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Meiri M, Bar-Oz G. Unraveling the diversity and cultural heritage of fruit crops through paleogenomics. Trends Genet 2024; 40:398-409. [PMID: 38423916 PMCID: PMC11079635 DOI: 10.1016/j.tig.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 03/02/2024]
Abstract
Abundant and plentiful fruit crops are threatened by the loss of diverse legacy cultivars which are being replaced by a limited set of high-yielding ones. This article delves into the potential of paleogenomics that utilizes ancient DNA analysis to revive lost diversity. By focusing on grapevines, date palms, and tomatoes, recent studies showcase the effectiveness of paleogenomic techniques in identifying and understanding genetic traits crucial for crop resilience, disease resistance, and nutritional value. The approach not only tracks landrace dispersal and introgression but also sheds light on domestication events. In the face of major future environmental challenges, integrating paleogenomics with modern breeding strategies emerges as a promising avenue to significantly bolster fruit crop sustainability.
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Affiliation(s)
- Meirav Meiri
- The Steinhardt Museum of Natural History and Israel National Center for Biodiversity Studies, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Guy Bar-Oz
- School of Archaeology and Maritime Cultures, University of Haifa, Haifa, 3498837 Mount Carmel, Israel
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2
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Millet CP, Allinne C, Vi T, Marraccini P, Verleysen L, Couderc M, Ruttink T, Zhang D, Sanchéz WS, Tranchant-Dubreuil C, Jeune W, Poncet V. Haitian coffee agroforestry systems harbor complex arabica variety mixtures and under-recognized genetic diversity. PLoS One 2024; 19:e0299493. [PMID: 38625928 PMCID: PMC11020479 DOI: 10.1371/journal.pone.0299493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 02/11/2024] [Indexed: 04/18/2024] Open
Abstract
Though facing significant challenges, coffee (Coffea arabica) grown in Haitian agroforestry systems are important contributors to rural livelihoods and provide several ecosystem services. However, little is known about their genetic diversity and the variety mixtures used. In light of this, there is a need to characterize Haitian coffee diversity to help inform revitalization of this sector. We sampled 28 diverse farms in historically important coffee growing regions of northern and southern Haiti. We performed KASP-genotyping of SNP markers and HiPlex multiplex amplicon sequencing for haplotype calling on our samples, as well as several Ethiopian and commercial accessions from international collections. This allowed us to assign Haitian samples to varietal groups. Our analyses revealed considerable genetic diversity in Haitian farms, higher in fact than many farmers realized. Notably, genetic structure analyses revealed the presence of clusters related to Typica, Bourbon, and Catimor groups, another group that was not represented in our reference accession panel, and several admixed individuals. Across the study areas, we found both mixed-variety farms and monovarietal farms with the historical and traditional Typica variety. This study is, to our knowledge, the first to genetically characterize Haitian C. arabica variety mixtures, and report the limited cultivation of C. canephora (Robusta coffee) in the study area. Our results show that some coffee farms are repositories of historical, widely-abandoned varieties while others are generators of new diversity through genetic mixing.
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Affiliation(s)
- Claude Patrick Millet
- IRD, UMR DIADE, CIRAD, Université Montpellier, Montpellier, France
- Faculté des Sciences de l’Agriculture et de l’Environnement, Université de Quisqueya, Port-au-Prince, Haiti
- Institut Agro, ABSys, Université Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Montpellier, France
- CIRAD, UMR ABSys, F-34398, Montpellier, France
| | - Clémentine Allinne
- Institut Agro, ABSys, Université Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Montpellier, France
- CIRAD, UMR ABSys, F-34398, Montpellier, France
- GECO, Université Montpellier, CIRAD, Montpellier, France
- CIRAD, UPR GECO, F-34398, Montpellier, France
| | - Tram Vi
- IRD, UMR DIADE, CIRAD, Université Montpellier, Montpellier, France
- Agricultural Genetics Institute (AGI), Hanoi, Vietnam
| | - Pierre Marraccini
- IRD, UMR DIADE, CIRAD, Université Montpellier, Montpellier, France
- CIRAD, UMR DIADE, Montpellier, France
| | - Lauren Verleysen
- Faculty of Sciences, Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- ILVO, Melle, Belgium
| | - Marie Couderc
- IRD, UMR DIADE, CIRAD, Université Montpellier, Montpellier, France
| | - Tom Ruttink
- ILVO, Melle, Belgium
- Ghent University, Ghent, Belgium
| | - Dapeng Zhang
- USDA-ARS, SPCL, Beltsville, Maryland, United States of America
| | | | | | - Wesly Jeune
- Faculté des Sciences de l’Agriculture et de l’Environnement, Université de Quisqueya, Port-au-Prince, Haiti
- AVSF, Pétion-Ville, Haïti
| | - Valérie Poncet
- IRD, UMR DIADE, CIRAD, Université Montpellier, Montpellier, France
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3
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Perigo CV, Haber LL, Facanali R, Vieira MAR, Torres RB, Bernacci LC, Guimarães EF, Baitello JB, Sobral MEG, Quecini V, Marques MOM. Essential Oils of Aromatic Plant Species from the Atlantic Rainforest Exhibit Extensive Chemical Diversity and Antimicrobial Activity. Antibiotics (Basel) 2022; 11:antibiotics11121844. [PMID: 36551501 PMCID: PMC9774909 DOI: 10.3390/antibiotics11121844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/07/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Microbial resistance, caused by the overuse or inadequate application of antibiotics, is a worldwide crisis, increasing the risk of treatment failure and healthcare costs. Plant essential oils (EOs) consist of hydrophobic metabolites with antimicrobial activity. The antimicrobial potential of the chemical diversity of plants from the Atlantic Rainforest remains scarcely characterized. In the current work, we determined the metabolite profile of the EOs from aromatic plants from nine locations and accessed their antimicrobial and biocidal activity by agar diffusion assays, minimum inhibitory concentration, time-kill and cell-component leakage assays. The pharmacokinetic properties of the EO compounds were investigated by in silico tools. More than a hundred metabolites were identified, mainly consisting of sesqui and monoterpenes. Individual plants and botanical families exhibited extensive chemical variations in their EO composition. Probabilistic models demonstrated that qualitative and quantitative differences contribute to chemical diversity, depending on the botanical family. The EOs exhibited antimicrobial biocidal activity against pathogenic bacteria, fungi and multiple predicted pharmacological targets. Our results demonstrate the antimicrobial potential of EOs from rainforest plants, indicate novel macromolecular targets, and contribute to highlighting the chemical diversity of native species.
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Affiliation(s)
| | - Lenita L. Haber
- Vegetables Research Center, Brazilian Agricultural Research Corporation, Brasília 70351-970, Brazil
| | | | | | | | | | - Elsie F. Guimarães
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro 22460-030, Brazil
| | - João B. Baitello
- Instituto Florestal do Estado de São Paulo, São Paulo 02377-000, Brazil
| | - Marcos E. G. Sobral
- Natural Sciences Department, Campus Dom Bosco, Universidade Federal de São João del-Rei, São João del Reio 36301-160, Brazil
| | - Vera Quecini
- Grape and Wine Research Center, Brazilian Agricultural Research Corporation, Bento Gonçalves 95701-008, Brazil
- Correspondence: (V.Q.); (M.O.M.M.); Tel.: +55-(54)-3455-8000 (V.Q.); +55-(19)-3202-1700 (M.O.M.M.)
| | - Marcia Ortiz M. Marques
- Instituto Agronômico, Campinas 13075-630, Brazil
- Correspondence: (V.Q.); (M.O.M.M.); Tel.: +55-(54)-3455-8000 (V.Q.); +55-(19)-3202-1700 (M.O.M.M.)
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4
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Rayne A, Blair S, Dale M, Flack B, Hollows J, Moraga R, Parata RN, Rupene M, Tamati‐Elliffe P, Wehi PM, Wylie MJ, Steeves TE. Weaving place‐based knowledge for culturally significant species in the age of genomics: Looking to the past to navigate the future. Evol Appl 2022; 15:751-772. [PMID: 35603033 PMCID: PMC9108313 DOI: 10.1111/eva.13367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 02/16/2022] [Accepted: 02/24/2022] [Indexed: 11/28/2022] Open
Abstract
Relationships with place provide critical context for characterizing biocultural diversity. Yet, genetic and genomic studies are rarely informed by Indigenous or local knowledge, processes, and practices, including the movement of culturally significant species. Here, we show how place‐based knowledge can better reveal the biocultural complexities of genetic or genomic data derived from culturally significant species. As a case study, we focus on culturally significant southern freshwater kōura (crayfish) in Aotearoa me Te Waipounamu (New Zealand, herein Aotearoa NZ). Our results, based on genotyping‐by‐sequencing markers, reveal strong population genetic structure along with signatures of population admixture in 19 genetically depauperate populations across the east coast of Te Waipounamu. Environment association and differentiation analyses for local adaptation also indicate a role for hydroclimatic variables—including temperature, precipitation, and water flow regimes—in shaping local adaptation in kōura. Through trusted partnerships between community and researchers, weaving genomic markers with place‐based knowledge has both provided invaluable context for the interpretation of data and created opportunities to reconnect people and place. We envisage such trusted partnerships guiding future genomic research for culturally significant species in Aotearoa NZ and beyond.
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Affiliation(s)
- Aisling Rayne
- University of Canterbury School of Biological Sciences Christchurch New Zealand
| | | | - Matthew Dale
- Waterscape Connections Ltd Dunedin New Zealand
- Te Rūnanga o Ngāi Tahu Dunedin New Zealand
| | - Brendan Flack
- Kāti Huirapa Rūnaka ki Puketeraki Karitane New Zealand
| | | | - Roger Moraga
- Tea Break Bioinformatics Ltd Palmerston North New Zealand
| | | | - Makarini Rupene
- University of Canterbury Ngāi Tahu Research Centre Christchurch New Zealand
- Environment Canterbury Christchurch New Zealand
| | | | - Priscilla M Wehi
- University of Otago, Centre for Sustainability Dunedin New Zealand
| | - Matthew J Wylie
- Kāti Huirapa Rūnaka ki Puketeraki Karitane New Zealand
- The New Zealand Institute for Plant and Food Research Limited Nelson New Zealand
| | - Tammy E Steeves
- University of Canterbury School of Biological Sciences Christchurch New Zealand
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5
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Bowles E, Jeon HB, Marin K, MacLeod P, Fraser DJ. Freshwater fisheries monitoring in northern ecosystems using Indigenous ecological knowledge, genomics, and life history: Insights for community decision-making. Facets (Ott) 2022. [DOI: 10.1139/facets-2021-0049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Natural resources in northern regions are often data-limited because they are difficult and expensive to access. Indigenous ecological knowledge (IEK) can provide information similar to, different from, or complementary to Western scientific data (WSD). We evaluated the general hypothesis that congruence in outcomes of IEK and WSD for population monitoring parameters is determined by temporal and spatial scale of the knowledge type. Parameters included population structure, degree of philopatry, morphological variation (and conservation status for one species), and genomics was a key Western scientific method. We evaluated this hypothesis in three subsistence and recreational fisheries (walleye, lake trout, and northern pike) in Mistassini Lake, Quebec, Canada. Concordance of outcomes was varied. IEK provided richer information on the biology, distribution, and morphological variation observable with the eyes. However, IEK cannot “see” into the genome, and WSD identified population structure and history more precisely than IEK. Both knowledge types could “see” change in populations, and the nature of what was seen both converged and was complementary. Determining when IEK and WSD are complementary or reach common conclusions may allow Indigenous communities to use both together, or one knowledge type over another when either is more desired, appropriate, or time- or cost-efficient to adopt.
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Affiliation(s)
- Ella Bowles
- Concordia University, 7141 Sherbrooke St. West, Montreal, QC H4B 1R6, Canada
- Current affiliation: Canadian Wildlife Service, 351 Boulevard St. Joseph, Gatineau, QC J8Y 3Z5, Canada
| | - Hyung-Bae Jeon
- Concordia University, 7141 Sherbrooke St. West, Montreal, QC H4B 1R6, Canada
| | - Kia Marin
- Concordia University, 7141 Sherbrooke St. West, Montreal, QC H4B 1R6, Canada
| | - Pamela MacLeod
- Cree Nation of Mistissini, 187 Main Street, Mistissini, QC G0W 1C0, Canada
| | - Dylan J. Fraser
- Concordia University, 7141 Sherbrooke St. West, Montreal, QC H4B 1R6, Canada
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Rimlinger A, Duminil J, Lemoine T, Avana ML, Chakocha A, Gakwavu A, Mboujda F, Tsogo M, Elias M, Carrière SM. Shifting perceptions, preferences and practices in the African fruit trade: the case of African plum (Dacryodes edulis) in different cultural and urbanization contexts in Cameroon. JOURNAL OF ETHNOBIOLOGY AND ETHNOMEDICINE 2021; 17:65. [PMID: 34749757 PMCID: PMC8576868 DOI: 10.1186/s13002-021-00488-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Understanding the perceptions, preferences and management practices associated with intraspecific variability of emblematic African tree crops is critical for their sustainable management. In this paper, we examine how the agrobiodiversity of a fruit tree species native to Central Africa, the African plum tree (Dacryodes edulis), is perceived and managed by Cameroonian cultivators. METHODS Semi-structured interviews and tree surveys were conducted over four months with 441 African plum tree owners from three different ethnic groups (Bamileke, Bassa, Beti) in urban, peri-urban and rural areas. Questions focused on trees owners' perceptions-including the local nomenclature-preferences and management practices related to African plum trees and their intraspecific agrobiodiversity. RESULTS Across the three ethnic groups in the study area, more than 300 different local varietal names were recorded. These were mainly based on morphological and organoleptic traits, with two-thirds of the names referring to fruit size, skin color and fruit taste. The same traits were used by tree owners to describe their fruit preferences, but their relative importance in shaping fruit preferences varied among groups. The preferences of urban dwellers from different ethnic groups when purchasing African plum fruit focused on the fruit's taste characteristics, while those of rural dwellers differed among ethnic groups. In rural areas, where African plums are sold and consumed by their growers, the preferences of Bassa consumers reflect quantity (fruit size) over quality (fruit taste or skin color) considerations. These preferences are reflected in the choice of seeds used for planting. Bassa owners sought seeds from trees with large fruits (with 34.8% of Bassa owners giving top priority to this trait as a selection criterion) to a significantly greater extent than Bamileke and Beti owners who prioritized taste and skin color instead. Among tree growers who selectively retained African plum trees in their fields, 44% considered tree productivity as a primary selection criterion. CONCLUSIONS Findings linking perceptions of and preferences for fruit traits to intraspecific tree diversity, with attention to inter-ethnic and rural-urban differences, will help design locally specific measures to conserve the agrobiodiversity of African plum in the context of its ongoing domestication.
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Affiliation(s)
- Aurore Rimlinger
- SENS, IRD, CIRAD, Univ Paul Valery Montpellier 3, Univ Montpellier, Montpellier, France.
- DIADE, Univ Montpellier, CIRAD, IRD, BP 64501, 34394, Montpellier, France.
- Institute of Geography and Sustainability, Faculty of Geosciences and Environment, University of Lausanne, 1015, Lausanne, Switzerland.
| | - Jérôme Duminil
- DIADE, Univ Montpellier, CIRAD, IRD, BP 64501, 34394, Montpellier, France
| | - Taïna Lemoine
- CEFE Univ Montpellier - CNRS - EPHE - IRD - Univ Paul Valéry, 34293, Montpellier, France
| | - Marie-Louise Avana
- Faculty of Agronomy and Agricultural Sciences, Forestry Department, University of Dschang, BP 222, Dschang, Cameroon
| | - Armel Chakocha
- Faculty of Agronomy and Agricultural Sciences, Forestry Department, University of Dschang, BP 222, Dschang, Cameroon
| | - Alexis Gakwavu
- Faculty of Agronomy and Agricultural Sciences, Forestry Department, University of Dschang, BP 222, Dschang, Cameroon
| | - Franca Mboujda
- DIADE, Univ Montpellier, CIRAD, IRD, BP 64501, 34394, Montpellier, France
- Faculty of Agronomy and Agricultural Sciences, Forestry Department, University of Dschang, BP 222, Dschang, Cameroon
| | | | - Marlène Elias
- The Alliance of Bioversity International and CIAT, Via di San Domenico, 1, 00153, Rome, Italy
| | - Stéphanie M Carrière
- SENS, IRD, CIRAD, Univ Paul Valery Montpellier 3, Univ Montpellier, Montpellier, France.
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7
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Hosni H, Diallo A, Morcillo F, Vaissayre V, Collin M, Tranchant-Dubreuil C, Dussert S, Joët T, Castaño F, Marquínez X, Stauffer FW, Hodel DR, Castillo Mont JJ, Adam H, Jouannic S, Tregear JW. Redox-related gene expression and sugar accumulation patterns are altered in the edible inflorescence produced by the cultivated form of pacaya palm (Chamaedorea tepejilote). ANNALS OF BOTANY 2021; 128:231-240. [PMID: 33978714 PMCID: PMC8324030 DOI: 10.1093/aob/mcab060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/07/2021] [Indexed: 05/23/2023]
Abstract
BACKGROUND AND AIMS The pacaya palm is a dioecious neotropical palm species that is exploited in Latin America for its male inflorescence, which is edible when immature. It is cultivated, in a non-intensive manner, in Guatemala, where a morphotype occurs that produces much larger, more highly branched inflorescences compared with wild palms. We sought to identify molecular factors underlying this phenotypic divergence, which is likely to be a product of domestication. METHODS We performed RNA-seq-based studies on immature pacaya palm male inflorescences in order to identify genes that might be directly or indirectly affected in their expression in relation to domestication. We also measured the accumulation of a range of soluble sugar molecules to provide information on the biochemical status of the two different types of material. KEY RESULTS A total of 408 genes were found to display significantly different expression levels between the wild and cultivated morphotypes. Three different functional categories were found to be enriched in the gene set that was upregulated in the cultivated morphotype: redox balance; secondary metabolism; and transport. Several sugars were found to accumulate at higher levels in inflorescences of the cultivated morphotype, in particular myo-inositol, fructose and glucose. CONCLUSIONS The observed upregulation of redox-related genes in the cultivated morphotype is corroborated by the observation of higher myo-inositol accumulation, which has been shown to be associated with enhanced scavenging of reactive oxygen species in other plants and which may affect meristem activity.
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Affiliation(s)
- Hanene Hosni
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Abdoulaye Diallo
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Fabienne Morcillo
- CIRAD, DIADE, Montpellier, France
- DIADE, Université de Montpellier, Institut de Recherche pour le Développement, Montpellier, France
| | - Virginie Vaissayre
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Myriam Collin
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | | | - Stéphane Dussert
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Thierry Joët
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Felipe Castaño
- Universidad Industrial de Santander, Escuela de Biología, Calle, Bucaramanga, Colombia
| | - Xavier Marquínez
- Universidad Nacional de Colombia, Departamento de Biología, Carrera, Bogotá, Colombia
| | - Fred W Stauffer
- Conservatoire et Jardin botaniques de la Ville de Genève, Université de Genève, Laboratoire de Systématique Végétale et Biodiversité, Chambésy, Switzerland
| | - Donald R Hodel
- University of California, Cooperative Extension, Alhambra, CA, USA
| | | | - Hélène Adam
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Stefan Jouannic
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - James W Tregear
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
- For correspondence. E-mail
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8
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Pérez-Escobar OA, Bellot S, Przelomska NAS, Flowers JM, Nesbitt M, Ryan P, Gutaker RM, Gros-Balthazard M, Wells T, Kuhnhäuser BG, Schley R, Bogarín D, Dodsworth S, Diaz R, Lehmann M, Petoe P, Eiserhardt WL, Preick M, Hofreiter M, Hajdas I, Purugganan M, Antonelli A, Gravendeel B, Leitch IJ, Torres Jimenez MF, Papadopulos AST, Chomicki G, Renner SS, Baker WJ. Molecular clocks and archaeogenomics of a Late Period Egyptian date palm leaf reveal introgression from wild relatives and add timestamps on the domestication. Mol Biol Evol 2021; 38:4475-4492. [PMID: 34191029 PMCID: PMC8476131 DOI: 10.1093/molbev/msab188] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in the Persian Gulf, and its evolution appears to have been influenced by gene flow from two wild relatives, P. theophrasti, currently restricted to Crete and Turkey, and P. sylvestris, widespread from Bangladesh to the West Himalayas. Genomes of ancient date palm seeds show that gene flow from P. theophrasti to P. dactylifera may have occurred by ∼2,200 years ago, but traces of P. sylvestris could not be detected. We here integrate archeogenomics of a ∼2,100-year-old P. dactylifera leaf from Saqqara (Egypt), molecular-clock dating, and coalescence approaches with population genomic tests, to probe the hybridization between the date palm and its two closest relatives and provide minimum and maximum timestamps for its reticulated evolution. The Saqqara date palm shares a close genetic affinity with North African date palm populations, and we find clear genomic admixture from both P. theophrasti, and P. sylvestris, indicating that both had contributed to the date palm genome by 2,100 years ago. Molecular-clocks placed the divergence of P. theophrasti from P. dactylifera/P. sylvestris and that of P. dactylifera from P. sylvestris in the Upper Miocene, but strongly supported, conflicting topologies point to older gene flow between P. theophrasti and P. dactylifera, and P. sylvestris and P. dactylifera. Our work highlights the ancient hybrid origin of the date palms, and prompts the investigation of the functional significance of genetic material introgressed from both close relatives, which in turn could prove useful for modern date palm breeding.
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Affiliation(s)
| | - Sidonie Bellot
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Natalia A S Przelomska
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Jonathan M Flowers
- Center for Genomics and Systems Biology, New York University Abu Dhabi, United Arab Emirates
| | - Mark Nesbitt
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Philippa Ryan
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | | | - Muriel Gros-Balthazard
- French National Research Institute for Sustainable Development, Montpellier, BP 64501 - 34394 Cedex 5, France
| | - Tom Wells
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3QU, UK
| | | | - Rowan Schley
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Diego Bogarín
- Lankester Botanical Garden, University of Costa Rica, San José, 302-7050, Costa Rica
| | - Steven Dodsworth
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Rudy Diaz
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | | | - Peter Petoe
- Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Wolf L Eiserhardt
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Michaela Preick
- Institute of Biochemistry and Biology, University of Potsdam, 14469 Potsdam, Germany
| | - Michael Hofreiter
- Institute of Biochemistry and Biology, University of Potsdam, 14469 Potsdam, Germany
| | - Irka Hajdas
- Department of Earth Sciences, ETH Zurich, 8092, Switzerland
| | - Michael Purugganan
- Center for Genomics and Systems Biology, New York University Abu Dhabi, United Arab Emirates
| | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,Department of Plant Sciences, University of Oxford, Oxford, OX1 3QU, UK.,Gothenburg Global Biodiversity Centre and Department of Biological and Environmental Sciences, University of Gothenburg, 413 19, Sweden
| | | | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Maria Fernanda Torres Jimenez
- Gothenburg Global Biodiversity Centre and Department of Biological and Environmental Sciences, University of Gothenburg, 413 19, Sweden
| | - Alexander S T Papadopulos
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, University of Bangor, Bangor LL57 2UW, UK
| | - Guillaume Chomicki
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Susanne S Renner
- Department of Biology, Washington University, Saint Louis, MO 63130, USA
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9
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Abstract
Resurrection genomics is an alternative to ancient DNA approaches in studying the genetics and evolution of past and possibly extinct populations. By reviving biological material such as germinating ancient seeds from archaeological and paleontological sites, or historical collections, one can study genomes of lost populations. We applied this approach by sequencing the genomes of seven Judean date palms (Phoenix dactylifera) that were germinated from ∼2,000 y old seeds recovered in the Southern Levant. Using this genomic data, we were able to document that introgressive hybridization of the wild Cretan palm Phoenix theophrasti into date palms had occurred in the Eastern Mediterranean by ∼2,200 y ago and examine the evolution of date palm populations in this pivotal region two millennia ago. Seven date palm seeds (Phoenix dactylifera L.), radiocarbon dated from the fourth century BCE to the second century CE, were recovered from archaeological sites in the Southern Levant and germinated to yield viable plants. We conducted whole-genome sequencing of these germinated ancient samples and used single-nucleotide polymorphism data to examine the genetics of these previously extinct Judean date palms. We find that the oldest seeds from the fourth to first century BCE are related to modern West Asian date varieties, but later material from the second century BCE to second century CE showed increasing genetic affinities to present-day North African date palms. Population genomic analysis reveals that by ∼2,400 to 2,000 y ago, the P. dactylifera gene pool in the Eastern Mediterranean already contained introgressed segments from the Cretan palm Phoenix theophrasti, a crucial genetic feature of the modern North African date palm populations. The P. theophrasti introgression fraction content is generally higher in the later samples, while introgression tracts are longer in these ancient germinated date palms compared to modern North African varieties. These results provide insights into crop evolution arising from an analysis of plants originating from ancient germinated seeds and demonstrate what can be accomplished with the application of a resurrection genomics approach.
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Vandebroek I, Picking D, Tretina J, West J, Grizzle M, Sweil D, Green U, Lindsay D. Root Tonics and Resilience: Building Strength, Health, and Heritage in Jamaica. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.640171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Jamaican root tonics are fermented beverages made with the roots, bark, vines (and dried leaves) of several plant species, many of which are wild-harvested in forest areas of this Caribbean island. These tonics are popular across Jamaica, and also appreciated among the Jamaican diaspora in the United States, Canada, and the United Kingdom. Although plants are the focal point of the ethnobotany of root tonics, interviews with 99 knowledgeable Jamaicans across five parishes of the island, with the goal of documenting their knowledge, perceptions, beliefs, and oral histories, showed that studying these tonics solely from a natural sciences perspective would serve as an injustice to the important sociocultural dimensions and symbolism that surround their use. Jamaican explanations about root tonics are filled with metaphorical expressions about the reciprocity between the qualities of “nature” and the strength of the human body. Furthermore, testimonies about the perceived cultural origins, and reasons for using root tonics, provided valuable insights into the extent of human hardship endured historically during slavery, and the continued struggle experienced by many Jamaicans living a subsistence lifestyle today. On the other hand, the popularity of root tonics is also indicative of the resilience of hard-working Jamaicans, and their quest for bodily and mental strength and health in dealing with socioeconomic and other societal challenges. Half of all study participants considered Rastafari the present-day knowledge holders of Jamaican root tonics. Even though these tonics represent a powerful informal symbol of Jamaican biocultural heritage, they lack official recognition and development for the benefit of local producers and vendors. We therefore used a sustainable development conceptual framework consisting of social, cultural, economic, and ecological pillars, to design a road map for a cottage industry for these artisanal producers. The four steps of this road map (growing production, growing alliances, transitioning into the formal economy, and safeguarding ecological sustainability) provide a starting point for future research and applied projects to promote this biocultural heritage product prepared with Neglected and Underutilized Species (NUS) of plants.
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