Editorial::Phenomics

publishersversionPeer reviewe

Teaching genetics, genomics and related disciplines to Erasmus students in English, language versus conceptual weaknesses

[SPA] El alto número de alumnos Erasmus nos llevó a iniciar la docencia en inglés en el curso 2000-1. Se han impartido asignaturas optativas como Biología Molecular Aplicada, Ingeniería Genética Vegetal y Genómica, cursos de master: Herramientas de Genómica en Investigación o troncales como Genética. La evaluación se ha llevado a cabo con presentaciones orales, y desde 2009 se ha añadido un examen tipo test. El examen test criba a los alumnos sin conocimientos básicos y falta de atención a las clases. Presentar un artículo de investigación requiere tutorías debido a la densidad de la escritura científica comparada con la de los textos para estudiantes. Los estudiantes de grado obtuvieron notas similares independientemente de su origen. Por el contrario, los estudiantes de master españoles obtuvieron notas significativamente mejores. Esta discrepancia podría deberse a que los alumnos extranjeros de grado tienen un nivel de conocimientos previo parecido a los españoles para las asignaturas. Sin embargo, en el master, los españoles eligen por afinidad temática mientras que los extranjeros lo hacen porque se oferta en inglés. El principal predictor del éxito de los alumnos no es que la asignatura se imparta en inglés, sino el grado de conocimientos previos relacionados con la materia impartida. [ENG] As a result of a relative important number of Erasmus students we started to teach in English in 2000-2001. Throughout the years the courses included optional courses like Applied Molecular Biology, and Plant Genetic Engineering for undergraduates, Genomics for graduate students, Genomic tools in research for master and compulsory courses like Genetics. Despite the offer of the different courses in English, the main predictor for the students success was a general knowledge of biological concepts and genetics rather than their English level beyond a certain minimal threshold. Grading was performed on the basis of an oral presentation of a scientific paper and since 2009 we included a short multiple-choice test of basic concepts. Both proved difficult but the multiple choice weeded out those students that did not do the everyday work of attendance. The preparation of a scientific paper required tutorial guidance as a result of the density of the scientific writing as compared to regular undergraduate textbooks. Undergraduate students graded equal irrespective of their origin while graduate students were significantly better when coming from Spanish universities probably as a result of choosing the subject based on previous knowledge and not on the language used

Desarrollo de herramientas genómicas y proteómicas de diagnóstico para el Sistema Murciano de Salud

La presentación muestra las líneas de investigación del grupo de Genética: •Control genético del tamaño de los órganos. •Desarrollo de herramientas de genómica. –Genotecas ultranormalizadas. –Mapeo de baja y alta resolución. –Identificación de fragmentos de ADN exógeno insertos en genomas complejos. –Desarrollo de vectores de expresión para genética y genómica inversa.Fundación Séneca. Ministerio de Educación y Ciencia. Fondo Social Europeo

El papel de las coaliciones promotoras en la evolución de las políticas de reporudcción humana asistida e investigación biomédica en España (1985-2010)

En este trabajo se estudia la función de las coaliciones promotoras en las políticas de reproducción humana asistida e investigación biomédica en España, durante el periodo de 1985 hasta el 2010. Desde el nacimiento del primer niño gracias a un FIV (fertilización in vitro) en España, las políticas sanitarias en especial las biotecnológicas han sufrido cambios.En este caso el marco teórico sobre el que se ha trabajado es el de las coaliciones promotoras, iniciada por Sabatier y Jenkins – Smith, y posteriormente por Éric Montpetit, Christine Rothmayr y Frédéric Varone, tendremos en cuenta que son políticas consideradas morales y se han aplicado al periodo y país. Para el estudio se ha hecho un profundo análisis de la legislación, los debates parlamentarios, prensa, informes y artículos de los principales actores que pertenecieron a las distintas coaliciones; finalmente 25 entrevistas con políticos, investigadores (bioética y biólogos), altos funcionarios, médicos, al igual que miembros de la Iglesia Católica que participaron en estas políticas durante el periodo de estudio.Como resultado de este proceso de estudio se llegaron a determinadas hipótesis que añaden a dichas teorías y matizan el marco teórico. Una de las peculiaridades frente a otros países, el deseo de los profesionales médicos españoles de una legislación aprobada rápidamente que proporcionara seguridad jurídica. La implicación de los investigadores y las organizaciones de pacientes en el proceso de toma de decisiones acompañando mientras los debates sobre reproducción se desplazaban hacia la investigación (investigación con células madre y clonación). La deconstrucción de la Iglesia Católica y su influencia, no ya como un mero observador sino como un jugador principal, y de sus distintas tendencias, especialmente los Jesuitas, como negociadores (brokers) entre los escépticos de la investigación y los emprendedores

Development of loss of function alleles based on CRISPR/CAS9 to study flower and fruit development

[SPA] El sistema CRISPR/Cas9 se ha convertido en la tecnología más útil para obtener alelos nuevos al estar basada en el proceso local de reparación de ADN activado localmente por la rotura del ADN. El complejo CRISPR/Cas9 es guiado por una molécula guía de ARN que le da especificidad de acción sobre una secuencia de ADN concreta. El objetivo del trabajo es desarrollar una colección de alelos en genes de interés relacionados con el desarrollo de la flor y fruto. [ENG] The CRISPR/cas9 system has taken over the methodologies to obtain new alleles as it is based on DNA repair mechanisms activated locally by DNA breakage. The CRISPR/Cas9 complex is driven by a guide RNA conferring specificity of action on a given DNA sequence. The aim of the work is to develop a set of alleles in genes of interest involved in flower and fruit development.The experiments will be conducted in Institute of Plant Biotechnology (IBV), Cartagena within Polytechnic University of Cartagena

Impact of crop diversification and low-input farming on soil microbial diversity

[SPA] Las comunidades microbianas existen en los ecosistemas de suelo y son indicadoras de su calidad. Los microorganismos en el suelo, proveen y contribuyen a los grandes ciclos geoquímicos del carbono y nitrógeno. Determinan las características físico-químicas y proveen de forma localizada de nitrógeno, sulfuro, fostato en la agricultura. El presente proyecto enfoca la determinación de comunidades microbiológicas, incluyendo especies y abundancia por medio de secuenciación de nueva generación de ADN de diferentes áreas agrícolas. Los datos generados van a dar una información muy amplia sobre las comunidades microbianas del suelo y el impacto de diferentes prácticas agrícolas sobre su estructura. [ENG] Microbial community existing in soil ecosystems is a major indicator of soil quality. Microorganisms in soil provide and/or contribute major biogeochemical cycles of carbon and nitrogen. They shape soil characteristics physically and chemically along with providing for Nitrogen, Sulphur, Phosphate and other nutritional cycles in agricultural areas locally. This project focuses on determination of soil microbiome community as the types of species existing and the abundance of each species through next-generation sequencing of 16S ribosomal metagenomic DNA from different agricultural areas. The overall data will provide a vast range of information of soil microbial community structure and the effect of different agricultural practices on community structure.This thesis is carried out in correlation with Plant Biotechnology Institute, Cartagena and Polytechnic University of Cartagena, Cartagena. Diverfarming Project is funded by European Union (H2020 project)

Development of loss of function alleles based on CRISPR/CAS9 to study flower and fruit development

[SPA] El sistema CRISPR/Cas9 se ha convertido en la tecnología más útil para obtener alelos nuevos al estar basada en el proceso local de reparación de ADN activado localmente por la rotura del ADN. El complejo CRISPR/Cas9 es guiado por una molécula guía de ARN que le da especificidad de acción sobre una secuencia de ADN concreta. El objetivo del trabajo es desarrollar una colección de alelos en genes de interés relacionados con el desarrollo de la flor y fruto. [ENG] The CRISPR/cas9 system has taken over the methodologies to obtain new alleles as it is based on DNA repair mechanisms activated locally by DNA breakage. The CRISPR/Cas9 complex is driven by a guide RNA conferring specificity of action on a given DNA sequence. The aim of the work is to develop a set of alleles in genes of interest involved in flower and fruit development.The experiments will be conducted in Institute of Plant Biotechnology (IBB), Cartagena within Polytechnic University of Cartagena. This work is supported by BFU2017-88300-C2-1-R

Role of molecular markers in environmental studies on the example of the endangered species Cistus heterophyllus

[SPA] Este estudio tiene como objetivo analizar un conjunto de marcadores moleculares para el rastreo de eventos de hibridación en la población de una especie en peligro de extinción de la familia Cistaceae, Cistus heterophyllus subsp. carthaginensis limitada a una sola población natural en el noreste de España. En esta población coocurren individuos con fenotipo silvestre y fenotipos híbridos, descritos antes en Africa como C. × clausonis, lo que sugiere eventos de hibridación entre esta población en peligro de extinción y una especie localmente abundante, Cistus albidus. Hemos aplicado marcadores plastídicos y la region internos inter-espaciados (ITS) de la ADN ribosómico como marcadores para su aplicación en la población mencionada. Observamos heteroplasmia en C. heterophyllus y C. × clausonis local, pero no en C. albidus. La región de ITS fue analizada en poblaciones geograficamente aisladas de Cistus heterophyllus, Cistus albidus y posibles híbridos entre estos dos especies. Depnediendo de individuo o población, C. × clausonis filogenéticamente parece más a Cistus heterophyllus o Cistus albidus y problamente está relacionado a la homogenización de variación por evolution concertada. [ENG] This study aims to analyse a set of molecular markers for tracing hybridization events in the population of an endangered species from the Cistaceae family, Cistus heterophyllus subsp. carthaginensis limited to only one natural population in the north-eastern Spain. In this population individuals with wild type and hybrid phenotypes, described before in Africa as C. × clausonis, co-occure, suggesting hybridization events between the endangered population and the locally abundant Cistus albidus. We applied plastid DNA and internal transcribed spacer (ITS) region of the ribosomal DNA as markers in the aforementioned population. We observed heteroplasmy for rpoB and rpoC1 plastid genes in C. heterophyllus and the local C. × clausonis, but not in C. albidus. The ITS region was analysed in geographically isolated populations of Cistus heterophyllus, Cistus albidus and possible hybrids of these two species. Depending on the individual and population, C. × clausonis phylogenetically resembles more either Cistus heterophyllus or Cistus albidus and it might be related to the homogenization of variation between repeat types through concerted evolution.This work was funded by the Comunidad Autónoma de la Región de Murcia Project “Molecular markers in conservation and management of the flora of Murcia Region”

Editorial: Spectroscopy for Crop and Product Phenotyping

Spectroscopy is a viable technique for exploring plant biochemistry in an efficient, accurate and typically non-destructive manner (Schie et al., 2018). By taking advantage of the properties of plant biomolecules and metabolites in different regions of the electromagnetic spectrum, advances have been made that allow for investigations into previously inaccessible aspects of biology in real-time (Akhgar et al., 2020). Other important advances involve disease diagnostics, early stress detection and plant product quality assessment (Gemperline et al., 2016). High-throughput technologies for nucleotide sequence analysis and detection of sequence variation have been increasingly used for plant genotyping and other fields of genetic testing. Polymerase chain reaction (PCR) is a simple and rapid method that can detect molecular genetic polymorphisms in basic and applied research applications. An important prospective use of PCR-based genotyping assays is to perform large-scale phenotyping analyses (Suyama and Matsuki, 2015), mutant screens, and comparative physiological analyses for Marker Assisted Breeding. This Research Topic highlights novel and innovative applications of all spectroscopic techniques that aim for characterization in plants in order to understand plant growth and productivity. Studies featuring impactful and innovative applications of well-established methodologies such as Raman spectroscopy, Near-infrared spectroscopy, Fluorescence resonance energy transfer, hyperspectral imaging, or a novel combination of spectrometric measurement techniques and novel spectrometric techniques were invited, resulting in 8 published articles. Infrared and Near-infrared spectroscopy (NIR) spectroscopy Infrared spectroscopy (Gillie et al., 2000) is becoming an increasingly popular and promising technology in agricultural and agri-food industries to measure intact, fresh, and unfrozen samples directly. The field of infrared spectroscopy is complex and comprehensive and could lead to specialized solutions for the agricultural sector in general, and for the viticultural industry in particular. Wyngaard et al., show that infrared spectroscopy is implemented for continuous monitoring of key metabolites in grapevine organs throughout the growing season. The observed spectral changes led to the classification of grapevine organs, providing individualized calibrations to compensate for the heterogeneity in grapevines, as well as developing more robust prediction models. Near-infrared spectroscopy is a non-destructive, fast, and low-cost method to measure the biochemicals for screening plant samples. Armstrong et al., investigate the feasibility of single kernel NIR spectroscopy for rapid determination of protein, oil, and weight in intact single sorghum seeds, highlighting the use of this non-destructive and quick method for screening these traits in sorghum breeding and industry applications. In the work of Ejaz et al., biochemical components of sorghum were predicted for enhancing grain sorting efficiency for food, feed, and fuel, using Fourier-transform NIR spectroscopy. Raman Spectroscopy-based Plant Pathology Diagnostics Raman spectroscopy (RS) is a label-free, non-invasive, non-destructive spectroscopic technique that is effective for studying the chemical structure of analyzed samples (Cialla-May et al., 2022). This technique has been widely used among biochemists, and has now found applications in agronomy, plant pathology and physiology for analysis of plant health status. Changes in plant biochemistry can be probed by Raman spectroscopy, allowing its use in confirmatory diagnosis of plant pathology. Dou et al., use RS to develop the diagnosis of Huanglongbing, a devastating disease caused by Candidatus Liberibacter spp. (Ca. L. asiaticus). By using a combination of HPLC and image studies of leaves, they created a ground truth concept demonstrating that a given signature in RS corresponds to increased p-coumaric acid and decreased lutein in infected grapefruit leaves. Since Raman spectroscopy can be used to resolve stress-induced changes in plant biochemistry on the molecular level, it represents a prospective and rapid technique for agronomy and plant pathology. Farber et al., show that RS can be used for highly accurate identification of stalk rot caused by Colletotrichum graminicola in maize at both early and late stages of disease progression, via spectroscopic analysis of both leaves and stalks. High-Resolution Microscopy and Spectrometry Approach The rhizosphere is a hotspot for microbial activity, organic carbon input, and carbon turnover in soils (Ilhardt et al., 2019). Several stand-alone and combinatorial methods have been developed to investigate the chemistry and the role of microbes in soil and the rhizosphere. Bandara et al., present a novel approach that allows simultaneous microbial identification and chemical analysis of the rhizosphere at a spatial resolution ranging from micro- to nanometers. This new method allows for comprehensive study of the spatio-temporal organization of nutrients and microbes in the rhizosphere at an unprecedented scale and provides a platform for a mechanistic understanding of complex patterns of interactions between roots, the microbiome and soil using a correlative microscopy approach. Lohse et al., present a novel workflow using laser desorption ionization combined with mass spectrometric imaging to directly analyze plant metabolites in a complex soil matrix. The target metabolites were detected with a spatial resolution of 25 μm in the root and surrounding soil, based on accurate masses using ultra-high mass resolution laser desorption ionization Fourier-transform ion cyclotron resonance mass spectrometry. Direct molecular imaging allows a non-targeted or targeted analysis of plant metabolites in undisturbed soil samples, paving the way to study the turnover of root-derived organic carbon in the rhizosphere with high chemical and spatial resolution. PCR genotyping Single-nucleotide polymorphisms (SNPs) represent the smallest type of genetic differences in DNA between biological samples (Campbell et al., 2015). SNP analysis has emerged as one of the most powerful tools employed over a wide range of research, from small-scale student-led investigations of specific SNPs to high-throughput microarray technologies to analyze thousands of SNPs simultaneously. Kalendar et al., propose a modification to improve the version of the existing Allele-specific PCR method that is similar to the Kompetitive allele specific PCR (KASP) technique for genotyping SNPs based on fluorescence resonance energy transfer (FRET). This new technique is based on the simultaneous presence of two components in the PCR: an allele-specific mixture (allele-specific and common primers), and a template-independent detector mixture that contains two to four universal probes and a single universal quencher oligonucleotide (Kalendar et al., 2022). The SNP site is positioned preferably at a penultimate base in each allele-specific primer, which increases the reaction specificity and allele discrimination. The proposed method was used for SNP genotyping in barley genes HvSAP16 and HvSAP8, and is suitable for bi-allelic uniplex, 3- or 4-allelic variants, or different SNPs in a multiplex format that can be used in a range of applications including medical, forensic, or any study involving SNP genotyping. Overall, the research collected on this Research Topic highlights innovative and promising applications of all spectroscopic techniques for characterizing plants to understand plant growth, productivity, and disease resistance, and for PCR-based genotyping to perform large-scale mutant screens, comparative analysis for Marker Assisted Breeding.Non peer reviewe

Genetic and molecular analysis of Gigantea, a gene involved in adaptation to climate via regulation of the circadian clock in Solanaceae

[SPA] El metabolismo, fisiología y comportamiento de los organismos vivos cambia entre el día y la noche. Estas oscilaciones biológicas se deben al reloj circadiano, un sistema endógeno que regula la mayoría de los procesos biológicos. En el reino vegetal, uno de los genes involucrados en esta regulación es Gigantea. Aunque fue descubierto en los años 50, sus funciones biológicas y moleculares no se conocen con detalle y son objeto de intenso trabajo debido a su importancia en la adaptación. En este proyecto de tesis pretendemos analizar cambios fenotípicos y bioquímicos relacionados con el silenciamiento de Gigantea en solanáceas. [ENG] The metabolism, physiology, and also the behaviour of most living beings, profoundly changes between day and night. These biological oscillations happen due to the circadian rhythm, an endogenous clock that regulates most of biological events. In the plant kingdom, one of the genes involved in this important regulation is Gigantea. Although discovered in the past century, some of its functions, at the molecular level, are unclear and still a source of intense scientific research. In this thesis project we will try to analyze phenotypic and biochemical changes induced by gene silencing in Solanaceae with the aim to better understand the function of Gigantea.I would like to thank the Institute of Plant Biotechnology (IBV), especially my director and co-director of thesis, Dr. Julia Rosl Weiss and Dr. Marcos Egea Gutiérrez-Cortines for their willingness and their valuable advice. This works is part of projects BFU-2013-45148-R and Seneca 19398/PI/1