Anthracnose, caused by <i>Colletotrichum truncatum</i>, is a major disease of lentil (<i>Lens culinaris</i> Medik.) on the Canadian prairies. Resistance to the more virulent race Ct0 of the pathogen is extremely rare within the <i>L. culinaris</i> gene pool thus resistance is being introgressed from <i>Lens ervoides</i>. The overall hypothesis of this project was that resistance derived from <i>Lens ervoides</i> accession L-01-827A would provide uniquely low levels of resistance to <i>Colletotrichum truncatum</i>. Individual studies were performed to: i) test field-resistance of interspecific lines; ii) develop a cutting-method to generate replicated phenotypic data on single plants; iii) study the deterioration of resistance between the juvenile phase (JP) and adult phases (AP) in the line CDC Redberry; and iv) examine genetic control of resistance in a susceptible and partially resistant background. Field evaluations of <i>L. culinaris x L. ervoides</i> lines indicated resistance genes from the wild species will provide unprecedented levels of disease control and heritability of the trait was estimated to be moderate. Single plant phenotyping of resistance is unreliable, thus the feasibility of using clonal propagation of individual plants to generate replicated ratings was evaluated. Results showed consistency in segregation ratios between cutting and seedling-derived plants of the same population, thus the method was utilized for testing of genetic control of segregating populations. CDC Redberry showed varying disease levels depending on the age of the plants with resistance acquisition in the JP that decreased as the plants proceeded through the AP. The F₁, F₂ and F_2:3 generations of two introgression populations were tested for resistance. Resistance from <i>L. ervoides</i> to both races of <i>C. truncatum</i> appeared to be due to the same gene(s) or from the same linkage block in both populations. Models for genetic control were consistent between F₂ and F_2:3 generations, however were different between the populations depending on whether the interspecific line was crossed into a susceptible or partially resistant <i>L. culinaris</i> background. However duplicate recessive epistasis seemed to control susceptibility in the susceptible background and when JP resistance was not a factor. There were significant differences between the JP and AP on more than a third of the F₂s tested supporting different resistance gene action based on growth phase. Resistance in the JP seemed to be due to dominant and recessive epistasis. It was postulated that the the populations may have had segregation distortion commonly found in interspecific populations, thus the previously described genotypes for cotyledon colour and albino plants were used to test the hypothesis of segregation distortion. Segregation of these traits were found to be similarly distorted to previously reported interspecific <i>L. culinaris x L. ervoides</i> populations supporting the hypothesis that continued segregation distortion was found in the introgression populations. Overall, it was found that resistance derived from <i>L. ervoides</i> accession L-01-827A is a highly effective source for the lentil breeding program, however the result suggest more than one backcross to <i>L. culinaris</i> be necessary to properly integrate the resistance genes to eventually obtain fully fertile, adapted lentil cultivars.

Anthracnose, caused by <i>Colletotrichum truncatum</i>, is a major disease of lentil (<i>Lens culinaris</i> Medik.) on the Canadian prairies. Resistance to the more virulent race Ct0 of the pathogen is extremely rare within the <i>L. culinaris</i> gene pool thus resistance is being introgressed from <i>Lens ervoides</i>. The overall hypothesis of this project was that resistance derived from <i>Lens ervoides</i> accession L-01-827A would provide uniquely low levels of resistance to <i>Colletotrichum truncatum</i>. Individual studies were performed to: i) test field-resistance of interspecific lines; ii) develop a cutting-method to generate replicated phenotypic data on single plants; iii) study the deterioration of resistance between the juvenile phase (JP) and adult phases (AP) in the line CDC Redberry; and iv) examine genetic control of resistance in a susceptible and partially resistant background. Field evaluations of <i>L. culinaris x L. ervoides</i> lines indicated resistance genes from the wild species will provide unprecedented levels of disease control and heritability of the trait was estimated to be moderate. Single plant phenotyping of resistance is unreliable, thus the feasibility of using clonal propagation of individual plants to generate replicated ratings was evaluated. Results showed consistency in segregation ratios between cutting and seedling-derived plants of the same population, thus the method was utilized for testing of genetic control of segregating populations. CDC Redberry showed varying disease levels depending on the age of the plants with resistance acquisition in the JP that decreased as the plants proceeded through the AP. The F₁, F₂ and F_2:3 generations of two introgression populations were tested for resistance. Resistance from <i>L. ervoides</i> to both races of <i>C. truncatum</i> appeared to be due to the same gene(s) or from the same linkage block in both populations. Models for genetic control were consistent between F₂ and F_2:3 generations, however were different between the populations depending on whether the interspecific line was crossed into a susceptible or partially resistant <i>L. culinaris</i> background. However duplicate recessive epistasis seemed to control susceptibility in the susceptible background and when JP resistance was not a factor. There were significant differences between the JP and AP on more than a third of the F₂s tested supporting different resistance gene action based on growth phase. Resistance in the JP seemed to be due to dominant and recessive epistasis. It was postulated that the the populations may have had segregation distortion commonly found in interspecific populations, thus the previously described genotypes for cotyledon colour and albino plants were used to test the hypothesis of segregation distortion. Segregation of these traits were found to be similarly distorted to previously reported interspecific <i>L. culinaris x L. ervoides</i> populations supporting the hypothesis that continued segregation distortion was found in the introgression populations. Overall, it was found that resistance derived from <i>L. ervoides</i> accession L-01-827A is a highly effective source for the lentil breeding program, however the result suggest more than one backcross to <i>L. culinaris</i> be necessary to properly integrate the resistance genes to eventually obtain fully fertile, adapted lentil cultivars.

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

Tesis por compendio / Alimentar a la futura población en crecimiento en un contexto de cambio climático exige nuevos enfoques y herramientas de mejora genética para desarrollar nuevas variedades de cultivos que sean resilientes y eficientes en el uso de los recursos. Entre las hortalizas, la berenjena (Solanum melongena) es reconocida como un cultivo importante y como tal está incluida en el Anexo 1 del Tratado Internacional sobre los Recursos Fitogenéticos para la Alimentación y la Agricultura, que incluye 34 cultivos considerados como los más relevantes para la humanidad. Antes del inicio de esta tesis, se disponía de pocas herramientas genéticas y genómicas para la mejora genética de la berenjena, las cuales se revisan en un capítulo introductorio. Asimismo, hemos reconocido la importancia de los parientes silvestres de la berenjena, que apenas se han utilizado en la mejora genética de la misma. A este respecto, para hacer un uso más eficiente de los parientes silvestres en la mejora genética, propusimos un enfoque ambicioso, llamado "introgressiomics", que consiste en un desarrollo sistemático y masivo de materiales que lleven introgresiones de parientes silvestres (CWR), los cuales generalmente son una fuente inexplorada e desaprovechada de variación genética. Los trabajos realizados en esta tesis están relacionados con la aplicación de este enfoque a la berenjena. En este marco, los objetivos generales de la tesis son el desarrollo de la información y herramientas genéticas y genómicas en el acervo genético de la berenjena, utilizando un enfoque multidisciplinario y multifacético para la mejora genética en el desarrollo de nuevas variedades mejoradas y resistentes usando especies relacionadas como fuente de variación. Concretamente, en el primer capítulo de esta tesis, secuenciamos el transcriptoma de dos especies relacionadas con la berenjena, la silvestre Solanum incanum y la especie cultivada africana S. aethiopicum, que tienen un gran interés en la mejora genética de la berenjena. Los transcriptomas se ensamblaron en 83,905 y 87,084 unigenes para S. incanum y S. aethiopicum respectivamente, los cuales fueron extensivamente anotados estructuralmente y funcionalmente. La busqueda de variantes alélicas identificó decenas de miles de polimorfismos intraespecíficos e interespecíficos, así como alrededor de un millar de SSRs en cada especie. En el segundo capítulo, un subconjunto de esos marcadores (11 SSRs y 35 SNPs) se analizaron para confirmar su utilidad para la huella genética, la evaluación de la diversidad y el establecimiento de relaciones entre las berenjenas cultivadas (común, escarlata y gboma). Observamos que los SSRs y los SNPs proporcionaron resultados diferentes en el establecimiento de las relaciones, lo que sugiere que cada tipo de marcador muestreó diferentes niveles de variación genética. Sin embargo, aunque ambos marcadores proporcionaron un nivel similar de información, los SNPs parecen proporcionar una mejor resolución que los SSRs para materiales filogenéticamente más distantes. En el tercer capítulo, para ampliar la estimación de la diversidad genética y las relaciones genéticas entre y dentro de las especies silvestres y cultivadas pertenecientes al complejo berenjena, realizamos un genotipado masivo, mediante un enfoque de genotipado por secuenciación, de 76 accesiones pertenecientes a 17 especies del acervo genético primario, secundario y terciario de la berenjena común. De los 75,399 sitios polimórficos identificados, 12,859 se asociaron a regiones CDS y se usaron para establecer una evaluación exhaustiva y detallada de la diversidad alélica natural y las relaciones genéticas en el acervo genético de la berenjena utilizando tres enfoques diferentes (estructura jerárquica de la población, dendrograma basado en UPGMA y análisis de PCoA). En el cuatro capítulo, desarrollamos un mapa genético interespecífico entre S. incanum y S. melongena, vinculado a otros / Feeding the future burgeoning population in a climate change scenario demands new breeding approaches and tools to develop new resource-efficient and resilient crop varieties. Among vegetable crops, eggplant (Solanum melongena) is recognized as an important food crop and as such is included in the Annex 1 of the International Treaty on Plant Genetic Resources for Food and Agriculture, which includes 34 crops considered as most relevant for mankind. Before the start of this thesis, few genetic and genomic tools and resources for eggplant breeding, which are reviewed in an introductory chapter, were available. We have recognized the importance of wild eggplant relatives, which have been barely used in eggplant breeding. In this respect, in order to make a more efficient use of wild relatives in plant breeding, we proposed an ambitious approach, called "introgressiomics", consisting of a systematic and massive development of materials carrying introgressions from crop wild relatives (CWRs), which usually are an unexplored and unexploited source of genetic variation for breeding traits. The works done in this thesis are related to the application of the introgressiomics approach to eggplant. In this framework, the general objectives of the thesis are the development of genetic and genomic information and tools in eggplant genepool, using a multidisciplinary and multi-pronged approach to assist eggplant breeding in the development of new improved and resilient varieties using eggplant relatives as a source of variation. Specifically, in the first chapter of this thesis, we sequenced the transcriptome of two eggplant related species, the wild Solanum incanum and the cultivated S. aethiopicum, that have a great interest in eggplant breeding. The transcriptomes were assembled in 83,905 and 87,084 unigenes for S. incanum and S. aethiopicum respectively, which were extensively structurally and functionally annotated. The variant call analysis identified tens of thousands intraspecific and interspecific polymorphisms, as well as around a thousand of SSRs in each species. In the second chapter, a subset of those markers (11 SSRs and 35 SNPs) was tested for confirming their usefulness for genetic fingerprinting, diversity evaluation and the establishment of relationships in cultivated eggplant (common, scarlet and gboma) genepools. We observed that SSRs and SNPs provided different results in the establishment of the relationships, suggesting that each marker type sampled different levels of genetic variation. However, although both markers provided a similar level of information, SNPs seem to provide a better resolution than SSRs for materials phylogenetically more distant. In the third chapter, in order to broaden the estimation of the genetic diversity and genetic relationships among and within wild and cultivated species belonging to eggplant complexes, we performed a massive genotyping, by a genotype-by-sequencing approach, of 76 accessions belonging to 17 species from the primary, secondary and tertiary genepool of common eggplant. Out of 75,399 polymorphic sites identified, 12,859 were associated to CDS regions and used to establish an exhaustive and detailed evaluation of the natural allelic diversity and genetic relationships in eggplant genepool using three different approaches (hierarchical population structure, UPGMA-based dendrogram, and PCoA analysis). In the four chapter, we developed an interspecific genetic map between S. incanum and S. melongena, linked to four previous eggplant maps and to one tomato map. A total of 243 molecular markers were successfully mapped consisting of 42 COSII, 99 SSRs, 88 AFLPs, 9 CAPS, 4 SNPs and one morphological polymorphic markers encompassed 1085 cM distributed in 12 linkage groups. Based on the syntheny with tomato, the candidate genes involved in the core chlorogenic acid synthesis pathway in eggplant (PAL, C4H, 4CL, HCT, C3¿H, HQT), five polyphenol oxidase genes (PPO1, PPO2, PPO3, PP / Alimentar la futura població en creixement en un context de canvi climàtic exigeix nous enfocaments i eines de millora genètica per desenvolupar noves varietats de cultius que siguin resilients i eficients en l'ús dels recursos. Entre les hortalisses, l'albergínia (Solanum melongena) és reconeguda com un cultiu important i com a tal està inclosa en l'Annex 1 del Tractat Internacional sobre els Recursos Fitogenètics per a l'Alimentació i l'Agricultura, que inclou 34 cultius considerats com els més rellevants per a la humanitat. Abans de l'inici d'aquesta tesi, es disposava de poques eines genètiques i genòmiques per a la millora genètica de l'albergínia, les quals es revisen en un capítol introductori. Així mateix, hem reconegut la importància dels parents silvestres de l'albergínia, que tot just s'han utilitzat en la millora genètica de la mateixa. Referent a això, per fer un ús més eficient dels parents silvestres a la millora genètica, vam proposar un enfocament ambiciós, anomenat "introgressiomics", que consisteix en un desenvolupament sistemàtic i massiu de materials que portin introgresions de parents silvestres (CWR), els quals generalment són una font inexplorada i desaprofitada de variació genètica. Els treballs realitzats en aquesta tesi estan relacionats amb l'aplicació d'aquest enfocament a l'albergínia. En aquest marc, els objectius generals de la tesi són el desenvolupament de la informació i eines genètiques i genòmiques en el patrimoni genètic de l'albergínia, utilitzant un enfocament multidisciplinari i multifacètic per a la millora genètica en el desenvolupament de noves varietats millorades i resistents emprent spècies relacionades com a font de variació. Concretament, en el primer capítol d'aquesta tesi, seqüenciem el transcriptoma de dues espècies relacionades amb l'albergínia, la silvestre Solanum incanum i l'espècie cultivada africana S. aethiopicum, que tenen un gran interès en la millora genètica de l'albergínia. Els transcriptomes s'ensamblaren en 83,905 i 87,084 unigenes per S. incanum i S. aethiopicum respectivament, els quals van ser extensivament anotats estructuralment i funcionalment. La recerca de variants al·lèliques va identificar desenes de milers de polimorfismes intraespecífics i interespecífics, així com al voltant d'un miler de SSRs en cada espècie. En el segon capítol, un subconjunt d'aquests marcadors (11 SSRs i 35 SNPs) es van analitzar per confirmar la seva utilitat per l'empremta genètica, l'avaluació de la diversitat i l'establiment de relacions entre les albergínies conreades (comú, escarlata i gboma). Observem que els SSRs i els SNPs van proporcionar resultats diferents en l'establiment de les relacions, el que suggereix que cada tipus de marcador va mostrejar diferents nivells de variació genètica. No obstant això, encara que tots dos marcadors van proporcionar un nivell similar d'informació, els SNPs semblen proporcionar una millor resolució que els SSRs per materials filogenèticament més distants. En el tercer capítol, per a ampliar l'estimació de la diversitat genètica i les relacions genètiques entre i dins de les espècies silvestres i conreades pertanyents al complex albergínia, vam realitzar un genotipat massiu, mitjançant un enfocament de genotipat per seqüenciació, de 76 accessions pertanyents a 17 espècies del patrimoni genètic primari, secundari i terciari de l'albergínia comuna. Dels 75,399 llocs polimòrfics identificats, 12,859 es van associar a regions CDS i es van usar per a establir una avaluació exhaustiva i detallada de la diversitat al·lèlica natural i les relacions genètiques en el patrimoni genètic de l'albergínia utilitzant tres enfocaments diferents (estructura jeràrquica de la població, dendrograma basat en UPGMA i anàlisi de PCoA). En el quart capítol, desenvolupem un mapa genètic interespecífic entre S. incanum i S. melongena, vinculat a altres quatre mapes anterior / Gramazio, P. (2018). GENETICS AND GENOMICS OF CULTIVATED EGGPLANTS AND WILD RELATIVES [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/104605 / Compendio

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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