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

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.

The world faces severe challenges in providing food security for a growing world population during climate change. This puts pressure on modern agriculture, including adapting crops to new environments and cultivation on less acreage. The tools for adapting crops exist within a species' genetic diversity.  Crop wild relatives (CWR) are wild taxa with a close genetic relationship to our crops. CWRs contain a breadth of genetic adaption for various habitats due to their wide geographical distribution. This invaluable diversity of genes is essential for improving breeding of crops and therefore needs to be sustainably conserved in situ to prevent the loss of the future crop adaptation.  Fragaria vesca appears on the list of priority CWRs for conservation within the Nordic region.  To create an efficient conservation strategy for F. vesca, knowledge about the genetic differences between populations within the Nordic region must be obtained. Therefore, this study aimed to optimise PCR protocol for 10 microsatellite primers in F. vasca. The annealing temperature was successfully optimised for all 10 primer pairs. Two of the primer pairs revealed intra-specific diversity. The study also found support for the earlier discovered genetic divergence between Icelandic and other European populations.

A growing world population means an increase in crop demand. At the same time climate change threatens food security as crops may become maladapted to a new environment. We need to adapt crops to increase crop yield and become resistant to a changed environment to meet this. Crop wild relatives (CWR), which have a genetic relatedness with our crops, will be of importance as a genetic resource for crop adaption and needs to be protected. Vaccinium myrtillus is one of the prioritized species on the Nordic countries CWR priority list. Here I report PCR protocols that can be used for amplifying microsatellites, or SSRs, within V. myrtillus for use in analyses of genetic diversity within and between populations. PCRs with varying annealing temperatures (Ta) were performed. An optimal Ta for the primer pair was found for four SSR loci, and for four SSR loci, an approved Ta was found. These eight primer pairs can be used to amplify SSRs for analyses of the genetic diversity between V. myrtillus populations. This is needed to evaluate which populations to focus on in conservation programmes to ensure a broad genetic diversity usable in crop adaptation to meet increasing crop demand and climate change.

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.

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In the future, food security will face significant challenges due to climate change and a growing world population. One approach to make agriculture more sustainable is to preserve biodiversity by utilizing crop wild relatives as a source of genetic material. These crop wild relatives are closely related to today’s cultivated crops and can be an important asset to combat food insecurity. Gaining more knowledge about a species’ genetic diversity through microsatellite analysis is an important step for future conservation and potential utilization in crop improvement. However, before these studies can take place the microsatellite markers have to be optimized for PCR. In this study, eleven microsatellite markers were optimized for bilberry individuals. Optimized annealing temperatures were found for all markers and most of them had amplification in three or more of the individuals tested from Sweden, Finland and Iceland. Ten out of the eleven tested markers were regarded suitable for future genetic diversity analyses. The eleventh, VCB-C00694, was considered unsuitable due to formation of primer dimers and not amplifying in several individuals. By assessing the genetic diversity of bilberry, Vaccinium myrtillus, it opens up the possibility to enrich their domesticated relative the American blueberry, Vaccinium corymbosum, by introducing new genetic variety. In relation to this, the increased knowledge about genetic diversity among bilberries in the Nordic can lead to better understanding of their need for conservation.

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.

Sugar beet and its wild relatives share a base chromosome number of nine and similar chromosome morphologies. Yet, interspecific breeding is impeded by chromosome and sequence divergence that is still not fully understood. Since repetitive DNAs are among the fastest evolving parts of the genome, we investigated, if repeatome innovations and losses are linked to chromosomal differentiation and speciation. We traced genome and chromosome-wide evolution across 13 beet species comprising all sections of the genera Beta and Patellifolia. For this, we combined short and long read sequencing, flow cytometry, and cytogenetics to build a comprehensive framework that spans the complete scale from DNA to chromosome to genome. Genome sizes and repeat profiles reflect the separation into three gene pools with contrasting evolutionary patterns. Among all repeats, satellite DNAs harbor most genomic variability, leading to fundamentally different centromere architectures, ranging from chromosomal uniformity in Beta and Patellifolia to the formation of patchwork chromosomes in Corollinae/Nanae. We show that repetitive DNAs are causal for the genome expansions and contractions across the beet genera, providing insights into the genomic underpinnings of beet speciation. Satellite DNAs in particular vary considerably between beet genomes, leading to the evolution of distinct chromosomal setups in the three gene pools, likely contributing to the barriers in beet breeding. Thus, with their isokaryotypic chromosome sets, beet genomes present an ideal system for studying the link between repeats, genomic variability, and chromosomal differentiation and provide a theoretical fundament for understanding barriers in any crop breeding effort.