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GIRASOL Lic. Jeremías Zubrzycki UNIVERSIDAD DE BUENOS AIRES Facultad de Farmacia y Bioquímica ESTUDIO DE LA RESISTENCIA A Sclerotinia sclerotiorum EN LINEAS ENDOCRIADAS DE GIRASOL Tesis presentada para optar al título de Doctor de la Universidad de Buenos Aires en el área Biotecnología Lic. Jeremías Zubrzycki Directora de tesis: Norma Paniego Director asistente de tesis: Gerardo Cervigni Consejera de Estudios: Carina Rivolta Instituto de Biotecnología, CICVyA, INTA Castelar Buenos Aires, 2014 ESTUDIO DE LA RESISTENCIA A Sclerotinia sclerotiorum EN LINEAS ENDOCRIADAS DE GIRASOL RESUMEN La podredumbre húmeda del capítulo (PHC), causada por Sclerotinia sclerotiorum, es una de las limitante más importantes para el cultivo del girasol. Este trabajo tuvo como objetivo identificar las regiones del genoma de girasol asociadas a resistencia a PHC para sustentar el desarrollo de estrategias de mejoramiento asistido que permitan acelerar el proceso de creación de nuevos genotipos con resistencia a la enfermedad. Para alcanzar este objetivo se trabajó con una población de 135 líneas recombinantes endocriadas (RILs) obtenidas del cruzamiento entre las líneas PAC2 (resistencia moderada a PHC) x RHA266 (susceptible a PHC), se estableció un protocolo para corroborar la pureza genética de las RILs entre ensayos, se saturó un mapa genético de girasol con marcadores funcionales de tipo mutaciones simples (SNP), se realizaron evaluaciones a campo y se llevaron adelante estudios para la identificación de las regiones responsables de la resistencia a PHC. Para establecer el protocolo de pureza genética de genotipos de girasol se analizaron 40 marcadores de tipo SSR distribuidos en los 17 grupos de ligamiento. En una segunda etapa se seleccionaron diez marcadores capaces de discriminar de manera inequívoca a las RILs que componen la población, y que combinan tamaños de fragmentos y marca fluorescentes de tal manera que pueden resolverse claramente en una única corrida de electroforesis capilar. Este protocolo se implementó sobre todas las RILs después de cada proceso de multiplicación. Con el fin de automatizar y abaratar los costos de implementación del protocolo se desarrolló un ensayo multiplexado de PCR. Para la saturación del mapa genético PAC2 x RHA266 con marcadores de tipo SNP se implementaron diferentes estrategias, inicialmente se utilizó la metodología de resolución de moléculas heteroduplex mediante cromatografía líquida de alta precisión en condiciones desnaturalizantes, mediante secuenciación de ADN y por último se diseñó un ensayo multiplexado de 384 marcadores SNPs usando la tecnología GoldenGate-Veracode (Illumina) basado en variantes alélicas presentes en genes candidatos asociados a respuestas a estreses bióticos y abióticos. En total se sumaron sesenta y nueve SNPs a la matriz genotípica que contenía 327 AFLPs, 229 SSRs, 8 EST-SSRs y 2 InDels. Estos marcadores fueron ordenados en 17 grupos de ligamiento (GLs) con un valor mínimo de LOD = 4 y una frecuencia de recombinación máxima de 0,35. El mapa resultante posee 2823,8 cM y una densidad media de 4,57 cM por loci. La población de mapeo fue evaluada para resistencia a PHC en la EEA INTA Balcarce durante 4 campañas utilizando un diseño en bloques completos aleatorizados con tres repeticiones. Las ascosporas del patógeno fueron inoculadas sobre capítulos en estadio R 5.2 mediante aspersión mecánica con una concentración de 2500 esporas/mL. Se registraron los datos de incidencia (IEMAX), severidad (SEV21), intensidad (INT21) y período de incubación (PI). El mapeo de QTLs de resistencia se llevó a cabo mediante el mapeo por intervalo compuesto. En todos los caracteres, la mayoría de los QTLs identificados mostraron coeficientes de determinación altos, en coincidencia con los moderados a altos valores de heredabilidades obtenidas. Estos parámetros indican que tanto la selección fenotípica como la indirecta serán eficientes. Para el carácter IEMAX fueron identificados 9 QTLs. Cuatro de los mismos fueron consistentes sobre un segmento comprendido por genes candidatos SNPs ubicados contiguos sobre 10 cM en el GL 15. No sólo por su reproducibilidad, sino también por las magnitudes de sus R2 (hasta 24%), esta sección genómica es una de la más importante para la tolerancia a IEMAX. Por otra parte, tanto para los 9 QTLs de SEV21 como para los 12 de INT21, su expresión está circunscripta a un ambiente determinado. Para PI, fueron encontrados 6 QTLs, de los que una única región genómica sobre el GL 10 parece ser consistente en dos de las campañas consideradas. A través del uso de marcadores compartidos, el análisis comparativo con otros mapas de girasol permitió corroborar la co-localización de QTLs para PHC en los grupos de ligamiento 1, 2, 8, 10, 11, 12, 15 y 16. La dispersión en el genoma de los QTLs identificados para los caracteres, confirman la base genética amplia y compleja que hace a la resistencia al PHC del girasol. Este trabajo ha permitido profundizar el conocimiento de dichas regiones, resaltando la importancia de la contribución de las fuentes localizadas en los GL 10 y 15, que se presentan como candidatas a ser analizadas con más detalle para avanzar en la identificación de genes responsables que contribuyan a entender la complejidad de las bases genéticas que gobiernan la resistencia. Asimismo, los marcadores asociados a los QTLs descriptos en esta Tesis podrán ser usados por los programas de mejoramiento en el desarrollo de genotipos con mejor desempeño ante el PHC. La integración de datos obtenidos por el grupo de trabajo en relación a la caracterización de nuevas fuentes de resistencia para PHC, que incluyen además el análisis de una población de mapeo por asociación constituida por 135 líneas de base genética amplia asociadas al programa de mejoramiento, permitió localizar otros factores asociados a la resistencia en el mapa genético de girasol. De esta manera, tres genes candidato asociados a niveles bajos de incidencia a PHC por mapeo de asociación se localizaron, en los grupos de ligamiento 10, 14, y 15 en las proximidades de los QTL definidos en esta Tesis. A partir de este trabajo se logró acotar el estudio de la resistencia a PHC a un conjunto reducido de regiones del genoma de girasol sobre las cuales se puede avanzar a partir de distintas aproximaciones de la genómica y la genética para localizar los componentes funcionales responsables de la expresión del fenotipo de interés. Palabras claves: Sclerotinia sclerotiorum, podredumbre húmeda del capítulo, girasol, mapeo de QTL, SNPs, genes candidatos. GENETIC ANALYSIS OF PARTIAL RESISTANCE TO Sclerotinia HEAD ROT IN SUNFLOWER. ABSTRACT Sclerotinia head rot (SHR) caused by Sclerotinia sclerotiorum is one of the most important limiting factors in sunflower crop. This study aimed to identify regions of the sunflower genome associated with resistance to SHR, in order to support the development of assisted breeding strategies to accelerate the process of creating new genotypes with resistance to disease. A population of 135 Recombinant Inbred Lines (RILs) from cross PAC2 (moderatly resistant to SHR) with RHA266 (susceptible to SHR) was used in this study. First, we established a protocol to confirm the intertrial RIL’s genetic purity and subsequently saturated a sunflower genetic map with SNP markers. We also conducted field evaluations. Finally, we performed studies to identify those regions responsible for SHR resistance. For the protocol of genetic purity, 40 SSR markers, which were distributed in 17 linkage groups, were analyzed. At a second stage, 10 markers were selected. These selected markers were able to unequivocally discriminate RILs in this population and also combined fragment sizes and fluorescent marks in such a way that they can be clearly resolved in a single run of capillary electrophoresis. This protocol was implemented in every RIL after every multiplication process. In order to automate and reduce the costs of implementing the protocol, we developed a multiplex PCR assay. Different strategies were implemented in order to saturate PAC2 x RHA266 genetic map with SNP markers. Initially, resolution of heteroduplex molecules was performed by high precision liquid chromatography under denaturing conditions, by DNA sequencing. Then, a 384-SNP-marker multiplex assay was designed, by using Golden Gate-Veracode (Illumina). This multiplex assay was based on allelic variants present in candidate genes associated with biotic and abiotic stress responses. Sixty-nine SNPs were added to the genotypic array already containing 327 AFLPs, 229 SSRs, 8 EST-SSRs and 2 InDels. These markers were sorted into 17 linkage groups (LGs) with a minimum LOD = 4 and a maximum recombination frequency of 0.35. The resulting map has 2823.8 cM and has an average density of 4.57 cm loci. The mapping population was evaluated for resistance to SHR in EEA INTA Balcarce over four seasons using a randomized complete-block design with three replications. Pathogen ascospores were inoculated over R 5.2 stage capitula by mechanical spraying with a 2500 spores/ml concentration. Incidence data (IEMAX), severity (SEV21), intensity (INT21) and incubation period (IP) were recorded. Resistance QTL mapping was performed using the Composite Interval Mapping (CIM). In all characters, most of the identified QTLs showed high determination coefficients, in coincidence with moderate to high heritability obtained values. These parameters indicate that both phenotypic and indirect selection will be efficient. Nine QTLs were identified for IEMAX. Four of them were consistent over a genomic region composed of adjacent SNP candidate genes located over 10 cM on LG 15. This is one of the most important genomic sections for IEMAX tolerance, not only for their reproducibility, but for their R2 magnitudes (up to 24%). Moreover, the expression of the 9 QTLs of SEV21 as well as of the 12 QTLs of INT21 was circumscribed to a given environment. Six QTLs were found for IP, of which a single genomic region on LG 10 appears to be consistent in two of the considered seasons. Through the use of sheared markers, comparative analyses with other sunflower maps allowed to corroborate QTL co-location for SHR in linkage groups 1, 2, 8, 10, 11, 12, 15 and 16.
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