Doctor of Philosophy / Genetics Interdepartmental Program - Plant Pathology / Jesse A. Poland / A major challenge for 21st century plant geneticists is to predict plant performance based on genetic information. This is a daunting challenge, especially when there are thousands of genes that control complex traits as well as the extreme variation that results from the environment where plants are grown. Rapid advances in technology are assisting in overcoming the obstacle of connecting the genotype to phenotype. Next generation sequencing has provided a wealth of genomic information resulting in numerous completely sequenced genomes and the ability to quickly genotype thousands of individuals. The ability to pair the dense genotypic data with phenotypic data, the observed plant performance, will culminate in successfully predicting cultivar performance. While genomics has advanced rapidly, phenomics, the science and ability to measure plant phenotypes, has slowly progressed, resulting in an imbalance of genotypic to phenotypic data. The disproportion of high-throughput phenotyping (HTP) data is a bottleneck to many genetic and association mapping studies as well as genomic selection (GS). To alleviate the phenomics bottleneck, an affordable and portable phenotyping platform, Phenocart, was developed and evaluated. The Phenocart was capable of taking multiple types of georeferenced measurements including normalized difference vegetation index and canopy temperature, throughout the growing season. The Phenocart performed as well as existing manual measurements while increasing the amount of data exponentially. The deluge of phenotypic data offered opportunities to evaluate lines at specific time points, as well as combining data throughout the season to assess for genotypic differences. Finally in an effort to predict crop performance, the phenotypic data was used in GS models. The models combined molecular marker data from genotyping-by-sequencing with high-throughput phenotyping for plant phenotypic characterization. Utilizing HTP data, rather than just the often measured yield, increased the accuracy of GS models. Achieving the goal of connecting genotype to phenotype has direct impact on plant breeding by allowing selection of higher yielding crops as well as selecting crops that are adapted to local environments. This will allow for a faster rate of improvement in crops, which is imperative to meet the growing global population demand for plant products.

The rapid expansion of high-throughput phenotyping (HTP) platforms in agronomic research has led to a major shift in plant science towards time-series phenotyping that can track plant development through its life stages, providing an opportunity to dissect the genetic basis of longitudinal traits. Plant breeders can now phenotype large populations during the growing season and promote the desirable genetic gain for the traits of interest in specific time points within their breeding program. The biggest challenge is to use the various tools in a practical way to understand the many complexities of plant growth and development and breeding implications. This dissertation explores interdisciplinary frameworks to assess different applications of HTP for longitudinal traits in soybean breeding. We provide a review outlining the current analytical approaches in quantitative genetics and genomics to adequately use high-dimensional phenomic data. Examples, advantages, and pitfalls of each approach, and future research directions and opportunities are explored. Among longitudinal traits in soybean, average canopy coverage (ACC) and above-ground biomass (AGB) are promising traits to strategic improve yield gain. Soybean ACC is highly heritable, with a high genetic correlation to yield and can be effectively measured by unmanned aerial systems (UAS). This study reveals that progeny rows selection using yield given ACC (Yield|ACC) selected the most top-ranking lines in advanced yield trials, which emphasizes the value of HTP of ACC for selection in the early stages of soybean breeding. In addition, we developed a HTP methodology to predict soybean AGB over several days after planting (DAP) and assessed the quantitative genomic properties of temporal AGB using random regression models (RRM). Our results show that AGB narrow-sense heritability estimates fluctuated over time and the genetic correlation of AGB between DAP decreased as the days went further apart. Considering the trait heritability, high prediction accuracies suggest that AGB is a good indicator trait for genomic selection in soybean breeding. Different genomic regions were found to be associated with AGB over time with potential time-specific SNPs playing a role in the trait expression. Similarly, candidate genes were identified with potential different patterns of expression over time. This study presents novel genetic knowledge for longitudinal traits in soybean and may contribute to the development of new cultivars with high yield and optimized AGB. This is the first application of RRM for genomic evaluation of a longitudinal trait in soybean and provides a foundation that RRM can be an effective approach to understand the temporal genetic architecture of a longitudinal trait in other crops.

The study of human cranial morphology has a long and contentious history. This study is the first large scale analysis of ecoregion specific human cranial modularity and integration. It utilizes an analysis of morphometric craniofacial variation and ecoregion affinity to better understand the environmental contribution to biological shape. This study tested three hypotheses. First, that there was variation in craniofacial shape that was linked to an individual’s ecoregion. Second, that there were ecoregion specific patterns of cranial modularity. And third, that the patterns of cranial integration (or the level of covariation between any two modules) were also associated with an individual’s ecoregion, and that different environments would result in different patterns of modular dependence and independence. Three-dimensional scans of 298 human crania were collected from museums, representing four higher level ecoregions and 11 lower-level ecoregions. Each cranium was mapped and placed within two hierarchical ecoregions. By examining ecoregions, instead of individual climatic variables, this analysis gives a more complete picture of how the environment is influencing cranial variation. Modules, or relatively independent morphological regions of the crania, were identified and their level of integration was assessed for every ecoregion. Modular integration is an analysis of the relative strength of the covariation between any two modules, and previous research theorized that changes in integration reflected changes in modular independence during development (Bastir and Rosas, 2005; Hall, 2005; Raff, 1996). The variation in strength between modules, both intrapopulation and interpopulation, were assessed and various explanations were explored. This analysis found that each ecoregion exhibited significantly different craniofacial shape from one another. Patterns of integration were also variable by ecoregion, suggesting that the ecological shape variation observed was solidified early in development. This study also identified the presence of a nasal module in each ecoregion. Overall, the findings of this study demonstrate that human crania are variable by ecoregion and that environmental conditions have led to ecoregion specific patterns of cranial modular integration. / Anthropology

Le commerce mondial et les mouvements humains accroissent les probabilités de transport à longue distance de propagules, et leur introduction dans de nouvelles aires géographiques. Dans certains cas, des espèces récemment établies peuvent devenir dominantes dans la communauté envahie. Malgré les menaces sur les communautés natives et le fonctionnement des écosystèmes, les invasions biologiques constituent des expériences naturelles qui permettent d’étudier les processus éco-évolutifs en temps réel, notamment l’impact de nouvelles interactions biotiques sur la composition et la dynamique des communautés, l’adaptation rapide à de nouvelles conditions environnementales, ou la dispersion en limite de répartition. Les îles océaniques sont particulièrement sensibles aux invasions biologiques en raison de la faible diversité de leurs communautés natives. Dans les terres australes françaises, le carabique marcheur Merizodus soledadinus, natif de Patagonie, a été accidentellement introduit à Kerguelen en 1913. La présente étude vise à comprendre les principaux mécanismes à l’origine du succès invasif de cet insecte aux Iles Kerguelen. Un large ensemble de méthodes ont été utilisée pour explorer les traits écologiques de M. soledadinus, des populations à la molécule. Les analyses génétiques confortent l’hypothèse historique d’un unique évènement d’introduction dans un seul site des Iles Kerguelen. Les populations échantillonnées le long du gradient d’invasion ne montrent pas de structuration génétique. Les traits phénotypiques mesurés montrent une forte différentiation entre les individus selon le temps de résidence des populations, confirmant l’hypothèse de tri spatial des populations au cours de l’expansion géographique. Nous avons démontré que l’expansion géographique et la sélection d’habitats par M. soledadinus est principalement gouvernée par la disponibilité en eau, comme le suggère par la forte sensibilité des adultes au stress hydrique. En parallèle, la colonisation d’habitats en altitude dépend des conditions thermiques, qui semblent être contraignantes pour cet insecte à partir de 200m d’altitude. La colonisation d’habitats d’altitude progresse pourtant, probablement assistée par le changement climatique. Pour finir, les adultes M. soledadinus sont longévifs et actifs toute l’année. Les connaissances apportées sur l’écologie de M. soledadinus et sur la dynamique de son expansion géographique suggèrent la poursuite de la colonisation de l’archipel par ce prédateur. L’ensemble de ces connaissances pourraient être utiles à la paramétrisation d’un modèle d’expansion géographique, qui permettrait de définir les routes de dispersion et les taux d’expansion, dans l’objectif d’assister les mesures de gestion par les agents de la Réserve naturelle des Terres Australes et Antarctiques Françaises. / Global trade and human movements increase the likelihood of long-distance transportation of propagules and their subsequent introduction into new geographic regions. In some instances, newly established species can become dominant in invaded communities, at the expense of native species. Besides threatening invaded communities and ecosystem functions, biological invasions constitute natural experiments that allow to study eco-evolutionary processes in real time, including the occurrence of new biotic interactions affecting community composition, rapid adaptation to novel environmental conditions, or dispersal evolution at range margins. Because of their impoverished native communities, oceanic islands’ ecosystems are particularly sensitive to biological invasions, and the French subantarctic islands are no exception. For instance, the flightless predatory carabid beetle Merizodus soledadinus is native from the southern tip of South America, and has been accidentally introduced to the Kerguelen Islands in 1913. In the present work, we aimed at understanding the main mechanisms underlying the invasive success of this insect at the Kerguelen Islands. Using a vast array of methodologies, ecological features of M. soledadinus were investigated with analytical procedures scaling from population to molecule through the individual level. Genetic investigations support the historically-based hypothesis of a single introduction event at a unique location of the Kerguelen Islands. No genetic structure was observed among individuals sampled from different populations along the invasion gradient. We tested the hypothesis of spatial sorting of populations during range expansion, by exploring phenotypic changes among individuals sampled along the invasion gradient. The measured phenotypic traits revealed major differentiation of adults according to the residence time of their populations, confirming the occurrence of spatial sorting of populations during geographic expansion. We also demonstrated that the geographic expansion of M. soledadinus, and microhabitat selection, are primarily governed by the availability of water resources, as suggested by the high sensitivity to water stress of adults of this ground beetle. In parallel, colonisation of altitudinal habitats is governed by thermal conditions, which seem to be physiologically constraining from 200m asl onwards. As the altitudinal distribution of M. soledadinus still extends, we concluded that ongoing climatic changes play a pivotal role in this expansion. Finally, adults of this ground beetle are long-lived and active year-round. The ecological knowledge of M. soledadinus characteristics and spatial expansion dynamics suggest that the colonisation process of the Kerguelen archipelago by this species will continue. Altogether, these data could be used for parametrising range expansion models that would delineate dispersal pathways and expansion rates, in the objective to assist stakeholders’ management decisions.

<p>Improved phenotyping technologies and data analytic strategies have the potential to reduce the phenotyping bottleneck in breeding programs, increase the number of genotypes that can be evaluated, and improve genetic gain of maize. Ear photometry and remote sensing were evaluated in this dissertation for their integration into breeding programs to understand the development of grain yield in diverse germplasm and to better predict yield performance. Ear photometry was used in Chapter 2 to characterize the testcross performance of temperate and tropical inbred lines. The effect of heterosis among the temperate heterotic groups was more noticeable in the ear-related characteristics rather than kernel-size characteristics. Yield components were generally more heritable than grain yield per ear, so they were explored for their use in multi-trait genomic prediction for grain yield on a plot or ear basis in Chapter 3. Multi-trait genomic prediction of grain yield was improved where ear characteristics were known in the testing set compared with single-trait genomic prediction.  Additionally, single-trait genomic prediction was more accurate in the temperate germplasm compared to the tropical germplasm. Thus, ear photometry is an efficient method to quickly assess yield components in maize and improve yield prediction in certain circumstances. In Chapter 4, the effect of row selection, plot size, and plot trimming on remote sensing trait repeatability and prediction accuracy of biomass yield in sorghum or grain yield in maize was evaluated. Decreased plot size and configuration has been suggested to increase the number of genotypes that can be evaluated per unit area. In this study, larger plot sizes were favorable for increasing repeatability and excluding outer rows improved predictive modelling. Plot trimming was never shown to be significantly different from non-trimmed plots in this study. Genomic prediction is another way to minimize experimental size and phenotypic data collection and was evaluated in Chapter 5. A reaction norm was used to model the trajectory of hybrid yield performance across a gradient of 86 environments. The heritability and prediction accuracy of grain yield were both improved in the higher-yielding environments compared to the lower-yielding environments. Single nucleotide polymorphisms with the highest magnitude of effects were selected in each environment. Twenty-one SNPs were selected indicating many SNPs were selected in multiple environments. Candidate genes in linkage disequilibrium with many of these SNPs were previously reported as stress adaptions. Genomic prediction and remote sensing were integrated for prediction of grain yield in Chapter 6. Heritability of remote sensing traits generally improved throughout the growing season. Prediction accuracy of BLUPs were improved through an integrated phenomic and genomic prediction model for all scenarios tested. In summary, ear photometry and remote sensing are technologies to evaluate large populations for unique plant trait characteristics that can be used in combination with genomic prediction to improve understanding of grain yield development and grain yield prediction.</p>

Die Untersuchung des Phänotyps bringt z.B. bei genetischen Krankheiten ein Verständnis der zugrunde liegenden Mechanismen mit sich. Aufgrund dessen wurden neue Technologien wie RNA-Interferenz (RNAi) entwickelt, die Genfunktionen entschlüsseln und mehr phänotypische Daten erzeugen. Interpretation der Ergebnisse solcher Versuche ist insbesondere bei heterogenen Daten eine große Herausforderung. Wenige Ansätze haben bisher Daten über die direkte Verknüpfung von Genotyp und Phänotyp hinaus interpretiert. Diese Dissertation zeigt neue Methoden, die Entdeckungen in Phänotypen über Spezies und Methodik hinweg ermöglichen. Es erfolgt eine Erfassung der verfügbaren Datenbanken und der Ansätze zur Analyse ihres Inhalts. Die Grenzen und Hürden, die noch bewältigt werden müssen, z.B. fehlende Datenintegration, lückenhafte Ontologien und der Mangel an Methoden zur Datenanalyse, werden diskutiert. Der Ansatz zur Integration von Genotyp- und Phänotypdaten, PhenomicDB 2, wird präsentiert. Diese Datenbank assoziiert Gene mit Phänotypen durch Orthologie über Spezies hinweg. Im Fokus sind die Integration von RNAi-Daten und die Einbindung von Ontologien für Phänotypen, Experimentiermethoden und Zelllinien. Ferner wird eine Studie präsentiert, in der Phänotypendaten aus PhenomicDB genutzt werden, um Genfunktionen vorherzusagen. Dazu werden Gene aufgrund ihrer Phänotypen mit Textclustering gruppiert. Die Gruppen zeigen hohe biologische Kohärenz, da sich viele gemeinsame Annotationen aus der Gen-Ontologie und viele Protein-Protein-Interaktionen innerhalb der Gruppen finden, was zur Vorhersage von Genfunktionen durch Übertragung von Annotationen von gut annotierten Genen zu Genen mit weniger Annotationen genutzt wird. Zuletzt wird der Prototyp PhenoMIX präsentiert, in dem Genotypen und Phänotypen mit geclusterten Phänotypen, PPi, Orthologien und weiteren Ähnlichkeitsmaßen integriert und deren Gruppierungen zur Vorhersage von Genfunktionen, sowie von phänotypischen Wörtern genutzt. / In diseases with a genetic component, examination of the phenotype can aid understanding the underlying genetics. Technologies to generate high-throughput phenotypes, such as RNA interference (RNAi), have been developed to decipher functions for genes. This large-scale characterization of genes strongly increases phenotypic information. It is a challenge to interpret results of such functional screens, especially with heterogeneous data sets. Thus, there have been only few efforts to make use of phenotype data beyond the single genotype-phenotype relationship. Here, methods are presented for knowledge discovery in phenotypes across species and screening methods. The available databases and various approaches to analyzing their content are reviewed, including a discussion of hurdles to be overcome, e.g. lack of data integration, inadequate ontologies and shortage of analytical tools. PhenomicDB 2 is an approach to integrate genotype and phenotype data on a large scale, using orthologies for cross-species phenotypes. The focus lies on the uptake of quantitative and descriptive RNAi data and ontologies of phenotypes, assays and cell-lines. Then, the results of a study are presented in which the large set of phenotype data from PhenomicDB is taken to predict gene annotations. Text clustering is utilized to group genes based on their phenotype descriptions. It is shown that these clusters correlate well with indicators for biological coherence in gene groups, such as functional annotations from the Gene Ontology (GO) and protein-protein interactions. The clusters are then used to predict gene function by carrying over annotations from well-annotated genes to less well-characterized genes. Finally, the prototype PhenoMIX is presented, integrating genotype and phenotype data with clustered phenotypes, orthologies, interaction data and other similarity measures. Data grouped by these measures are evaluated for theirnpredictiveness in gene functions and phenotype terms.

Retosios ligos (RL) – tai ypač mažai paplitusios ligos (gyvybei pavojų keliančios arba lėtai sekinančios ligos), kuriomis Europos Sąjungoje (ES) serga ne daugiau kaip 5 iš 10 000 asmenų. Pirmą kartą terminą „retosios ligos“ 1978 metais pavartojo Neilas A. Holtzmanas. Kiekviena RL ES serga apie 246 000 žmonių. Iš viso RL, kurių žinoma 5 000 – 8 000, kokiu nors gyvenimo etapu suserga apie 6% ES gyventojų ir tai yra 29 – 36 mln. ligonių. Lietuvoje sergančių RL galėtų būti apie 200 000 žmonių. Dauguma RL yra genetinės ligos (jos sudaro 80%), o likusios – kitų kategorijų retos vėžio formos, autoimuninės ligos, įgimtos raidos anomalijos, toksinės ir infekcinės ligos. Habilitacijos procedūrai teikiamų mokslo darbų apžvalgoje nagrinėtos 22 mokslinės publikacijos. Istoriniai šaltiniai apie RL gali būti anatominių preparatų muziejai, antikvarinės knygos medicinine tematika, tautosaka. Apžvalgoje nagrinėta Vilniaus universiteto Medicinos fakulteto anatominių preparatų kolekcija, kurioje nustatytas unikalus žmogaus anotocefalijos atvejis ir 11 kitų nozologinių RL (įgimtų anomalijų) vienetų. Pagrindinės priemonės žinioms apie RL turtinti ir klinikiniams moksliniams tyrimams plėtoti yra registrai ir duomenų bazės. Tai vienintelis būdas kaupti duomenis, kad būtų galima gauti pakankamo dydžio imtis epidemiologiniams ir (arba) klinikiniams tyrimams. Apžvalgoje nagrinėtos autopsijų ir Lietuvos paveldimų ligų ir įgimtų anomalijų (LIRECA) duomenų bazės, kurių analizės metu taikyti statistiniai... [toliau žr. visą tekstą] / Rare diseases (RD) – life menacing or slowly emaciating diseases of extremely low incidence (less than 5 cases in 10,000 EU inhabitants). The term was launched by Neil A. Holtzman in 1978. There are about 5,000 – 8,000 RD, each manifesting itself in some life stage of about 6% of EU population, that amounts from 29 to 36 million people. In Lithuania that would make about 200,000 people. The majority of RD are genetic (80%), the remaining consist of rare cancer forms, autoimmune diseases, inborn developmental anomalies, toxic or contagious illnesses. The author presented an analytical review of 22 publications on RD. Historical indications about RD could be found in anatomical museums, ancient medical books, and folk art. In the collection of anatomical specimens of Medical Faculty of Vilnius University the author has discovered a unique case of human anotocephaly and eleven more nosological entities of RD (congenital anomalies). The main sources for information on RD are registers and data bases. This is the only way to obtain sufficient samples for epidemiologic and/or clinical research. Lithuanian Register of Congenital Anomalies (LIRECA) and autopsies data base were reviewed by the author and analyzed by statistical research models applicable in registration of RD, in particular Poisson linear model and logistic (binomic) regression. Analysis of standardized remainders confirmed their adequacy and suitability. Biological asymmetry was evaluated by analysis of... [to full text]

L'utilisation de variétés présentant des résistances quantitatives polygéniques est une pratique respectueuse de l'environnement et potentiellement durable pour lutter contre les bioagresseurs. Les résistances quantitatives sont cependant mal connues et encore peu exploitées. Via l'étude de l'interaction Capsicum spp. / Phytophthora capsici, les objectifs sont de (i) caractériser la diversité naturelle de l'hôte pour le phénotype quantitatif de résistance, (ii) décrire la diversité au QTL Pc5.1, déterminant majeur de la résistance, conservé chez les géniteurs et efficace à large spectre, et (iii) déterminer le profil d'évolution moléculaire aux gènes candidats de Pc5.1. L'évaluation du niveau de résistance de ressources génétiques de Capsicum spp. et du spectre de résistance d'un panel d'accessions a permis d'identifier de nouveaux géniteurs de forte résistance au spectre large et a fourni un set d'isolats différenciant les accessions selon leur spectre. Le polymorphisme à Pc5.1 a été révélé par séquençage haut débit. Globalement, Pc5.1 présente un polymorphisme nucléotidique plus élevé que le reste du génome. Les accessions résistantes sont très peu divergentes au QTL, signe d'une forte conservation intra- et inter-génique, alors que les accessions sensibles sont plus polymorphes. Aux gènes candidats, deux haplotypes majeurs ont été identifiés, l'un présent quasi exclusivement chez des accessions résistantes et l'autre chez des accessions sensibles, ce qui confirme la forte conservation du locus et la divergence entre résistants et sensibles. Le déséquilibre de liaison mesuré aux gènes candidats étant fort, surtout chez les C. annuum, 65% des polymorphismes sont significativement associés à la résistance. Cette étude a mis en évidence le caractère contraint de l'allèle de résistance à Pc5.1 et interroge sur l'origine et l'histoire évolutive du QTL, en relation avec sonefficacité à large spectre. Il semble qu'une localisation proche du centromère limite les recombinaisons au locus et que la divergence entre les sensibles et les résistants soit un événement ancien. La détermination de la nature moléculaire et de l'histoire évolutive de Pc5.1 sera poursuivie en approfondissant les analyses de divergence des séquences et en se focalisant sur la validation fonctionnelle des gènes candidats déjà en cours. / An environmentally friendly and potentially durable strategy to control diseases is the breeding for varieties displaying quantitative polygenic resistances. However a few is known about quantitative resistances, which are thus underexploited. Through the investigation of the Capsicum spp. / Phytophthora capsici interaction, this study aimed to (i) phenotype natural host diversity for the quantitative resistance, (ii) describe the nucleotide diversity at the QTL Pc5.1, a major determinant of resistance that is retrieved among genitors and is broad-spectrum, and (iii) explore the pattern of molecular evolution at Pc5.1 candidate genes. Through the phenotyping for level of resistance in Capsicum spp. genetic resources and spectrum of resistance in a sample of accessions, novel genitors displaying strong and broadspectrum resistance have been identified, and a set of isolates that differentiate accessions according to their resistance spectrum has been established. High-throughput sequencing has been exploited to identify polymorphisms at Pc5.1. Nucleotide diversity at Pc5.1 is higher than over the genome. Resistant accessions displayed low divergence thatindicates high intra- and inter-genic conservation, while susceptible accessions are more polymorphic than resistant ones. At the candidate genes, two major haplotypes have been identified, one being almost exclusively exhibited by resistant accessions and the other by susceptible ones, which reinforces the assessments that the QTL is highly conserved and that resistant and susceptible accessions are divergent. Linkage disequilibrium at candidate genes being high, particularly for C. annuum, 65% of polymorphisms are in significant association with resistance. By highlightingthe constraint pattern of selection at Pc5.1, this study wonders about the origin and the evolution history of the QTL, in relation to its broad-spectrum efficiency. A close proximity with the centromere region seems to restrict recombinations at the QTL, and divergence between resistant and susceptible may be an ancient event. The investigation of the molecular function and the pattern of evolution of Pc5.1 will be continued through in depth study of the acquired sequences and functional validation of candidate genes already ongoing.

Tesis por compendio / [ES] El trabajo realizado en la presente tesis pretende contribuir a la puesta en valor de las variedades tradicionales valencianas de tomate. En primer lugar se aborda la caracterización de una colección de 69 entradas de variedades valencianas de tomate de ocho tipos varietales ('De Borseta', 'Cherry', 'Cor¿, 'De Penjar', 'Plana', 'De Pruna', 'Redona' y 'Valenciana') con 64 descriptores convencionales y 38 características del Tomato Analyzer. Se ha puesto de manifiesto que el uso de forma complementaria de la herramienta fenómica del Tomato Analyzer es una nueva estrategia para la caracterización y clasificación de las variedades locales de tomate, así como para la distinción entre tipos varietales relacionados. A pesar del uso generalizado de los descriptores estandarizados de tomate, hay poca información sobre los efectos ambientales sobre los valores de los descriptores y sobre su herencia. La evaluación de 12 entradas de tomate procedentes de siete tipos varietales en tres ambientes diferentes (cultivo convencional aire libre, cultivo ecológico aire libre e invernadero) mediante el uso de 36 descriptores, ha permitido establecer la influencia del sistema de cultivo sobre estos descriptores, encontrándose una amplia gama de variación, y demostrando su utilidad para describir los materiales de tomate, su diversidad y relaciones. Por otra parte, puede ser muy interesante asociar características saludables como un elevado contenido en vitaminas o sustancias antioxidantes beneficiosas para la salud. El análisis de 69 entradas locales valencianas de tomate procedentes de ocho tipos varietales para caracteres como contenido en distintos azúcares, ácidos y antioxidantes puso de manifiesto diferencias significativas entre los tipos varietales ensayados para la mayoría de las características. Los tipos varietales 'Cherry' y 'De Penjar' presentaban mayor materia seca, contenido de sólidos solubles, acidez titulable, índice de sabor, ß-caroteno, ácido ascórbico, fenólicos totales y actividad antioxidante que los otros grupos. Los resultados obtenidos serán útiles para la diferenciación, mejora y selección de variedades locales de tomate con propiedades organolépticas mejoradas. Los estudios de caracterización y tipificación de las variedades tradicionales de tomate son imprescindibles para detectar factores que dificultan su puesta en valor y fomento de la explotación comercial. En este sentido, dentro de esta tesis se han caracterizado 3 poblaciones de tomate 'Valenciana d'El Perelló'. La menor productividad de las selecciones ensayadas en comparación con el control comercial parece ser debida a una concentración de la producción en los 2-3 primeros ramilletes de la planta. En el programa de selección y mejora del tomate 'Valenciana d¿El Perelló' que se ha realizado se dispone de selecciones con una distribución de cuajado mucho más uniforme. Por otra parte, una forma muy interesante de potenciar su cultivo, es obtener variedades resistentes al ToMV, derivándose un conjunto de linajes de este tomate con el gen Tm22 que confiere resistencia al ToMV. En cuanto a la adaptación a las condiciones agroclimáticas locales de las variedades tradicionales, esta característica es fundamental de este tipo de variedades. Así, las plantas de tomate del tipo 'De Penjar', han sido cultivadas tradicionalmente en la región mediterránea. Estos materiales están adaptados a condiciones de campo abierto bajo condiciones de bajo consumo de recursos. Sin embargo, el cultivo bajo invernadero se está expandiendo debido al aumento de su demanda. La evaluación de 12 variedades (siete entradas tradicionales, tres selecciones y dos híbridos) del tipo 'De Penjar' en cultivo al aire libre y en cultivo bajo invernadero ha revelado un alto impacto del ambiente de cultivo sobre las propiedades morfológicas, agronómicas y químicas de variedades de tomate 'De Penjar'y sugiere la necesidad de desarrollar variedade / [CA] El treball realitzat en la present tesi pretén contribuir a la posada en valor de les varietats tradicionals valencianes de tomàquet. En primer lloc s'aborda la caracterització d'una col·lecció de 69 entrades de varietats valencianes de tomàquet de vuit tipus varietals ( 'De Borseta', 'Cherry', 'Cor',' De penjar ',' Plana ',' De Pruna ', 'Redona' i 'Valenciana') amb 64 descriptors convencionals i 38 característiques del Tomato Analyzer. S'ha posat de manifest que l'ús de forma complementària de l'eina fenómica del Tomato Analyzer és una nova estratègia per a la caracterització i classificació de les varietats locals de tomàquet, així com per la distinció entre tipus varietals relacionats. Malgrat l'ús generalitzat dels descriptors estandarditzats de tomàquet, hi ha poca informació sobre els efectes ambientals sobre els valors dels descriptors i sobre la seva herència. L'avaluació de 12 entrades de tomàquet procedents de set tipus varietals en tres ambients diferents (cultiu convencional aire lliure, cultiu ecològic aire lliure i hivernacle) mitjançant l'ús de 36 descriptors, ha permès establir la influència del sistema de cultiu sobre aquests descriptors, trobant una àmplia gamma de variació, i demostrant la seva utilitat per descriure els materials de tomàquet, la seva diversitat i relacions. D'altra banda, pot ser molt interessant associar característiques saludables com un elevat contingut en vitamines o substàncies antioxidants beneficioses per a la salut. L'anàlisi de 69 entrades locals valencianes de tomàquet procedents de vuit tipus varietals per a caràcters com a contingut en diferents sucres, àcids i antioxidants va posar de manifest diferències significatives entre els tipus varietals assajats per a la majoria de les característiques. Els tipus varietals 'Cherry' i 'De penjar' presentaven major matèria seca, contingut de sòlids solubles, acidesa, índex de gust, ß-carotè, àcid ascòrbic, fenòlics totals i activitat antioxidant que els altres grups. Els resultats obtinguts seran útils per a la diferenciació, millora i selecció de varietats locals de tomàquet amb propietats organolèptiques millorades. Els estudis de caracterització i tipificació de les varietats tradicionals de tomàquet són imprescindibles per detectar factors que en dificulten la posada en valor i foment de l'explotació comercial. En aquest sentit, dins d'aquesta tesi s'han caracteritzat març poblacions de tomàquet 'Valenciana d'El Perelló'. La menor productivitat de les seleccions assajades en comparació amb el control comercial sembla ser deguda a una concentració de la producció en els 2-3 primers ramells de la planta. En el programa de selecció i millora del tomàquet 'Valenciana d'El Perelló' que s'ha realitzat es disposa de seleccions amb una distribució de quallat molt més uniforme. D'altra banda, una forma molt interessant de potenciar el seu cultiu, és obtenir varietats resistents al ToMV, derivant un conjunt de llinatges d'aquest tomàquet amb el gen Tm22 que confereix resistència al ToMV. Pel que fa a l'adaptació a les condicions agroclimàtiques locals de les varietats tradicionals, aquesta característica és fonamental d'aquest tipus de varietats. Així, les plantes de tomàquet del tipus 'De penjar', han estat cultivades tradicionalment a la regió mediterrània. Aquests materials estan adaptats a condicions de camp obert sota condicions de baix consum de recursos. No obstant això, el cultiu sota hivernacle s'està expandint causa de l'augment de la seva demanda. L'avaluació de 12 varietats (set entrades tradicionals, 3 seleccions i dues híbrids) del tipus 'De penjar' en cultiu a l'aire lliure i en cultiu sota hivernacle ha revelat un alt impacte de l'ambient de cultiu sobre les propietats morfològiques, agronòmiques i químiques de varietats de tomàquet 'De Penjar'y suggereix la necessitat de desenvolupar varietats específiques adaptades a cultiu baix hivernacle / [EN] The work carried out in this thesis aims to contribute to the valorisation of the traditional Valencian tomato varieties. First, the characterization of a collection of 69 entries of Valencian tomato varieties of eight varietal types ('De Borseta', 'Cherry', 'Cor',' De Penjar ',' Plana ',' De Pruna ', 'Redona' and 'Valenciana') with 64 conventional descriptors and 38 characteristics of the Tomato Analyzer. It has been shown that the complementary use of the Tomato Analyzer's phenomic tool is a new strategy for the characterization and classification of local tomato varieties, as well as for the distinction between related varietal types. Despite the widespread use of standardized tomato descriptors, there is little information about the environmental effects on the values of the descriptors and their inheritance. The evaluation of 12 entries of tomato from seven varietal types in three different environments (conventional open air cultivation, open air ecological cultivation and greenhouse) through the use of 36 descriptors, has allowed to establish the influence of the cultivation system on these descriptors, being a wide range of variation, and demonstrating its usefulness to describe tomato materials, their diversity and relationships. On the other hand, it can be very interesting to associate healthy characteristics such as a high content of vitamins or antioxidant substances beneficial to health. The analysis of 69 Valencian local tomato entries from eight varietal types for characters as content in different sugars, acids and antioxidants revealed significant differences between the varietal types tested for most of the characteristics. The varietal types 'Cherry' and 'De Penjar' had higher dry matter, content of soluble solids, acidity, flavor index, ß-carotene, ascorbic acid, total phenolic and antioxidant activity than the other groups. The results obtained will be useful for the differentiation, improvement and selection of local tomato varieties with improved organoleptic properties. Characterization and typification studies of traditional tomato varieties are essential to detect factors that make it difficult to value and promote commercial exploitation. In this sense, within this thesis 3 populations of tomato 'Valenciana d'El Perelló' have been characterized. The lower productivity of the selections tested compared to the commercial control seems to be due to a concentration of the production in the first 2-3 bunches of the plant. In the program of selection and improvement of the tomato 'Valenciana d'El Perelló' that has been made, selections are available with a much more uniform fruit set distribution. On the other hand, a very interesting way to enhance their crop is to obtain varieties resistant to ToMV, deriving a set of lineages of this tomato with the Tm22 gene that confers resistance to ToMV. Regarding the adaptation to the local agroclimatic conditions of the traditional varieties, this characteristic is fundamental of this type of varieties. Thus, tomato plants of the 'De Penjar' type have traditionally been grown in the Mediterranean region. These materials are adapted to open field conditions under conditions of low resource consumption. However, greenhouse cultivation is expanding due to the increase in demand. The evaluation of 12 varieties (seven traditional entrances, three selections and two hybrids) of the 'De Penjar' type in outdoor cultivation and in greenhouse cultivation has revealed a high impact of the cultivation environment on the morphological, agronomic and chemical properties of varieties of tomato 'De Penjar' and suggests the need to develop specific varieties adapted to greenhouse cultivation. / Figás Moreno, MDR. (2019). CARACTERIZACIÓN, TIPIFICACIÓN, SELECCIÓN Y MEJORA GENÉTICA DE VARIEDADES VALENCIANAS DE TOMATE [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/119449 / Compendio

[ES] La tesis abarca una serie de estudios destinados a mejorar los programas de selección genética para aumentar la eficiencia alimentaria en dos etapas de la vida productiva de los cerdos: lactación y crecimiento. En los capítulos 2 al 5 se exploraron diversas metodologías y fuentes de información (genética, genómica y fenómica) para lograr este objetivo. La eficiencia alimentaria durante la lactación es un sistema complejo de rasgos fenotípicos interrelacionados. En el Capítulo 2 se usaron modelos de ecuaciones estructurales para inferir las asociaciones causales entre la ingesta diaria de alimento, el balance de peso de la cerda, la ganancia de peso de la camada, el balance de espesor de grasa dorsal y el peso metabólico de la cerda. Se analizaron datos de 1.100 cerdas de un experimento de selección divergente para la eficiencia en cerdos en crecimiento. Se utilizó el algoritmo de causación inductiva para definir el modelo de ecuaciones estructurales. Los resultados indicaron que la ingesta diaria de alimento y la ganancia diaria de peso de la camada influenciaban el balance diario de peso de la cerda, con coeficientes estructurales medios de 0.12 y -0.03, respectivamente. Posteriormente, el balance diario de peso de la cerda impactó en el balance diario del grosor de la grasa dorsal y en el peso metabólico de la cerda, con coeficientes estructurales de 0,70 y -1,22, respectivamente. Se evaluaron diferentes estrategias de selección. Las estrategias de selección que no dependían de registros de ingesta alimentaria resultaron igualmente efectivas, aunque aumentar la ganancia de peso de la camada reduciendo o manteniendo constante la ingesta alimentaria sin deteriorar la condición corporal de la cerda parece difícil. En el Capítulo 3 se exploraron los beneficios de métodos de multi-output y stacking para mejorar la precisión de la predicción de la eficiencia alimentaria a partir del genotipo de cerdos en crecimiento. Se analizaron datos de 5.828 cerdos y 45.610 SNPs, implementando cuatro estrategias diferentes. Modelos de random forest y support vector regression fueron entrenados con diferentes subconjuntos de variables predictoras (de 200 a 3000 SNPs más informativos). La estrategia estándar, que utilizaba solo los genotipos como predictores, mostró el mejor rendimiento. Con el algoritmo random forest y los 1.000 SNPs más informativos, la correlación de Spearman promedio fue 0.23 (0.04). En cuanto a la fenotipado de alto rendimiento, se propuso el uso de los acelerómetros y las cámaras para obtener información sobre el comportamiento animal. En el Capítulo 4, 16 conejos fueron equipados con acelerómetros y grabados durante 2 semanas. Se segmentaron las series temporales en ventanas de tiempo de diferentes tamaños (1, 3, 5, 7 y 9 segundos) y se calcularon 41 características por ventana. Modelos de random forest, support vector machine y gradient boosting fueron entrenados para clasificar estados activos/inactivos. El modelo de random forest, con una ventana de 9 segundos y las 5 características más importantes, alcanzó una precisión mediana de 1 y una recall mediana de 0.93. Finalmente, en el Capítulo 5 se combinó un algoritmo de seguimiento por detección con un sistema de identificación por radiofrecuencia para rastrear doce cerdos de un corral de los cuales tres cerdos tenían marcas de pelaje únicas que facilitaban su distinción visual. Se implementaron el algoritmo You Only Look Once (v8) para detección y el algoritmo BoT-SORT para seguimiento. Los cerdos con pelajes similares se rastrearon durante un promedio de 49 minutos, mientras que los cerdos con marcas únicas se rastrearon 152 minutos, con una coincidencia del 90% o más con la verdad absoluta. Esta combinación de dispositivos representa un avance significativo en la identificación, seguimiento y trazabilidad de animales en grupo. / [CA] La tesi comprén una sèrie d'estudis destinats a millorar els programes de selecció genètica per a augmentar l'eficiència alimentària en dos etapes de la vida productiva dels porcs: lactació i creixement. En els capítols 2 al 5 es van explorar diverses metodologies i fonts d'informació (genètica, genòmica i fenómica) per a aconseguir este objectiu. L'eficiència alimentària durant la lactació és un sistema complex de trets fenotípics interrelacionats. En el Capítol 2 es van usar models d'equacions estructurals per a inferir les associacions causals entre la ingesta diària d'aliment, el balanç de pes de la truja, l'augment de pes de la ventrada, el balanç del gruix del greix dorsal i el pes metabòlic de la truja. Es van analitzar dades de 1.100 truges d'un experiment de selecció divergent per a l'eficiència en porcs en creixement. Es va utilitzar l'algorisme de causación inductiva per a definir el model d'equacions estructurals. Els resultats van indicar que la ingesta diària d'aliment i l'augment diari de pes de la ventrada van influir en el balanç diari de pes de la truja, amb coeficients estructurals mitjans posteriors de 0,12 i -0.03, respectivament. Posteriorment, el balanç diari de pes de la truja va impactar en el balanç diari del gruix del greix dorsal i en el pes metabòlic de la truja, amb coeficients estructurals de 0,70 i -1,22, respectivament. Es van avaluar diferents estratègies de selecció. Les estratègies de selecció que no depenien de registres d'ingesta alimentària van resultar igualment efectives, encara que augmentar el pes de la ventrada reduint o mantenint constant la ingesta alimentària sense deteriorar la condició corporal de la truja sembla difícil. En el Capítol 3 es van explorar els beneficis de mètodes de multi-output i stacking per a millorar la precisió de la predicció de l'eficiència alimentària a partir del genotip de porcs en creixement. Es van analitzar dades de 5.828 porcs i 45.610 SNPs, implementant quatre estratègies diferents. Models de random forest i support vector regression van ser entrenats amb diferents subconjunts de variables predictores (de 200 a 3000 SNPs més informatius). L'estratègia estàndard, que utilitzava només els genotips com a predictors, va mostrar el millor rendiment. Amb l'algorisme random forest i els 1.000 SNPs més informatius, la correlació de Spearman mitjana va ser 0.23 (0.04). Quant a la fenotipat d'alt rendiment, es va proposar l'ús dels acceleròmetres i càmeres per a obtindre informació sobre el comportament animal. En el Capítol 4, 16 conills van ser equipats amb acceleròmetres i gravats durant 2 setmanes. Es van segmentar les sèries temporals en finestres de temps de diferents grandàries (1, 3, 5, 7 i 9 segons) i es van calcular 41 característiques per finestra. Models de random forest, support vector machine i gradient boosting van ser entrenats per a classificar estats actius/inactius. El model de random forest, amb una finestra de 9 segons i les 5 característiques més importants, va aconseguir una precisió mitjana d'1 i una recall mitjana de 0.93. Finalment, en el Capítol 5 es va combinar un algorisme de seguiment per detecció amb un sistema d'identificació per radiofreqüència per a rastrejar dotze porcs d'un corral dels quals tres tenien marques de pelatge úniques que facilitaven la seua distinció visual. Es van implementar l'algorisme You Only Look Onze (v8) per a detecció i l'algorisme Bot-SORT per a seguiment. Els porcs amb pelatges similars es van rastrejar durant una mitjana de 49 minuts, mentres que els porcs amb marques úniques es van rastrejar 152 minuts, amb una coincidència del 90% o més amb la veritat absoluta. Esta combinació de dispositius representa un avanç significatiu en la identificació, seguiment i traçabilitat d'animals en grup. / [EN] The thesis comprises a series of studies aimed at improving genetic selection programs to increase feed efficiency at two stages of the productive life of pigs: lactation and growth. In Chapters 2 to 5, various methodologies and sources of information (genetics, genomics, and phenomics) were explored to achieve this goal. Feed efficiency during lactation is a complex system of interrelated phenotypic traits. In Chapter 2, structural equation models were used to infer the causal associations between daily feed intake, sow weight balance, litter weight gain, backfat thickness balance, and sow metabolic body weight. Data from 1,100 sows from a divergent selection experiment for efficiency in growing pigs were analysed. The inductive causation algorithm was used to define the structural equation model. Results indicated that daily feed intake and daily litter weight gain influenced daily sow weight balance, with average structural coefficients of 0.12 and -0.03, respectively. Subsequently, daily sow weight balance impacted daily backfat thickness balance and sow metabolic body weight, with structural coefficients of 0.70 and -1.22, respectively. Different selection strategies were evaluated. Selection strategies that did not rely on feed intake records proved equally effective, although increasing litter weight gain while reducing or maintaining constant feed intake without deteriorating the sow's body condition seems challenging. In Chapter 3, the benefits of multi-output and stacking methods to improve the accuracy of predicting feed efficiency from the genotype of growing pigs were explored. Data from 5,828 pigs and 45,610 SNPs were analysed, implementing four different strategies. Random forest and support vector regression models were trained with different subsets of predictor variables (from 200 to 3,000 of the most informative SNPs). The standard strategy, which used only genotypes as predictors, showed the best performance. With the random forest algorithm and the top 1,000 SNPs, the average Spearman correlation was 0.23 (0.04). Regarding high-throughput phenotyping, the use of accelerometers and cameras to obtain information on animal behaviour was proposed. In Chapter 4, 16 rabbits were equipped with accelerometers and filmed for 2 weeks. The time series were segmented into time windows of different sizes (1, 3, 5, 7, and 9 seconds), and 41 features were calculated per window. Random forest, support vector machine, and gradient boosting models were trained to classify active/inactive states. The random forest model, with a 9-second window and the 5 most important features, achieved a median precision of 1 and a median recall of 0.93. Finally, in Chapter 5, a tracking-by-detection algorithm was combined with a radio frequency identification system to track twelve pigs in a pen, three of which had unique coat markings that facilitated visual distinction. The You Only Look Once (v8) algorithm was implemented for detection and the BoT-SORT algorithm for tracking. Pigs with similar coat markings were tracked for an average of 49 minutes, while pigs with unique markings were tracked for 152 minutes, with a 90% or higher match with the ground truth. This combination of devices represents a significant advancement in the identification, tracking, and traceability of animals in groups. / Mora Fenoll, M. (2024). New insights for enhancing feed efficiency [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/211262