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van Aubel G, Van Cutsem E, Emond A, Métillon G, Cordier É, Van Cutsem P. Dual Transcriptomic and Metabolomic Analysis of Elicited Flax Sheds Light on the Kinetics of Immune Defense Activation Against the Biotrophic Pathogen Oidium lini. PHYTOPATHOLOGY 2024:PHYTO02240070KC. [PMID: 38748518 DOI: 10.1094/phyto-02-24-0070-kc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2024]
Abstract
Flax (Linum usitatissimum) grown under controlled conditions displayed genotype-dependent resistance to powdery mildew (Oidium lini) following COS-OGA (comprising chitosan- and pectin-derived oligomers) elicitor application. The present study reveals a two-step immune response in plants preventively challenged with the elicitor: an initial, rapid response characterized by the transcription of defense genes whose protein products act in contact with or within the cell wall, where biotrophic pathogens initially thrive, followed by a prolonged activation of cell wall peroxidases and accumulation of secondary metabolites. Thus, dozens of genes encoding membrane receptors, pathogenesis-related proteins, and wall peroxidases were initially overexpressed. Repeated COS-OGA treatments had a transient effect on the transcriptome response while cumulatively remodeling the metabolome over time, with a minimum of two applications required for maximal metabolomic shifts. Secondary metabolites, in particular terpenoids and phenylpropanoids, emerged as major components of this secondary defense response alongside pathogenesis-related proteins and wall peroxidases. The sustained accumulation of secondary metabolites, even after cessation of elicitation, contrasted with the short-lived transcriptomic response. Wall peroxidase enzyme activity also exhibited cumulative effects, increasing strongly for weeks after a third elicitor treatment. This underscores the plasticity of the plant immune response in the face of a potential infection, and the need for repeated preventive applications to achieve the full protective potential of the elicitor.
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Affiliation(s)
- Géraldine van Aubel
- Biology Department, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
- FytoFend S.A., 5032 Isnes, Belgium
| | | | - Amélie Emond
- Biology Department, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | | | - Émilie Cordier
- Biology Department, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Pierre Van Cutsem
- Biology Department, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
- FytoFend S.A., 5032 Isnes, Belgium
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2
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Landoni B, Suárez-Montes P, Habeahan RHF, Brennan AC, Pérez-Barrales R. Local climate and vernalization sensitivity predict the latitudinal patterns of flowering onset in the crop wild relative Linum bienne Mill. ANNALS OF BOTANY 2024; 134:117-130. [PMID: 38482916 PMCID: PMC11161566 DOI: 10.1093/aob/mcae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 03/13/2024] [Indexed: 06/09/2024]
Abstract
BACKGROUND AND AIMS The timing of flowering onset is often correlated with latitude, indicative of climatic gradients. Flowering onset in temperate species commonly requires exposure to cold temperatures, known as vernalization. Hence, population differentiation of flowering onset with latitude might reflect adaptation to the local climatic conditions experienced by populations. METHODS Within its western range, seeds from Linum bienne populations (the wild relative of cultivated Linum usitatissimum) were used to describe the latitudinal differentiation of flowering onset to determine its association with the local climate of the population. A vernalization experiment including different crop cultivars was used to determine how vernalization accelerates flowering onset, in addition to the vernalization sensitivity response among populations and cultivars. Additionally, genetic differentiation of L. bienne populations along the latitudinal range was scrutinized using microsatellite markers. KEY RESULTS Flowering onset varied with latitude of origin, with southern populations flowering earlier than their northern counterparts. Vernalization reduced the number of days to flowering onset, but vernalization sensitivity was greater in northern populations compared with southern ones. Conversely, vernalization delayed flowering onset in the crop, exhibiting less variation in sensitivity. In L. bienne, both flowering onset and vernalization sensitivity were better predicted by the local climate of the population than by latitude itself. Microsatellite data unveiled genetic differentiation of populations, forming two groups geographically partitioned along latitude. CONCLUSIONS The consistent finding of latitudinal variation across experiments suggests that both flowering onset and vernalization sensitivity in L. bienne populations are under genetic regulation and might depend on climatic cues at the place of origin. The association with climatic gradients along latitude suggests that the climate experienced locally drives population differentiation of the flowering onset and vernalization sensitivity patterns. The genetic population structure suggests that past population history could have influenced the flowering initiation patterns detected, which deserves further work.
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Affiliation(s)
- Beatrice Landoni
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
- Department of Biosciences, University of Milan, Milan, Italy
| | | | | | | | - Rocío Pérez-Barrales
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
- Botany Department, University of Granada, Granada, Spain
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3
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Brescia F, Sillo F, Franchi E, Pietrini I, Montesano V, Marino G, Haworth M, Zampieri E, Fusini D, Schillaci M, Papa R, Santamarina C, Vita F, Chitarra W, Nerva L, Petruzzelli G, Mennone C, Centritto M, Balestrini R. The 'microbiome counterattack': Insights on the soil and root-associated microbiome in diverse chickpea and lentil genotypes after an erratic rainfall event. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:459-483. [PMID: 37226644 PMCID: PMC10667653 DOI: 10.1111/1758-2229.13167] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 05/05/2023] [Indexed: 05/26/2023]
Abstract
Legumes maintain soil fertility thanks to their associated microbiota but are threatened by climate change that causes soil microbial community structural and functional modifications. The core microbiome associated with different chickpea and lentil genotypes was described after an unexpected climatic event. Results showed that chickpea and lentil bulk soil microbiomes varied significantly between two sampling time points, the first immediately after the rainfall and the second 2 weeks later. Rhizobia were associated with the soil of the more productive chickpea genotypes in terms of flower and fruit number. The root-associated bacteria and fungi were surveyed in lentil genotypes, considering that several parcels showed disease symptoms. The metabarcoding analysis revealed that reads related to fungal pathogens were significantly associated with one lentil genotype. A lentil core prokaryotic community common to all genotypes was identified as well as a genotype-specific one. A higher number of specific bacterial taxa and an enhanced tolerance to fungal diseases characterized a lentil landrace compared to the commercial varieties. This outcome supported the hypothesis that locally adapted landraces might have a high recruiting efficiency of beneficial soil microbes.
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Affiliation(s)
- Francesca Brescia
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Fabiano Sillo
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Elisabetta Franchi
- Eni S.p.A.R&D Environmental & Biological LaboratoriesSan Donato MilaneseItaly
| | - Ilaria Pietrini
- Eni S.p.A.R&D Environmental & Biological LaboratoriesSan Donato MilaneseItaly
| | - Vincenzo Montesano
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyBernalda (MT)Italy
| | - Giovanni Marino
- Institute for Sustainable Plant ProtectionNational Research Council of ItalySesto FiorentinoItaly
| | - Matthew Haworth
- Institute for Sustainable Plant ProtectionNational Research Council of ItalySesto FiorentinoItaly
| | - Elisa Zampieri
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Danilo Fusini
- Eni S.p.A.R&D Environmental & Biological LaboratoriesSan Donato MilaneseItaly
| | - Martino Schillaci
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Roberto Papa
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Chiara Santamarina
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Federico Vita
- Department of Bioscience, Biotechnology and EnvironmentUniversity of Bari Aldo MoroBariItaly
| | - Walter Chitarra
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and EconomicsConeglianoItaly
| | - Luca Nerva
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and EconomicsConeglianoItaly
| | | | - Carmelo Mennone
- Azienda Pantanello, ALSIA Research Center Metapontum AgrobiosBernalda (MT)Italy
| | - Mauro Centritto
- Institute for Sustainable Plant ProtectionNational Research Council of ItalySesto FiorentinoItaly
- ENI‐CNR Water Research Center ‘Hypatia of Alexandria’ALSIA Research Center Metapontum AgrobiosBernaldaItaly
| | - Raffaella Balestrini
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
- ENI‐CNR Water Research Center ‘Hypatia of Alexandria’ALSIA Research Center Metapontum AgrobiosBernaldaItaly
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4
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Altınışık NE, Kazancı DD, Aydoğan A, Gemici HC, Erdal ÖD, Sarıaltun S, Vural KB, Koptekin D, Gürün K, Sağlıcan E, Fernandes D, Çakan G, Koruyucu MM, Lagerholm VK, Karamurat C, Özkan M, Kılınç GM, Sevkar A, Sürer E, Götherström A, Atakuman Ç, Erdal YS, Özer F, Erim Özdoğan A, Somel M. A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition. SCIENCE ADVANCES 2022; 8:eabo3609. [PMID: 36332018 PMCID: PMC9635823 DOI: 10.1126/sciadv.abo3609] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked innovations in symbolism, technology, and diet. We present 13 ancient genomes (c. 8500 to 7500 cal BCE) from Pre-Pottery Neolithic Çayönü in the Tigris basin together with bioarchaeological and material culture data. Our findings reveal that Çayönü was a genetically diverse population, carrying mixed ancestry from western and eastern Fertile Crescent, and that the community received immigrants. Our results further suggest that the community was organized along biological family lines. We document bodily interventions such as head shaping and cauterization among the individuals examined, reflecting Çayönü's cultural ingenuity. Last, we identify Upper Mesopotamia as the likely source of eastern gene flow into Neolithic Anatolia, in line with material culture evidence. We hypothesize that Upper Mesopotamia's cultural dynamism during the Neolithic Transition was the product not only of its fertile lands but also of its interregional demographic connections.
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Affiliation(s)
- N. Ezgi Altınışık
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Duygu Deniz Kazancı
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Ayça Aydoğan
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Hasan Can Gemici
- Department of Settlement Archaeology, Middle East Technical University, 06800 Ankara, Turkey
| | - Ömür Dilek Erdal
- Husbio-L Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Savaş Sarıaltun
- Department of Museology and Cultural Heritage Management, Çanakkale Onsekiz Mart University, Çanakkale 17100, Turkey
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Dilek Koptekin
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey
| | - Kanat Gürün
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Ekin Sağlıcan
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey
| | - Daniel Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
- CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Gökhan Çakan
- Husbio-L Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Meliha Melis Koruyucu
- Husbio-L Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Vendela Kempe Lagerholm
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Cansu Karamurat
- Department of Settlement Archaeology, Middle East Technical University, 06800 Ankara, Turkey
| | - Mustafa Özkan
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Gülşah Merve Kılınç
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100 Sıhhiye, Ankara, Turkey
| | - Arda Sevkar
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Elif Sürer
- Department of Modeling and Simulation, Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Çiğdem Atakuman
- Department of Settlement Archaeology, Middle East Technical University, 06800 Ankara, Turkey
| | - Yılmaz Selim Erdal
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
- Husbio-L Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Füsun Özer
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Aslı Erim Özdoğan
- Department of Archaeology, Çanakkale Onsekiz Mart University, Çanakkale 17100, Turkey
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
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Melelli A, Jamme F, Beaugrand J, Bourmaud A. Evolution of the ultrastructure and polysaccharide composition of flax fibres over time: When history meets science. Carbohydr Polym 2022; 291:119584. [DOI: 10.1016/j.carbpol.2022.119584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/30/2022] [Accepted: 05/04/2022] [Indexed: 11/28/2022]
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6
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Huang H. Discovery and Domestication of New Fruit Trees in the 21st Century. PLANTS 2022; 11:plants11162107. [PMID: 36015410 PMCID: PMC9413266 DOI: 10.3390/plants11162107] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022]
Abstract
The exploration and use of wild plant resources goes back to our rooted history of human civilization over about 20,000 years ago, before Ancient Mesopotamia in the Valley of the Tigris and Euphrates where barley, lentil and wheat were first domesticated [...]
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Affiliation(s)
- Hongwen Huang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China
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7
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Environmental effects on the spread of the Neolithic crop package to South Asia. PLoS One 2022; 17:e0268482. [PMID: 35816489 PMCID: PMC9273075 DOI: 10.1371/journal.pone.0268482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/29/2022] [Indexed: 11/19/2022] Open
Abstract
The emergence of Neolithic economies and their spread through Eurasia was one of the most crucial transitions of the Holocene, with different mechanisms of diffusion—demic, cultural—being proposed. While this phenomenon has been exhaustively studied in Europe, with repeated attempts to model the speed of Neolithic diffusion based on radiocarbon dates, much less attention has been devoted to the dispersal towards the East, and in particular to South Asia. The Neolithic in the latter region at least partly derived from southwest Asia, given the presence of “founder crops” such as wheat and barley. The process of their eastward diffusion, however, may have been significantly different to the westward dispersal, which was mainly due to demic diffusion, as local domesticates were already available and farming was already practiced in parts of South Asia. Here, we use radiocarbon dates specifically related to the spread of the southwest Asian Neolithic crops to model the speed of dispersal of this agricultural package towards South Asia. To assess potential geographical and environmental effects on the dispersal, we simulate different speeds depending on the biomes being crossed, employing a genetic algorithm to search for the values that most closely approach the radiocarbon dates. We find that the most important barrier to be crossed were the Zagros mountains, where the speed was lowest, possibly due to topography and climate. A large portion of the study area is dominated by deserts and shrublands, where the speed of advance, albeit closer to the range expected for demic diffusion, was lower than observed in Europe, which can also potentially be attributed to environmental constraints in the adaptation of the crops. Finally, a notable acceleration begins in the Indus valley, exceeding the range of demic diffusion in the tropical and subtropical environments east of the Indus. We propose that the latter is due to the rapid diffusion among populations already familiar with plant cultivation.
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8
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Jiang C, Lei M, Guo Y, Gao G, Shi L, Jin Y, Cai Y, Himmelbach A, Zhou S, He Q, Yao X, Kan J, Haberer G, Duan F, Li L, Liu J, Zhang J, Spannagl M, Liu C, Stein N, Feng Z, Mascher M, Yang P. A reference-guided TILLING by amplicon-sequencing platform supports forward and reverse genetics in barley. PLANT COMMUNICATIONS 2022; 3:100317. [PMID: 35605197 PMCID: PMC9284286 DOI: 10.1016/j.xplc.2022.100317] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 02/13/2022] [Accepted: 03/11/2022] [Indexed: 05/26/2023]
Abstract
Barley is a diploid species with a genome smaller than those of other members of the Triticeae tribe, making it an attractive model for genetic studies in Triticeae crops. The recent development of barley genomics has created a need for a high-throughput platform to identify genetically uniform mutants for gene function investigations. In this study, we report an ethyl methanesulfonate (EMS)-mutagenized population consisting of 8525 M3 lines in the barley landrace "Hatiexi" (HTX), which we complement with a high-quality de novo assembly of a reference genome for this genotype. The mutation rate within the population ranged from 1.51 to 4.09 mutations per megabase, depending on the treatment dosage of EMS and the mutation discrimination platform used for genotype analysis. We implemented a three-dimensional DNA pooling strategy combined with multiplexed amplicon sequencing to create a highly efficient and cost-effective TILLING (targeting induced locus lesion in genomes) platform in barley. Mutations were successfully identified from 72 mixed amplicons within a DNA pool containing 64 individual mutants and from 56 mixed amplicons within a pool containing 144 individuals. We discovered abundant allelic mutants for dozens of genes, including the barley Green Revolution contributor gene Brassinosteroid insensitive 1 (BRI1). As a proof of concept, we rapidly determined the causal gene responsible for a chlorotic mutant by following the MutMap strategy, demonstrating the value of this resource to support forward and reverse genetic studies in barley.
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Affiliation(s)
- Congcong Jiang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Miaomiao Lei
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yu Guo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Guangqi Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijie Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yanlong Jin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Cai
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Shenghui Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuefeng Yao
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jinhong Kan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Georg Haberer
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Fengying Duan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Manuel Spannagl
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Chunming Liu
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Zongyun Feng
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany.
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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Komarnytsky S, Retchin S, Vong CI, Lila MA. Gains and Losses of Agricultural Food Production: Implications for the Twenty-First Century. Annu Rev Food Sci Technol 2021; 13:239-261. [PMID: 34813357 DOI: 10.1146/annurev-food-082421-114831] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The world food supply depends on a diminishing list of plant crops and animal livestock to not only feed the ever-growing human population but also improve its nutritional state and lower the disease burden. Over the past century or so, technological advances in agricultural and food processing have helped reduce hunger and poverty but have not adequately addressed sustainability targets. This has led to an erosion of agricultural biodiversity and balanced diets and contributed to climate change and rising rates of chronic metabolic diseases. Modern food supply chains have progressively lost dietary fiber, complex carbohydrates, micronutrients, and several classes of phytochemicals with high bioactivity and nutritional relevance. This review introduces the concept of agricultural food systems losses and focuses on improved sources of agricultural diversity, proteins with enhanced resilience, and novel monitoring, processing, and distribution technologies that are poised to improve food security, reduce food loss and waste, and improve health profiles in the near future. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Slavko Komarnytsky
- Plants for Human Health Institute, North Carolina State University, Kannapolis, North Carolina; .,Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina
| | - Sophia Retchin
- Kenan-Flagler Business School, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Chi In Vong
- Plants for Human Health Institute, North Carolina State University, Kannapolis, North Carolina; .,Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina
| | - Mary Ann Lila
- Plants for Human Health Institute, North Carolina State University, Kannapolis, North Carolina; .,Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina
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10
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Harnessing the Wild Relatives and Landraces for Fe and Zn Biofortification in Wheat through Genetic Interventions—A Review. SUSTAINABILITY 2021. [DOI: 10.3390/su132312975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Micronutrient deficiencies, particularly iron (Fe) and zinc (Zn), in human diets are affecting over three billion people globally, especially in developing nations where diet is cereal-based. Wheat is one of several important cereal crops that provide food calories to nearly one-third of the population of the world. However, the bioavailability of Zn and Fe in wheat is inherently low, especially under Zn deficient soils. Although various fortification approaches are available, biofortification, i.e., development of mineral-enriched cultivars, is an efficient and sustainable approach to alleviate malnutrition. There is enormous variability in Fe and Zn in wheat germplasm, especially in wild relatives, but this is not utilized to the full extent. Grain Fe and Zn are quantitatively inherited, but high-heritability and genetic correlation at multiple locations indicate the high stability of Fe and Zn in wheat. In the last decade, pre-breeding activities have explored the potential of wild relatives to develop Fe and Zn rich wheat varieties. Furthermore, recent advances in molecular biology have improved the understanding of the uptake, storage, and bioavailability of Fe and Zn. Various transportation proteins encoding genes like YSL 2, IRT 1, OsNAS 3, VIT 1, and VIT 2 have been identified for Fe and Zn uptake, transfer, and accumulation at different developing stages. Hence, the availability of major genomic regions for Fe and Zn content and genome editing technologies are likely to result in high-yielding Fe and Zn biofortified wheat varieties. This review covers the importance of wheat wild relatives for Fe and Zn biofortification, progress in genomics-assisted breeding, and transgenic breeding for improving Fe and Zn content in wheat.
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11
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Melelli A, Shah DU, Hapsari G, Cortopassi R, Durand S, Arnould O, Placet V, Benazeth D, Beaugrand J, Jamme F, Bourmaud A. Lessons on textile history and fibre durability from a 4,000-year-old Egyptian flax yarn. NATURE PLANTS 2021; 7:1200-1206. [PMID: 34518667 DOI: 10.1038/s41477-021-00998-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Flax has a long and fascinating history. This plant was domesticated around 8,000 BCE1 in the Fertile Crescent area2, first for its seeds and then for its fibres1,3. Although its uses existed long before domestication, residues of flax yarn dated 30,000 years ago have been found in the Caucasus area4. However, Ancient Egypt laid the foundations for the cultivation of flax as a textile fibre crop5. Today flax fibres are used in high-value textiles and in natural actuators6 or reinforcements in composite materials7. Flax is therefore a bridge between ages and civilizations. For several decades, the development of non- or micro-destructive analysis techniques has led to numerous works on the conservation of ancient textiles. Non-destructive methods, such as optical microscopy8 or vibrational techniques9,10, have been largely used to investigate archaeological textiles, principally to evaluate their degradation mechanisms and state of conservation. Vibrational spectroscopy studies can now benefit from synchrotron radiation11 and X-ray diffraction measurement in the archaeometric study of historical textiles12,13. Conservation of mechanical performance and the ultrastructural differences between ancient and modern flax varieties have not been examined thus far. Here we examine the morphological, ultrastructural and mechanical characteristics of a yarn from an Egyptian mortuary linen dating from the early Middle Kingdom (Eleventh Dynasty, ca. 2033-1963 BCE) and compare them with a modern flax yarn to assess the quality and durability of ancient flax fibres and relate these to their processing methods. Advanced microscopy techniques, such as nano-tomography, multiphoton excitation microscopy and atomic force microscopy were used. Our findings reveal the cultural know-how of this ancient civilization in producing high-fineness fibres, as well as the exceptional durability of flax, which is sometimes questioned, demonstrating their potential as reinforcements in high-technology composites.
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Affiliation(s)
| | - Darshil U Shah
- Centre for Natural Material Innovation, Department of Architecture, University of Cambridge, Cambridge, UK
| | - Gemala Hapsari
- FEMTO-ST Institute, Department of Applied Mechanics, UMR CNRS 6174, University of Franche-Comté, Besançon, France
| | | | - Sylvie Durand
- INRAE, UR1268 BIA Biopolymères Interactions Assemblages, Nantes, France
| | - Olivier Arnould
- LMGC, Université de Montpellier, UMR CNRS 5508, Montpellier, France
| | - Vincent Placet
- FEMTO-ST Institute, Department of Applied Mechanics, UMR CNRS 6174, University of Franche-Comté, Besançon, France
| | | | - Johnny Beaugrand
- INRAE, UR1268 BIA Biopolymères Interactions Assemblages, Nantes, France
| | - Frédéric Jamme
- Synchrotron SOLEIL, DISCO beamline, Gif-sur-Yvette, France
| | - Alain Bourmaud
- Univ. Bretagne Sud, UMR CNRS 6027, IRDL, Lorient, France.
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12
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Riel-Salvatore J, Lythe A, Albornoz AU. New insights into the spatial organization, stratigraphy and human occupations of the Aceramic Neolithic at Ganj Dareh, Iran. PLoS One 2021; 16:e0251318. [PMID: 34407112 PMCID: PMC8372917 DOI: 10.1371/journal.pone.0251318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 04/23/2021] [Indexed: 12/01/2022] Open
Abstract
The Aceramic Neolithic site of Ganj Dareh (Kermanshah, Iran) is arguably one of the most significant sites for enhancing our understanding of goat domestication and the onset of sedentism. Despite its central importance, it has proven difficult to obtain contextually reliable data from it and integrate the site in regional syntheses because it was never published in full after excavations ceased in 1974. This paper presents the Ganj Dareh archive at Université de Montréal and shows how the documentation and artifacts it comprises still offer a great deal of useful information about the site. In particular, we 1) present the first stratigraphic profile for the site, which reveals a more complex depositional history than Smith's five-level sequence; 2) reveal the presence of two possible pre-agricultural levels (H-01 and P-01); 3) explore the spatial organization of different levels; 4) explain possible discrepancies in the radiocarbon dates from the site; 5) show some differences in lithic technological organization in levels H-01 and P-01 suggestive of higher degrees of residential mobility than subsequent phases of occupation at the site; and 6) reanalyze the burial data to broaden our understanding of Aceramic Neolithic mortuary practices in the Zagros. These data help refine our understanding of Ganj Dareh's depositional and occupational history and recenter it as a key site to improve our understanding the Neolithization process in the Middle East.
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Affiliation(s)
- Julien Riel-Salvatore
- Département d’Anthropologie, Laboratoire d’Archéologie de l’Anthropocène, Université de Montréal, Montréal, QC, Canada
| | - Andrew Lythe
- Département d’Anthropologie, Laboratoire d’Archéologie de l’Anthropocène, Université de Montréal, Montréal, QC, Canada
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13
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Hruby K, Cendrowska M, Chasan R, Groman-Yaroslavski I, Rosenberg D. The function of the south-Levantine Late Chalcolithic and Early Bronze Age basalt vessels bearing circumferential depressions: Insights from use-wear analyses. PLoS One 2021; 16:e0252535. [PMID: 34086750 PMCID: PMC8177471 DOI: 10.1371/journal.pone.0252535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/17/2021] [Indexed: 11/23/2022] Open
Abstract
One of the most characteristic aspects of the Late Chalcolithic and Early Bronze Age periods in the southern Levant is the appearance of large assemblages of basalt vessels. These vessels, frequently meticulously made, appear sometimes a considerable distance from the raw material sources and are found mainly at habitation sites. While these and their prestigious value have been widely discussed in the past, their function is still obscure. In the current paper, we address their functionality through microscopic use-wear analysis. Emphasis was placed on basalt vessels with a distinct wear pattern–circumferential depressions, which appear along the perimeter of their interior bases. The documented traces were compared to results of an experimental study we conducted to characterize the effects of abrasion, grinding, and lubrication on basalt surfaces. The results of the comparative experimental study suggest that the circumferential depression was formed from a repetitive rotational activity using a narrow-ended tool. Further, it seems that two material types acted in combination as the circling device and processed material. One was hard and abrasive, such as stone, and the other was semi-resilient, such as wood or mineral powder. Water was likely used as a lubricant in the rotational process. While the actual function of the bowls bearing the circumferential depressions is not entirely clear, the use-wear analyses suggest that they may have been devices involved in craft industries, used for processing materials unrelated to food (minerals in particular). Whatever the exact function was, it clear that this use continued from the Chalcolithic through the Early Bronze Age, providing evidence for functional continuity between these two periods.
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Affiliation(s)
- Karolina Hruby
- Laboratory for Ground Stone Tools Research, Zinman Institute of Archaeology, University of Haifa, Haifa, Israel
- * E-mail:
| | | | - Rivka Chasan
- Laboratory for Ground Stone Tools Research, Zinman Institute of Archaeology, University of Haifa, Haifa, Israel
| | - Iris Groman-Yaroslavski
- The Use-Wear Analysis Laboratory, Zinman Institute of Archaeology, University of Haifa, Haifa, Israel
| | - Danny Rosenberg
- Laboratory for Ground Stone Tools Research, Zinman Institute of Archaeology, University of Haifa, Haifa, Israel
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14
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Preece C, Jones G, Rees M, Osborne CP. Fertile Crescent crop progenitors gained a competitive advantage from large seedlings. Ecol Evol 2021; 11:3300-3312. [PMID: 33841785 PMCID: PMC8019021 DOI: 10.1002/ece3.7282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/24/2020] [Accepted: 01/21/2021] [Indexed: 12/03/2022] Open
Abstract
Cereal domestication during the transition to agriculture resulted in widespread food production, but why only certain species were domesticated remains unknown. We tested whether seedlings of crop progenitors share functional traits that could give them a competitive advantage within anthropogenic environments, including higher germination, greater seedling survival, faster growth rates, and greater competitive ability.Fifteen wild grass species from the Fertile Crescent were grown individually under controlled conditions to evaluate differences in growth between cereal crop progenitors and other wild species that were never domesticated. Differences in germination, seedling survival, and competitive ability were measured by growing a subset of these species as monocultures and mixtures.Crop progenitors had greater germination success, germinated more quickly and had greater aboveground biomass when grown in competition with other species. There was no evidence of a difference in seedling survival, but seed size was positively correlated with a number of traits, including net assimilation rates, greater germination success, and faster germination under competition. In mixtures, the positive effect of seed mass on germination success and speed of germination was even more beneficial for crop progenitors than for other wild species, suggesting greater fitness. Thus, selection for larger seeded individuals under competition may have been stronger in the crop progenitors.The strong competitive ability of Fertile Crescent cereal crop progenitors, linked to their larger seedling size, represents an important ecological difference between these species and other wild grasses in the region. It is consistent with the hypothesis that competition within plant communities surrounding human settlements, or under early cultivation, benefited progenitor species, favoring their success as crops.
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Affiliation(s)
- Catherine Preece
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
- PLECO (Plants and Ecosystems)Department of BiologyUniversity of AntwerpWilrijkBelgium
| | - Glynis Jones
- Department of ArchaeologyUniversity of SheffieldSheffieldUK
| | - Mark Rees
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Colin P. Osborne
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
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15
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Salavert A, Zazzo A, Martin L, Antolín F, Gauthier C, Thil F, Tombret O, Bouby L, Manen C, Mineo M, Mueller-Bieniek A, Piqué R, Rottoli M, Rovira N, Toulemonde F, Vostrovská I. Direct dating reveals the early history of opium poppy in western Europe. Sci Rep 2020; 10:20263. [PMID: 33219318 PMCID: PMC7679390 DOI: 10.1038/s41598-020-76924-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/02/2020] [Indexed: 11/11/2022] Open
Abstract
This paper aims to define the first chrono-cultural framework on the domestication and early diffusion of the opium poppy using small-sized botanical remains from archaeological sites, opening the way to directly date minute short-lived botanical samples. We produced the initial set of radiocarbon dates directly from the opium poppy remains of eleven Neolithic sites (5900–3500 cal BCE) in the central and western Mediterranean, northwestern temperate Europe, and the western Alps. When possible, we also dated the macrobotanical remains originating from the same sediment sample. In total, 22 samples were taken into account, including 12 dates directly obtained from opium poppy remains. The radiocarbon chronology ranges from 5622 to 4050 cal BCE. The results show that opium poppy is present from at least the middle of the sixth millennium in the Mediterranean, where it possibly grew naturally and was cultivated by pioneer Neolithic communities. Its dispersal outside of its native area was early, being found west of the Rhine in 5300–5200 cal BCE. It was introduced to the western Alps around 5000–4800 cal BCE, becoming widespread from the second half of the fifth millennium. This research evidences different rhythms in the introduction of opium poppy in western Europe.
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Affiliation(s)
- Aurélie Salavert
- Unité Mixte de Recherche (UMR) Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle (MNHN), Centre National de Recherche Scientifique (CNRS), Alliance Sorbonne Université, Paris, France.
| | - Antoine Zazzo
- Unité Mixte de Recherche (UMR) Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle (MNHN), Centre National de Recherche Scientifique (CNRS), Alliance Sorbonne Université, Paris, France
| | - Lucie Martin
- Laboratory of Prehistoric Archaeology and Anthropology, University of Geneva, Geneva, Switzerland.,UMR EDYTEM, CNRS, Université Grenoble Alpes, Université Savoie Mont-Blanc, Chambéry, France
| | - Ferran Antolín
- Integrative Prehistory and Archaeological Science (IPAS), Universität Basel, Basel, Switzerland
| | - Caroline Gauthier
- Laboratoire des Sciences du Climat et de l'Environnement (LSCE), CNRS, Commissariat à l'Energie Atomique (CEA), Université de Versailles Saint-Quentin, Paris-Saclay, Paris, France
| | - François Thil
- Laboratoire des Sciences du Climat et de l'Environnement (LSCE), CNRS, Commissariat à l'Energie Atomique (CEA), Université de Versailles Saint-Quentin, Paris-Saclay, Paris, France
| | - Olivier Tombret
- Unité Mixte de Recherche (UMR) Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle (MNHN), Centre National de Recherche Scientifique (CNRS), Alliance Sorbonne Université, Paris, France.,UMR Histoire Naturelle de L'Homme Préhistorique, Musée de L'Homme, MNHN, Paris, France
| | - Laurent Bouby
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Claire Manen
- UMR TRACES, CNRS, Université Toulouse Jean Jaurès, Toulouse, France
| | - Mario Mineo
- Museo delle Civiltà - Museo Preistorico Etnografico "Luigi Pigorini", Rome, Italy
| | | | - Raquel Piqué
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Mauro Rottoli
- Laboratorio Di Archeobiologia Dei Musei Civici Di Como, Department of Humanities, Università Degli Studi Di Trento, Trento, Italy
| | - Núria Rovira
- UMR Archéologie Des Sociétés Méditerranéennes, Université Paul-Valéry Montpellier 3, CNRS, Ministère de La Culture Et de La Communication, Inrap/LabEx Archimède, Montpellier, France
| | - Françoise Toulemonde
- Unité Mixte de Recherche (UMR) Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle (MNHN), Centre National de Recherche Scientifique (CNRS), Alliance Sorbonne Université, Paris, France
| | - Ivana Vostrovská
- Faculty of Arts, Palacký University Olomouc, Olomouc, Czech Republic
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16
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Caracuta V, Alex B, Regev L, Regev J, Mintz E, Barzilai O, Hershkovitz I, Boaretto E. The Marine Isotope Stage 3 landscape around Manot Cave (Israel) and the food habits of anatomically modern humans: New insights from the anthracological record and stable carbon isotope analysis of wild almond (Amygdalus sp.). J Hum Evol 2020; 160:102868. [DOI: 10.1016/j.jhevol.2020.102868] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 01/29/2023]
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17
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Living off the land: Terrestrial-based diet and dairying in the farming communities of the Neolithic Balkans. PLoS One 2020; 15:e0237608. [PMID: 32817620 PMCID: PMC7444498 DOI: 10.1371/journal.pone.0237608] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/29/2020] [Indexed: 01/01/2023] Open
Abstract
The application of biomolecular techniques to archaeological materials from the Balkans is providing valuable new information on the prehistory of the region. This is especially relevant for the study of the neolithisation process in SE Europe, which gradually affected the rest of the continent. Here, to answer questions regarding diet and subsistence practices in early farming societies in the central Balkans, we combine organic residue analyses of archaeological pottery, taxonomic and isotopic study of domestic animal remains and biomolecular analyses of human dental calculus. The results from the analyses of the lipid residues from pottery suggest that milk was processed in ceramic vessels. Dairy products were shown to be part of the subsistence strategies of the earliest Neolithic communities in the region but were of varying importance in different areas of the Balkan. Conversely, milk proteins were not detected within the dental calculus. The molecular and isotopic identification of meat, dairy, plants and beeswax in the pottery lipids also provided insights into the diversity of diet in these early Neolithic communities, mainly based on terrestrial resources. We also present the first compound-specific radiocarbon dates for the region, obtained directly from absorbed organic residues extracted from pottery, identified as dairy lipids.
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18
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Petrova P, Petrov K. Lactic Acid Fermentation of Cereals and Pseudocereals: Ancient Nutritional Biotechnologies with Modern Applications. Nutrients 2020; 12:E1118. [PMID: 32316499 PMCID: PMC7230154 DOI: 10.3390/nu12041118] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/09/2020] [Accepted: 04/15/2020] [Indexed: 02/07/2023] Open
Abstract
Grains are a substantial source of macronutrients and energy for humans. Lactic acid (LA) fermentation is the oldest and most popular way to improve the functionality, nutritional value, taste, appearance and safety of cereal foods and reduce the energy required for cooking. This literature review discusses lactic acid fermentation of the most commonly used cereals and pseudocereals by examination of the microbiological and biochemical fundamentals of the process. The study provides a critical overview of the indispensable participation of lactic acid bacteria (LAB) in the production of many traditional, ethnic, ancient and modern fermented cereals and beverages, as the analysed literature covers 40 years. The results reveal that the functional aspects of LAB fermented foods are due to significant molecular changes in macronutrients during LA fermentation. Through the action of a vast microbial enzymatic pool, LAB form a broad spectrum of volatile compounds, bioactive peptides and oligosaccharides with prebiotic potential. Modern applications of this ancient bioprocess include the industrial production of probiotic sourdough, fortified pasta, cereal beverages and "boutique" pseudocereal bread. These goods are very promising in broadening the daily menu of consumers with special nutritional needs.
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Affiliation(s)
- Penka Petrova
- Institute of Microbiology, Bulgarian Academy of Sciences, Acad. G. Bonchev, Str. Bl. 26, 1113 Sofia, Bulgaria
| | - Kaloyan Petrov
- Institute of Chemical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev, Str. Bl. 103, 1113 Sofia, Bulgaria
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19
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Kosterin OE, Bogdanova VS, Mglinets AV. Wild pea (Pisum sativum L. subsp. elatius (Bieb.) Aschers. et Graebn. s.l.) at the periphery of its range: Zagros Mountains. Vavilovskii Zhurnal Genet Selektsii 2020; 24:60-68. [PMID: 33659782 PMCID: PMC7716565 DOI: 10.18699/vj20.596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Characteristics of wild peas and their habitats at the periphery of the range are interesting with respect to their potential importance for pre-breeding programs aimed at selection for different environmental conditions. However, wild pea diversity in peripheral regions is insufficiently represented in the existing germplasm collections. In such regions, wild pea populations are rare, small in size and suffer from climatic change and land exploitation, hence their focused search is strongly desirable. A two-week-long expedition to Iran in May 2017 revealed two small populations of the wild pea (Pisum sativum subsp. elatius) in the Zagros Mts, in Aligudarz and Khorramabad Districts of Lorestan Province, Iran, at elevations of 1841 and 1971 m a.s.l., respectively. Their habitats are briefly described. Two pea accessions derived from them, CE9 and CE10, were characterised for some visible and molecular characters. These peas appeared to belong to the evolutionary lineage B, recognised by us earlier in P. sativum as opposed to the so-called lineage AC. They contain a unique non-conservative substitution in subtype 5 of histone H1 and turned to be most related to some wild pea accessions originating from southern and south-eastern Turkey and Golan Heights. Scarce information available on wild pea occurrence in Iran suggests their existence in the south-western principal slope of Zagros Mts and southern principal slopes of Elborz and Kopet Dagh Mts. It was found that wild peas representing the evolutionary lineage B produce poorly open and poorly coloured flowers (as reported by us earlier) only in the greenhouse conditions but normally pigmented and open flowers in the wild and mesh houses at open air in Israel. Some issues of pea taxonomy are discussed.
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Affiliation(s)
- O E Kosterin
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - V S Bogdanova
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A V Mglinets
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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20
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Sertse D, You FM, Ravichandran S, Cloutier S. The Complex Genetic Architecture of Early Root and Shoot Traits in Flax Revealed by Genome-Wide Association Analyses. FRONTIERS IN PLANT SCIENCE 2019; 10:1483. [PMID: 31798617 PMCID: PMC6878218 DOI: 10.3389/fpls.2019.01483] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/25/2019] [Indexed: 05/05/2023]
Abstract
Roots are fundamental organs for water and nutrient uptake as well as for signal transduction in response to biotic and abiotic stresses. Flax has a shallow tap root system that relies mostly on top soil nutrient and moisture resources. The crop can easily be outcompeted by weeds or other crops in intercropping systems, especially in moisture deficit conditions. However, there is a wide range of variation among genotypes in terms of performance under scarce resources such as moisture limitation. Here we phenotyped 15 root, two shoot traits and shoot to root dry weight ratio on 115 flax accessions grown in a hydroponic pouch system and performed a genome-wide association study (GWAS) based on seven different models to identify quantitative trait loci underlying these traits. Significant variation among genotypes was observed for the two shoot and 12 of the 14 root traits. Shoot dry weight was correlated with root network volume, length, surface area, and root dry weight (r > 0.5, P < 0.001) but not significantly correlated with root depth (r = 0.033, P > 0.05). The seven GWAS models detected a total of 228 quantitative trait nucleotides (QTNs) for 16 traits. Most loci, defined by an interval of 100 kb up and downstream of the QTNs, harbored genes known to play role(s) in root and shoot development, suggesting them as candidates. Examples of candidate genes linked to root network QTNs included genes encoding GRAS transcription factors, mitogen-activated protein kinases, and auxin related lateral organ boundary proteins while QTN loci for shoot dry weight harbored genes involved in photomorphogenesis and plant immunity. These results provide insights into the genetic bases of early shoot and root development traits in flax that could be capitalized upon to improve its root architecture, particularly in view of better withstanding water limiting conditions during the cropping season.
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Affiliation(s)
- Demissew Sertse
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Frank M. You
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sridhar Ravichandran
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sylvie Cloutier
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
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21
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Wood D, Lenné JM. A natural adaptive syndrome as a model for the origins of cereal agriculture. Proc Biol Sci 2019; 285:rspb.2018.0277. [PMID: 29563270 DOI: 10.1098/rspb.2018.0277] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 02/26/2018] [Indexed: 11/12/2022] Open
Abstract
A novel explanation of the origin of cereal agriculture is proposed, based on the ecology and adaptive morphology of wild cereals ancestral to our founder cereals (einkorn, emmer and barley). Wild cereals are unusually large-seeded. A natural evolutionary-ecological syndrome relates large seed, awns and monodominance (LAM). Awns bury attached seeds in the soil, protecting seed from fire; buried seed needs to be large to emerge on germination; large seeds, growing without competition from small-seeded plants, will produce monodominant vegetation. Climatic and edaphic instability at the Pleistocene-Holocene boundary would have provided an impetus for the spread of annual ruderal grasses. LAM grassland provided an obvious natural model for the origins of cereal agriculture. Subsequent field management would mimic the natural niche (MNN). The fact that monodominance is a long-standing character of the natural LAM syndrome validates cereal monocultures (now producing most of our food). An alternative explanation of crop domestication, by auditioning a great range of species for a human-constructed niche (NCT), is rejected.
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Affiliation(s)
- David Wood
- North Oldmoss Croft, Fyvie, Turriff, Aberdeenshire AB53 8NA, UK
| | - Jillian M Lenné
- North Oldmoss Croft, Fyvie, Turriff, Aberdeenshire AB53 8NA, UK
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22
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Dietrich L, Meister J, Dietrich O, Notroff J, Kiep J, Heeb J, Beuger A, Schütt B. Cereal processing at Early Neolithic Göbekli Tepe, southeastern Turkey. PLoS One 2019; 14:e0215214. [PMID: 31042741 PMCID: PMC6493732 DOI: 10.1371/journal.pone.0215214] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 03/29/2019] [Indexed: 11/24/2022] Open
Abstract
We analyze the processing of cereals and its role at Early Neolithic Göbekli Tepe, southeastern Anatolia (10th / 9th millennium BC), a site that has aroused much debate in archaeological discourse. To date, only zooarchaeological evidence has been discussed in regard to the subsistence of its builders. Göbekli Tepe consists of monumental round to oval buildings, erected in an earlier phase, and smaller rectangular buildings, built around them in a partially contemporaneous and later phase. The monumental buildings are best known as they were in the focus of research. They are around 20 m in diameter and have stone pillars that are up to 5.5 m high and often richly decorated. The rectangular buildings are smaller and–in some cases–have up to 2 m high, mostly undecorated, pillars. Especially striking is the number of tools related to food processing, including grinding slabs/bowls, handstones, pestles, and mortars, which have not been studied before. We analyzed more than 7000 artifacts for the present contribution. The high frequency of artifacts is unusual for contemporary sites in the region. Using an integrated approach of formal, experimental, and macro- / microscopical use-wear analyses we show that Neolithic people at Göbekli Tepe have produced standardized and efficient grinding tools, most of which have been used for the processing of cereals. Additional phytolith analysis confirms the massive presence of cereals at the site, filling the gap left by the weakly preserved charred macro-rests. The organization of work and food supply has always been a central question of research into Göbekli Tepe, as the construction and maintenance of the monumental architecture would have necessitated a considerable work force. Contextual analyses of the distribution of the elements of the grinding kit on site highlight a clear link between plant food preparation and the rectangular buildings and indicate clear delimitations of working areas for food production on the terraces the structures lie on, surrounding the circular buildings. There is evidence for extensive plant food processing and archaeozoological data hint at large-scale hunting of gazelle between midsummer and autumn. As no large storage facilities have been identified, we argue for a production of food for immediate use and interpret these seasonal peaks in activity at the site as evidence for the organization of large work feasts.
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Affiliation(s)
- Laura Dietrich
- German Archaeological Institute, Orient Department, Berlin, Germany
- * E-mail: (LD); (JM)
| | - Julia Meister
- University of Würzburg, Institute of Geography and Geology, Würzburg, Germany
- * E-mail: (LD); (JM)
| | - Oliver Dietrich
- German Archaeological Institute, Orient Department, Berlin, Germany
| | - Jens Notroff
- German Archaeological Institute, Orient Department, Berlin, Germany
| | - Janika Kiep
- Freie Universität Berlin, Institute of Geographical Sciences, Berlin, Germany
| | | | - André Beuger
- German Archaeological Institute, Orient Department, Berlin, Germany
| | - Brigitta Schütt
- Freie Universität Berlin, Institute of Geographical Sciences, Berlin, Germany
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23
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Sertse D, You FM, Ravichandran S, Cloutier S. The genetic structure of flax illustrates environmental and anthropogenic selections that gave rise to its eco-geographical adaptation. Mol Phylogenet Evol 2019; 137:22-32. [PMID: 30978393 DOI: 10.1016/j.ympev.2019.04.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 04/06/2019] [Accepted: 04/08/2019] [Indexed: 01/15/2023]
Abstract
Flax, one of the eight founder crops of agriculture, has been cultivated for its oil and/or fiber for millennia. Understanding genetic divergence and geographic origins of germplasm in line with their cultivation history and ecological adaptation are essential for conservation and breeding. Here we performed a genome-wide assessment based on more than 51,000 single nucleotide polymorphic sites defining 383 flax accessions from a core collection representing 37 flax growing countries. Population structure analysis resulted in a total of 12 populations that were pooled into four major groups: Temperate, South Asian, Abyssinian and Mediterranean. The vast majority (n = 335) belonged to the Temperate group that comprised eight populations including one dominated by fiber flax. Genetic variation between fiber and oil morphotypes was less pronounced than variation within morphotypes. The genetic variation among groups and populations was attributed in part to eco-geographic and anthropogenic factors. Genetic signatures indicated loci under strong selection by environmental factors such as day length. A high concentration of private haplotypes were observed in the South Asian, Mediterranean and Abyssinian populations despite their low genotype representation, hinting at the long history of the crop in these regions. The addition of genotypes from these three regions would enrich the core collection by capturing a wider genetic breadth for breeding and conservation.
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Affiliation(s)
- Demissew Sertse
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada; Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
| | - Frank M You
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Sridhar Ravichandran
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada; Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada.
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UPLC-MS metabolome based classification of Lupinus and Lens seeds: A prospect for phyto-equivalency of its different accessions. Food Res Int 2019; 115:379-392. [DOI: 10.1016/j.foodres.2018.11.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 10/19/2018] [Accepted: 11/02/2018] [Indexed: 02/06/2023]
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25
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Kılınç GM, Koptekin D, Atakuman Ç, Sümer AP, Dönertaş HM, Yaka R, Bilgin CC, Büyükkarakaya AM, Baird D, Altınışık E, Flegontov P, Götherström A, Togan İ, Somel M. Archaeogenomic analysis of the first steps of Neolithization in Anatolia and the Aegean. Proc Biol Sci 2018; 284:rspb.2017.2064. [PMID: 29167366 DOI: 10.1098/rspb.2017.2064] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 10/20/2017] [Indexed: 12/20/2022] Open
Abstract
The Neolithic transition in west Eurasia occurred in two main steps: the gradual development of sedentism and plant cultivation in the Near East and the subsequent spread of Neolithic cultures into the Aegean and across Europe after 7000 cal BCE. Here, we use published ancient genomes to investigate gene flow events in west Eurasia during the Neolithic transition. We confirm that the Early Neolithic central Anatolians in the ninth millennium BCE were probably descendants of local hunter-gatherers, rather than immigrants from the Levant or Iran. We further study the emergence of post-7000 cal BCE north Aegean Neolithic communities. Although Aegean farmers have frequently been assumed to be colonists originating from either central Anatolia or from the Levant, our findings raise alternative possibilities: north Aegean Neolithic populations may have been the product of multiple westward migrations, including south Anatolian emigrants, or they may have been descendants of local Aegean Mesolithic groups who adopted farming. These scenarios are consistent with the diversity of material cultures among Aegean Neolithic communities and the inheritance of local forager know-how. The demographic and cultural dynamics behind the earliest spread of Neolithic culture in the Aegean could therefore be distinct from the subsequent Neolithization of mainland Europe.
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Affiliation(s)
- Gülşah Merve Kılınç
- Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativaegen 7, Stockholm 114 18, Sweden
| | - Dilek Koptekin
- Department of Health Informatics, Middle East Technical University, Ankara 06800, Turkey
| | - Çiğdem Atakuman
- Department of Settlement Archaeology, Middle East Technical University, Ankara 06800, Turkey
| | - Arev Pelin Sümer
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
| | - Handan Melike Dönertaş
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, Hinxton CB10 1SD, UK
| | - Reyhan Yaka
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
| | - Cemal Can Bilgin
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
| | | | - Douglas Baird
- Department of Archaeology, Classics, and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK
| | - Ezgi Altınışık
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.,A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativaegen 7, Stockholm 114 18, Sweden
| | - İnci Togan
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
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Weide A, Riehl S, Zeidi M, Conard NJ. A systematic review of wild grass exploitation in relation to emerging cereal cultivation throughout the Epipalaeolithic and aceramic Neolithic of the Fertile Crescent. PLoS One 2018; 13:e0189811. [PMID: 29293519 PMCID: PMC5749723 DOI: 10.1371/journal.pone.0189811] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/01/2017] [Indexed: 11/18/2022] Open
Abstract
The present study investigates the occurrence of wild grasses at Epipalaeolithic and aceramic Neolithic sites in the Near East in order to assess their role in subsistence economies alongside the emergence of cereal cultivation. We use Chogha Golan in the foothills of the central Zagros Mountains (ca. 11.7-9.6 ka cal. BP) as a case study, where the archaeobotanical data suggest the frequent exploitation of a complex of wild grasses for almost 2,000 years. Domesticated emmer replaced these wild grasses as the major food resources towards the end of occupation at the site (ca. 9.8 ka cal. BP). We discuss possible implications of this development and conclude that the traditional concept of pre-domestication cultivation seems unsuited for explaining the patterns from Chogha Golan. These data are in good accordance with the overall picture in the Zagros Mountains, where wild grasses were routinely gathered throughout the early Holocene. In contrast, wild grasses were gradually replaced by wild cereals in the Levantine corridor since the end of the Pleistocene. However, several sites located in this region provide evidence for a continuous exploitation of wild grasses alongside emerging cereal cultivation and most of these taxa were part of the earliest segetal floras that evolved with the appearance of domestic cereals throughout the 11th millennium cal. BP. Some sites contemporary to the Pre-Pottery Neolithic B still provide evidence for the usage of wild grasses, which possibly reflects the utilization of edible arable weeds and continuous gathering of wild grasses by more mobile groups.
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Affiliation(s)
- Alexander Weide
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
- * E-mail:
| | - Simone Riehl
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
- Tübingen Senckenberg Center for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Mohsen Zeidi
- Tübingen Senckenberg Center for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany
| | - Nicholas J. Conard
- Tübingen Senckenberg Center for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany
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Liu X, Lister DL, Zhao Z, Petrie CA, Zeng X, Jones PJ, Staff RA, Pokharia AK, Bates J, Singh RN, Weber SA, Motuzaite Matuzeviciute G, Dong G, Li H, Lü H, Jiang H, Wang J, Ma J, Tian D, Jin G, Zhou L, Wu X, Jones MK. Journey to the east: Diverse routes and variable flowering times for wheat and barley en route to prehistoric China. PLoS One 2017; 12:e0187405. [PMID: 29095896 PMCID: PMC5667820 DOI: 10.1371/journal.pone.0187405] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/15/2017] [Indexed: 11/18/2022] Open
Abstract
Today, farmers in many regions of eastern Asia sow their barley grains in the spring and harvest them in the autumn of the same year (spring barley). However, when it was first domesticated in southwest Asia, barley was grown between the autumn and subsequent spring (winter barley), to complete their life cycles before the summer drought. The question of when the eastern barley shifted from the original winter habit to flexible growing schedules is of significance in terms of understanding its spread. This article investigates when barley cultivation dispersed from southwest Asia to regions of eastern Asia and how the eastern spring barley evolved in this context. We report 70 new radiocarbon measurements obtained directly from barley grains recovered from archaeological sites in eastern Eurasia. Our results indicate that the eastern dispersals of wheat and barley were distinct in both space and time. We infer that barley had been cultivated in a range of markedly contrasting environments by the second millennium BC. In this context, we consider the distribution of known haplotypes of a flowering-time gene in barley, Ppd-H1, and infer that the distributions of those haplotypes may reflect the early dispersal of barley. These patterns of dispersal resonate with the second and first millennia BC textual records documenting sowing and harvesting times for barley in central/eastern China.
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Affiliation(s)
- Xinyi Liu
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO, United States of America
- * E-mail:
| | - Diane L. Lister
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
| | - Zhijun Zhao
- Institutue of Archaeology, Chinese Academy of Social Sciences, Beijing, China
| | - Cameron A. Petrie
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
| | - Xiongsheng Zeng
- Institute for the History of Natural Sciences, Chinese Academy of Sciences, Beijing, China
| | - Penelope J. Jones
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
| | - Richard A. Staff
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
- Scottish Universities Environmental Research Centre (SUERC), University of Glasgow, East Kibride, United Kingdom
| | | | - Jennifer Bates
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
| | - Ravindra N. Singh
- Department of AIHC and Archaeology, Banaras Hindu University, Varnasi, India
| | - Steven A. Weber
- Department of Anthropology, Washington State University, Vancouver, WA, United States of America
| | | | - Guanghui Dong
- Key Laboratory of Western China’s Environmental Systems, Lanzhou University, Lanzhou, China
| | - Haiming Li
- Key Laboratory of Western China’s Environmental Systems, Lanzhou University, Lanzhou, China
| | - Hongliang Lü
- Department of Archaeology, Sichuan University, Chengdu, China
| | - Hongen Jiang
- Department of History of Science and Archaeometry, University of Chinese Academy of Sciences, Beijing, China
| | - Jianxin Wang
- School of Cultural Heritage, Northwest University, Xi’an, China
| | - Jian Ma
- School of Cultural Heritage, Northwest University, Xi’an, China
| | - Duo Tian
- School of Cultural Heritage, Northwest University, Xi’an, China
| | - Guiyun Jin
- School of History and Culture, Shandong University, Jinan, China
| | - Liping Zhou
- Laboratory for Earth Surface Processes, Peking University, Beijing, China
| | - Xiaohong Wu
- School of Archaeology and Museology, Peking University, Beijing, China
| | - Martin K. Jones
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
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Abbo S, Gopher A. Near Eastern Plant Domestication: A History of Thought. TRENDS IN PLANT SCIENCE 2017; 22:491-511. [PMID: 28434795 DOI: 10.1016/j.tplants.2017.03.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 02/28/2017] [Accepted: 03/20/2017] [Indexed: 06/07/2023]
Abstract
The Agricultural Revolution and plant domestication in the Near East (among its components) have fascinated generations of scholars. Here, we narrate the history of ideas underlying plant domestication research since the late 19th century. Biological and cultural perspectives are presented through two prevailing models: one views plant domestication as a protracted, unconscious evolutionary mutualistic (noncentric) process. The second advocates a punctuated, knowledge-based human initiative (centric). We scrutinize the research landscape while assessing the underlying evolutionary and cultural mechanisms. A parsimony measure indicates that the punctuated-centric view better accords with archaeological records, and the geobotany and biology of the species, and requires fewer assumptions. The protracted alternative requires many assumptions, does not account for legume biology, fails to distinguish domestication from postdomestication changes, and, therefore, is less parsimonious.
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Affiliation(s)
- Shahal Abbo
- The Levi Eshkol School of Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel.
| | - Avi Gopher
- The Sonia and Marco Nadler Institute of Archaeology, Tel Aviv University, Ramat Aviv 6997801, Israel
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Tayeh N, Aubert G, Pilet-Nayel ML, Lejeune-Hénaut I, Warkentin TD, Burstin J. Genomic Tools in Pea Breeding Programs: Status and Perspectives. FRONTIERS IN PLANT SCIENCE 2015; 6:1037. [PMID: 26640470 PMCID: PMC4661580 DOI: 10.3389/fpls.2015.01037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 11/09/2015] [Indexed: 05/07/2023]
Abstract
Pea (Pisum sativum L.) is an annual cool-season legume and one of the oldest domesticated crops. Dry pea seeds contain 22-25% protein, complex starch and fiber constituents, and a rich array of vitamins, minerals, and phytochemicals which make them a valuable source for human consumption and livestock feed. Dry pea ranks third to common bean and chickpea as the most widely grown pulse in the world with more than 11 million tons produced in 2013. Pea breeding has achieved great success since the time of Mendel's experiments in the mid-1800s. However, several traits still require significant improvement for better yield stability in a larger growing area. Key breeding objectives in pea include improving biotic and abiotic stress resistance and enhancing yield components and seed quality. Taking advantage of the diversity present in the pea genepool, many mapping populations have been constructed in the last decades and efforts have been deployed to identify loci involved in the control of target traits and further introgress them into elite breeding materials. Pea now benefits from next-generation sequencing and high-throughput genotyping technologies that are paving the way for genome-wide association studies and genomic selection approaches. This review covers the significant development and deployment of genomic tools for pea breeding in recent years. Future prospects are discussed especially in light of current progress toward deciphering the pea genome.
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Affiliation(s)
| | | | | | | | - Thomas D. Warkentin
- Crop Development Centre, College of Agriculture and Bioresources, University of SaskatchewanSaskatoon, SK, Canada
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Nasiri J, Naghavi MR, Kayvanjoo AH, Nasiri M, Ebrahimi M. Precision assessment of some supervised and unsupervised algorithms for genotype discrimination in the genus Pisum using SSR molecular data. J Theor Biol 2015; 368:122-32. [PMID: 25591889 DOI: 10.1016/j.jtbi.2015.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 11/06/2014] [Accepted: 01/01/2015] [Indexed: 10/24/2022]
Abstract
For the first time, prediction accuracies of some supervised and unsupervised algorithms were evaluated in an SSR-based DNA fingerprinting study of a pea collection containing 20 cultivars and 57 wild samples. In general, according to the 10 attribute weighting models, the SSR alleles of PEAPHTAP-2 and PSBLOX13.2-1 were the two most important attributes to generate discrimination among eight different species and subspecies of genus Pisum. In addition, K-Medoids unsupervised clustering run on Chi squared dataset exhibited the best prediction accuracy (83.12%), while the lowest accuracy (25.97%) gained as K-Means model ran on FCdb database. Irrespective of some fluctuations, the overall accuracies of tree induction models were significantly high for many algorithms, and the attributes PSBLOX13.2-3 and PEAPHTAP could successfully detach Pisum fulvum accessions and cultivars from the others when two selected decision trees were taken into account. Meanwhile, the other used supervised algorithms exhibited overall reliable accuracies, even though in some rare cases, they gave us low amounts of accuracies. Our results, altogether, demonstrate promising applications of both supervised and unsupervised algorithms to provide suitable data mining tools regarding accurate fingerprinting of different species and subspecies of genus Pisum, as a fundamental priority task in breeding programs of the crop.
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Affiliation(s)
- Jaber Nasiri
- Department of Agronomy and Plant Breeding, Division of Molecular Plant Genetics, College of Agricultural & Natural Resources, University of Tehran, Karaj, Tehran, Iran.
| | - Mohammad Reza Naghavi
- Department of Agronomy and Plant Breeding, College of Agricultural & Natural Resources, University of Tehran, Karaj, Tehran, Iran.
| | | | - Mojtaba Nasiri
- School of Life Sciences, Biomedical Science, Division of Molecular Biology, University of Sussex, Falmer, Brighton, UK.
| | - Mansour Ebrahimi
- Department of Biology, School of Basic Sciences, University of Qom, Qom, Iran.
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31
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Langlie BS, Mueller NG, Spengler RN, Fritz GJ. Agricultural origins from the ground up: archaeological approaches to plant domestication. AMERICAN JOURNAL OF BOTANY 2014; 101:1601-17. [PMID: 25326610 DOI: 10.3732/ajb.1400145] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The timing, geographical locations, causes, and consequences of crop domestication have long been major concerns of archaeologists, and agricultural origins and dispersals are currently more relevant than ever to scientists seeking solutions to elusive problems involving food insecurity and global health disparities. Perennial research issues that archaeologists continue to tackle include (1) thinking outside centers of origin that were based on limited and insufficient past knowledge; (2) distinguishing between single and multiple domestications of specific crops; (3) measuring the pace of domestication; and (4) decoupling domestication from agricultural economies. Paleoethnobotanists have expanded their toolkits to include analysis of ancient and modern DNA and have added increasingly sophisticated techniques in the field and the laboratory to derive precise chronological sequences to assess morphological changes in ancient and often fragmentary archaeobotanical remains and to correctly interpret taphonomy and context. Multiple lines of archaeological evidence are ideally brought together, and whenever possible, these are integrated with information from complementary sources. We discuss current perspectives and anthropological approaches to research that have as their goals the fuller and broader understanding of ancient farming societies, the plants that were domesticated, the landscapes that were created, and the culinary legacies that were passed on.
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Affiliation(s)
- BrieAnna S Langlie
- Department of Anthropology, CB 1114, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130 USA
| | - Natalie G Mueller
- Department of Anthropology, CB 1114, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130 USA
| | - Robert N Spengler
- Department of Anthropology, CB 1114, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130 USA
| | - Gayle J Fritz
- Department of Anthropology, CB 1114, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130 USA
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Abstract
Early Neolithic sedentary villagers started cultivating wild cereals in the Near East 11,500 y ago [Pre-Pottery Neolithic A (PPNA)]. Recent discoveries indicated that Cyprus was frequented by Late PPNA people, but the earliest evidence until now for both the use of cereals and Neolithic villages on the island dates to 10,400 y ago. Here we present the recent archaeological excavation at Klimonas, which demonstrates that established villagers were living on Cyprus between 11,100 and 10,600 y ago. Villagers had stone artifacts and buildings (including a remarkable 10-m diameter communal building) that were similar to those found on Late PPNA sites on the mainland. Cereals were introduced from the Levant, and meat was obtained by hunting the only ungulate living on the island, a small indigenous Cypriot wild boar. Cats and small domestic dogs were brought from the mainland. This colonization suggests well-developed maritime capabilities by the PPNA period, but also that migration from the mainland may have occurred shortly after the beginning of agriculture.
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Goring-Morris AN, Belfer-Cohen A. Neolithization Processes in the Levant. CURRENT ANTHROPOLOGY 2011. [DOI: 10.1086/658860] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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36
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Piperno DR. The Origins of Plant Cultivation and Domestication in the New World Tropics. CURRENT ANTHROPOLOGY 2011. [DOI: 10.1086/659998] [Citation(s) in RCA: 267] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Bar-Yosef O. Climatic Fluctuations and Early Farming in West and East Asia. CURRENT ANTHROPOLOGY 2011. [DOI: 10.1086/659784] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Zhao Z. New Archaeobotanic Data for the Study of the Origins of Agriculture in China. CURRENT ANTHROPOLOGY 2011. [DOI: 10.1086/659308] [Citation(s) in RCA: 264] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Özdoğan M. Archaeological Evidence on the Westward Expansion of Farming Communities from Eastern Anatolia to the Aegean and the Balkans. CURRENT ANTHROPOLOGY 2011. [DOI: 10.1086/658895] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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