Environmental niche variation and evolutionary diversification of the Brachypodium distachyon grass complex species in their native circum-Mediterranean range

PREMISE OF THE STUDY: We conducted environmental niche modeling (ENM) of the Brachypodium distachyon s.l. complex, a model group of two diploid annual grasses ( B. distachyon , B. stacei ) and their derived allotetraploid ( B. hybridum) , native to the circum-Mediterranean region. We (1) investigated the ENMs of the three species in their native range based on present and past climate data; (2) identifi ed potential overlapping niches of the diploids and their hybrid across four Quaternary windows; (3) tested whether speciation was associated with niche divergence/conservatism in the complex species; and (4) tested for the potential of the polyploid outperforming the diploids in the native range. M ETHODS: Geo-referenced data, altitude, and 19 climatic variables were used to construct the ENMs. We used paleoclimate niche models to trace the potential existence of ancestral gene fl ow among the hybridizing species of the complex. KEY RESULTS: Brachypodium distachyon grows in higher, cooler, and wetter places, B. stacei in lower, warmer, and drier places, and B. hybridum in places with intermediate climatic features. Brachypodium hybridum had the largest niche overlap with its parent niches, but a similar distribution range and niche breadth. C ONCLUSIONS: Each species had a unique environmental niche though there were multiple niche overlapping areas for the diploids across time, suggesting the potential existence of several hybrid zones during the Pleistocene and the Holocene. No evidence of niche divergence was found, suggesting that species diversifi cation was not driven by ecological speciation but by evolutionary history, though it could be associated to distinct environmental adaptations.

Molecular tools to improve chestnut management: El Bierzo as a case study

The European chestnut (Castanea sativa Mill.) is a multipurpose species that has been widely cultivated around the Mediterranean basin since ancient times. New varieties were brought to the Iberian Peninsula during the Roman Empire, which coexist since then with native populations that survived the last glaciation. The relevance of chestnut cultivation has being steadily growing since the Middle Ages, until the rural decline of the past century put a stop to this trend. Forest fires and diseases were also major factors. Chestnut cultivation is gaining momentum again due to its economic (wood, fruits) and ecologic relevance, and represents currently an important asset in many rural areas of Europe. In this Thesis we apply different molecular tools to help improve current management strategies. For this study we have chosen El Bierzo (Castile and Leon, NW Spain), which has a centenary tradition of chestnut cultivation and management, and also presents several unique features from a genetic perspective (next paragraph). Moreover, its nuts are widely appreciated in Spain and abroad for their organoleptic properties. We have focused our experimental work on two major problems faced by breeders and the industry: the lack of a fine-grained genetic characterization and the need for new strategies to control blight disease. To characterize with sufficient detail the genetic diversity and structure of El Bierzo orchards, we analyzed DNA from 169 trees grafted for nut production covering the entire region. We also analyzed 62 nuts from all traditional varieties. El Bierzo constitutes an outstanding scenario to study chestnut genetics and the influence of human management because: (i) it is located at one extreme of the distribution area; (ii) it is a major glacial refuge for the native species; (iii) it has a long tradition of human management (since Roman times, at least); and (iv) its geographical setting ensures an unusual degree of genetic isolation. Thirteen microsatellite markers provided enough informativeness and discrimination power to genotype at the individual level. Together with an unexpected level of genetic variability, we found evidence of genetic structure, with three major gene pools giving rise to the current population. High levels of genetic differentiation between groups supported this organization. Interestingly, genetic structure does not match with spatial boundaries, suggesting that the exchange of material and cultivation practices have strongly influenced natural gene flow. The microsatellite markers selected for this study were also used to classify a set of 62 samples belonging to all traditional varieties. We identified several cases of synonymies and homonymies, evidencing the need to substitute traditional classification systems with new tools for genetic profiling. Management and conservation strategies should also benefit from these tools. The avenue of high-throughput sequencing technologies, combined with the development of bioinformatics tools, have paved the way to study transcriptomes without the need for a reference genome. We took advantage of RNA sequencing and de novo assembly tools to determine the transcriptional landscape of chestnut in response to blight disease. In addition, we have selected a set of candidate genes with high potential for developing resistant varieties via genetic engineering. Our results evidenced a deep transcriptional reprogramming upon fungal infection. The plant hormones ET and JA appear to orchestrate the defensive response. Interestingly, our results also suggest a role for auxins in modulating such response. Many transcription factors were identified in this work that interact with promoters of genes involved in disease resistance. Among these genes, we have conducted a functional characterization of a two major thaumatin-like proteins (TLP) that belongs to the PR5 family. Two genes encoding chestnut cotyledon TLPs have been previously characterized, termed CsTL1 and CsTL2. We substantiate here their protective role against blight disease for the first time, including in silico, in vitro and in vivo evidence. The synergy between TLPs and other antifungal proteins, particularly endo-p-1,3-glucanases, bolsters their interest for future control strategies based on biotechnological approaches.

Influence of new integrated pest management strategies on aphidophagous predators in horticultural crops

El 1 de enero de 2014 entró en vigor la Directiva Europea 2009/128/CE sobre uso sostenible de plaguicidas y el Real Decreto 1311/2012 por el cual se traspone dicha normativa comunitaria al ámbito nacional. Estos reglamentos establecen el marco legal por el que las explotaciones agrícolas deben cumplir los principios generales de la Gestión Integrada de Plagas (GIP). Los principios de la GIP dan preferencia a aquellos métodos de control que sean sostenibles y respetuosos con el medio ambiente, dando prioridad al control biológico, al físico y a otros de carácter no químico. Sin embargo, el uso de insecticidas selectivos con los enemigos naturales es necesario en ocasiones para el adecuado manejo de las plagas en cultivos hortícolas. Por ello, el objetivo general de esta Tesis ha sido aportar conocimientos para la mejora del control de plagas en cultivos hortícolas, mediante la integración de estrategias de lucha biológica, física y química. La primera de las líneas de investigación de esta Tesis se centró en el estudio del efecto de la presencia dos depredadores, larvas Chrysoperla carnea y adultos de Adalia bipunctata, en la dispersión del virus de transmisión no persistente Cucumber mosaic virus (CMV) y del virus de transmisión persistente Cucurbit aphid-borne yellows virus (CABYV), transmitidos por el pulgón Aphis gosypii en cultivo de pepino. La tasa de transmisión de CMV fue baja para los dos tiempos de evaluación ensayados (1 y 5 días), debido al limitado movimiento de su vector A. gossypii. Las plantas que resultaron infectadas se localizaron próximas a la fuente de inóculo central y la presencia de ambos enemigos naturales no incrementó significativamente el porcentaje de plantas ocupadas por pulgones ni la tasa de transmisión de CMV. Los patrones de distribución de A. gossypii y de CMV tan solo fueron coincidentes en las proximidades de la planta central infectada en la que se liberaron los insectos. En los ensayos con CABYV, la presencia de C. carnea y de A. bipunctata respectivamente provocó un incremento significativo de la dispersión de A. gossypii tras 14 días, pero no tras 7 días desde la liberación de los insectos. La reducción en el número inicial de pulgones en la planta central infectada con CABYV fue siempre mayor tras la liberación de C. carnea en comparación con A. bipunctata. Sin embargo, la tasa de transmisión de CABYV y su distribución espacial no se vieron significativamente modificadas por la presencia de ninguno de los depredadores, ni tras 7 días ni tras 14 días desde el inicio de los ensayos. Al igual que se estudió el efecto de la presencia de enemigos naturales en el comportamiento de las plagas y en la epidemiología de las virosis que transmiten, en una segunda línea de investigación se evaluó el posible efecto del consumo de pulgones portadores de virus por parte de los enemigos naturales. Este trabajo se llevó a cabo en el Laboratorio de Ecotoxicología del Departamento de Entomología de la Universidade Federal de Lavras (UFLA) (Brasil). En él se evaluó la influencia en los parámetros biológicos del enemigo natural Chrysoperla externa al alimentarse de Myzus persicae contaminados con el virus de transmisión persistente Potato leafroll virus (PLRV). El consumo de M. persicae contaminados con PLRV incrementó significativamente la duración de la fase larvaria, reduciendo también la supervivencia en comparación a otras dos dietas a base de M. persicae no contaminados con el virus y huevos del lepidóptero Ephestia kuehniella. La duración de la fase de pupa de C. externa no difirió significativamente entre las dietas a base de pulgones contaminados con PLRV y pulgones no contaminados, pero ambas fueron menores que con la dieta con huevos de E. kuehniella. Sin embargo, ni la supervivencia en la fase de pupa ni los parámetros reproductivos de los adultos emergidos mostraron diferencias significativas entre las dietas evaluadas. Por el contrario, la supervivencia de los adultos durante los 30 primeros días desde su emergencia sí se vio significativamente afectada por la dieta, siendo al término de este periodo del 54% para aquellos adultos de C. externa que durante su fase larvaria consumieron pulgones con PLRV. Dentro de la GIP, una de las estrategias de carácter físico que se emplean para el control de plagas y enfermedades en cultivos hortícolas protegidos es el uso de plásticos con propiedades fotoselectivas de absorción de la radiación ultravioleta (UV). Por ello, la tercera línea de investigación de la Tesis se centró en el estudio de los efectos directos e indirectos (mediados por la planta) de condiciones especiales de baja radiación UV sobre el crecimiento poblacional del pulgón A. gossypii y los parámetros biológicos del enemigo natural C. carnea, así como sobre las plantas de pepino en las que se liberaron los insectos. Los ensayos se realizaron en jaulones dentro de invernadero, utilizándose en el primero de ellos plantas de pepino sanas, mientras que en el segundo las plantas de pepino fueron previamente infectadas con CABYV para estudiar de qué manera afectaba la incidencia del virus en las mismas condiciones. Las condiciones de baja radiación UV (bajo plástico Térmico Antivirus®) ejercieron un efecto directo en las fases iniciales del cultivo de pepino, promoviendo su crecimiento, mientras que en fases más avanzadas del cultivo indujeron un aumento en el contenido en nitrógeno de las plantas. Las plantas de pepino que fueron sometidas a mayor intensidad de radiación UV (bajo plástico Térmico Blanco®) al inicio del cultivo mostraron un engrosamiento significativo de las paredes de las células epidérmicas del haz de las hojas, así como de la cutícula. El uso del plástico Térmico Antivirus®, utilizado como barrera fotoselectiva para crear condiciones de baja radiación UV, no alteró con respecto al plástico Térmico Blanco® (utilizado como control) el desarrollo poblacional del pulgón A. gossypii ni los parámetros biológicos evaluados en el depredador C. carnea. En el segundo experimento, realizado con plantas infectadas con CABYV, la incidencia de la virosis enmascaró las diferencias encontradas en experimento con plantas sanas, reduciendo aparentemente la influencia de las distintas condiciones de radiación UV. Por último, para el desarrollo de las estrategias de GIP es importante estudiar los posibles efectos secundarios que los plaguicidas pueden tener en los enemigos naturales de las plagas. Es por ello que en la Tesis se evaluaron la toxicidad y los efectos subletales (fecundidad y fertilidad) de flonicamida, flubendiamida, metaflumizona, spirotetramat, sulfoxaflor y deltametrina en los enemigos naturales C. carnea y A. bipunctata. Los efectos secundarios fueron evaluados por contacto residual tanto para larvas como para adultos de ambos enemigos naturales en condiciones de laboratorio. Flonicamida, flubendiamida, metaflumizona y spirotetramat fueron inocuos para larvas de último estadio y adultos de C. carnea y A. bipunctata. Por este motivo, estos insecticidas se presentan como buenos candidatos para ser incorporados dentro de programas de GIP en combinación con estos enemigos naturales para el control de plagas de cultivos hortícolas. Sulfoxaflor fue ligeramente tóxico para adultos de C. carnea y altamente tóxico para larvas de último estadio de A. bipunctata. Para A. bipunctata, sulfoxaflor y deltametrina fueron los compuestos más dañinos. Deltametrina fue también el compuesto más tóxico para larvas y adultos de C. carnea. Por tanto, el uso de deltametrina y sulfoxaflor en programas de GIP debería tomarse en consideración cuando se liberasen cualquiera de estos dos enemigos naturales debido al comportamiento tóxico que mostraron en condiciones de laboratorio. ABSTRACT On 1 January 2014 came into effect the Directive 2009/128/EC of the European Parliament about sustainable use of pesticides and the Royal Decree 1311/2012 that transposes the regulation to the Spanish level. These regulations establish the legal framework that agricultural holdings must adhere to in order to accomplish the general principles of Integrated Pest Management (IPM). The guidelines of IPM give priority to sustainable and eco-friendly pest control techniques, such as biological and physical measures. Nevertheless, the use of pesticides that are selective to natural enemies is sometimes a necessary strategy to implement accurate pest management programs in horticultural protected crops. Therefore, the general objective of this Thesis was to contribute to the improvement of pest management strategies in horticultural crops, by means of the integration of biological, physical and chemical techniques. The first research line of this Thesis was focused on the evaluation of the effects of two aphidophagous predators, Chrysoperla carnea larvae and Adalia bipunctata adults, on the spread of the non-persistently transmitted Cucumber mosaic virus (CMV, Cucumovirus) and the persistently transmitted Cucurbit aphid-borne yellows virus (CABYV, Polerovirus), by the aphid vector Aphis gossypii in a cucumber crop under greenhouse conditions. The CMV transmission rate was generally low, both after 1 and 5 days, due to the limited movement of its aphid vector A. gossypii. Infected plants were mainly located around the central virusinfected source plant, and the percentage of aphid occupation and CMV-infected plants did not differ significantly in absence and presence of natural enemies. The distribution patterns of A. gossypii and CMV were only coincident close to the central plant where insects were released. In the CABYV experiments, the presence of C. carnea larvae and A. bipunctata adults induced significant A. gossypii dispersal after 14 days but not after 7 days. The reduction in the initial aphid population established in the central plant was always higher for C. carnea than for A. bipunctata. Nevertheless, CABYV spread was not significantly modified by the presence of each predator either in the short term (7 days) or in the long term (14 days). Furthermore, the percentage of CABYV-infected plants did not significantly differ when each natural enemy was present in any evaluation period. It is important to evaluate the influence that natural enemies have on pest dynamics and on the spread of viral diseases, but it should be also taken into account the possible effect on the performance of natural enemies when they feed on preys that act as vectors of viruses. Thus, in a second research line developed in the Laboratory of Ecotoxicology, Department of Entomology, of the Universidade Federal de Lavras (UFLA) (Brazil), it was evaluated the performance of Chrysoperla externa under the condition of consuming Myzus persicae acting as vector of Potato leafroll virus (PLRV). The diet composed of PLRV-infected M. persicae significantly increased the length and reduced the survival rate, of the larval period in regard to the other two diets, composed of non-infected M. persicae and Ephestia kuehniella eggs. The lengths of the pupal stage were not significantly different between the aphid diets, but both were significantly shorter than that of E. kuehniella eggs. Neither pupal survival nor reproductive parameters revealed significant differences among the diets. Nevertheless, the adult survival curves during the first 30 days after emergence showed significant differences, reaching at the end of this interval a value of 54% for those C. externa adults fed on PLRVinfected aphids during their larval period. According to the IPM guidelines, one of the physical strategies for the control of pests and diseases in horticultural protected crops is the use of plastic films with photoselective properties that act as ultraviolet (UV) radiation blocking barriers. In this sense, the third research line of the Thesis dealt with the study of the direct and plant-mediated influence of low UV radiation conditions on the performance of the aphid A. gossypii and on the biological parameters of the natural enemy C. carnea, as well as on the cucumber plants where insects were released. The experiments were conducted inside cages under greenhouse conditions, using for the first one healthy cucumber plants, while for the second experiment the cucumber plants were previously infected with CABYV in order to assess the influence of the virus in the same conditions. The low UV radiation conditions (under Térmico Antivirus® plastic film) seemed to exert a direct effect in the early stages of cucumber plants, enhancing their growth, and in an increasing nitrogen content at further developmental stages. The higher UV radiation exposure (under Térmico Blanco® plastic film) in the early stages of the cucumber crop induced the thickening of the adaxial epidermal cell walls and the cuticle of leaves. The use of Térmico Antivirus® plastic film as a photoselective barrier to induce low UV radiation conditions did not modify, in regard to Térmico Blanco® plastic film (used as control), neither the population development of A. gossypii nor the studied biological parameters of the predator C. carnea. In the second experiment, done with CABYV-infected cucumber plants, the incidence of the virus seemed to mask the direct and plant-mediated influence of the different UV radiation conditions. In last term, for the development of IPM strategies it is important to study the potential side effects that pesticides might have on natural enemies. For this reason, in the Thesis were tested the toxicity and sublethal effects (fecundity and fertility) of flonicamid, flubendiamide, metaflumizone, spirotetramat, sulfoxaflor and deltamethrin on the natural enemies C. carnea and A. bipunctata. The side effects of the active ingredients of the insecticides were evaluated with residual contact tests for the larvae and adults of these predators under laboratory conditions. Flonicamid, flubendiamide, metaflumizone and spirotetramat were innocuous to last instar larvae and adults of C. carnea and A. bipunctata. Therefore, these pesticides are promising candidates for being incorporated into IPM programs in combination with these natural enemies for the control of particular greenhouse pests. In contrast, sulfoxaflor was slightly toxic to adults of C. carnea and was highly toxic to last instar larvae of A. bipunctata. For A. bipunctata, sulfoxaflor and deltamethrin were the most damaging compounds. Deltamethrin was also the most toxic compound to larvae and adults of C. carnea. In accordance with this fact, the use of sulfoxaflor and deltamethrin in IPM strategies should be taken into consideration when releasing either of these biological control agents, due to the toxic behavior observed under laboratory conditions.

The family of DOF transcription factors in Brachypodium distachyon: phylogenetic comparison with rice and barley DOFs and expression profiling

ABSTRACT: Transcription factors (TFs) are proteins that have played a central role both in evolution and in domestication, and are major regulators of development in living organisms. Plant genome sequences reveal that approximately 7% of all genes encode putative TFs. The DOF (DNA binding with One Finger) TF family has been associated with vital processes exclusive to higher plants and to their close ancestors (algae, mosses and ferns). These are seed maturation and germination, light-mediated regulation, phytohormone and plant responses to biotic and abiotic stresses, etc. In Hordeum vulgare and Oryza sativa, 26 and 30 different Dof genes, respectively, have been annotated. Brachypodium distachyon has been the first Pooideae grass to be sequenced and, due to its genomic, morphological and physiological characteristics, has emerged as the model system for temperate cereals, such as wheat and barley. RESULTS: Through searches in the B. distachyon genome, 27 Dof genes have been identified and a phylogenetic comparison with the Oryza sativa and the Hordeum vulgare DOFs has been performed. To explore the evolutionary relationship among these DOF proteins, a combined phylogenetic tree has been constructed with the Brachypodium DOFs and those from rice and barley. This phylogenetic analysis has classified the DOF proteins into four Major Cluster of Orthologous Groups (MCOGs). Using RT-qPCR analysis the expression profiles of the annotated BdDof genes across four organs (leaves, roots, spikes and seeds) has been investigated. These results have led to a classification of the BdDof genes into two groups, according to their expression levels. The genes highly or preferentially expressed in seeds have been subjected to a more detailed expression analysis (maturation, dry stage and germination). CONCLUSIONS: Comparison of the expression profiles of the Brachypodium Dof genes with the published functions of closely related DOF sequences from the cereal species considered here, deduced from the phylogenetic analysis, indicates that although the expression profile has been conserved in many of the putative orthologs, in some cases duplication followed by subsequent divergence may have occurred (neo-functionalization).

Genetic characterization of chestnut (Castanea sativa Mill.) orchards and traditional nut varieties in El Bierzo, a glacial refuge and major cultivation site in Northwestern Spain

This paper presents a detailed genetic study of Castanea sativa in El Bierzo, a major nut production region with interesting features. It is located within a glacial refuge at one extreme of the distribution area (northwest Spain); it has a centenary tradition of chestnut management; and more importantly, it shows an unusual degree of genetic isolation. Seven nuclear microsatellite markers were selected to analyze the genetic variability and structure of 169 local trees grafted for nut production. We analyzed in the same manner 62 local nuts. The selected loci were highly discriminant for the genotypes studied, giving a combined probability of identity of 6.1 × 10−6. An unprecedented density of trees was sampled for this project over the entire region, and nuts were collected representing 18 cultivars marketed by local producers. Several instances of misclassification by local growers were detected. Fixation index estimates and analysis of molecular variance (AMOVA) data are supportive of an unexpectedly high level of genetic differentiation in El Bierzo, larger than that estimated in a previous study with broader geographical scope but based on limited local sampling (Pereira-Lorenzo et al., Tree Genet Genomes 6: 701–715, 2010a). Likewise, we have determined that clonality due to grafting had been previously overestimated. In line with these observations, no significant spatial structure was found using both a model-based Bayesian procedure and Mantel’s tests. Taken together, our results evidence the need for more fine-scale genetic studies if conservation strategies are to be efficiently improved.