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19 aprile 2014

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TOPICS for XXIX cicle

TOPICS for XXIX  cicle

Number of PhD positions: one PhD position with grant

Research topic:

New chemometric tools for food characterization through imaging and spectroscopy

The development of new chemometric tools for efficient extraction of useful information from data measured using fast and nondestructive techniques, such as NIR spectroscopy, RGB imaging and hyperspectral imaging is a strategic research area, due to the great importance concerning its strong interdisciplinary nature. In fact, the knowledge led by multivariate analysis of data acquired using these emerging analytical techniques is transversal to many research fields in science and agri-food technologies. The topics of the present research work will deal with the development of analytical methods for the fast characterization of food matrices in their complex form, i.e. without the need of sample pretreatment before analysis. The information contained in data measured using different analytical techniques, including both fast and nondestructive methods and classical analytical techniques such as chromatography that will be employed as reference methods, will be extracted by means of blind analysis algorithms developed ad-hoc, aiming to model the chemical, physical and technological characteristics of the food samples.

Scientific tutor:

Prof. Alessandro Ulrici (SSD CHIM/01)


Required skills:

The candidate is required to have at least a basic knowledge of the theory beyond the mostly diffused techniques of experimental design and of multivariate analysis (e.g., FD, PCA, PLS, PLSDA, signal processing ) and of their main applications for the characterization and valorization of agricultural and food products. Among the instrumental techniques, the rapid and non-destructive ones, such as infrared spectroscopy (especially FT-NIRS) and imaging techniques, will play a major role. The scientific profile of the candidate must prove a basic understanding of these topics.


Number of PhD positions: one PhD position with grant

Tutor prof. Angela Conte


There is increased interest for the intimate interactions between the colonic functions and the luminal ecology. Colon has an important role in the salvage and absorption, after bacterial metabolism, of some nutrients not absorbed in small intestine (peptides, polyphenols, carbohydrates...). Normal colonic flora not only metabolizes compounds but also hold pathogens at bay by several mechanisms. Administration of exogenous microorganisms so-called probiotics, has therapeutic effect inhibiting bowel inflammation in humans.

The aim of this study is:

1) to investigate some physiological properties of bioactive peptides obtained from bovine milk by microbial metabolism with Lactobacillus ramnosus.

2) to investigate the biological activity of polyphenol metabolites produced by Lactobacillus ramnosus

Genetic and epigenetic control of phenotpypic variation in Zygosacchatomyces rouxii complex, a common group of food spoilage yeasts

Number of PhD positions: one PhD position with grant

Tutor prof. Paolo Giudici


Traditionally, genetic changes, which include chromosomal rearrangement and spontaneous mutations, are considered driving forces for phenotypic variation, genome evolution and genetic disease. More recently, monogenetic cell-to-cell variability (so called phenotypic heterogeneity) has been also found to play an important role for the survival of a clonal population in the face of fluctuating environments. The phenotypic heterogeneity is metastable variation in cellular parameters generated by epigenetic mechanisms. Zygosaccharomyces rouxii and relative species are common food spoilage yeasts, suitable to survive in high aw environments. High interstrain phenotypic and genetic variability has been recently observed in a group of Z. rouxii related yeasts referred to as Z. rouxii complex (Solieri et al 2013; Solieri et al. in preparation). Moreover, cell-to cell variability in monoclonal population has also been observed (Solieri et al., 2013). However, the key proteins regulating such nongenetic heterogeneity remain elusive in Z. rouxii complex, as well as chromosomal rearrangements underlying the genetic variation. The present PhD project is aimed to:

1)     identify chromosomal hot spots of genetic rearrangements, with a focus on telomeric mating-type (/MAT/) genes and other multi-copy genes

2)     provide cell-image evidences of cell-to cell variability in isogenic  Z. rouxii populations (swith from budding to pseudohyphal growth)in response to the environmental changes

3)     study the role of at least one epigenetic controller of this heterogeneity, such asHsp90p

Number of PhD positions: one PhD position with grant

Research topic:

Ancient DNA and Archaeobotany Research to investigate local origins of wild cereals

Knowledge about the history of agriculture and the patterns of speciation and variation of domesticated species may have important implications regarding current agricultural, anthropological and ecological issues. This research focuses on the analysis of wild cereals from rockshelters located in central Sahara. Plant remains, accumulated in archaeological layers and protected by deterioration processes, are chronologically dated from about 7000 to 5000 years before present. Macroremains especially consist of caryopses in an extraordinary good status of preservation, and they are evidence of the presence of species that today are locally extinct. Among the wild cereals there are species of Panicum and Sorghum. This approach will shed light on the evolutionary lines that led to the contemporary species of minor cereals in the central Saharan area. By means of biomolecular and phylogenetic investigation, and especially by ancient DNA (aDNA) Research it would be possible to reveal new elements of the evolutionary history of wild cereals.

Scientific tutors:

Dr. Laura Arru (SSD BIO/04)


Dr. Anna Maria Mercuri (BIO/02)

Required skills:

The candidate is required to have familiarity with the main archaeobotanical and biomolecular techniques. For the selection purpose, it would be considered preferential title to possess knowledge on use of optical and scanning microscopes and systematic morphological analysis, on DNA extraction and amplification from ancient plant material, and on molecular skills such as DNA sequencing and DNA barcoding. It is also mandatory the availability to spend - from the beginning - a period of about six months/one year in a European/American lab to refine the molecular techniques of this quite delicate field of Research.

Number of PhD positions: one PhD position with grant

Research topic I:

Seed transmission of bacteria in tomato and cucurbits and assessment of seed health

Healthy seeds are key to high crop yields, underpinning European and global food security. A wide range of diseases and pests are carried by seed and as well as spreading and increasing old problems, new problems may be introduced into the European Community countries via this route. There are currently opportunities to improve seed quality control by implementing emerging novel methodologies. The research  project will aim to study and understand the transmission (seed to plant and plant to seed) of bacterial pathogens affecting tomato (Xanthomonas vesicatoria and Clavibacter michiganensis subsp. michiganensis) and cucurbits (Acidovorax citrulli). Extensive field trials are planned during the spring-summer period. Additionally, the project will attempt to develop efficient DNA/RNA extraction methods from seed and generic Real-Time PCR assays in order to implement the detection methods of seed transmitted bacteria. Finally, the project will improve methods for sanitation of seed contaminated by bacteria using either bacterial antagonists or biomolecules.

Research topic II:

The role of microbial communities (PGPB and PGPF) in the induction of systemic resistance in plants

Microbial communities associated with plants have being extensively studied during the last years. Among those communities there are several microorganism which may have a positive effect on crop plants, either by inhibiting plant pathogens or by promoting growth of plants, they are associated with (or both). During the research programme, two pathosystems will be taken into account: 1) Pear and its most important bacterial pathogen, Erwinia amylovora; 2) Tomato and Rhizoctonia solani (plus another fungus affecting the aerial part of the host plant). The possible induction of a systemic resistance in the host plant will be studied through a transcriptomic approach, i.e. the study of a set of transcripts produced by the host plants and associated with the presence/inoculation of particular PGPB or PGPF used to induce resistance to the pathogens.

Scientific tutor for both topics:

Prof. Emilio  Stefani (SSD AGR/12)


Required skills for research topic I:

The candidate is required to have a basic knowledge of plant pathology and plant bacteriology in particular. He/she should be familiar with the planning of field trials for studying the epidemiology and expression of bacterial diseases in vegetable crops. Knowledge of experimental design and statistical analysis of epidemiological data is also desirable. Basic microbiological techniques (media preparation, sterilization, plating, plant inoculation, DNA extraction from bacteria, PCR) are also required. Finally, the prospective candidate should have a very good knowledge of the English language, written and spoken.

Required skills for research topic II:

The candidate is required to have a basic knowledge of molecular plant pathology and plant biotechnology. He/she should be familiar with DNA/RNA extraction and purification from plants and its analysis. Some knowledge of metagenomics, AFLP, RT-PCR, HPLC and Next Generation Sequencing (NGS) would be greatly appreciated. Finally, the prospective candidate should have a very good knowledge of the English language, written and spoken.





RESEARCH TOPICS: ?Molecular characterization of insect populations feeding on animal organic matter?

The presence of non-indigenous species in new areas and regions can be due to natural shift but can also be increased by human accidental or conscious transport. In these new regions, the allochthonous species can proliferate, spread, and persist to the detriment of the environment and human safety. The invasive species threaten native biodiversity, disrupt ecological processes, and cause significant economic losses. In the last years the main attention to invasive species was focused on plant related species or on disease carrier insects whereas few attention has been paid on species able to contaminate animal organic matter or able to cause myiasis.
The present project deals with the molecular characterization of species related with protein rich substrata, such as dry meat and fish as well as fresh meat or living organisms, from different Italian, European and overseas population, in order to create a database useful for the identification of the species, of the populations and of their geographical origin.

Dr Stefano Vanin

Dr Lara Maistrello

The candidate for this PhD program should have a degree in Biotechnology, Biology or similar, basic entomological knowledge and advanced knowledge in molecular biology particularly: DNA extraction, DNA amplification (via PCR), cloning, sequencing. In addition knowledge about DNA dataset managing and sequence analysis (Clustalw, BLAST) are required.

Research topics : Intestinal microbiota, bifidobacteria and bioactivation of phytochemicals

Prof. Maddalena Rossi

The candidate should present a broad knowledge and training in the scientific and practical aspects of biotechnology and microbiology. The candidate needs a biotechnological background, with a strong interest in chemistry, molecular biology, microbial ecology. It is necessary that the candidate is prone to spend at least one year in a foreign laboratory to develop and apply new techniques.


RESEARCH TOPICS: "Development of practical strategies for pest control in the food production and storage chain"

Food products are subject to continuous hazards from animal pests that may occur at any stage of the production and storage chain. Among the measures that enterprises should take to ensure food safety there is pest control (EC Reg. 852/2004 and EC Reg. 854/2004), that should be carried out by applying a rational management of the productive processes and enabling procedures of internal monitoring and "self-control" strategies. Behind these operations it is important to have an analysis tool that allows to handle all the complex issues linked to the achievement of the pest management checklist and to the development of a specific survey of the different species of pests, that should be different according to the type of food commodity and the position in the production/storage chain. The aim of this project is to provide an instrument to enable a truly effective pest monitoring, to understand where to look and how to discriminate and interpret the different results. These elements are necessary to objectively identify the problems in order to take appropriate pest proofing solutions and a proper integrated pest management.


Dr Lara Maistrello

Required skills
Degree in Biology, Natural Sciences, Agricultural Sciences or similar. Good knowledge of food/stored products pests and good practical experience in pest management.



Research topics :
Characterization and evaluation of grapevine germplasm in Emilia Romagna using genetic, chemical and molecular markers. In the frame of a 3 years research project funded by 11 Bank Foundations (Ager).

Key points of the three year activity will be the characterization and evaluation of local main and minor grapevine cultivars of Emilia Romagna region, by means of ampelographic and ampelometric descriptors and the microsatellite profile, the analysis of grape berries phenolics and volatiles; the histo-anatomical features of leaf and berry related to susceptibility to biotic stresses with the specific aims of establish the basis of information for the exploitation of regional viticulture, the improvement of wine quality, the individuation of useful traits for low input systems of cultivation and the proposal of new products. The results will contribute to the implementation of the Italian Vitis database. The PhD student will acquire knowledge in several scientific fields such as chemistry, molecular biology, botanics and viticulture. In addition the work of the PhD student will be inserted in the frame of a research project involving the major schools for viticultural sciences in Italy (Universities of Torino, Milano, Pisa, Palermo, National Council of Research- Torino) enabling to improve his knowledge in one of the most interesting agronomical species cultivated in Italy and in Europe. The research collaborations with the other project members and the participation of the supervisors to European projects (Grapegen 06 and Cost Action) will also guarantee the possibility for the PhD student to spend part of the time in foreign Institutions or to participate to workshops or attend specialization classes abroad.

Required skills
Knowledge of botany, chemistry, arboriculture and viticulture, ecophysiology, methods of fruit composition analysis and quality evaluation; methods of inventory, collection, conservation, characterization and evaluation of fruit tree genetic resources.

Scientific Tutor :
Prof. Cristina Bignami
Dr.ssa Serena Anna Imazio

Prof. Andrea Antonelli



Research topics : Fate, metabolism and biological effect of food polyphenols and their metabolites in human.
Study of the biological activity of polyphenol-derived metabolites with particular emphasis on their antiglycative activity and their ability to interact with plasmatic proteins and enzymes. Dietary polyphenols are thought to be beneficial in reducing the incidence of degenerative diseases such as cardiovascular disease and certain types of cancers. Although a proportion of these dietary bioactive compounds are absorbed intact, more likely the real determinants of the biological activity of dietary polyphenols are their major metabolites. Following ingestion, infact, phenolic compounds undergo extensive metabolism during their passage through the gastrointestinal tract and, with very few exceptions, only metabolites of the parent compounds enter the circulatory system.

Scientific Tutor: prof. Angela Conte

Required skills: The applicant must have a good knowledge of food biochemistry, human nutritional needs and metabolism.

Research topic:
Studies on the epidemiology and biological control of the bacterial canker of Actinidia
The bacterial canker is the most severe disease of Actinidia sp. and its causal agent is the bacterium Pseudomonas syringae pv. actinidiae (Psa). The disease is not well understood so far and the research will focus on some aspects of the disease cycle, such as the pathogen penetration sites into the host plant, the role of pollen and fruits in spreading the bacterium, the epiphytic life of the pathogen on host and non host plants. A second important task is the study of the epiphytic and endophytic microbial communities, in order to identify possible antagonists to be used in biological control of the disease, together with conventional pesticides. A third task is to fingerprint Psa populations in order to allow an evolutionary study through genotyping and phylotyping.

Scientific tutor:
Prof. Emilio Stefani

Required skills
The prospective candidate is an enthusiastic and skilled, young scientist, with a good written and spoken knowledge of English and Italian and a very good computer literacy. An excellent academic profile and a sound knowledge of molecular plant pathology and plant-microbe interaction is required, as well as a good expertise in DNA technologies (extraction, purification, amplification, characterization, sequencing) applied to microorganisms. The research to be done also includes the design and evaluation of several field experiments, thus the statistical analysis of epidemiological data shouldn?t be a problem for the eligible candidate. Additional experience in numerical taxonomy and population genetics would be desirable.


Title: Food safety and innovative technologies in bioconservation
Research topics :

Study of bacteriocin-producers LAB (Lactic Acid Bacteria) and of their bacteriocins to be used as starters and natural preservatives to improve quality and safety in food field.
Antibacterial activity evaluation of natural antimicrobial substances (bacteriocins, spice extracts, lysozyme, chitosan) and living bacteriocin-producers strains entrapped in coatings applied to PET films for food packaging applications

Study of biological characteristics influencing the virulence and responsible of selective pressure in microorganisms isolated from food, clinical and environmental samples; evaluation of survival of pathogens (Legionella pneumophila) and opportunistic bacteria (Aeromonas hydrophila, Pseudomonas spp.) and their interaction in different ecosystems and in the biofilm production.

Evaluation of the chemo-antibiotic resistance in bacteria of clinical, environmental, food and animal origin. Identification and characterization of genetic determinants encoding for antibiotic-resistance, antibacterial activity and virulence factors through recombination mechanisms and molecular researches.

Scientific Tutor:
Prof. Moreno Bondi
Prof. Patrizia Messi

Required skills

The candidate would present a good knowledge of food, environmental and clinical microbiology, with particular reference to the role of microorganisms in the production and prevention of food degradation and food borne infections. Specific skills on the food packing field and on the study of biological characters responsible for selective pressure such as the production of antibacterial substances (bacteriocins and BLS), ability to form biofilm, etc., are also desirable. Experience in the fields previously reported can be important.


Research topics :
Identification and molecular mapping of loci responsible of bolting time in lettuce.

A recognized problem for lettuce crop is early bolting (i.e. flowering) in the field before harvesting time. A lettuce plant starting to bolt synthesizes secondary metabolites that render the crop unsaleable. Therfore delayed bolting is a desirable trait in commercial lettuce varieties as it helps preserving the quality of lettuces sold for consumption and allows the grower more time to harvest the crop. During this Ph. D. thesis a molecular linkage maps will be produced on genetic materials exhibiting polimorphism for the bolting induction trait, in order to find the most significative association between markers and loci controlling it.

Required skills
Knowledge of horticulture, plant genetics, plant genomics, horticultural plant breeding, plant biotechnology, methods of marker-assisted selection, of linkage map construction and of linkage mapping, including bioinformatics.

Scientific Tutors:
Dr. Enrico Belfanti


Prof. Nicola Pecchioni


Research topics :
Plant genomics for improvement of production

The advent of plant genomics and of genomics platforms allowed in the last few years to move from small plant genome sequencing (e.g. Arabidopsis) to sequencing projects of large genome crops. One result of the last revolution of technologies known as new generation sequencing (NGS) is the partial shift of genomics research from model plants to globally important crop species. It is aim of the present project the application of plant genomics tools to understand mechanisms limiting crop yields. The final aim being the improvement of quantity and quality of the production of agricultural plants strategic for the italian and european economy.

Required skills
Knowledge of plant genetics, plant genomics, plant breeding, plant ecophysiology, plant biotechnology, methods of marker-assisted and genomic-assisted selection, including bioinformatics.

Scientific Tutor:

Prof. Nicola Pecchioni

1) Number of PhD propositions : one PhD position with grant.

RESEARCH TOPICS: Starters, probiotics, and fermentative processes towards
traditional and functional foods.

The project aims to investigate metabolic and physiologic properties of
probiotic bacteria and microbial starters (e.g. yeasts and lactic acid
bacteria) in order to exploit them in the development of innovative
functional foods and in food manufacturing to improve safety and product

SCIENTIFIC TUTORS: prof.ssa Maddalena Rossi

2) Number of PhD propositions : one PhD position with grant.


Genomics and bioinformatics in the model plant Brachypodium distachyon for the study of yield potential of cereals
The species so far the most used as model plant, Arabidopsis thaliana, has provided a wealth of useful informations and valuable tools for understanding plant biology. However, Arabidopsis is too phylogenetically distant from the temperate cereals to be used as a model system for cereal-specific metabolisms and responses to the environment. For this reason, together with the growing use of cereal crop species as "models" for themselves, recently Brachypodium distachyon has been proposed as new model for grasses and temperate cereals like barley and wheats. Brachypodium has available diploid accessions, lab-suited size and short life cycle, autogamy, simple growth requirements, a small (about 271 Mbp) sequenced and annotated genome publically available, genetic and genomic tools developed so far.
It is aim of the present PhD project to apply most recent genomic and bioinformatic tools, like e.g. NGS techniques, to study and validate candidate genes for explaining mechanisms of tolerance to yield potential limitations like biotic and abiotic stresses. Among biotic, the leaf rust fungus Puccinia brachypodii, and among abiotic low temperature. The results obtained, in a faster time than in a complex cereal genome like that of barley or of wheat, will serve as a basis to transfer this knowledge to major cereals. It is required fluent knowledge of at least one language of EU but more will constitute preferential title; the student will be asked to move for 1 to 3 short (6 months) periods to other laboratories of the Brachypodium research community to share results and technologies. It will be required for the PhD student to publish one scientific article per year.
Tutor Prof. Nicola Pecchioni

Acetic acid bacteria as oxidative catalysts in industrial processes.

The research project is devoted to develop reproducible and efficient
methods for the exploitation of acetic acid bacteria as biocatalysts
in industrial processes.
The project includes two main parts:
-         study of stress factors affecting industrial application of
acetic acid bacteria
-         strategy to exploit metabolic potential of acetic acid
bacteria for innovative industrial products.



Despite their great economical impact as pests of the major crops, aphids have been not deeply studied at a molecular level and in particular the structure and evolution of their chromosomes have been almost neglected. Sex chromosomes (consisting in two X chromosomes in females and only one X in males) have been partially studied at a cytogenetic level and they resulted highly enriched of heterochromatin, but at present only one X-related gene has been identified and few studies aimed to analyze their evolution has been carried out. At this regard, for instance, even if X chromosomes play an important role in the sex determination there isn?t any result indicating which genes on X chromosomes drive the male/female differentiation. The aim of the present project is to analyse the X related genes  of the peach potato aphid Myzus persicae, generally considered one of the more serious pest on a wide range of agricultural and horticultural crops, in which it can cause substantial direct feeding and cosmetic damage as well as transmitting more than 100 virus diseases. M. persicae X chromosomes will be dissected using a laser catapulting microdissector and amplified by whole genome amplification PCR. Aphid sex chromosome dissection is facilitated by the large dimensions of the X chromosomes that are generally at least 10 µm long. The DNA sequences obtained from the dissected chromosomes will be amplified and marked for generating chromosome specific painting probes to be used for in situ hybridization experiments (ZOO-FISH) comparing the composition of the X chromosomes in highly related  and less related species looking for gene syntheny. We also plan to use the DNA isolated by microdissection to construct a X chromosome-specific library that will be wholly sequence by 454 sequencing. This approach will be facilitated by the presence of the wholly sequenced genome of the aphid A. pisum. The availability of a chromosome specific library will allow us to analyze a) the sequence composition of the X chromosomes in M. persicae, b) to identify the groups of genic syntheny, c) their conservativeness d) to evaluate the rearrangements occurred during the evolution of more or less related taxa. Moreover, we plan to screen the X chromosome-specific library for the presence of repetitive elements including transposons and retrotransposons and other repetitive elements. The presence of mobile elements in the aphid genome is particularly intriguing since in many populations, and sometimes in a whole species, aphid reproduction is based on apomictic parthenogenesis lacking therefore not only sexual reproduction but also crossing over recombination. It could be therefore very intriguing looking for recombinational events due to mobile elements in parthenogenetic aphid making possible the evaluation of the role of specific DNA sequences (satellites, transposable elements, etc.) in genetic variability and chromosomal rearrangements. The identification of genes located on the X chromosomes will also allow us to go in depth in the study the sex determination mechanisms in aphids and to verify the presence of dosage compensation mechanisms between XX females and XO males. Gene dosage compensation has been observed in some insects species (such as the XX-XY system in Drosophila), but is not present in Lepidoptera with the ZZ/ZW sex determination system. Insects with XX/XO sex determination have never been studied making also this goal absolutely innovative. At this regard it must be stressed that the role of dosage compensation in the evolution of sex chromosomes has been very recently debated since the Ohno hypothesis has been denied buy RNA sequencing studies carried out in human and mouse. The interest in the identification of chromosome rearrangements is emphasized in M. persicae where chromosome translocations have been related to changes toward insecticide resistance. In particular a translocation 1-3 has been related to increased resistance levels against organophosphate insecticides in aphid populations isolated in UK. In Italy several M. persicae population have been isolated with different levels of organophosphates resistance but no information are available on their karyotype. Specific probes obtained by microdissection could therefore allow us the identification of chromosome markers to be used for the management of resistant aphid populations in the field. Chromosome microdissection provided interesting clues about karyotype evolution in mammals, birds, and, more recently, in plants but it has been so far scarcely applied in insects. This approach (combined to 454 sequencing) could allow us to go in depth in the study of genes and repetitive elements localized on X chromosomes in aphids also opening new applicative perspectives. Indeed our project will provide useful tools for sex chromosome researches, especially for the study of genetic control of sex determination and sex differentiation in aphid species and for the identification of chromosomal markers related to insecticide resistance.
Tutor Prof. Giancarlo Manicardi


Molecular dissection of QTL controlling the high and low temperature growth of wine yeast.

Required skills
The successful candidates should have a Master degree in Food sciences and Technology, Biotechnology, Biology, or Food control and safety. Basic knowledge of the main molecular biology procedures, as well as experience in using microbiology equipments and microorganism management are required. Knowledge of bioinformatics and software tools for sequence analysis are a plus. The candidate should show a real interest for industrial microbiology and bio-statistics. Further, the candidate should be a team-player and should have excellent knowledge of English.
Tutor prof. Paolo Giudici


Secondary metabolites in plants: properties and effects on plants and human health
Different stresses in plants can promote the formation of reactive oxygen species (ROS), which in turn generate oxidative stress. Plants at this point produce different secondary metabolites with antioxidant properties, in order to limit the damage. Many of these compounds have been shown to have important positive effects on the plants themselves, and on human health, for example by showing antioxidant and chemopreventive properties. The PhD project includes the study of these secondary metabolites and their applications.

Tutor: Dott. Laura Arru


Plant genomics for improvement of crop production
The advent of plant genomics and of genomics platforms allowed in the last few years to move to sequencing projects of large genome crops. One result of the last revolution of technologies known as new generation sequencing (NGS) is the partial shift of genomics research from model plants to globally important crop species. It is aim of the present project the application of plant genomics tools to crop species, to directly understand mechanisms limiting crop yields. The final aim being the improvement of quality and quantity of the production of agricultural plants strategic for the Italian and European economy. The required skills for a candidate are: knowledge of plant genetics, plant genomics, plant breeding, plant ecophysiology, plant biotechnology, methods of marker-assisted selection, basic bioinformatics. It is required fluent knowledge of at least one language of EU but more will constitute preferential title. It will be required for the PhD student to publish one scientific article per year.

Tutor: Dott. Enrico Francia





General Topics of the School

The research activity of the School of Doctorate concern production, processing, as well as chemistry, technology, quality and safety of food. Each topic is developed in a particular course. Vegetal and animal production, including growing techniques, cattle breeding, pest control are the main topic of the course of Science, Technology, and Biotechnology in Agriculture. Consumer and environment respect along with high quality production and food industry needs are the main concerns of these topics. The new applications of molecular genetics in agriculture are also extensively studied.

Process and product innovation are the main topics of the Food Science, Technology, and Biotechnology course. Food technology, microbiology, chemistry, biochemistry, and molecular biology are the main fields involved in these topics. Raw material quality and its aptitude to processing is also matter of concern, as well as innovative food packaging technologies.


Crop physiology: research of crop plant ideotype for low-input farming

The need to reduce inputs in modern farming systems must necessarily go together either the maintenance or the increase of yields for crop plants, because of the increasing world demand of commodities. It is asked to agronomic research not only to find ways to optimize and save inputs, but also to design new physiological ideotypes of crop plants that are more responding in the field to this double objective. This is the object of the research, to individuate physiological types that are more suitable to stabilize yields in low input conditions, in a chosen species, and for the Italian environments.

Product innovation for diversification strategies and business development in agribusiness

The international trade liberalization of agricultural products cuts down the business income of European farmers. It is necessary to develop diversification strategies in farm productions in order to have new opportunities, for example different uses of agricultural commodities and new particular consumer demands. Product innovation is increasingly important for the European agriculture. This is a very complex subject, a lot of elements are involved in it: technical knowledge, management, marketing, business strategies, political decisions, agricultural policy. The first purpose of this research is to analyse these arguments using economic theory and empirical analysis in the agricultural sector. The second purpose is to give indications and to define operating rules to indentify, check, transfer, implement the product innovations in the agricultural sector.

Fine mapping of resistance genes to root-knot nematodes

The goal of the ph.D project will be the study of the genes involved in the resistance to Root-Knot Nematodes (RKN, Meloidogyne spp.) in common bean (Phaseolus vulgaris L.). Starting point of the research will be the genetic materials (breeding lines, segregating progenies, etc.) developed by the Centro per le Colture Industriali di Bologna (CRA-CIN, Research Center for Industrial Crops) and the derived molecular markers associated to the different resistance sources studied during the last years. The multidisciplinary project will try to connect breeding experience and different genomic tools with the final aim to identify the genes that are regulating the nematode resistance, for example by saturating the flanking regions surrounding the genes with different molecular markers, and trying to clarify the regulation and the expression of those resistance genes.

Construction of a high resolution map of wheat chromosome 5A

The goal of the project is the construction of a high density molecular map that is needed for anchoring BAC contigs to a genetic map, in order to obtain a physical map for sequencing. Several mapping populations will be used during the project, and different parallel marker development approaches. The model species Brachypodium dystachion will be used for searching orthologous sequences. The computational effort for the map construction, together with the association of markers found with agronomically relevant traits will be part of the project.

Quality Improvement of fruit productions

The aim of the research is to understand the critical environmental and physiological factors that can improve the fruit productions, through the interaction with the agronomic management. This will include the study of how such factors affect the fruit quality. The results of the action of the key factors will be analyzed, as quality traits as well as compounds with nutraceutical value, not only on the fresh product of the chosen species, but also on the transformed products.

Innovation and quality in organic zootechny

PhD students activity will be carried out in the agro-zootechnical field, with particular attention to the effects of innovative farming technologies, alternative to the current conventional ones, on animal products quality. In detail, the attitude of raw materials to be processed into highly safe and high value added products will be investigated. Further, attention will be paid to the relationships between organic pig farming and the quality of the finished products. Finally, the characteristics of carcass and meat obtained from local swine breeds, reared according to the organic system, will be defined.

Increase of anthocyanin production in tomato

Anthocyanins are water-soluble pigments widely distributed throughout the plant kingdom. Beside their physiological roles in plants, several positive effects of anthocyanins in the diet have been described, and interest grew in anthocyanin pigments, and in food plants containing anthocyanins, because of their possible health benefits as antioxidants. The main objective of the research will be the study of the role of anthocyanins in the response to biotic and abiotic stresses. In particular, it will be evaluated the tolerance/susceptibility to abiotic (chilling) and biotic (Alternaria infection) stresses of single and double mutants of an available collection of mutants impaired in anthocyanin content. The research will also deal with the identification of the alleles of candidate genes that could explain the mutations, selected among regulatory elements of the anthocyanin biosynthesis pathway.

Food Microbiology

The research activity of Food Microbiology group focuses microbial ecology associated to safety and stability of foods. The research activity includes: i) the knowledge of food ecosystems; ii) the transformation and preservation techniques; iii) the microbial activities to obtain metabolites useful for biotechnological applications.

Our experimental approaches include the integration of classical methodology and metabolomics and metagenomics to characterise the microbial diversity in food ecosystems as well as their potential exploitation in innovative microbial processes.

Yeasts, acetic acid bacteria and lactic acid bacteria involved in fermented foods production are the main microbial groups investigated through poliphasic identification and technological characterisation, and about 2,000 strains have been collected as bioresource for selection and genetic improvement of strains useful for wine, vinegar, beer, sourdough and cheese production.


Biological activity and metabolism of naturally occurring compounds. In particular, their protection against oxidative stress and protein glycation and their ability to modulate the biochemical activity of digestive enzymes.

Evaluation of the food flavour profile with an electronic nose

Food flavours have been traditionally studied by gas chromatography. More recently, the use of electronic sensors is gaining interest in this field.

The study of relationships among composition, food quality, and the response of an electronic nose to several foodstuffs is the main objective of this research topic. In addition, the problem of off-flavours and taints can be considered as well for its great concern in food industry. Among the others, food taints could derive from technological process, poor storage conditions, and occasional contamination. The study of relationships among composition, food quality, and the response of an electronic nose is the main objective of this research topic. The correlations among sensory analysis, GC determinations, and electronic nose responses applied to different matrices (food, raw materials and packaging materials) will be considered.

Meat production, meat processing and quality assessment.

Pork production requires high standards of quality to meet the consumers’ expatiations and the need of transformation industry. The former requires healthy product, with low levels of fat and cholesterol; the latter look at the fatty acid composition, which is a matter of great concern for its implication in curing for its higher oxidability. In addition, the outbreak of defects in pig thighs (superficial veining, red skin, blood splash etc.) can cause a high incidence of rejects at seasoning. Hybrids and genetic selection for leaner carcasses modify lipid characteristics, becoming richer of unsaturated fatty acids. Although favourable for human nutrition, an increase of these substances may cause oxidation problems, especially for long-seasoned products such as Italian seasoned ham. Chemical composition of fat, sensory and rheological attributes of final products, the influence of farm factors, the characteristics of backfat and intramuscular fat for the improvement of ham quality in PDO dry-curing, and the study of the qualitative characteristics of the carcass and meat of farm animals are the main research objectives.

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