Dissertations / Theses on the topic 'Crop Wild relatives (CWRs)'

Crop wild relatives are important for agriculture due to the genetic richness they possess. They have been used in plant breeding to develop high yielding varieties; varieties with improved resistance to biotic and abiotic stresses, and enhanced nutritional content. Securing their conservation in the long-term is critical to enable the continuous development of crops’ varieties able to respond to future challenges. The work presented in this thesis is a contribution to the effort of understanding the ex situ conservation gaps of crop wild relatives, their expected response to climate change and their needs for conservation. Methods used in this thesis include species distribution modelling, gap analyses, a case study assessing the preliminary IUCN Red List categories, species distribution projections onto future climate change scenarios, and an estimation of the global value of crop wild relatives based on their likelihood of being used in plant breeding, and the contributions of their associated crops to human diets and agricultural production systems. The methods used here can be applied to more crop genepools for global conservation planning, and can also be adapted for analysis at the regional and national level. The results presented here are being used to improve the conservation of the wild relatives of 29 crops.

As the global population rises, the demand for food increases which underscores a need for improvement in food security. Disease pressures are a major concern surrounding sustainable agriculture. Static crop populations, containing little to no genetic diversity, are vulnerable to diverse pathogen populations. Wild relatives of crop plants are a reservoir for new disease resistance traits that can be introgressed into cultivated crops. The identification of novel disease resistance is of paramount importance because pathogen co-evolution is not only defeating current resistance genes (R genes) but chemical controls as well. Phytophthora sojae (P. sojae), the causal agent of Phytophthora root and stem rot disease, reduces soybean harvests worldwide. We developed an approach to screen for new R genes that recognize core effectors from P. sojae. We expect R genes identified by these screens to be durable because P. sojae requires core effectors for virulence. We utilized effector-based screening to probe Glycine soja germplasm with core RXLR effectors from P. sojae to search for novel R genes. We developed segregating populations from crosses of P. sojae resistant G. soja germplasm with susceptible G. max cultivar Williams to determine inheritance of potential R genes in germplasm that responded to core effectors. We are using marker assisted breeding to map disease resistance traits in recombinant inbred (RI) lines. To better understand pathosystems, we examined host resistance and susceptibility using bioinformatics. We analyzed the interaction between Arabidopsis thaliana ecotype Col-0 and Hyaloperonospora arabidopsidis isolate Emwa1 using a publicly available RNA time-course experiment. We describe a new algorithm to sort genes into time-point specific clusters using activation and repression parameters. Gene ontology annotations were used to identify defense genes with unique expression profiles, and A. thaliana null mutants for these genes were significantly more susceptible to Emwa1 than wild-type. We plan to use these tools to rapidly identify and guide introgression of durable disease resistance into crop species.
Ph. D.

Modern crop varieties contain limited genetic diversity. Demand from an expanding human population requires crop yields to increase substantially, however, a low capacity for adaptation may leave crops susceptible to environmental change, threatening future food security. Crop wild relatives (CWR) are a valuable, but threatened, genetic resource containing more genetic diversity than their cultivated relatives that can be utilised by plant breeders to improve the resilience of new crop varieties. This thesis researches methodologies to facilitate systematic, active conservation of CWR and their genetic diversity within a national context using the UK and its devolved administrations as an exemplar. Methods involve the development of CWR inventori es, gap analyses, assessment of CWR habitat preferences , a case study seeking to justify the establishment of the first UK CWR genetic reserve on The Lizard Peninsula, Cornwall and finally, exploration of the use of next generation sequencing as a tool for targeting collection of accessions to fill genetic gaps in genebanks. A key success of this research was the involvement of stakeholders, bridging the gap between research and practice. The methods used can now be applied to other countries and can be integrated into European and global conservation planning, contributing to improved future food security.

Climate change is predicted to have far-reaching deleterious impacts worldwide; agriculture in particular is expected to be effected by significant loss of suitable land and crop yields in the world’s most populous and poorest regions. Crop wild relatives (CWR) are a rich source of underutilised genetic diversity which could help to mitigate climate change for agriculture through breeding new resilient varieties. However, CWR are under-conserved and threatened in the wild. This thesis researches and develops systematic methodologies to advance knowledge and support action on in situ CWR conservation at the global level. Methods included developing a global inventory of CWR associated with crops important for food security worldwide, species distribution modelling, climate change analysis, in situ gap analysis, reserve planning and prioritisation, and, examining the congruence of CWR distributions with regions of high biodiversity and crop diversity. The methods described here can be applied to CWR at both the national and regional level to ensure robust in situ CWR conservation. A principal success of this research is the global CWR inventory, which has been used in several national strategies and as the basis of a major ex situ germplasm collection mission worldwide.

Agrobiodiversity are threatened due to habitat loss, land reclamation and fragmentation, spread of diseases and pests, genetic uniformity, genetic erosion, and other human activities. Crop wild relatives (CWR) are wild species that are more or less genetically related to crops that can be used to introgress useful genes for improvement of productivity, resistance to biotic and abiotic stresses and quality of cultivated crop. These valuable resources are threatened and untapped for crop improvements. Therefore, their conservation would be valuable and will contribute to maintaining and promoting the sustainability of crop diversity, facilitating agricultural production and supporting the increasing demand for food, feed and natural resources. This thesis tackle for the first time the diversity and conservation status of CWR in North Africa region. In order to achieve this goal, different methods, approaches and techniques were used. These are identifying CWR in the region (CWR checklist), prioritize the checklist, ex situ and in situ gap analyses, species distribution modelling, threat assessment using IUCN Red List categories, climate change assessment and molecular genetic analysis of wild barley (Hordeum vulgare subsp. spontaneum (C. Koch) Thell). The outcomes will assist in lay the foundations for future ex situ and in situ conservation, and subsequent use.

Human-induced land degradation and climate change can reduce agricultural productivity and increase susceptibility to food shortages at local and global scales. Planting perennial crop species, such as fruit and nut crops, may be an intervention strategy because of their beneficial contributions to sustainable agriculture and human nutrition. Many perennial temperate fruit and nut species are however, particularly vulnerable to frost events, drought, insufficient chill hours, and disease and insect outbreaks. Modifying these species to yield harvests under a wider range of biotic and abiotic conditions may increase the value and long-term viability of perennials in agroecosystems. This dissertation examines adaptation and ecogeography in temperate perennial fruit crops, using apple (Malus sensu lato) as an example for case studies. The resilience of feral domestic apple trees in abandoned farmstead orchards throughout the southwestern U.S. indicates plasticity in adapting to local environmental conditions. Dendrochronology reveals these trees tend to persist where they have access to supplemental water, either as shallow groundwater or irrigation. While domestic apples are cultivated under a range of growing conditions, wild relatives of agricultural crops may further expand the cultivable range of the species. Crop wild relatives are species closely related to agricultural species, including progenitors that may contribute beneficial traits to crops. Sampling the genetic variation in crop wild relatives may benefit from ecological genetics and GIS theory to reveal genetic structure. The Pacific crabapple is an example of a wild apple relative that may contain genetic variation useful in apple breeding. Species distribution modeling of the Pacific crabapple identifies a narrow climatic window of suitable habitat along the northern Pacific coast, and genetic fingerprinting reveals a highly admixed genetic structure with little evidence of natural or cultural selection. While the moist coastal Pacific Northwest is not necessarily characteristic of many apple-growing regions, the species may have useful adaptations transferable to domestic apples. Genetic resources offer a promising source of raw material for adapting crops to future agricultural environments; their characterization, conservation, and use may offer important contributions to adaptation and use of perennial crops in agro-ecosystems.

Un requisito previo en cualquier programa de conservación de Recursos Fitogenéticos es la la estimación de la diversidad existente. El inventario de las especies parientes de cultivos prioritarios en Venezuela (PSC) se basó en los principales Catálogos de Flora del país, seleccionando los taxones próximamente relacionados con los cultivos. Se incluyeron 47 géneros, 217 especies y 228 taxones, correspondientes a 28 familias botánicas. De éstas, las que tienen mayor riqueza son: Fabaceae, Solanaceae, Araceae, Lauraceae, Dioscoreaceae, Poaceae, Rosaceae y Myrtaceae. Existen 26 especies endémicas, pertenecientes a los géneros Xanthosoma, Persea, Dioscorea, Prunus y Manihot. Los géneros nativos con especies del pool genético primario del cultivo son Manihot, Solanum (Sección Petota), Lycopersicon, Ananas, Capsicum, Dioscorea, Xanthosoma, Phaseolus, Theobroma, Ipomoea, Gossypium, Arracacia y Psidium. El número de taxones evaluados según los criterios de la IUCN es prácticamente nulo y la representación de accesiones venezolanas de PSC en los bancos de germoplasma nacionales e internacionales es muy baja. En relación con el estudio taxonómico del género Phaseolus, se reconocen tres especies en Venezuela: P. lunatus L., P. vulgaris L. y P. dumosus Macfad., que se diferencian fácilmente por la morfología de las flores, brácteas, bractéolas y legumbres. Phaseolus lunatus y P. vulgaris crecen en estado silvestre y cultivado y Phaseolus dumosus corresponde a la forma cultivada que se ha naturalizado. En relación al género Macroptilium, los resultados del análisis morfológico, molecular y biogeográfico de las especies del complejo Macroptilium gracile indican que los taxones pertenecen a una sola especie con tres taxones infraespecíficos, de los cuales dos son nuevas combinaciones: una subespecie no típica (Macroptilium gracile subsp. scolecocarpus (Piper) Berlingeri & M.B. Crespo, comb. nov.) y dos variedades en la subespecie tipo (M. gracile subsp. gracile var. gracile y M. gracile subsp. gracile var. subcoriaceum (Benth.) Berlingeri & M.B. Crespo, comb. nov.). Phaseolus diversifolius Pittier y P. unilobatus Pittier corresponden a sinonimias de Macroptilium gracile var. subcoriaceum y M. gracile var. gracile, respectivamente. En el género Macroptilium se reconocen seis especies en Venezuela: M. atropurpureum (DC.) Urb., M. lathyroides (L.) Urb., M. gracile (Poepp. ex Benth.) Urb., M. bracteatum (Nees & Mart.) Maréchal & Baudet, M. erythroloma (Mart. ex Benth.) Urb. y M. monophyllum (Benth.) Maréchal & Baudet. Macroptilium longepedunculatum (Mart. ex Benth.) Urb. y M. gracile (Poepp. ex Benth.) Urb., que algunos autores separan en el rango específico, corresponden a variedades extremas de una misma especie. Al tener prioridad el nombre M. gracile, M. longepedunculatum queda relegado a la sinonimia del primero.

Pigeonpea (Cajanus cajan) is a sub-tropical and tropical pulse rich in plant-based protein, carbohydrates, minerals, and vitamins. Helicoverpa armigera is the most devastating insect pest in pigeonpea. This study focussed on deciphering the molecular host plant resistance (HPR) mechanisms applied by Cajanus scarabaeoides a wild pigeonpea against insect using transcriptomic and proteomic studies. These HPR mechanisms were transferred to the cultivated pigeonpea via interspecific hybridisation, and they are stable at F2 generation. The study outcome provides a unique insight into the insect resistance mechanisms employed by C. scarabaeoides and lays the foundation for further studies and applications.

Dans les hauts plateaux des Andes entre le Pérou et la Bolivie, à 3 800 mètres d’altitude s’étend le lac Titicaca, berceau des civilisations précolombiennes et l’un des principaux centres mondiaux de domestication des espèces végétales cultivées pour l’agriculture. Cette région est reconnue comme le centre d’origine du quinoa, C. quinoa Willd. Elle concentre la plus grande diversité génétique du quinoa, tant pour les variétés paysannes cultivées que pour les espèces sauvages apparentées. Notre recherche a été conduite dans la région de Puno, Pérou, qui reste l’une des principales régions productrices de quinoa au monde. Le quinoa y présente une distribution spatiale selon un gradient climatique nord-sud et une différenciation en zones agroécologiques liée à l’altitude. Actuellement, sept principales espèces de parents sauvages du quinoa y sont présentes : C.ambrosioides L., C.incisum Poiret, C.pallidicaule Aellen, C.petiolare Kunth, C.hircinum Schrad., C.quinoa ssp. melanospermum Hunz. et C.carnosolum Moq. Cette diversité de ressources génétiques a une grande valeur pour l’évolution adaptative du quinoa notamment face aux effets du changement climatique. Notre thèse s’inscrit dans l’importance économique et culturelle du quinoa, étant à la fois une ressource alimentaire des régions andines et l’objet des marchés internationaux du fait de ses qualités nutritives. Cette opportunité économique peut avoir des impacts en termes de sécurité alimentaire, d’agrobiodiversité, et de gestion de l’agroécosystème. Cette thèse a analysé comment les communautés agricoles andines intègrent la présence des espèces de parents sauvages dans leurs pratiques de gestion et leurs pratiques agricoles autour du quinoa. Des cartographies participatives et des enquêtes ethnobotaniques ont été réalisées avec les membres de six villages choisis selon des critères biogéographiques. La modélisation chorématique a été appliquée à deux périodes, avant et après 1970, année charnière au Pérou pour l’agriculture, dans le but de montrer comment les dynamiques socio-spatiales du milieu andin se modifient, notamment en lien avec l’évolution de la culture du quinoa. La distribution des espèces de parents sauvages du quinoa apparaît fortement liée à l’organisation socio-spatiale de l’agroécosystème. Ces espèces sont maintenues par les villageois pour leurs multiples usages alimentaires, médicinaux et culturels, dans des espaces naturels, des zones pâturées, aux abords et également à l’intérieur des champs cultivés. Ceci est à la fois le résultat de la gestion dynamique organisée par les communautés rurales et des savoirs liés à ces espèces qui se transmettent de génération en génération. Cependant cette gestion est en train de changer sous la pression d’enjeux globaux liés au marché international du quinoa, dont les exigences impliquent de réduire la présence de parents sauvages dans les champs cultivés. En conclusion, la thèse aborde la durabilité des pratiques de gestion et des pratiques agricoles dans un objectif de conservation dynamique in situ de la biodiversité sauvage et cultivée. Une mise en perspective historique des résultats nous a permis de questionner l’évolution des pratiques de gestion de ces différentes espèces par les communautés locales. En termes d’implication, deux types de projets pourraient être réfléchis. Le développement de projets prenant en compte le maintien de la présence des parents sauvages du quinoa dans le champ cultivé est favorable à l’introduction de gènes d’intérêt pour aider le quinoa à s’adapter à des conditions écologiques changeantes sous les effets du changement climatique. Egalement, des projets spécifiques de conservation in situ de l’agrobiodiversité, qui considèrent l’espace naturel et l’espace cultivé comme un ensemble cohérent, représentent une voie de gestion de pools de gènes importante pour l’agriculture et l’alimentation mondiale
Lake Titicaca, the cradle of pre-Columbian civilizations and one of the world’s main centres of domestication for farmed plant species, lies 3,800 m above sea level in the central Andean Highlands between Peru and Bolivia. The region is acknowledged as the centre of origin of quinoa, Chenopodium quinoa Willd. The greatest genetic diversity of quinoa and its wild relatives is concentrated there. Our research was conducted in the Puno region (Peru), which remains one of the main quinoa producing regions in the world. Quinoa displays spatial distribution along a North-South climate gradient in the region, with differentiation into mostly elevation-related, agro-ecological zones that explain its genetic diversity. Seven main quinoa crop wild relatives currently exist there: C. ambrosioides L., C. incisum Poiret, C. pallidicaule Aellen, C. petiolare Kunth, C. hircinum Schrad., C. quinoa ssp. melanospermum Hunz. and C. carnosolum Moq. This diversity of plant genetic resources is of great value for the adaptive evolution of quinoa, especially under the effect of climate change. This PhD thesis deals with the economic and cultural importance of quinoa, which is both a food resource in the Andean regions and an international commodity due to its exceptional nutritional qualities (protein-rich). This economic opportunity may have impacts on local food security, agrobiodiversity and agro-ecosystem management. One way of investigating this issue is to examine how the distribution of crop wild relatives is linked to the way quinoa cultivation is spatially organized. The thesis analysed how Andean farming communities incorporate the presence of wild relatives in their quinoa-related management and farming practices. Participatory mapping and ethnobotanical surveys were carried out with members of six villages chosen according to biogeographical criteria along a North South gradient, combined with data related to elevation and the proximity to Lake Titicaca. In order to show how the socio-spatial dynamics of the Andean environment are changing, notably linked to changes in quinoa growing, chorematic modelling was applied to two periods, before and after 1970, which was a pivotal year for Peruvian farming (agrarian reform, territorial rights of indigenous communities). The distribution of quinoa crop wild relatives seems to be closely linked to how the agro-ecosystem is spatially organized. Local communities keep these species for their multiple food, medicinal and cultural uses in natural areas, grazing areas, around and in farmed fields. This results from the dynamic management organized by rural communities, and from knowledge of those species passed down through the generations, by both women and men. However, management is changing under the pressure of global challenges arising from the international quinoa market, which calls for fewer wild parents in farmed fields. To conclude, the thesis looks at the sustainability of management and farming practices with a view to dynamic in situ conservation of wild and cultivated biodiversity. Choremes are used to place the results in historical perspective, to see how the management of these different species by local communities is evolving. In terms of implications, two types of project could be considered. Developing projects that keep quinoa crop wild relatives in farmed fields promotes the introduction of genes of interest, helping quinoa to adapt to ecological conditions being modified by climate change. Likewise, specific projects for in situ conservation of agrobiodiversity, which consider natural and cultivated areas as a coherent whole, are a way of managing gene pools that is important for agriculture and for feeding the world

abstract: Since the Convention on Biological Diversity was established in 1992, more importance has been given to the conservation of genetic resources in the international community. In 2001, the International Treaty on Plant Genetic Resources for Food and Agriculture (PGRFA) focused on conserving plant genetic resources, including crop wild relatives (CWR). Some of these genetic resources hold desirable traits--such as transfer of plant disease resistance, improvement of nutritional content, or increased resistance to climate change--that can improve commercial crops. For many years, ex situex situ conservation was the prevalent form of protecting plant genetic resources. However, after PGRFA was published in 1998, in situ techniques have increasingly been applied to conserve wild relatives and enhance domesticated crops.In situ techniques are preferred when possible, since they allow for continued evolution of traits through natural selection, and viability of seed stock through continuous germination and regeneration. In my research, I identified regions in Bolivia and rated them according to their potential for successful programs of iin situ conservation of wild crop relatives. In particular, I analyzed areas according to the following criteria: a) The prevalence of CWRs. b) The impacts of climate change, land use change, population growth, and economic development on the continued viability of CWRs in an area. c) The socio-political and economic conditions that might impede or facilitate successful conservation programs and outcomes. This work focuses on three genera of particular importance in Bolivia: Peanut (Arachis spp.), Potato (Solanum spp.) and Quinoa (Chenopodium spp.). I analyzed the above factors for each municipality in Bolivia (the smallest scale for which appropriate data were available). The results indicate which municipalities are most likely to successfully engage in CWR conservation projects. Finally, I present guidelines for the creation of conservation projects that pinpoint some of the potential risks and difficulties with in situ conservation programs in Bolivia and more generally.
Dissertation/Thesis
M.S. Biology 2011

Crop wild relatives (CWR) are an indispensable and at the same time threatened genetic resources for plant breeding. The study uses wild species related to celery to demonstrate how genetic resources of CWRs can be actively maintained in their natural surroundings (in-situ). Genetic reserves should be designated for long term conservation of selected occurrences. The study presents the selection procedure in detail, aiming at the identification of occurrences and sites suitable for the designation of genetic reserves, the spatial model of a genetic reserve and first practical results of the project. The overall aim of the project is the establishment of a nationwide network of genetic reserves for Apium graveolens, Helosciadium repens, H. nodiflorum and H. inundatum, the four wild celery species native to Germany. Helosciadum repens (Jacq.) W.D.J.Koch is threatened by genetic erosion due to a decline in population numbers and sizes. The loss of any population is an irretrievable loss of diversity and opportunity to enhance crops in the future. Genetic reserves are one way to conserve these populations and their genetic potential. Twenty-seven populations were selected for the analysis in a decision process based on site information. Microsatellites (SSR) were used to elucidate the genetic diversity of German populations. A cluster analysis was performed to see if the individuals form clusters of similarity. For that, a discriminate analysis of principal components (DAPC) was conducted, as the inbreeding index indicated a high number of inbreeding events in the populations and thus discordance with HWE (Hardy-Weinberg equilibrium). The analysis identified six genetic groups, which coincide well with the geographic origin of the analysed plants. The allelic richness (mean counts of alleles per individual per population) was higher in the southern populations compared to the northern ones. This North-South discrepancy was also visible as a high heterogeneity in the cluster assignments in the DAPC analysis. These differences in genetic diversity might be a result of the biogeographic history of Europe, especially the last glacial maximum. For the establishment of genetic reserves, two populations were considered as most important: The population that differs the most from the average genetic composition and the population that represents the average genetic composition of a population the best. The two extremes of differentiation were interpreted as such that the former has a specific adaptation to its local environment, and the latter represents all populations the best. DifferInt was used to analyse the SSR data and validate the differentiation of all populations compared to a pool of populations. However, SSRs are not capable of detecting adaptive traits. Populations were additionally chosen from different eco-geographic units (EGU), to increase the chance of capturing different traits. EGUs (Naturräume) are areas of specific abiotic and biotic features. These features may influence selection pressures and induce local adaptations. Based on site parameters and genetic data, 14 most appropriate wild populations (MAWP) were identified for genetic reserves establishment. For H. repens, two eco-forms are known and described in the literature. Besides their different habitats (terrestrial/semi-terrestrial and aquatic) they can be differentiated by morphological traits. Leave and stolon sizes and flowering behaviour differ significantly. Furthermore, the roots of the aquatic forms do not anchor in soil but on other aquatic plants, wood or roots of trees, while the terrestrial form exhibits a shallow root system network similar to other perennial species. To this end, no genetic analysis was conducted to clarify the phylogenetic status of the putative forms and authors avoided the usage of any specific noun rather than form. The SSR data from the previous study was evaluated, particularly with regards to the two forms. Additionally, an ISSR analysis was conducted, and the data was used to perform a PCA. There was no genetic clustering regarding the two forms neither in the SSR nor in the ISSR data. Nonetheless, the North-South discrepancy in the genetic diversity that was visible in the DAPC plot was confirmed in the PCA of the ISSR data. However, markers may fail to detect quantitative variation for adaptively important traits. As the most obvious difference in the two habitats was the water availability, the adaptation of both forms to drought stress was studied by measuring the relative water content of leaves, system water content and water loss during drought stress conditions. The stomatal index was measured for different water treatment levels. The results indicate that phenotypic plasticity rather than genotypic adaptation is responsible for different H. repens phenotypes.