Species in the genus Vanilla represent important biological resources relevant to sustainable cultivation of the natural vanilla crop. Understanding the diversity and distributions of these species is key for the conservation and use of this agrobiodiversity. The Chocó region, which encompasses the humid tropical forest stretching from southern Panama through western Colombia and into northwest Ecuador, harbors a significant portion of the secondary gene pool of the vanilla crop, whose diversity is still incompletely documented. During our ongoing research into neotropical vanilla, and within the framework of the project “Vainilla Aroma Chocó”, we documented a distinct morphotype of Vanilla in disturbed tropical rainforest in the northern Colombian Pacific region. We undertook a thorough revision of herbarium material to determine taxonomic affinities, and we assessed conservation status. Vanilla pacifica sp. nov. is allied to the principal cultivated species, V. planifolia, and V. hartii. We provide a taxonomic description, illustrations, and observations on ecology and use. We evaluate conservation status and propose management actions. With only three subpopulations known, one in Colombia and two in northwest Ecuador, and a total of six documented individuals, V. pacifica is assessed as Critically Endangered [CR]. From our revision of herbarium material, we also report the occurrence of V. hartii in Colombia, bringing the total number of Vanilla species in Colombia to 28. This study further contributes to our knowledge of vanilla crop wild relatives and underlines the important role of community participation in biodiversity research and conservation.

Background: Nine Vanilla species have been reported in Mexico. Vanilla calyculata has been formally documented in Brazil, Colombia, El Salvador, Guatemala, Honduras, and Nicaragua. Its presence in Mexico has been suggested based on a single sterile specimen but its identity has not been confirmed, and no further records are known. Questions: Do the live individuals of Vanilla sp. found in Western Mexico correspond to Vanilla calyculata? Studied species: Vanilla calyculata. Study site and dates: Western Mexico, 2019-2025. Methods: Specimens of Vanilla sp. were collected and determined taxonomically using specialized literature. Mexican herbaria were widely consulted. The conservation status was assessed using the IUCN Red List criteria. Results: We confirmed the presence of Vanilla calyculata in Mexico based on wild specimens and herbarium records. This species is now known from three localities in Western Mexico, which increases its distribution up to 1,800 km northwards. The number of species of the Vanilla genus reported for Mexico increases to 10 and to three for the west of the country. The conservation status of V. calyculata in Mexico is C2a(i), “Critically Endangered - CR”, based on the IUCN criteria. Conclusions: This work contributes to the knowledge on the geographic distribution of the genus Vanilla in the Neotropical region, Mexican orchid diversity, and emphasizes the need for immediate actions to ensure the conservation of this important component of agrobiodiversity in Mexico.

Species in the genus Vanilla Plum. ex. Mill. (Orchidaceae) are of economic importance as wild relatives of the natural vanilla crop. Nonetheless, we still lack the taxonomic clarity necessary to effectively conserve and utilise this plant diversity. Colombia is at the centre of the distribution of Vanilla subgenus Xanata section Xanata Soto Arenas P.J.Cribb, the secondary gene pool for the vanilla crop. We undertook an extensive examination of Colombian national and international herbarium material, including type specimens for Vanilla calyculata Schltr., V. columbiana Rolfe, and V. phaeantha Rchb.f. We provide distribution maps for Vanilla phaeantha and V. calyculata in Colombia, and show that both V. phaeantha and V. calyculata are broadly sympatric within the type location of V. columbiana. Through examination of type material, we reassess the recently-proposed synonymy of Vanilla columbiana with V. calyculata. and concur with previous conclusions that the holotype of V. columbiana is a likely immature bud. Nonetheless, in both floral and vegetative traits, we consider that the greater affinity between Vanilla columbiana and V. phaeantha warrants their synonymy. Consequently, we resurrect the taxon Vanilla calyculata Schltr. Both Vanilla phaeantha and V. calyculata are native to Tropical Dry Forest, a highly threatened ecosystem. With a national Area of Occupancy of only 156 km2 and 68 km2 respectively, both species have a preliminary IUCN Red List classification of Endangered, EN: B2a,b(ii,iii,iv,v) at the national level. Representation of both species in in situ and ex situ conservation strategies requires improvement. With this taxonomic clarity, more thorough conservation evaluation and ecological studies can now be undertaken to inform the management plans for these species.

Orchids constitute one of the most spectacular radiations of flowering plants. However, their origin, spread across the globe, and hotspots of speciation remain uncertain due to the lack of an up-to-date phylogeographic analysis. We present a new Orchidaceae phylogeny based on combined high-throughput and Sanger sequencing data, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and c. 7% (1921) of the 29 524 accepted species, and use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distributions from the World Checklist of Vascular Plants. The orchids' most recent common ancestor is inferred to have lived in Late Cretaceous Laurasia. The modern range of Apostasioideae, which comprises two genera with 16 species from India to northern Australia, is interpreted as relictual, similar to that of numerous other groups that went extinct at higher latitudes following the global climate cooling during the Oligocene. Despite their ancient origin, modern orchid species diversity mainly originated over the last 5 Ma, with the highest speciation rates in Panama and Costa Rica. These results alter our understanding of the geographic origin of orchids, previously proposed as Australian, and pinpoint Central America as a region of recent, explosive speciation.

Assessing variation in root functional traits may offer novel insights into plant adaptations to changing environmental conditions. However, such studies, particularly on epiphytic species in tropical ecosystems, are still limited. Previous research has suggested that precipitation has a major impact on epiphyte survival and thus can be considered a candidate driver of epiphytic root trait variation, though compelling evidence is lacking. In this study, we investigated variation in 19 root functional traits in 43 epiphytic (36 species) and 14 terrestrial (7 species) orchids along an elevational gradient in Colombia and examined whether this variation is associated with differences in abiotic conditions. Contrary to previous studies, our findings did not associate trait variation with precipitation but revealed strong correlations with solar radiation, temperature, and water vapour pressure. The variation was particularly pronounced in traits related to the velamen radicum. Epiphytic and terrestrial orchids showed similar responses despite their different growth habits. Overall, these patterns suggest that higher sunlight and temperature conditions lead both orchid types to allocate more resources to root structures that mitigate abiotic stress, and highlight the role of other environmental factors in driving root trait variability.

Vanilla is an economically important crop for low-lying humid tropical regions, but cultivated plants face serious phytosanitary problems. Fusarium wilt is a devastating disease affecting vanilla crops, caused by the fungal pathogens Fusarium oxysporum f. sp. vanillae (Fov) and F. oxysporum f. sp. radicis-vanillae (Forv), part of the F. oxysporum species complex (FOSC). We characterized 29 fungal isolates from a vanilla crop and crop wild relatives (CWR) using molecular (EF1-α and ITS-rRNA loci) and morphological traits. Fusarium was the predominant genus, followed by Colletotrichum and Clonostachys. Four Fusarium species were identified: F. oxysporum (37.9%), Fusarium solani (20.7%), Fusarium pseudocircinatum (13.8%) and Fusarium concentricum (10.3%). The latter three species were isolated only from CWR and may represent latent pathogens. Fov was isolated from both the crop and CWR, while a Forv-affiliated isolate was also found in a vanilla crop, marking the first report in the neotropical region. The EF1-α locus provided greater genotype resolution, as well as having reference sequences for Forv. However, the fungal barcode ITS locus is widely applied. We recommend the continued use of both loci for Fusarium diagnosis in vanilla to facilitate early detection and the development of effective integrated crop management strategies.

The tropical Andean landscape has been dramatically transformed over the last century with remaining native forest limited to small fragments within a heterogeneous matrix of crops, cattle pastures, and urban environments. We aimed to explore the impact of habitat transformation on the population dynamics in an endemic twig epiphytic orchid located within the undisturbed forest and within modified matrix habitat in two regions with contrasting landscape structures: with a dominant shade coffee matrix and a dominant grassland matrix. Over 2 years, we surveyed 4,650 individuals of the Colombian endemic orchid, Rodriguezia granadensis. We undertook four post-breeding censuses in three sites in each region in both native forest and pasture sub-sites (12 sub-sites; 48 censuses in total), and constructed demographic transition matrices (n = 36). The transition probabilities were calculated using a Bayesian approach and population grow rates were evaluated using asymptotic models and elasticities using transient dynamics. Between regions, higher population growth rate and inertia (defined as the largest or smallest long-term population density with the same initial density distribution) was seen in the shade coffee-dominated landscape. Additionally, population growth rate and damping ratio was higher in forest compared with pasture, with lower convergence time for the forest subsites. These demographic patterns reveal the contrasting levels of population resilience of this orchid in different landscape structures with the more connected shade-coffee dominated landscape permitting some healthier populations with greater population growth and survival in forest than pasture. This study highlights that twig epiphyte colonization of isolated phorophytes in pastures should not be interpreted as a sign of a healthy population but as a temporal transitory period.

Fusarium wilt, caused by the fungus Fusarium oxysporum f. sp. vanillae (Fov), is a disease that results in significant losses in commercial vanilla production. The genera Ceratobasidium (Ceratobasidiaceae) and Tulasnella (Tulasnellaceae), which are often reported as mutualistic symbionts in orchids, belong to the form genus Rhizoctonia, a paraphyletic group of fungi with potential for pathogen biocontrol. We assayed the antagonistic properties of the form genus Rhizoctonia from the roots of neotropical orchids: two Tulasnella spp. isolates (Bv3 and Er1) and one Ceratobasidium sp. (Er19). In a dual culture, we found that form genus Rhizoctonia isolates can generate a biocontrol effect against Fusarium through the mechanisms of antibiosis and competition for space and nutrients. On histological observations, orchid root endophytes also demonstrated potential for mutualistic symbiosis development by establishing themselves on the surface and within the root tissue of Vanilla planifolia accessions multiplied in vitro (NSF021 and NSF092). However, in plant assays, the form genus Rhizoctonia isolates did not reduce symptom expression or disease development due to infection by Fov in the host. These results contribute to the knowledge of the interactions between tropical orchids and their microbiota and demonstrate the need for multidisciplinary studies for the implementation of integrated management strategies for Fusarium disease in commercial systems.

Vanilla is an economically important crop for low-lying humid tropical regions. World demand for natural vanilla is increasing, but cultivated plants face serious phytosanitary problems. The disease known as Fusarium wilt is mainly related to the fungus Fusarium oxysporum f. sp. vanillae, and for its management, the pathogen–host relationship must be understood. Four in vitro multiplied vanilla accessions were evaluated: two Vanilla planifolia from Colombia and Mexico, one from V. odorata, and one (1) F1 hybrid (V. rivasii × V. trigonocarpa). In addition, three isolates of Fusarium from different symptomatic plants present in small-scale agroforestry systems: (1Fov) F. oxysporum f. sp. vanillae from leaf, (2Fov) F. oxysporum f. sp. vanillae from root and (3Fs) F. solani also from root. Plants with two months of growth were inoculated in vitro by immersion of roots, and the development of Fusarium wilt was recorded for 15 days, using a severity scale to describe symptoms and to calculate the area under the disease progress curve (AUDPC). No statistical differences were found when analyzing the interaction between Fusarium isolates and vanilla accessions. However, when independently analyzing the design factor Fusarium isolates, there were significant differences; the 1Fov isolate of F. oxysporum f. sp. vanillae induced the highest symptoms as well as death in some plants of all accessions, while F. solani was considered a secondary pathogen. There were no statistical differences for the vanilla accessions factor, but the values of AUDPC and symptoms observed suggest a slight resistance in all the accessions. Therefore, it is suggested to explore the vanilla gene pool to generate multiplication material with resistance genes and to contribute with genetic improvement to successfully integrate the management of Fusarium wilt in commercial systems.

Natural vanilla is a high-value crop with demand increasing globally. Crop wild relatives (CWR) represent valuable agrobiodiversity and are prioritized in the Global Strategy for Plant Conservation. Vanilla species are naturally rare with historically infrequent botanical collections. Despite their importance as CWR, fewer than 10% of Vanilla species have been evaluated for the IUCN Red List. Colombia is a diversity center for Vanilla species, yet many remote regions are lacking detailed floristic characterization. We show that the participation of rural communities in scientific endeavor enhances capacity to register biodiversity. We report two Vanilla species in the under-explored region of the Serranía de las Quinchas in the mid–Magdalena River valley in Colombia, including the first report for Colombia of Vanilla karen-christianae. For this, and the second species, Vanilla dressleri, we present descriptions with photographic botanical illustrations, updated distribution maps, and preliminary conservation status assessment. Both species are of elevated conservation concern, categorized as Endangered – EN: B2a,b(ii,iii,iv,v) following IUCN criteria. Within Colombia, all recorded occurrences for both species fall outside protected areas. Vanilla crop wild relatives in Colombia have urgent conservation needs. The Serranía de las Quinchas is a priority for further botanical exploration for Vanilla, as well as other protected areas with appropriate habitat. In situ conservation should be complemented with ex situ actions. Community participation in biodiversity research is recommended in this and other remote regions as an integral step towards enhancing biodiversity research and community-based conservation.

Chapter 6 Conservation and Sustainable Use of Vanilla Crop Wild Relatives in Colombia Book Editor(s):Daphna Havkin-Frenkel, Daphna Havkin-Frenkel Rutgers University, NJ, USASearch for more papers by this authorFaith C. Belanger, Faith C. Belanger Rutgers University, NJ, USASearch for more papers by this author First published: 06 July 2018 https://doi.org/10.1002/9781119377320.ch6Citations: 4 AboutPDFPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShareShare a linkShare onFacebookTwitterLinked InRedditWechat Summary This chapter reviews research into vanilla Crop wild relatives (CWR), and identifies priorities for research, and actions necessary for conservation and sustainable use for the valuable genetic resources in Colombia. Given the importance of the microbiome for plant health, any long-term ex situ CWR conservation strategy for Vanilla genetic resources must also contemplate the simultaneous conservation of microbial symbionts. Continued exploration of Vanilla diversity in the country is necessary, and will likely result in further species being discovered. Comprehensive research program must include continued genomic, metabolomic, ecological and agronomical study of native Vanilla species, thereby informing effective conservation strategies, in addition to facilitating efficient use of genetic diversity in crop improvement programs. The ecology of Vanilla species in the wild is still underexplored, yet knowledge of ecological and physiological processes and traits in wild populations is of great value for the development of effective strategies for conservation and sustainable use. Citing Literature Handbook of Vanilla Science and Technology, Second Edition RelatedInformation

Crown architecture usually is heterogeneous as a result of foraging in spatially and temporally heterogeneous light environments. Ecologists are only beginning to identify the importance of temporal heterogeneity for light acquisition in plants, especially at the diurnal scale. Crown architectural heterogeneity often leads to a diurnal variation in light interception. However, maximizing light interception during midday may not be an optimal strategy in environments with excess light. Instead, long-lived plants are expected to show crown architectures and leaf positions that meet the contrasting needs of light interception and avoidance of excess light on a diurnal basis. We expected a midday depression in the diurnal course of light interception both at the whole-crown and leaf scales, as a strategy to avoid the interception of excessive irradiance. We tested this hypothesis in a population of guava trees (Psidium guajava L.) growing in an open tropical grassland. We quantified three crown architectural traits: intra-individual heterogeneity in foliage clumping, crown openness, and leaf position angles. We estimated the diurnal course of light interception at the crown scale using hemispheric photographs, and at the leaf scale using the cosine of solar incidence. Crowns showed a midday depression in light interception, while leaves showed a midday peak. These contrasting patterns were related to architectural traits. At the crown scale, the midday depression of light interception was linked to a greater crown openness and foliage clumping in crown tops than in the lateral parts of the crown. At the leaf scale, an average inclination angle of 45° led to the midday peak in light interception, but with a huge among-leaf variation in position angles. The mismatch in diurnal course of light interception at crown and leaf scales can indicate that different processes are being optimized at each scale. These findings suggest that the diurnal course of light interception may be an important dimension of the resource acquisition strategies of long-lived woody plants. Using a temporal approach as the one applied here may improve our understanding of the diversity of crown architectures found across and within environments.

A distinctive species, Vanilla denshikoira, is described from the North West Amazon, in Colombia, within the Guiana Shield region. The species has morphological features similar to those of species in the Vanilla planifolia group. It is an important addition to the vanilla crop wild relatives, bringing the total number of species in the V planifolia group to 21. Vanilla denshikoira is a narrow endemic, known from only a single locality, and highly vulnerable to anthropological disturbance. Under IUCN criteria it is categorized CR. The species has potential value as a non-timber forest product. We recommend a conservation program that includes support for circa situm actions implemented by the local communities.

Light is considered a non-limiting factor for vascular epiphytes. Nevertheless, an epiphyte's access to light may be limited by phorophyte shading and the spatio-temporal environmental patchiness characteristic of epiphytic habitats. We assessed the extent to which potential light interception in Rodriguezia granadensis, an epiphytic orchid, is determined by individual factors (plant size traits and leaf traits), or environmental heterogeneity (light patchiness) within the crown of the phorophyte, or both. We studied 104 adult plants growing on Psidium guajava trees in two habitats with contrasting canopy cover: a dry tropical forest edge, and isolated trees in a pasture. We recorded the number of leaves and the leaf area, the leaf position angles, and the potential exposure of the leaf surface to direct irradiance (silhouette area of the leaf blade), and the potential irradiance incident on each plant. We found the epiphytes experience a highly heterogeneous light environment in the crowns of P.guajava. Nonetheless, R.granadensis plants displayed a common light interception strategy typical of low-light environments, resembling terrestrial, forest understory plants. Potential exposure of the total leaf surface to direct irradiance correlated positively with plant size and within-plant variation in leaf orientation. In many-leaved individuals, within-plant variation in leaf angles produced complementary leaf positions that enhanced potential light interception. This light interception strategy suggests that, in contrast to current wisdom, enhancing light capture is important for vascular epiphytes in canopies with high spatio-temporal heterogeneity in light environments.

Background: Mycorrhizal interactions are ecologically important to understand the orchid biology since orchids depend on mycorrhizal fungi for seed germination.Objective: The aim of this study was to evaluate the ability of fungi isolated from the roots of Vanilla adult plants to induce symbiotic seed germination.Materials and Methods: Fruits from three native species of Vanilla from Colombia were collected to test symbiotic seed germination through experiments in vitro.First, the viability of the seeds was determined through scarification of the seeds using sand-paper and immersion of the embryos in a 1% tetrazolium chloride solution.Second, a surface-sterilized seeds suspension was added to the petri dishes that had an isolated fungus previously obtained from adult plants.Finally, the percentage of seed germination and the index of growth were calculated and the germination stages were morphologically characterized.A one-way analysis of variance (ANOVA) for evaluate differences among species was realized for seed viability variable.For seed germination trails, a factorial design was used and a generalized linear model with a gamma distribution and link function "Log" was performed.Results: With Ceratobasidium strains percentages of germination close to 80% were reached whereas, Tulasnella isolates promoted percentages close to 60%.At Vanilla species level, V. rivasii had the best performance for the variables evaluated.Conclusion: This study presented a new procedure for measuring Vanilla seed viability, as well as, it provided relevant information about seed development.Both Ceratobasidium and Tulasnella isolates can promote germination in Vanilla seeds.However, with the Ceratobasidium strains, higher stages of development were reached.

Background and Aims Improved understanding of the secondary gene pools of crops is essential for advancing genetic gain in breeding programmes. Common bean, Phaseolus vulgaris, is a staple crop with several wild relatives in its secondary gene pool. The year-long bean, P. dumosus, an important crop in Guatemala, is considered particularly closely related to P. vulgaris and a potential source of novel variation. However, the genetic diversity and relationship to other Phaseolus species of P. dumosus remain unclear. Methods We conducted the first comprehensive investigation of P. dumosus genetic diversity using both nuclear and chloroplast genome markers. Our nuclear marker set included over 700 markers present within the Phaseolus DArT (Diversity Arrays Technology) array, which we applied to P. dumosus and other relatives of P. vulgaris (including every secondary gene pool species: P. acutifolius, P. albescens, P. coccineus and P. costaricensis). Key Results Phaseolus dumosus arose from hybridization of P. vulgaris and P. coccineus, followed by at least two later hybridizations with sympatric congener populations. Existing P. dumosus collections have low genetic diversity. Conclusions The under-utilized crop P. dumosus has a complex hybrid origin. Further sampling in the region in which it arose may uncover additional germplasm for introgressing favourable traits into crops within the P. vulgaris gene pool.