superior de Estudios Sociales, Consejo Nacional de Investigaciones Científicas y Técnicas (ISES, CONICET), San Miguel de Tucumán, Argentina
- Instituto de Arqueología y Museo, Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán (IAM, FCN e IML, UNT), San Miguel de Tucumán, Argentina
| | - María del Pilar Babot
- Instituto Superior de Estudios Sociales, Consejo Nacional de Investigaciones Científicas y Técnicas (ISES, CONICET), San Miguel de Tucumán, Argentina
- Instituto de Arqueología y Museo, Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán (IAM, FCN e IML, UNT), San Miguel de Tucumán, Argentina
| | - Laure Benoit
- Centre d'Écologie Fonctionnelle et Évolutive CEFE, CNRS, Université de Montpellier, UPVM3, EPHE, IRD, Montpellier, France
| | - Concetta Burgarella
- UMR AGAP Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, CIRAD, INRA, SupAgro, Montpellier, France
| | - Sabrina Costa-Tártara
- Departamento de Tecnología, Universidad Nacional de Luján, Luján, Buenos Aires, Argentina
| | - Marie-Pierre Dubois
- Centre d'Écologie Fonctionnelle et Évolutive CEFE, CNRS, Université de Montpellier, UPVM3, EPHE, IRD, Montpellier, France
| | - Laurène Gay
- UMR AGAP Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, CIRAD, INRA, SupAgro, Montpellier, France
| | - Salomón Hocsman
- Instituto Superior de Estudios Sociales, Consejo Nacional de Investigaciones Científicas y Técnicas (ISES, CONICET), San Miguel de Tucumán, Argentina
- Instituto de Arqueología y Museo, Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán (IAM, FCN e IML, UNT), San Miguel de Tucumán, Argentina
| | - Margaux Jullien
- UMR AGAP Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, INRA, CIRAD, SupAgro, Montpellier, France
| | - Sara María Luisa López-Campeny
- Instituto Superior de Estudios Sociales, Consejo Nacional de Investigaciones Científicas y Técnicas (ISES, CONICET), San Miguel de Tucumán, Argentina
- Instituto de Arqueología y Museo, Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán (IAM, FCN e IML, UNT), San Miguel de Tucumán, Argentina
| | | | - Miguel Navascués
- Centre de Biologie pour la Gestion des Populations CBGP, INRA, IRD, CIRAD, SupAgro, Montpellier, France
- Institut de Biologie Computationnelle IBC, Montpellier, France
| | - Nurit Oliszewski
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán (FCN e IML, UNT), San Miguel de Tucumán, Argentina
- Instituto Superior de Estudios Sociales, Consejo Nacional de Investigaciones Científicas y Técnicas (ISES, CONICET), San Miguel de Tucumán, Argentina
| | - Elizabeth Pintar
- Social Sciences Division, Austin Community College, Austin, Texas, United States of Amrica
| | - Saliha Zenboudji
- Centre d'Écologie Fonctionnelle et Évolutive CEFE, CNRS, Université de Montpellier, UPVM3, EPHE, IRD, Montpellier, France
| | - Héctor Daniel Bertero
- Cátedra de Producción Vegetal, Facultad de Agronomía, Universidad de Buenos Aires, and IFEVA-CONICET, Buenos Aires, Argentina
| | - Richard Joffre
- Centre d'Écologie Fonctionnelle et Évolutive CEFE, CNRS, Université de Montpellier, UPVM3, EPHE, IRD, Montpellier, France
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Stitzer MC, Ross-Ibarra J. Maize domestication and gene interaction. THE NEW PHYTOLOGIST 2018; 220:395-408. [PMID: 30035321 DOI: 10.1111/nph.15350] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/05/2018] [Indexed: 05/24/2023]
Abstract
Contents Summary 395 I. Introduction 395 II. The genetic basis of maize domestication 396 III. The tempo of maize domestication 401 IV. Genetic interactions and selection during maize domestication 401 V. Gene networks of maize domestication alleles 404 VI. Implications of gene interactions on evolution and selection404 VII. Conclusions 405 Acknowledgements 405 References 405 SUMMARY: Domestication is a tractable system for following evolutionary change. Under domestication, wild populations respond to shifting selective pressures, resulting in adaptation to the new ecological niche of cultivation. Owing to the important role of domesticated crops in human nutrition and agriculture, the ancestry and selection pressures transforming a wild plant into a domesticate have been extensively studied. In Zea mays, morphological, genetic and genomic studies have elucidated how a wild plant, the teosinte Z. mays subsp. parviglumis, was transformed into the domesticate Z. mays subsp. mays. Five major morphological differences distinguish these two subspecies, and careful genetic dissection has pinpointed the molecular changes responsible for several of these traits. But maize domestication was a consequence of more than just five genes, and regions throughout the genome contribute. The impacts of these additional regions are contingent on genetic background, both the interactions between alleles of a single gene and among alleles of the multiple genes that modulate phenotypes. Key genetic interactions include dominance relationships, epistatic interactions and pleiotropic constraint, including how these variants are connected in gene networks. Here, we review the role of gene interactions in generating the dramatic phenotypic evolution seen in the transition from teosinte to maize.
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Affiliation(s)
- Michelle C Stitzer
- Department of Plant Sciences, University of California, Davis, Davis, CA, 95616, USA
- Center for Population Biology, University of California, Davis, Davis, CA, 95616, USA
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, University of California, Davis, Davis, CA, 95616, USA
- Center for Population Biology, University of California, Davis, Davis, CA, 95616, USA
- Genome Center, University of California, Davis, Davis, CA, 95616, USA
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Over a Thousand Years of Evolutionary History of Domestic Geese from Russian Archaeological Sites, Analysed Using Ancient DNA. Genes (Basel) 2018; 9:genes9070367. [PMID: 30037043 PMCID: PMC6070935 DOI: 10.3390/genes9070367] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 07/16/2018] [Accepted: 07/16/2018] [Indexed: 12/14/2022] Open
Abstract
The European domestic goose is a widely farmed species known to have descended from the wild greylag goose (Anser anser). However, the evolutionary history of this domesticate is still poorly known. Ancient DNA studies have been useful for many species, but there has been little such work on geese. We have studied temporal genetic variation among domestic goose specimens excavated from Russian archaeological sites (4th–18th centuries) using a 204 base pair fragment of the mitochondrial control region. Specimens fell into three different genetic clades: the domestic D-haplogroup, the F-haplogroup that includes both wild and domestic geese, and a clade comprising another species, the taiga bean goose. Most of the subfossil geese carried typical domestic D-haplotypes. The domestication status of the geese carrying F-haplotypes is less certain, as the haplotypes identified were not present among modern domestic geese and could represent wild geese (misclassified as domestics), introgression from wild geese, or local domestication events. The bones of taiga bean goose were most probably misidentified as domestic goose but the domestication of bean goose or hybridization with domestic goose is also possible. Samples from the 4th to 10th century were clearly differentiated from the later time periods due to a haplotype that was found only in this early period, but otherwise no temporal or geographical variation in haplotype frequencies was apparent.
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Pramod RK, Velayutham D, P K S, P S B, Zachariah A, Zachariah A, B C, S S S, P G, Dhinoth Kumar B, Iype S, Gupta R, Santhosh S, Thomas G. Complete mitogenome reveals genetic divergence and phylogenetic relationships among Indian cattle ( Bos indicus) breeds. Anim Biotechnol 2018; 30:219-232. [PMID: 29938580 DOI: 10.1080/10495398.2018.1476376] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Indigenous cattle of India belong to the species, Bos indicus and they possess various adaptability and production traits. However, little is known about the genetic diversity and origin of these breeds. To investigate the status, we sequenced and analyzed the whole mitochondrial DNA (mtDNA) of seven Indian cattle breeds. In total, 49 single-nucleotide variants (SNVs) were identified among the seven breeds analyzed. We observed a common synonymous SNV in the COII gene (m.7583G > A) of all the breeds studied. The phylogenetic analysis and genetic distance estimation showed the close genetic relationship among the Indian cattle breeds, whereas distinct genetic differences were observed between Bos indicus and Bos taurus cattle. Our results indicate a common ancestor for European Zwergzebu breed and South Indian cattle. The estimated divergence time demonstrated that the Bos indicus and Bos taurus cattle lineages diverged 0.92 million years ago. Our study also demonstrates that ancestors of present zebu breeds originated in South and North India separately ∼30,000 to 20,000 years ago. In conclusion, the identified genetic variants and results of the phylogenetic analysis may provide baseline information to develop appropriate strategies for management and conservation of Indian cattle breeds.
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Affiliation(s)
| | | | - Sajesh P K
- a AgriGenome Labs Pvt. Ltd., Smart City Kochi , India
| | - Beena P S
- a AgriGenome Labs Pvt. Ltd., Smart City Kochi , India
| | | | - Arun Zachariah
- c Department of Forest and Wildlife , Wayanad , Kerala , India
| | - Chandramohan B
- d National Institute of Science Education and Research , Jatni , India
| | - Sujith S S
- a AgriGenome Labs Pvt. Ltd., Smart City Kochi , India
| | - Ganapathi P
- e Bargur Cattle Research Station, Tamil Nadu Veterinary Animal Sciences University , Chennai , India
| | | | | | - Ravi Gupta
- f Medgenome Labs Pvt. Ltd. , Narayana Health City , Bommasandra , Bengaluru , India
| | - Sam Santhosh
- g SciGenom Research Foundation , Cheruthuruthy , India
| | - George Thomas
- g SciGenom Research Foundation , Cheruthuruthy , India
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Abstract
In this article, we attempt to integrate recent advances in our understanding of the relations between culture and genes into an emerging field—cultural genomics—and discuss its promises and theoretical and methodological challenges. We first provide a brief review of previous conceptualizations about the relations between culture and genes and then argue that recent advances in molecular evolution research has allowed us to reframe the discussion away from parallel genetic and cultural evolution to focus on the interactions between the two. After outlining the key issues involved in cultural genomics (unit of analysis, timescale, mechanisms, and direction of influence), we provide examples of research for the different levels of interactions between culture and genes. We then discuss ideological, theoretical, and methodological challenges in cultural genomics and propose tentative solutions.
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Convergent genomic signatures of domestication in sheep and goats. Nat Commun 2018; 9:813. [PMID: 29511174 PMCID: PMC5840369 DOI: 10.1038/s41467-018-03206-y] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/29/2018] [Indexed: 12/15/2022] Open
Abstract
The evolutionary basis of domestication has been a longstanding question and its genetic architecture is becoming more tractable as more domestic species become genome-enabled. Before becoming established worldwide, sheep and goats were domesticated in the fertile crescent 10,500 years before present (YBP) where their wild relatives remain. Here we sequence the genomes of wild Asiatic mouflon and Bezoar ibex in the sheep and goat domestication center and compare their genomes with that of domestics from local, traditional, and improved breeds. Among the genomic regions carrying selective sweeps differentiating domestic breeds from wild populations, which are associated among others to genes involved in nervous system, immunity and productivity traits, 20 are common to Capra and Ovis. The patterns of selection vary between species, suggesting that while common targets of selection related to domestication and improvement exist, different solutions have arisen to achieve similar phenotypic end-points within these closely related livestock species. The sheep and goat were domesticated ~10,500 years ago in the same region of the Middle-East. Here, Alberto et al compare the genomes of wild Asiatic mouflon and Bezoar ibex with that of domestics from local, traditional and improved breeds and find common targets of selection related to domestication and improvement in sheep and goats.
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Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds. Nat Commun 2018; 9:859. [PMID: 29491421 PMCID: PMC5830443 DOI: 10.1038/s41467-017-02809-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 12/03/2017] [Indexed: 12/30/2022] Open
Abstract
Domestication fundamentally reshaped animal morphology, physiology and behaviour, offering the opportunity to investigate the molecular processes driving evolutionary change. Here we assess sheep domestication and artificial selection by comparing genome sequence from 43 modern breeds (Ovis aries) and their Asian mouflon ancestor (O. orientalis) to identify selection sweeps. Next, we provide a comparative functional annotation of the sheep genome, validated using experimental ChIP-Seq of sheep tissue. Using these annotations, we evaluate the impact of selection and domestication on regulatory sequences and find that sweeps are significantly enriched for protein coding genes, proximal regulatory elements of genes and genome features associated with active transcription. Finally, we find individual sites displaying strong allele frequency divergence are enriched for the same regulatory features. Our data demonstrate that remodelling of gene expression is likely to have been one of the evolutionary forces that drove phenotypic diversification of this common livestock species. The domestication of plants and animals causes genomic changes underlying various morphologic, physiologic and behavioral changes. Here, Naval-Sanchez et al. provide a ChIP-Seq validated comparative functional annotation of the sheep genome, and show widespread evolution of proximal regulatory elements.
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Manin A, Corona-M E, Alexander M, Craig A, Thornton EK, Yang DY, Richards M, Speller CF. Diversity of management strategies in Mesoamerican turkeys: archaeological, isotopic and genetic evidence. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171613. [PMID: 29410864 PMCID: PMC5792941 DOI: 10.1098/rsos.171613] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/06/2017] [Indexed: 06/08/2023]
Abstract
The turkey (Meleagris gallopavo) represents one of the few domestic animals of the New World. While current research points to distinct domestication centres in the Southwest USA and Mesoamerica, several questions regarding the number of progenitor populations, and the timing and intensity of turkey husbandry remain unanswered. This study applied ancient mitochondrial DNA and stable isotope (δ13C, δ15N) analysis to 55 archaeological turkey remains from Mexico to investigate pre-contact turkey exploitation in Mesoamerica. Three different (sub)species of turkeys were identified in the archaeological record (M. g. mexicana, M. g. gallopavo and M. ocellata), indicating the exploitation of diverse local populations, as well as the trade of captively reared birds into the Maya area. No evidence of shared maternal haplotypes was observed between Mesoamerica and the Southwest USA, in contrast with archaeological evidence for trade of other domestic products. Isotopic analysis indicates a range of feeding behaviours in ancient Mesoamerican turkeys, including wild foraging, human provisioning and mixed feeding ecologies. This variability in turkey diet decreases through time, with archaeological, genetic and isotopic evidence all pointing to the intensification of domestic turkey management and husbandry, culminating in the Postclassic period.
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Affiliation(s)
- Aurelie Manin
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Eduardo Corona-M
- Centro INAH Morelos, Instituto Nacional de Antropología e Historia, Mexico
| | | | - Abigail Craig
- BioArCh, Department of Archaeology, University of York, York, UK
| | | | - Dongya Y. Yang
- Ancient DNA laboratory, Department of Archaeology, Simon Fraser University, Burnaby, BC, Canada
| | - Michael Richards
- Department of Archaeology, Simon Fraser University, Burnaby, BC, Canada
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Louwaars NP. Plant breeding and diversity: A troubled relationship? EUPHYTICA: NETHERLANDS JOURNAL OF PLANT BREEDING 2018; 214:114. [PMID: 30996394 PMCID: PMC6434984 DOI: 10.1007/s10681-018-2192-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 05/30/2018] [Indexed: 05/11/2023]
Abstract
Plant breeding collects, induces and rearranges genetic diversity followed by selection. Breeding may contribute to diversity in farmers' fields or significantly reduce it. History has numerous examples of both. The diversity of many crops have gone through domestication, dispersal and modernization bottlenecks. Between these major decreasing processes, diversity has picked up through different evolutionary processes, and plant breeding affected by policies. Major negative effects of plant breeding on diversity have been recorded following the modernization bottleneck, but alternative breeding strategies have come up as well, both in the formal system and in the interphase between formal and farmers' seed systems. Multiline breeding and participatory plant breeding are introduced as examples to also analyse effects of current developments in technology and policy. This paper intends to shed some light on the questions: how will current developments in technology and policy affect crop genetic diversity? Are we heading for a new bottleneck-either a molecular or a policy bottleneck, or a combination of both? Or could the future become more diverse? We look at the relationship between breeding, policies, and crop genetic diversity in farming systems with a birds-eye view. Notably because of current policy trends we warn for a new diversity bottleneck.
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Affiliation(s)
- Niels P. Louwaars
- Plantum, Netherlands Association for Plant Reproductive Materials, Gouda, The Netherlands
- Department of Law and Governance, Wageningen University, Wageningen, The Netherlands
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Thomas J, Kirby S. Self domestication and the evolution of language. BIOLOGY & PHILOSOPHY 2018; 33:9. [PMID: 29606782 PMCID: PMC5871649 DOI: 10.1007/s10539-018-9612-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 03/13/2018] [Indexed: 05/09/2023]
Abstract
We set out an account of how self-domestication plays a crucial role in the evolution of language. In doing so, we focus on the growing body of work that treats language structure as emerging from the process of cultural transmission. We argue that a full recognition of the importance of cultural transmission fundamentally changes the kind of questions we should be asking regarding the biological basis of language structure. If we think of language structure as reflecting an accumulated set of changes in our genome, then we might ask something like, "What are the genetic bases of language structure and why were they selected?" However, if cultural evolution can account for language structure, then this question no longer applies. Instead, we face the task of accounting for the origin of the traits that enabled that process of structure-creating cultural evolution to get started in the first place. In light of work on cultural evolution, then, the new question for biological evolution becomes, "How did those precursor traits evolve?" We identify two key precursor traits: (1) the transmission of the communication system through learning; and (2) the ability to infer the communicative intent associated with a signal or action. We then describe two comparative case studies-the Bengalese finch and the domestic dog-in which parallel traits can be seen emerging following domestication. Finally, we turn to the role of domestication in human evolution. We argue that the cultural evolution of language structure has its origin in an earlier process of self-domestication.
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Affiliation(s)
- James Thomas
- Centre for Language Evolution, University of Edinburgh, 3 Charles Street, Edinburgh, EH8 9AD UK
| | - Simon Kirby
- Centre for Language Evolution, University of Edinburgh, 3 Charles Street, Edinburgh, EH8 9AD UK
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Roucou A, Violle C, Fort F, Roumet P, Ecarnot M, Vile D. Shifts in plant functional strategies over the course of wheat domestication. J Appl Ecol 2017. [DOI: 10.1111/1365-2664.13029] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Agathe Roucou
- CEFE; CNRS; Univ. Montpellier; Univ Paul Valéry Montpellier 3; EPHE, IRD; Montpellier France
- LEPSE; Univ Montpellier; INRA; SupAgro Montpellier; Montpellier France
| | - Cyrille Violle
- CEFE; CNRS; Univ. Montpellier; Univ Paul Valéry Montpellier 3; EPHE, IRD; Montpellier France
| | - Florian Fort
- CEFE; Montpellier SupAgro; CNRS; Univ. Montpellier; Univ Paul Valéry Montpellier 3; EPHE, IRD; Montpellier France
| | - Pierre Roumet
- AGAP; Univ Montpellier; CIRAD; INRA; Montpellier SupAgro; Montpellier France
| | - Martin Ecarnot
- AGAP; Univ Montpellier; CIRAD; INRA; Montpellier SupAgro; Montpellier France
| | - Denis Vile
- LEPSE; Univ Montpellier; INRA; SupAgro Montpellier; Montpellier France
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Grossen C, Biebach I, Angelone-Alasaad S, Keller LF, Croll D. Population genomics analyses of European ibex species show lower diversity and higher inbreeding in reintroduced populations. Evol Appl 2017; 11:123-139. [PMID: 29387150 PMCID: PMC5775499 DOI: 10.1111/eva.12490] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 04/04/2017] [Indexed: 12/30/2022] Open
Abstract
Restoration of lost species ranges to their native distribution is key for the survival of endangered species. However, reintroductions often fail and long‐term genetic consequences are poorly understood. Alpine ibex (Capra ibex) are wild goats that recovered from <100 individuals to ~50,000 within a century by population reintroductions. We analyzed the population genomic consequences of the Alpine ibex reintroduction strategy. We genotyped 101,822 genomewide single nucleotide polymorphism loci in 173 Alpine ibex, the closely related Iberian ibex (Capra pyrenaica) and domestic goat (Capra hircus). The source population of all Alpine ibex maintained genetic diversity comparable to Iberian ibex, which experienced less severe bottlenecks. All reintroduced Alpine ibex populations had individually and combined lower levels of genetic diversity than the source population. The reintroduction strategy consisted of primary reintroductions from captive breeding and secondary reintroductions from established populations. This stepwise reintroduction strategy left a strong genomic footprint of population differentiation, which increased with subsequent rounds of reintroductions. Furthermore, analyses of genomewide runs of homozygosity showed recent inbreeding primarily in individuals of reintroduced populations. We showed that despite the rapid census recovery, Alpine ibex carry a persistent genomic signature of their reintroduction history. We discuss how genomic monitoring can serve as an early indicator of inbreeding.
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Affiliation(s)
- Christine Grossen
- Department of Evolutionary Biology and Environmental Studies University of Zürich Zürich Switzerland
| | - Iris Biebach
- Department of Evolutionary Biology and Environmental Studies University of Zürich Zürich Switzerland
| | - Samer Angelone-Alasaad
- Department of Evolutionary Biology and Environmental Studies University of Zürich Zürich Switzerland
| | - Lukas F Keller
- Department of Evolutionary Biology and Environmental Studies University of Zürich Zürich Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics Institute of Biology University of Neuchâtel Neuchâtel Switzerland
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Abstract
Archaeology is a field of research that relies largely on the remains of past humans and nonhuman animals and the traces of their interactions within a range of material conditions. In archaeology, as in sociocultural anthropology, the dominant analytical perspective on human–animal relations is ontologically anthropocentric: the study of the human use of nonhuman animals for the benefit of human beings, and scholarly inquiry that is largely for the sake of elucidating what nonhuman animals can tell us about the human condition. This review outlines the historical trajectory of Anglo-American archaeology's encounters with animal remains, and human–animal interactions, within this framework and considers recent attempts to move beyond anthropocentrism.
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Affiliation(s)
- Brian Boyd
- Department of Anthropology, Columbia University, New York, NY 10027
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Theofanopoulou C, Gastaldon S, O’Rourke T, Samuels BD, Messner A, Martins PT, Delogu F, Alamri S, Boeckx C. Self-domestication in Homo sapiens: Insights from comparative genomics. PLoS One 2017; 12:e0185306. [PMID: 29045412 PMCID: PMC5646786 DOI: 10.1371/journal.pone.0185306] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/11/2017] [Indexed: 02/07/2023] Open
Abstract
This study identifies and analyzes statistically significant overlaps between selective sweep screens in anatomically modern humans and several domesticated species. The results obtained suggest that (paleo-)genomic data can be exploited to complement the fossil record and support the idea of self-domestication in Homo sapiens, a process that likely intensified as our species populated its niche. Our analysis lends support to attempts to capture the "domestication syndrome" in terms of alterations to certain signaling pathways and cell lineages, such as the neural crest.
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Affiliation(s)
- Constantina Theofanopoulou
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
- Universitat de Barcelona Institute for Complex Systems, Barcelona, Spain
| | - Simone Gastaldon
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
- School of Psychology, University of Padova, Padova, Italy
| | - Thomas O’Rourke
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
| | - Bridget D. Samuels
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, United States of America
| | - Angela Messner
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
| | | | - Francesco Delogu
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Saleh Alamri
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
| | - Cedric Boeckx
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
- Universitat de Barcelona Institute for Complex Systems, Barcelona, Spain
- ICREA, Barcelona, Spain
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Abstract
One of the challenges in evaluating arguments for extending the conceptual framework of evolutionary biology involves the identification of a tractable model system that allows for an assessment of the core assumptions of the extended evolutionary synthesis (EES). The domestication of plants and animals by humans provides one such case study opportunity. Here, I consider domestication as a model system for exploring major tenets of the EES. First I discuss the novel insights that niche construction theory (NCT, one of the pillars of the EES) provides into the domestication processes, particularly as they relate to five key areas: coevolution, evolvability, ecological inheritance, cooperation and the pace of evolutionary change. This discussion is next used to frame testable predictions about initial domestication of plants and animals that contrast with those grounded in standard evolutionary theory, demonstrating how these predictions might be tested in multiple regions where initial domestication took place. I then turn to a broader consideration of how domestication provides a model case study consideration of the different ways in which the core assumptions of the EES strengthen and expand our understanding of evolution, including reciprocal causation, developmental processes as drivers of evolutionary change, inclusive inheritance, and the tempo and rate of evolutionary change.
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Affiliation(s)
- Melinda A. Zeder
- Program in Human Ecology and Archaeobiology, Department of Anthropology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution, Washington, DC 20560, USA
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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Livestock Animal Displacement on Rural Tourism Destinations: Placing Livestock's “Pest” Role in the Background. SUSTAINABILITY 2017. [DOI: 10.3390/su9081307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Kemp BM, Judd K, Monroe C, Eerkens JW, Hilldorfer L, Cordray C, Schad R, Reams E, Ortman SG, Kohler TA. Prehistoric mitochondrial DNA of domesticate animals supports a 13th century exodus from the northern US southwest. PLoS One 2017; 12:e0178882. [PMID: 28746407 PMCID: PMC5528258 DOI: 10.1371/journal.pone.0178882] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/19/2017] [Indexed: 01/24/2023] Open
Abstract
The 13th century Puebloan depopulation of the Four Corners region of the US Southwest is an iconic episode in world prehistory. Studies of its causes, as well as its consequences, have a bearing not only on archaeological method and theory, but also social responses to climate change, the sociology of social movements, and contemporary patterns of cultural diversity. Previous research has debated the demographic scale, destinations, and impacts of Four Corners migrants. Much of this uncertainty stems from the substantial differences in material culture between the Four Corners vs. hypothesized destination areas. Comparable biological evidence has been difficult to obtain due to the complete departure of farmers from the Four Corners in the 13th century CE and restrictions on sampling human remains. As an alternative, patterns of genetic variation among domesticated species were used to address the role of migration in this collapse. We collected mitochondrial haplotypic data from dog (Canis lupus familiaris) and turkey (Meleagris gallopavo) remains from archaeological sites in the most densely-populated portion of the Four Corners region, and the most commonly proposed destination area for that population under migration scenarios. Results are consistent with a large-scale migration of humans, accompanied by their domestic turkeys, during the 13th century CE. These results support scenarios that suggest contemporary Pueblo peoples of the Northern Rio Grande are biological and cultural descendants of Four Corners populations.
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Affiliation(s)
- Brian M. Kemp
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Kathleen Judd
- Laboratory of Molecular Anthropology and Ancient DNA, Washington State University, Pullman, Washington, United States of America
| | - Cara Monroe
- Department of Anthropology, Washington State University, Pullman, Washington, United States of America
| | - Jelmer W. Eerkens
- Department of Anthropology, University of California, Davis, California, United States of America
| | - Lindsay Hilldorfer
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Connor Cordray
- Laboratory of Molecular Anthropology and Ancient DNA, Washington State University, Pullman, Washington, United States of America
| | - Rebecca Schad
- Laboratory of Molecular Anthropology and Ancient DNA, Washington State University, Pullman, Washington, United States of America
| | - Erin Reams
- Laboratory of Molecular Anthropology and Ancient DNA, Washington State University, Pullman, Washington, United States of America
| | - Scott G. Ortman
- Department of Anthropology, University of Colorado, Boulder, Colorado, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Crow Canyon Archaeological Center, Cortez, Colorado, United States of America
| | - Timothy A. Kohler
- Department of Anthropology, Washington State University, Pullman, Washington, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Crow Canyon Archaeological Center, Cortez, Colorado, United States of America
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The Evolutionary Origin and Genetic Makeup of Domestic Horses. Genetics 2017; 204:423-434. [PMID: 27729493 DOI: 10.1534/genetics.116.194860] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/17/2016] [Indexed: 12/21/2022] Open
Abstract
The horse was domesticated only 5.5 KYA, thousands of years after dogs, cattle, pigs, sheep, and goats. The horse nonetheless represents the domestic animal that most impacted human history; providing us with rapid transportation, which has considerably changed the speed and magnitude of the circulation of goods and people, as well as their cultures and diseases. By revolutionizing warfare and agriculture, horses also deeply influenced the politico-economic trajectory of human societies. Reciprocally, human activities have circled back on the recent evolution of the horse, by creating hundreds of domestic breeds through selective programs, while leading all wild populations to near extinction. Despite being tightly associated with humans, several aspects in the evolution of the domestic horse remain controversial. Here, we review recent advances in comparative genomics and paleogenomics that helped advance our understanding of the genetic foundation of domestic horses.
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Shehata HR, Griffiths MW, Raizada MN. Seeds of the Wild Progenitor of Maize Possess Bacteria That Antagonize Foodborne Pathogens. Foodborne Pathog Dis 2017; 14:202-209. [DOI: 10.1089/fpd.2016.2225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Hanan R. Shehata
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada
- Department of Microbiology, School of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Mansel W. Griffiths
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
- Canadian Research Institute for Food Safety, University of Guelph, Guelph, Ontario, Canada
| | - Manish N. Raizada
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada
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50
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Caliebe A, Nebel A, Makarewicz C, Krawczak M, Krause-Kyora B. Insights into early pig domestication provided by ancient DNA analysis. Sci Rep 2017; 7:44550. [PMID: 28300151 PMCID: PMC5353713 DOI: 10.1038/srep44550] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/09/2017] [Indexed: 11/24/2022] Open
Abstract
Pigs (Sus scrofa) were first domesticated between 8,500 and 8,000 cal BC in the Near East, from where they were subsequently brought into Europe by agriculturalists. Soon after the arrival of the first domestic pigs in northern Europe (~4500 BC), farmers are thought to have started to incorporate local wild boars into their swine herds. This husbandry strategy ultimately resulted in the domestication of European wild boars. Here, we set out to provide a more precise geographic and temporal framework of the early management of suid populations in northern Europe, drawing upon mitochondrial DNA haplotype data from 116 Neolithic Sus specimens. We developed a quantitative mathematical model tracing the haplotypes of the domestic pigs back to their most likely geographic origin. Our modelling results suggest that, between 5000 and 4000 BC, almost all matrilines in the north originated from domesticated animals from the south of central Europe. In the following period (4000–3000 BC), an estimated 78–100% of domesticates in the north were of northern matrilineal origin, largely from local wild boars. These findings point towards a dramatic change in suid management strategies taking place throughout south-central and northern Europe after 4000 BC.
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Affiliation(s)
- Amke Caliebe
- Institute of Medical Informatics and Statistics, Kiel University, 24105 Kiel, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany
| | - Cheryl Makarewicz
- Institute of Prehistoric and Protohistoric Archaeology, Kiel University, 24098 Kiel, Germany
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Kiel University, 24105 Kiel, Germany
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany.,Max Planck Institute for the Science of Human History, 07745 Jena, Germany
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