Cultivation potential of Vanilla crop wild relatives in two contrasting land use systems
Tài liệu tham khảo
Adame-García, 2015, Molecular identification and pathogenic variation of Fusarium species isolated from Vanilla planifolia in Papantla Mexico, Bot. Sci., 93, 669, 10.17129/botsci.142
Aerts, 2011, Semi-forest coffee cultivation and the conservation of Ethiopian Afromontane rainforest fragments, For. Ecol. Manag., 261, 1034, 10.1016/j.foreco.2010.12.025
Aerts, 2013, Genetic variation and risks of introgression in the wild C offea arabica gene pool in south‐western E thiopian montane rainforests, Evolut. Appl., 6, 243, 10.1111/j.1752-4571.2012.00285.x
Azofeifa-Bolaños, 2014, Importancia y desafíos de la conservación de Vanilla spp.(Orquidaceae) en Costa Rica, Agron. Mesoam., 25, 189, 10.15517/am.v25i1.14220
Azofeifa-Bolaños, 2019, Efecto de la desinfección de segmentos nodales sobre el rendimiento morfogenético de vitroplantas de Vanilla planifolia Andrews, Agron. Mesoam., 30, 33, 10.15517/am.v30i1.32360
Bertola, 2021, Improvement of soil microbial diversity through sustainable agricultural practices and its evaluation by-omics approaches: A perspective for the environment, food quality and human safety, Microorganisms, 9, 1400, 10.3390/microorganisms9071400
Beule, 2020, Improved normalization of species count data in ecology by scaling with ranked subsampling (SRS): application to microbial communities, PeerJ, 8, 10.7717/peerj.9593
Bhai, 2000, Phytophthora rot–a new disease of vanilla (Vanilla planifolia Andrews) in India, J. Spices Aromat. Crops, 9, 73
Błasiak, 2021, The effects of tree and stand traits on the specific leaf area in managed scots pine forests of different ages, Forests, 12, 396, 10.3390/f12040396
Bory, S., Grisoni, M., Duval, M.F. and Besse, P., 2008. Biodiversity and preservation of vanilla: present state of knowledge. Genetic Resources and Crop Evolution, 55(4), pp.551–571.
Bramel, P., Frey, F. 2021. Global strategy for the conservation and use of Vanilla genetic resources. Global Crop Diversity Trust. Bonn, Germany.
Brunschwig, C., Collard, F.X., Lepers-Andrzejewski, S. and Raharivelomanana, P., 2017. Tahitian Vanilla (Vanilla× tahitensis): a Vanilla species with unique features. Active Ingredients from Aromatic and Medicinal Plants.
Callahan, 2016, DADA2: high-resolution sample inference from Illumina amplicon data, Nat. Methods, 13, 581, 10.1038/nmeth.3869
Caporaso, J.G., Lauber, C.L., Walters, W.A., Berg-Lyons, D., Lozupone, C.A., Turnbaugh, P.J.,. & Knight, R. , 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the national academy of sciences, 108(Supplement 1), 4516–4522.
Carbajal-Valenzuela, 2022, Microbial diversity in cultivated and feral vanilla vanilla planifolia orchids affected by stem and rot disease, Microb. Ecol., 84, 821, 10.1007/s00248-021-01876-8
Chambers, 2021, Genotyping-By-Sequencing diversity analysis of international Vanilla collections uncovers hidden diversity and enables plant improvement, Plant Sci., 311, 10.1016/j.plantsci.2021.111019
Chaparro, 2012, Manipulating the soil microbiome to increase soil health and plant fertility, Biol. Fertil. Soils, 48, 489, 10.1007/s00374-012-0691-4
Chen, 2021, Harnessing knowledge from maize and rice domestication for new crop breeding, Mol. Plant, 14, 9, 10.1016/j.molp.2020.12.006
Delgado-Baquerizo, 2016, Microbial diversity drives multifunctionality in terrestrial ecosystems, Nat. Commun., 7, 1, 10.1038/ncomms10541
Dempewolf, 2017, Past and future use of wild relatives in crop breeding, Crop Sci., 57, 1070, 10.2135/cropsci2016.10.0885
Díaz, 2016, The global spectrum of plant form and function, Nature, 529, 167, 10.1038/nature16489
Díez, 2017, Effects of light intensity on the morphology and CAM photosynthesis of Vanilla planifolia Andrews, Rev. Fac. Nac. De. Agron. Medellín, 70, 8023, 10.15446/rfna.v70n1.61736
Fasiolo, 2020, Scalable visualization methods for modern generalized additive models, Journal of computational and Graphical Statistics, 29, 78, 10.1080/10618600.2019.1629942
Favre, 2022, A genome-wide assessment of the genetic diversity, evolution and relationships with allied species of the clonally propagated crop Vanilla planifolia Jacks. ex Andrews, Genet. Resour. Crop Evol., 1
Fernandes, 2013, ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq, PLOS One, 8, 10.1371/journal.pone.0067019
Fierer, 2007, Toward an ecological classification of soil bacteria, Ecology, 88, 1354, 10.1890/05-1839
Flanagan, 2016, An integrated strategy for the conservation and sustainable use of native Vanilla species in Colombia, Lankesteriana, 16, 201, 10.15517/lank.v16i2.26007
Garbeva, 2004, Microbial diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness, Annu. Rev. Phytopathol., 42, 243, 10.1146/annurev.phyto.42.012604.135455
Gepts, 2004, Crop domestication as a long-term selection experiment, Plant Breed. Rev., 24, 1
Gillespie, 2021, Tree species mixing affects soil microbial functioning indirectly via root and litter traits and soil parameters in European forests, Funct. Ecol., 35, 2190, 10.1111/1365-2435.13877
Goettsch, 2021, Extinction risk of Mesoamerican crop wild relatives, Plants, People, Planet, 3, 775, 10.1002/ppp3.10225
Grisoni, 2021, The beautiful hills: half a century of vanilla (Vanilla planifolia Jacks. ex Andrews) breeding in Madagascar, Genet. Resour. Crop Evol., 68, 1691, 10.1007/s10722-021-01119-2
Hänke, H., Barkmann, J., Blum, L., Franke, Y., Martin, D.A., Niens, J., Osen, K., Uruena, V., Witherspoon, S.A. and Wurz, A., 2018. Socio-economic, land use and value chain perspectives on vanilla farming in the SAVA Region (north-eastern Madagascar): The Diversity Turn Baseline Study (DTBS) (No. 1806).
Harlan, 1971, Toward a rational classification of cultivated plants, Taxon, 20, 509, 10.2307/1218252
Harman, 2019, Symbiotic root-endophytic soil microbes improve crop productivity and provide environmental benefits, Scientifica, 2019
Havkin-Frenkel, 2018
Hodgkin, T. and Hajjar, R., 2007. Using crop wild relatives for crop improvement: trends and perspectives. Crop wild relative conservation and use, pp.535–548.
Holdridge, L.R., 1967. Life zone ecology. Life zone ecology., (rev. ed.).
Householder, 2010, Diversity, natural history, and conservation of Vanilla (Orchidaceae) in Amazonian wetlands of Madre de Dios, Peru, J. Bot. Res. Inst. Tex., 227
Johnson, 2021, Vanilla aerial and terrestrial roots host rich communities of orchid mycorrhizal and ectomycorrhizal fungi, Plants, People, Planet, 3, 541, 10.1002/ppp3.10171
Kalam, 2020, Recent understanding of soil acidobacteria and their ecological significance: a critical review, Front. Microbiol., 2712
Kappelle, 2016
Karremans, 2020, A reappraisal of Neotropical Vanilla. With a note on taxonomic inflation and the importance of alpha taxonomy in biological studies, Lankesteriana, 20, 395
Kassambara, A. and Mundt, F., 2017. "Package ‘factoextra’." Extract and visualize the results of multivariate data analyses.
Kattge, 2020, TRY plant trait database–enhanced coverage and open access, Glob. Change Biol., 26, 119, 10.1111/gcb.14904
Khan, 2020, Super-pangenome by integrating the wild side of a species for accelerated crop improvement, Trends Plant Sci., 25, 148, 10.1016/j.tplants.2019.10.012
Kielak, 2016, The ecology of Acidobacteria: moving beyond genes and genomes, Front. Microbiol., 7, 744, 10.3389/fmicb.2016.00744
Kohlmann, 2010, Biodiversity conservation in Costa Rica: a correspondence analysis between identified biodiversity hotspots (Araceae, Arecaceae, Bromeliaceae, and Scarabaeinae) and conservation priority life zones, Rev. Mex. De. Biodivers., 81, 511
Koyyappurath, 2015, Differential responses of vanilla accessions to root rot and colonization by fusarium oxysporum f. sp. radicis-vanillae, Front. Plant Sci., 6, 1125, 10.3389/fpls.2015.01125
La, 1998, Nutritive characteristics of vanilla, Chin. J. Trop. Crops, 2, 55
Laliberté, E., Legendre, P., Shipley, B. and Laliberté, M.E., 2014. Package ‘FD’. Measuring functional diversity from multiple traits, and other tools for functional ecology, pp.1–0.
Lavorel, 2012, How fundamental plant functional trait relationships scale‐up to trade‐offs and synergies in ecosystem services, J. Ecol., 100, 128, 10.1111/j.1365-2745.2011.01914.x
Lê, 2008, FactoMineR: an R package for multivariate analysis, J. Stat. Softw., 25, 1, 10.18637/jss.v025.i01
Legendre, 2001, Ecologically meaningful transformations for ordination of species data, Oecologia, 129, 271, 10.1007/s004420100716
Maitner, 2018, The bien r package: a tool to access the Botanical Information and Ecology Network (BIEN) database, Methods Ecol. Evol., 9, 373, 10.1111/2041-210X.12861
Marra, 2011, Practical variable selection for generalized additive models, Comput. Stat. Data Anal., 55, 2372, 10.1016/j.csda.2011.02.004
Martin, 2020, Land-use history determines ecosystem services and conservation value in tropical agroforestry, Conserv. Lett., 13, 10.1111/conl.12740
Martin, 2021, Shade-tree rehabilitation in vanilla agroforests is yield neutral and may translate into landscape-scale canopy cover gains, Ecosystems, 24, 1253, 10.1007/s10021-020-00586-5
Martin, D.A., Andrianisaina, F., Fulgence, T.R., Osen, K., Rakotomalala, A.A.N.A., Raveloaritiana, E., Soazafy, M.R., Wurz, A., Andriafanomezantsoa, R., Andriamaniraka, H., Andrianarimisa, A., Barkmann, J., Dröge, S., Grass, I., Guerrero-Ramirez, N., Hänke, H., Hölscher, D., Rakouth, B., Ranarijaona, H.L.T., and Kreft, H., 2022. Land-use trajectories for sustainable land system transformations: Identifying leverage points in a global biodiversity hotspot. Proceedings of the National Academy of Sciences, 119(7).
Martin, 2011, Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet. J., 17, 10, 10.14806/ej.17.1.200
Maruenda, 2013, Exploration of Vanilla pompona from the Peruvian Amazon as a potential source of vanilla essence: Quantification of phenolics by HPLC-DAD, Food Chem., 138, 161, 10.1016/j.foodchem.2012.10.037
Maxted, 2006, Towards a definition of a crop wild relative, Biodivers. Conserv., 15, 2673, 10.1007/s10531-005-5409-6
Maxted, 2007, Creation and use of a national inventory of crop wild relatives, Biol. Conserv., 140, 142, 10.1016/j.biocon.2007.08.006
McMurdie, 2013, phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data, PLOS One, 8, 10.1371/journal.pone.0061217
Meilleur, 2004, In situ conservation of crop wild relatives: status and trends, Biodivers. Conserv., 13, 663, 10.1023/B:BIOC.0000011719.03230.17
Meyer, 2013, Evolution of crop species: genetics of domestication and diversification, Nat. Rev. Genet., 14, 840, 10.1038/nrg3605
Oksanen, F.Guillaume Blanchet, Michael Friendly, Roeland Kindt, Pierre Legendre, Dan Mc.Glinn, Peter R. Minchin, R.B. O.'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Eduard Szoecs and Helene Wagner, 2020. vegan: Community Ecology Package. R package version 2.5–7. https://CRAN.R-project.org/package=vegan.
Osewold, 2022, Support trees in vanilla agroforests of Madagascar: diversity, composition and origin, Agrofor. Syst., 10.1007/s10457-022-00733-y
Osorio, 2014, Nutrient status and vegetative growth of Vanilla planifolia Jacks plants as affected by fertilization and organic substrate composition, Acta Agron., 63, 326, 10.15446/acag.v63n4.40754
Osterhoudt, 2017
Palama, 2009, Metabolic changes in different developmental stages of Vanilla planifolia pods, J. Agric. Food Chem., 57, 7651, 10.1021/jf901508f
Pérez-Silva, 2021, Quantification of the aromatic potential of ripe fruit of Vanilla planifolia (Orchidaceae) and several of its closely and distantly related species and hybrids, Eur. Food Res. Technol., 247, 1489, 10.1007/s00217-021-03726-w
Pinaria, 2010, Fusarium species associated with vanilla stem rot in Indonesia, Australas. Plant Pathol., 39, 176, 10.1071/AP09079
Porras-Alfaro, 2007, Mycorrhizal fungi of Vanilla: diversity, specificity and effects on seed germination and plant growth, Mycologia, 99, 510, 10.1080/15572536.2007.11832545
Puthur, 2005, Influence of light intensity on growth and crop productivity of Vanilla planifolia Andr. General and Applied, Plant Physiol., 31, 215
Quast, 2012, The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Res., 41, D590, 10.1093/nar/gks1219
Redden, 2015
Ross-Ibarra, 2007, Plant domestication, a unique opportunity to identify the genetic basis of adaptation, Proc. Natl. Acad. Sci. USA, 104, 8641, 10.1073/pnas.0700643104
Sandheep, 2014, Screening and identification of potential Trichoderma sp. against soil borne pathogens of vanilla (Vanilla planifolia), Indian J. Agric. Res., 48, 459, 10.5958/0976-058X.2014.01330.4
Sauvadet, 2019, Shade trees have higher impact on soil nutrient availability and food web in organic than conventional coffee agroforestry, Sci. Total Environ., 649, 1065, 10.1016/j.scitotenv.2018.08.291
Schlüter, 2007, Genetic variation in Vanilla planifolia (Orchidaceae), Econ. Bot., 61, 328, 10.1663/0013-0001(2007)61[328:GVIVPO]2.0.CO;2
Schneider, 2012, NIH Image to ImageJ: 25 years of image analysis, Nat. Methods, 9, 671, 10.1038/nmeth.2089
SINAC. 2018. Plan estratégico 2018–2025 Programa nacional corredores biológicos de Costa Rica. http://enbcr.go.cr/sites/default/files/sinac_2018_planestrategico_programa_nacional_de_corredores_biologicos_costa_rica.pdf (accessed 25 October 2020).
Soto Arenas, 2010, A revision of the Mexican and Central American species of Vanilla Plumier ex Miller with a characterization of their ITS region of the nuclear ribosomal DNA, Lankesteriana, 9, 285
Tanksley, 1997, Seed banks and molecular maps: unlocking genetic potential from the wild, Science, 277, 1063, 10.1126/science.277.5329.1063
Theis, 1957, A vanilla hybrid resistant to Fusarium root rot, Phytopathology, 47, 579
Van Der Heijden, 2008, The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems, Ecol. Lett., 11, 296, 10.1111/j.1461-0248.2007.01139.x
Van Heerwaarden, 2011, Genetic signals of origin, spread, and introgression in a large sample of maize landraces, Proc. Natl. Acad. Sci. USA, 108, 1088, 10.1073/pnas.1013011108
Vincent, 2013, A prioritized crop wild relative inventory to help underpin global food security, Biol. Conserv., 167, 265, 10.1016/j.biocon.2013.08.011
Wang, 2007, Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy, Appl. Environ. Microbiol., 73, 5261, 10.1128/AEM.00062-07
Watteyn, 2020, Vanilla distribution modeling for conservation and sustainable cultivation in a joint land sparing/sharing concept, Ecosphere, 11, 10.1002/ecs2.3056
Wood, S., 2017. Package “mgcv”: mixed GAM computation vehicle with GCV/AIC/REML smoothness estimation. Version.
Wood, 2002, GAMs with integrated model selection using penalized regression splines and applications to environmental modelling, Ecol. Model., 157, 157, 10.1016/S0304-3800(02)00193-X
Wurz, 2022, Win-win opportunities combining high yields with high multi-taxa biodiversity in tropical agroforestry, Nat. Commun., 13, 10.1038/s41467-022-30866-8
Xiong, 2015, Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota, Proteomics, 15, 3424, 10.1002/pmic.201400571
Xiong, 2017, Bio-fertilizer application induces soil suppressiveness against Fusarium wilt disease by reshaping the soil microbiome, Soil Biol. Biochem., 114, 238, 10.1016/j.soilbio.2017.07.016
Yoneda, 2021, Novel plant-associated acidobacteria promotes growth of common floating aquatic plants, duckweeds, Microorganisms, 9, 1133, 10.3390/microorganisms9061133
Yumurtaci, 2015, Utilization of wild relatives of wheat, barley, maize and oat in developing abiotic and biotic stress tolerant new varieties, Emir. J. Food Agric., 01, 10.9755/ejfa.v27i1.17852
Zeder, 2006, Documenting domestication: the intersection of genetics and archaeology, Trends Genet., 22, 139, 10.1016/j.tig.2006.01.007
Zhang, 2020, Spatial patterns and interspecific associations during natural regeneration in three types of secondary forest in the central part of the Greater Khingan Mountains, Heilongjiang Province, China, Forests, 11, 152, 10.3390/f11020152