2018 International CRAG “Severo Ochoa” PhD Program | Center for Research in Agricultural Genomics

The International “Severo Ochoa” PhD Program of the Centre for Research in Agricultural Genomics (CRAG) is advertising four PhD positions for 2019. This is a four-year program beginning in early 2019. Doctoral students enrolled in this program will obtain their PhD Degree from either the Autonomous University of Barcelona (UAB) or the University of Barcelona (UB). More information about the doctoral program at CRAG can be found here:https://www.cragenomica.es/crag-phd-program

Ministerio de Economia y CompetitividadIf interested in applying to the International CRAG “Severo Ochoa” PhD Program,please carefully read the Application requirements and procedureand check out allavailable projects.

Application deadline isFriday March 30, 2018. Shortlisted applicants will be interviewed during spring 2018. Successful applicants will start their PhD projects in early 2019.

This four-year PhD grant is funded by the “National Programme for the Promotion of Talent and its Employability 2016” from the Spanish Ministry of Economy and Competitiveness.

Application requirements and procedure

Eligibility

1. The program is aimed at international students who have completed one of the following options by September 2018:

  • studies that lead to an official Spanish (or from another country of the European Higher Education Area) university degree in Biology, Biochemistry, Biotechnology, or related areas and that have 300 credits (ECTS), of which at least 60 must correspond to master level.
  • a degree in a non-Spanish university not adapted to the European Higher Education Area that gives access to doctoral studies in Biology, Biochemistry, Biotechnology or related areas.

2. Candidates are selected exclusively on merit, on the basis of their curriculum. Academic grades and the curriculum of applicants are evaluated, as well as reference letters and a motivation letter. No selection criteria for positive or negative discrimination are applied.

3. Applicants should have obtained a degree after January 2015.

4. Candidates cannot be in possession of a PhD Degree.

5. Candidates cannot have been hired as predoctoral students for more than 12 months before the start of the CRAG “Severo Ochoa” PhD Program.

6. Candidates cannot have started a pre-doctoral fellowship funded by the Spanish “Plan Estatal de Investigación, Desarrollo e Innovación Tecnológica” or any previous “Plan Nacional”.

How to apply

Applicants should complete and submit the on-line application throughCRAGjobs.

Applicants will be asked to upload the following documents:

  • Curriculum vitae
  • A motivation letter, including a brief summary of work experience and a statement of research interests and career goals (2 pages maximum).
  • A scanned copy of the student’s certified Academic Record, including a detailed record of study / transcript (a list of attended courses and corresponding grades): these documents must show the grades attained in exam periods.
  • Copy of passport (international applicants only).
  • Any additional files considered relevant to the application, but please only provide documents that are important to support it. Do not overload the application with certificates and documents of lesser significance.

In addition, applicants must ensure the submission of two reference letters from university lecturers or scientists with whom the applicant has studied or worked. Letters should be sent directly by the referees toPhDprogram@cragenomica.es, and should also be received by the application deadline,March 30, 2018.Only letters with official letterhead and signature will be accepted. Candidates are responsible for ensuring that referees submit these letters, and should consider that referees may need some time to prepare and send their letters within the deadline. Applications without reference letters will not be considered.

Pleasedownloadreferee request.

The doctoral program is in English. Therefore, a good knowledge of English is absolutely required. We encourage candidates to support the application with scores of internationally valid language exams like TOEFL or other tests. However, they are not mandatory: a verifiable education in English, or a reasonably long stay in an English speaking country are also convincing.

In the motivation letter,applicants should indicate up to two research projects in which they would like to work, in order of preference(seeAvailable Projects, below). Moreover, if candidates have a particular interest in any one of these projects, they should also indicate it. More information on the research activities of each group can be found at CRAG website.

Applicants must submit information in English (CV, and motivation letter including summary of work experience). If the certified academic records are not in English, Catalan or Spanish, applicants must also attach a translation in one of these languages.

Applicants must upload all the required documents asPDF files of less than 10MB.

Please note that we can only consider applications that are complete.

Selection procedure

Applications will be reviewed through a selection process involving CRAG group leaders, including the Principal Investigators that will host the fellows. Students are preselected according to their written application, grades, and reference letters.

Short-listed candidates will be interviewed during spring 2018. Candidates who are accepted for the program will be notified by email shortly after the interview period. These PhD positions are funded by the Spanish Ministry of Economy and Competitiveness (MINECO) and CRAG. CRAG will assist the selected candidates to submit the required documents at the Spanish MINECO website in summer 2018. Applicants who have not been successful but have received a positive evaluation will be put on a waiting list to cover possible renunciations and future positions.

Available Projects

2018 CRAG SO – 1: Genetic dissection of factors influencing fruit flesh color in melon

Principal Investigators: Jordi Garcia-Mas and Manuel Rodríguez-Concepción

Efforts are ongoing to identify genes underlying important agronomic traits affecting fruit quality and production in melon. Among them, flesh color is an important commercial trait, and ripe melons with white, green and orange flesh are available depending on the accumulation of plastid-localized chlorophyll and carotenoid pigments1. The accumulation of the pro-vitamin A carotenoid β-carotene is controlled by the Orange (CmOr) gene, which encodes a chaperone protein that promotes the differentiation of chromoplasts². Plants that carry the dominant allele CmOr (Gf/-) bear orange-fleshed melons, while the recessive Cmor (gf/gf) allele results in either white or green flesh melons³. The white/green phenotype is controlled by a second locus Wf, where the dominant (Wf/-) and recessive (wf/wf) plants bear white and green-fleshed melons, respectively³. The identity of the Wf gene, located in chromosome VIII, is still unknown. The identification of Wf and the analysis of its genetic interactions with Gf would provide a powerful tool to manipulate melon flesh color and nutritional content and contribute to better understanding the development of different plastid types. A RIL population derived from “Piel de sapo” and “Védrantais” allowed the identification of both loci involved in flesh color⁴. The mapping interval of Wf spans 233 Kb and contains 32 annotated genes, including candidates encoding proteins required for normal photosynthetic functions and chloroplast development. This PhD project proposes to progress our understanding on the genetic control of fruit flesh color by (1) identifying the Wf gene, (2) studying the genetic interactions between the different Wf and Gf alleles, and (3) characterizing the biological function of the encoded proteins. This multidisciplinary project involves the integration of several approaches and the collaboration of the laboratories led by Jordi Garcia-Mas (Program of Plant and Animal Genomics) and Manuel Rodriguez-Concepcion (Program of Plant Metabolism and Metabolic Engineering).

References:¹Chayut et al. BMC Plant Biol.15, 274 (2015), ²Tzuri et al. Plant J.82, 267-279 (2015), ³Clayberg Rep. Cucurbit Genet. Coop.15, 53 (1992), ⁴Pereira et al. manuscript in preparation

2018 CRAG SO – 2: The hidden nature of the Arabidopsis peptidome: Analyses of the Arabidopsis flower development gene regulatory network

Principal Investigator: José Luis Riechmann

The current global, dynamic view of the gene regulatory networks underlying plant development is primarily based on measuring gene expression at the transcriptome level, thus overlooking the substantial role that is played by regulatory processes occurring after mRNA is made. Moreover, evidence has accummulated over the past few years pointing to the existence of a substantial but uncharted fraction of the eukaryotic proteome that is mainly composed of small proteins (peptidome), of roles and functions yet to be discovered. Recent advances in proteomics and high-throughput analyses of translating RNAs (ribosome profiling) have begun to address this challenge, and evidence for functional peptides encoded by sORFs is accumulating. Using Arabidopsis flower development as the model and primary experimental system, the research projects aims to address two key questions: what is the nature and extent of the Arabidopsis peptidome? and, what are the specific functions carried out by this potential myriad of novel peptides/small proteins? Research will involve a combination of genomic, proteomic, genetic technologies as well as bioinformatic approaches.

2018 CRAG SO – 3: Role of microRNAs (miRNAs) in plant immunity: crosstalk between nutrient homeostasis and disease resistance in rice and Arabidopsis

Principal Investigator: Blanca San Segundo

Plants are constantly challenged with numerous adverse environmental conditions, including biotic and abiotic stresses. To survive under such conditions, plants have evolved a variety of mechanisms to perceive and respond in the most appropriated manner to each type of stress. MicroRNAs (miRNAs) are emerging as versatile regulators of gene expression in adaptive responses of plants to environmental stresses. MiRNAs are short regulatory non-coding RNAs that guide gene silencing. The main goal of the project is to decipher miRNA-mediated processes underlying resistance to pathogen infection in plants, and to identify interconnected regulations between disease resistance and nutrient homeostasis. These studies will be carried out in rice and Arabidopsis (model systems for functional genomics in monocotyledonous and dicotyledonous plant species, respectively). The specific objectives are: i) to characterize the relevance of miRNAs in crosstalk between phosphate signaling and immune responses; and ii) to elucidate the role of miR7695, a rice-specific miRNA characterized in our group, in controlling iron homeostasis in the context of disease resistance; and iii) to identify molecular mechanisms governing the interaction between phosphate and iron signaling in disease resistance. The project integrates forward and reverse genetic approaches (CRISPR/Cas9 genome editing, overexpression, mutant analysis), deep sequencing and bioinformatics analyses, nutritional assessments, cytological and histological analysis. The results here obtained and the knowledge generated will contribute to the establishment of novel concepts in the field of plant/pathogen interaction. This should finally help to define new strategies to improve disease resistance in plants that will also benefit breeding programs for crop protection.

2017 CRAG SO – 4: Understanding plant domestication through the genomic analysis of ancient emmer wheat from Egypt

Principal Investigator: Laura Botigué

Plant domestication is a topic of interest in a broad range of research fields such as agronomics, genome evolution, archaeology or anthropology. Past limitations in the study of the early domestication process can now be overcome by including ancient samples in crop genomic analysis. Our lab has access to emmer wheat samples excavated in Egypt dated from the Neolithic up to the Roman period. This project aims to extract the DNA from these ancient samples and sequence it to perform downstream genomic analyses that will allow us to answer several questions regarding wheat domestication. Specifically, the PhD candidate will use cutting-edge bioinformatic and statistical tools to work on i) investigating the genomic architecture of Egyptian wheat population through time, including modern wheat; ii) characterizing known phenotypic traits in the ancient samples such as the non-shattering phenotype, and iii) identifying regions of the genome selected during domestication through the comparison of the observed evolution of allele frequencies and computational simulations.

This project is a collaborative effort with University College London and Warwick University and presents an opportunity to learn and develop a wide range of techniques to perform genomic analysis and computational modelling. As a result, new aspects of cereal domestication will be discovered, and a step forward in the identification of genomic regions of interest for domestication will have been made. Furthermore, the PhD student will analyse for the first time genetic data from ancient specimens from different time periods.

Source:www.cragenomica.es