Desarrollo Y Aplicación De Herramientas Genómicas Para La Mejora De Especies Cucurbitáceas Por Calidad Y Resistencia a Enferm

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Desarrollo Y Aplicación De Herramientas Genómicas Para La Mejora De Especies Cucurbitáceas Por Calidad Y Resistencia a Enferm Desarrollo y aplicación de herramientas genómicas para la mejora de especies cucurbitáceas por calidad y resistencia a enfermedades. TESIS DOCTORAL Presentada por: Cristina Esteras Gómez Dirigida por: Dra. María Belén Picó Sirvent Valencia, mayo 2012 Agradecimientos Quiero expresar mi agradecimiento de forma muy especial a la directora de esta Tesis, la Dra. Belén Picó, por su constante apoyo durante todos estos años, por tantas enseñanzas recibidas y por la total confianza que ha depositado siempre en mí. Así mismo, me gustaría agradecer al Dr. Fernando Nuez, director del COMAV, el haberme dado la posibilidad de realizar los trabajos de la presente Tesis doctoral en el marco de varios proyectos desarrollados en dicho Instituto. Desearía dar las gracias también a todos aquellos que han colaborado de una forma u otra a que saliera adelante este trabajo, en especial a Cristina Roig, que tantas cosas me ha enseñado y con la que tantas horas he pasado en el laboratorio, a José Blanca, Antonio Monforte, Joaquín Cañizares, Pello Ziarsolo y los investigadores de otras instituciones con las que se ha colaborado como el IRTA, IFAPA y la Universidad de Nápoles Federico II. También agradecer todo su apoyo a todos mis compañeros del COMAV, con los que he compartido tantas horas, y en especial a los que “conviven” conmigo en el despacho, a Alicia, Javi y Santi, por sus inestimables consejos siempre que las cosas no salían, su ayuda y sus risas en tantos otros momentos. Y, por supuesto, a todos aquellos que en algún momento u otro han pertenecido al grupo de Cucurbitáceas del COMAV, en especial a Eva y Mercè. Finalmente, mi más profundo agradecimiento a mi familia, sin la cual nada de esto habría sido posible, y en especial a Juanra, por toda su paciencia en los malos momentos. 3 ABSTRACT Melon (Cucumis melo ) and summer squash (Cucurbita pepo ) are economically important cucurbits cultivated worldwide. New, better-adapted, cultivars, resistant to pests and diseases, and varieties displaying better quality traits are required to optimize their production and to meet market demands. Crop breeding must be carried out efficiently and competitively, using the existing genetic knowledge and the molecular tools available for each species. The development of genomic tools to speed up Cucurbits breeding programs is the main objective of this Doctoral Thesis. Molecular markers are essential tools for the construction of genetic maps, for an efficient MAS selection, for QTL (Quantitative Trait Loci ) analysis and mapping and for the development of new breeding populations. Molecular markers are also necessary tools for biodiversity analysis. High-quality markers, such as microsatellites (Simple Sequence Repeats, SSRs) and SNPs (Single Nucleotide Polymorphisms) have been developed and/or validated for both species in this Thesis. The generation of sequence information, required for the development of SSRs and SNPs has dramatically changed in the last 6 years due to the advent of new technological advances. In fact, a fairly complete melon transcriptome has been produced using high-throughput 454 sequencing (NGS, Next Generation Sequencing) and combining the newly produced ESTs with the previously existing Sanger sequences. The melon transcriptome characterization presented is the most complete to date (53.252 unigenes with over 63% of them annotated). The generation of large SSRs and SNPs collections for these species, by mapping the ESTs (Expressed Sequence Tags) against the new version of the transcriptome has been a great achievement starting a new era in melon breeding. The obtained collection of molecular markers (more than 3.000 SSRs and 38.000 SNPs) has allowed the construction of melon maps with increased marker density. 5 Similar resources have been developed for the first time in C. pepo . SSRs identified in the C. pepo transcriptome sequencing project has been applied to localize landraces with favourable commercial traits and whose alleles might be exploited in breeding programs. Likewise, the usefulness of both EST-SSRs and genomic SSRs for depicting genetic relationships has been proved. On the other hand, the employment of the first SNP set identified for Cucurbita through a massive genotyping platform, GoldenGate, has been a success (90%). The genetic map obtained, with more than 300 SNPs, has allowed to map a large set of QTLs related to early flowering, femaleness tendency, shape, size and fruit color, and other traits of interest in breeding. Therefore, these works report the validation and application of previously developed markers and the generation of new genomic tools to speed up the breeding process of these crops. The paper-based format of this Thesis confirms the interest of the obtained results. 6 RESUMEN El melón (Cucumis melo ) y el calabacín ( Cucurbita pepo ) son especies cucurbitáceas de gran importancia económica a nivel nacional y mundial. Para optimizar su producción se requiere de la obtención de nuevas variedades mejor adaptadas a los sistemas de cultivo, más resistentes frente a nuevas enfermedades o plagas y con mejores características organolépticas, que respondan a las cada vez mayores exigencias del mercado. La mejora debe realizarse de una forma eficiente y competitiva, apoyándose en los crecientes conocimientos genéticos en estas dos especies y en los últimos avances biotecnológicos. El desarrollo de herramientas genómicas con el fin de impulsar la mejora de estos cultivos es el principal objetivo de la presente Tesis doctoral. El desarrollo de marcadores moleculares es esencial para la construcción de mapas genéticos, para la realización de una selección más eficiente, para el análisis y cartografía de QTLs (Quantitative Trait Loci ) y para el desarrollo de líneas de premejora, además de ser una herramienta fundamental para el análisis de la biodiversidad. En esta Tesis se han desarrollo y/o validado marcadores de alta calidad, de tipo microsatélite (Simple Sequence Repeats, SSRs) y SNPs (Single Nucleotide Polymorphisms), para estas dos especies. La generación de información de secuencia, necesaria para el desarrollo de este tipo de marcadores, ha cambiado en el transcurso de los trabajos presentados en la Tesis, habiéndose abordado finalmente la secuenciación del transcriptoma de melón mediante técnicas de secuenciación de alto rendimiento (NGS, Next Generation Sequencing). La obtención de grandes colecciones de SSRs y SNPs en ambas especies, resultado del ensamblaje de ESTs (Expressed Sequence Tags) procedentes de secuencias Sanger previamente disponibles y de las nuevas secuencias obtenidas por secuenciación masiva, ha supuesto un gran avance para estas especies no 7 modelo, permitiendo la construcción de mapas más densos en melón y del primer mapa basado en SNPs en calabacín. En melón, la caracterización del transcriptoma presentada es, con 53.252 unigenes, de los cuales el 63% están anotados funcionalmente con términos GO, la más completa que existe. Este transcriptoma ha proporcionado una valiosa información para la anotación del genoma, actualmente en fase de publicación. Además de la identificación de más de 3.000 SSRs y 38.000 SNPs, ha supuesto el desarrollo de herramientas bioinformáticas para la selección de marcadores polimórficos entre diversos morfotipos de interés, lo que abre camino a una nueva era en la mejora de este cultivo. La aplicación de los SSRs identificados gracias a la secuenciación del transcriptoma de C. pepo ha servido para localizar cultivares tradicionales cuya riqueza alélica podría ser explotada con fines comerciales. Asimismo, ha confirmado la eficacia de los EST-SSRs frente a los de origen genómico para estudios de variabilidad. Por otra parte, la utilización de los primeros SNPs identificados para Cucurbita ha supuesto la primera aplicación, con un 90% de éxito, de una plataforma de genotipado masivo, GoldenGate, en este género. El mapa genético basado en más de 300 SNPs ha permitido cartografiar un amplio conjunto de QTLs relacionados con la precocidad de la floración, la tendencia femenina de la planta, la forma, tamaño y coloración del fruto, además de otros caracteres que resultan de gran interés para la mejora. Por tanto, estos trabajos suponen la validación y la aplicación de marcadores previamente desarrollados y la generación de nuevas herramientas genómicas que supondrán la aceleración del proceso de mejora de estos cultivos. El formato de la Tesis basado en artículos ya publicados por el grupo confirma el interés de los resultados obtenidos. 8 RESUM El meló ( Cucumis melo ) i la carabasseta ( Cucurbita pepo ) són espècies cucurbitàcies de gran importància econòmica a nivell nacional i mundial. Per a optimitzar la seua producció es requereix de l´obtenció de noves varietats millor adaptades als sistemes de conreu, més resistents a noves malalties o plagues i amb millors característiques organolèptiques, que responguen a les cada vegada majors exigències del mercat. La millora ha de realitzar-se d´una forma eficient i competitiva, basant-se en els creixents coneiximents genètics en aquestes dues espècies i en els últims avançaments biotecnològics. El desenvolupament de ferramentes genòmiques per a impulsar la millora d´aquests conreus és el principal objectiu de la present Tesi doctoral. El desenvolupament de marcadors moleculars és essencial per a la construcció de mapes genètics, per a la realització d´una selecció més eficient, per a l´anàlisi i cartografia de QTLs (Quantitative Trait Loci ) i per al desenvolupament de línies de premillora, a més de
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