Phenotypic modelling of plant adaptation
Daniela Bustos-Korts, Wageningen University
November, 2022
Courses activated in 2021-22 academic year
METABOLOMIC APPROACHES IN AGRICULTURAL SCIENCE: FROM SAMPLE EXTRACTION TO BIOINFORMATIC ANALYSIS ANALYSIS (3CFU)
December 2021
AIMS
The course will focus on metabolomic strengths and on its weaknesses, its potential application in life science, and all the steps involved in the metabolomics workflow, from sample extraction to bioinformatic data analysis and interpretation.
Through lectures, case study and practicals, this course aims to provide the student with a high degree of familiarity with the equipment and experimental methods that underlie the study of complex biological systems using a powerful tool such as metabolomics.
TO BE AQUIRED
Basic knowledges on metabolomic and its potential use in plant and agricultural science as well as basic knowledge in data handling and analysis
14 December 2021
09-11
Fabrizio Araniti
Introduction to plant metabolomic
11-13
Natasha Spadafora
Comprehensive analytical workflow for the study of the volatilome to determine food quality and safety by automated sample preparation coupled with GC (GCxGC)-MS
14-16
Bhakti Prinsi
Targeted analysis of plant secondary metabolites by LC-ESI-MS/MS: a case study in basil
15 December 2021
09-11
Metabolomics: Age-old Technologies to Emerging Computational Tools and Resources
Biswapriya Biswavas Misra
11-13
MS-DIAL, a versatile tool in MS-based metabolomics efforts: Hands-on tutorial
Biswapriya Biswavas Misra
14-16
Untargeted metabolomics for authenticity and traceability in the agro-food chain
Luigi Lucini
16 Dicember 2021
09-13
Practical course on metabolomic tools: from peaks intensities extraction to data analysis
Fabrizio Araniti
14-16
Integrated Analysis of Transcriptome and Metabolome dataset in plants
Antonella Muto
Other courses putatively activated in 2021-22 academic year
Exploitation of variability in woody crops (3CFU)
AIMS
Understanding of the genetic variability in tree crops
TO BE AQUIRED
Tools for preserving and exploiting the genetic variability in tree crops.
PROGRAMME
I. Phenotipic variability in woody species. BASSI, CIRILLI (1 CFU, 6 h)
Basic elements of sistematic pomology in pome and stone fruits, olive, grape and citrus. Main tools for varietal characterization.
Preserving byodiversity: genetic resources collection. Cultivar evaluation and identification.
Breeding principles: qualitative and quantitative traits. Main breeding goal and selection criteria: yield, quality, resistance to biotic and abiotic stresses.
II. Genotipic variability in woody specie and its exploitation: grape as a case study. DE LORENZIS, FAILLA (1 CFU,6 h)
Grapevines genetic resources for breeding of wine, table grapes and rootstock. Phenotyping. Genetic structure of grapevine germplasm. Grapevine domestication: sylvestris vs sativa. Genetic bases of some phenotypic traits: muscat flavor, color, bunch shape. Phenotyping for rootstock resistance to abiotic stress
III. Sequencing the genome of heterozygous species. POZZI, ROSSINI (1CFU, 6 h)
Application of next generation sequencing in grape. Advanced breeding: marker assisted selection; gene pyramiding; genomic selection. Next generation breeding: use of genome bioediting and biotechnologies in grape.
Genomic approaches for dissection and improvement of fruit quality traits in peach. Introduction to peach and fruit quality traits. Breeding goals and traditional approaches. Genomics tools to support breeding - examples through selected case studies: MAS for a Mendelian trait, markers for maturity date and aroma. Challenges and opportunities: complex traits dissection and improvement - towards genomic selection in peach; phenotyping complex traits - texture.
Safety and wellness of agricultural operators (3CFU)
Course objectives and skills requested
The course is aimed to offer a specific skill about the evaluation and management of the most important risks encountered in the agricultural activity, both for the possible accidents and the occupational diseases onset.
The participating PhD students are requested to have a basic knowledge about the agricultural system and the main means of production (machinery, fertilizers, pesticides, etc.).
PROGRAMME
Principles of ergonomics and evaluation methodologies Guidetti, Riccardo (1CFU, 6 h)
a) principles of biomechanics
b) the upper and lower limbs; the spine
c) the risks of biomechanical overload
d) ergonomics
e) the OCRA (OCcupational Repetitive Action)
f) application examples in agriculture
Equipment for the application of plant protection products (sprayer machinery) Facchinetti, Davide (1CFU, 6 h)
a) The correct and sustainable use of the sprayer machinery, with particular reference to the environmental impact reduction of the treatments and the operator protection
b) The safety in the use of agricultural machinery: a) general overview
The safety in the use of agricultural machinery Domenico,Pessina (1CFU, 6 h)
1) analysis of the most critical situations:
a) the tractor roll-over
b) analysis of the most critical situations: the PTO cardan shaft
2) Analisys and solutions to control the most dangerous ergonomics parameters in agriculture:
a) noise
b) vibrations
Senescence and quality of flowers and vegetables exploitation of variability in woody crops (3CFU) Antonio Ferrante
AIMS
Description of the internal and external factors that affect the plant and argon development and senescence. Relationship with the quality of produce and strategies for preserving the quality during postharvest life.
TO BE AQUIRED
Understanding the mechanisms behind the senescence processes and tools to delay the senescence preserving the quality of horticultural produce.
PROGRAMME
I. Introduction
The fruit and leaf development and quality changes during ripening and senescene.
II Plant hormones and senescence
Physiological, biochemical, and molecular changes induced by the plant hormones and senescence regulation using the plant hormone inhibitors. Use of biotechnological tools for modifying the quality and produce preservation.
III Technological advanced tools for reducing the senescence.
Use of low temperature, controlled or modified atmosphere for slowing down the degenerative processes associated to produce senescence.
Sustainability in animal production (3CFU)
AIMS
Understanding the main aspects of sustainability in animal productions and identification of improvement strategies
TO BE AQUIRED
Tools for identifying strategies for improving animal production sustainability.
PROGRAMME
I. Environmental impact of animal productions. Sandrucci, Anna Alfea (0.5 CFU, 3 h)
The challenges of sustainability in animal production. Environmental impact of animal productions: GHG emissions, eutrophication, acidification, land use. Factors influencing environmental impact of animal products
II. Mitigation strategies of environmental impact of animal production. Alberto Tamburini (0.5 CFU,3 h)
Agriculture and Climate Change. Methane and ruminal fermentations. Mitigation potential. Food diet changes drive to mitigation. Milk productivity. Feed rations. Carbon sink. Technology and mitigation.
III. Life Cycle Assessment of environmental impact of animal production chains: methodological approaches and application cases. Luciana Bava (0.5 CFU, 3 h)
Life Cycle assessment: what is it? Life Cycle assessment: example from scientific literature. The phases according to EN ISO 14040. Goal and scope. Functional unit. System boundaries. Allocation. Inventory analysis. Impact assessment. Interpretation. Life Cycle Costing. Social Life Cycle
IV. Sustainable livestock systems in developing countries. Matteo Crovetto (0.5 CFU, 3 h)
Contribute of food of animal origin to human diet in developed and developing countries. Undernourishment in the world. Crop and animal production systems: intensive, semi-intensive, extensive. Mixed and small-scale farms
V. Precision feeding for a sustainable animal husbandry. Luca Rapetti (0.5 CFU, 3 h)
What is the precision feeding? Total mixed ration. E-feeders. Technologies to measure nutritional processes. Environmental impact of N and N metabolism in ruminants. Effect of Precision Feeding management on N excretion and production. The enteric methane. Selected strategies for enteric methane mitigation.
VI. Animal welfare for a sustainable animal husbandry. Silvana Mattiello (0.5 CFU, 3 h)
Definition of animal welfare. Why talking about animal welfare? European approach to the evaluation of
animal welfare: animal-based vs resource-based indicators. New trends: positive welfare and animals’ emotions. New technologies for the evaluation and labelling of animal welfare.
SUSTAINABLE CROP PROTECTION (3CFU)
AIMS
To supply knowledge and tools concerning new strategies for plant disease and parasite containment.
TO BE AQUIRED
Basic knowledge on plant parasites and their effects: new tools for their containment.
PROGRAMME
I. Elusive plant pathogens: endophytism and parasitism. Basic of biocontrol for plant pathogen containment. Bianco, Piero Attilio (0.25 CFU, 1,5 h)
New technologies are disclosing surprising interactions among plants and their inner "world". New insights for their relationships are source of new knowledge and new triggers to develop innovative plant disease control strategies.
II. Biological control of insect pests: from SIT to symbiotic control, Montagna, Matteo (0.5 CFU,3 h)
Agriculture and Climate Change. Methane and ruminal fermentations. Mitigation potential. Food diet changes drive to mitigation. Milk productivity. Feed rations. Carbon sink. Technology and mitigation.
III. The complex epidemiology of plant diseases associated with uncultivable pathogens: multidisciplinary approaches applied to develop sustainable control strategies. Quaglino, Fabio (0.5 CFU, 3 h)
General features of uncultivable pathogens. Phytoplasmas as case study: main properties (etiology, epidemiology, host-pathogen interactions). Molecular epidemiology as starting point for developing control strategies. Sustainable integrated approaches to control phytoplasma diseases.
IV. Resistance to plant pathogen: the case of grapevine and Plasmopara viticola; Patogen resistance to fungicides. Toffolatti, Silvia (0.5 CFU, 3 h)
Can we exploit plant resistance for the disease management? Description of the plant defense mechanisms in different grapevine species, available and emerging sources of resistance and durability of resistance. Challenges in fungicide management of the disease: definition of fungicide resistance, selection of resistant strains and management of resistance through anti-resistance strategies.
V. Plant Secondary Metabolites: Pathophysiologial Role in Planta and Health-Promoting Effects in Human. Iriti, Marcello (0.5 CFU, 3 h)
Chemical structure, biosynthesis and tissue localization of phytochemicals. Chemical ecology. Resistance/tolerance to biotic/abiotic/environmental stresses. Plant innate immunity: elicitors and plant activators. Bioactive phytochemicals of food and medicinal plants: health benefits in human.
VI. Allelopathy & Allelochemicals. Vitalini (0.25 CFU, 1,5 h)
Plant-plant interactions and introduction to allelopathy. Allelochemicals: chemical structure and biosynthesis. Release and activity of allelochemicals. Allelopathy in crop protection. Case studies: Lolium multiflorum and Peucedanum ostruthium.
VII. Beneficial bacteria as inoculants and members of the microbiota: case study on biocontrol of fungal pathogens of lettuce. Passera (0.25 CFU, 1,5 h)
Biocontrol of plant pathogens. Native and exogenous beneficial microbes. Endophytic and epiphytic microbiota: functions and characteristics. Case study example of the application of exogenous bacterial inoculants on the control of fungal pathogens and effects on the microbiota of lettuce plants.
VIII. Use of bacterial biostimulants for improving crops yield ad quality. Cocetta, Giacomo (0,25 CFU, 1,5 h). Biostimulants, a general overview and classification. Beneficial effects of bacterial biostimulants on crops agronomical traits. Crops quality as affected by bacterial biostimulants application at harvest and during shelf life. Case studies related to vegetable crops treated with bacterial biostimulants.
Nitrogen nutrition in crops: Agronomy, Biochemistry, and food quality (3CFU)
AIMS
The course will address topics related to the management of nitrogen fertilization and nitrogen metabolism in plants as well as analyze the impact of nitrogen input on crop production from the quantitative and qualitative point of view.
TO BE AQUIRED
Base knowledge in agronomy and plant biology
PROGRAMME
The following aspects will be considered:
- Nitrogen fertilization: environmental impacts and EU legislation on nitrates. Espen, Luca (2 h)
- Economic aspects on nitrogen fertilizer management. Corsi, Stefano (2 h)
- Nitrogen metabolism in plants: a physiological and biochemical perspective. Prinsi, Bhakti (4 h), Espen, Luca (2 h)
- Different approaches for estimating Nitrogen Use Efficiency (NUE). Araniti, Fabrizio (2 h)
- Possible strategies for lowering nitrate content in leafy vegetables. Cocetta, Giacomo (2 h)
- Optimization of nitrogen fertilization: new and old agronomical practices. Confalonieri, Roberto (2 h)
- Storage protein content and quality in legume seeds (2h). Scarafoni, Alessio (2 h)
--------------------------------------------------------------------------------------------------
Courses activated in 2020-21 academic year
Nitrogen nutrition in crops: Agronomy, Biochemistry, and Food Quality (3CFU)
September 2021
All lessons will take in the classroom Pellizzi
AIMS
The course will address topics related to the management of nitrogen fertilization and nitrogen metabolism in plants as well as it will analyse the impact of nitrogen input on crop production from the quantitative and qualitative point of view.
TO BE AQUIRED
Base knowledge in agronomy and plant biology
PROGRAMME
14 september 2021
9.30 - 11.30
Nitrogen fertilization: environmental impacts and EU legislation on nitrates
Espen, Luca
11.30 -13.30
Uptake and sensing of nitrogen nutrients by plants
Prinsi, Bhakti
14.30 - 16.30
Nitrogen assimilation: molecular and biochemical events
Espen, Luca
15 september 2021
9.30 – 11.30
Nitrogen metabolism in plants: new insight and open questions.
Prinsi, Bhakti
11.30 - 13.30
Storage protein content and quality in legume seeds
Scarafoni, Alessio
14.30 - 16.30
Different approaches for estimating Nitrogen Use Efficiency (NUE).
Araniti, Fabrizio
16 September 2021
9.30 – 11.30
Possible strategies for lowering nitrate content in leafy vegetables.
Cocetta, Giacomo
11.30 -13.30
Optimization of nitrogen fertilization: new and old agronomical practices.
Confalonieri, Roberto
14.30 – 16.30
Economic aspects on nitrogen fertilizer management.
Corsi, Stefano
Safety and wellness of agricultural operators (3CFU)
September 2021
Course objectives and skills requested
The course is aimed to offer a specific skill about the evaluation and management of the most important risks encountered in the agricultural activity, both for the possible accidents and the occupational diseases onset.
The participating PhD students are requested to have a basic knowledge about the agricultural system and the main means of production (machinery, fertilizers, pesticides, etc.).
PROGRAMME
Principles of ergonomics and evaluation methodologies Guidetti, Riccardo (1CFU, 6 h)
a) principles of biomechanics
b) the upper and lower limbs; the spine
c) the risks of biomechanical overload
d) ergonomics
e) the OCRA (OCcupational Repetitive Action)
f) application examples in agriculture
Equipment for the application of plant protection products (sprayer machinery) Facchinetti, Davide (1CFU, 6 h)
a) The correct and sustainable use of the sprayer machinery, with particular reference to the environmental impact reduction of the treatments and the operator protection
b) The safety in the use of agricultural machinery: a) general overview
The safety in the use of agricultural machinery Domenico,Pessina (1CFU, 6 h)
1) analysis of the most critical situations:
a) the tractor roll-over
b) analysis of the most critical situations: the PTO cardan shaft
2) Analisys and solutions to control the most dangerous ergonomics parameters in agriculture:
a) noise
b) vibrations
SUSTAINABLE CROP PROTECTION (3CFU)
September 2021
AIMS
To supply knowledge and tools concerning new strategies for plant disease and parasite containment.
TO BE AQUIRED
Basic knowledge on plant parasites and their effects: new tools for their containment.
PROGRAMME
I. Elusive plant pathogens: endophytism and parasitism. Basic of biocontrol for plant pathogen containment. Bianco, Piero Attilio (0.25 CFU, 1,5 h)
New technologies are disclosing surprising interactions among plants and their inner "world". New insights for their relationships are source of new knowledge and new triggers to develop innovative plant disease control strategies.
II. Biological control of insect pests: from SIT to symbiotic control, Montagna, Matteo (0.5 CFU,3 h)
Agriculture and Climate Change. Methane and ruminal fermentations. Mitigation potential. Food diet changes drive to mitigation. Milk productivity. Feed rations. Carbon sink. Technology and mitigation.
III. The complex epidemiology of plant diseases associated with uncultivable pathogens: multidisciplinary approaches applied to develop sustainable control strategies. Quaglino, Fabio (0.5 CFU, 3 h)
General features of uncultivable pathogens. Phytoplasmas as case study: main properties (etiology, epidemiology, host-pathogen interactions). Molecular epidemiology as starting point for developing control strategies. Sustainable integrated approaches to control phytoplasma diseases.
IV. Resistance to plant pathogen: the case of grapevine and Plasmopara viticola; Patogen resistance to fungicides. Toffolatti, Silvia (0.5 CFU, 3 h)
Can we exploit plant resistance for the disease management? Description of the plant defense mechanisms in different grapevine species, available and emerging sources of resistance and durability of resistance. Challenges in fungicide management of the disease: definition of fungicide resistance, selection of resistant strains and management of resistance through anti-resistance strategies.
V. Plant Secondary Metabolites: Pathophysiologial Role in Planta and Health-Promoting Effects in Human. Iriti, Marcello (0.5 CFU, 3 h)
Chemical structure, biosynthesis and tissue localization of phytochemicals. Chemical ecology. Resistance/tolerance to biotic/abiotic/environmental stresses. Plant innate immunity: elicitors and plant activators. Bioactive phytochemicals of food and medicinal plants: health benefits in human.
VI. Allelopathy & Allelochemicals. Vitalini (0.25 CFU, 1,5 h)
Plant-plant interactions and introduction to allelopathy. Allelochemicals: chemical structure and biosynthesis. Release and activity of allelochemicals. Allelopathy in crop protection. Case studies: Lolium multiflorum and Peucedanum ostruthium.
VII. Beneficial bacteria as inoculants and members of the microbiota: case study on biocontrol of fungal pathogens of lettuce. Passera (0.25 CFU, 1,5 h)
Biocontrol of plant pathogens. Native and exogenous beneficial microbes. Endophytic and epiphytic microbiota: functions and characteristics. Case study example of the application of exogenous bacterial inoculants on the control of fungal pathogens and effects on the microbiota of lettuce plants.
VIII. Use of bacterial biostimulants for improving crops yield ad quality. Cocetta, Giacomo (0,25 CFU, 1,5 h). Biostimulants, a general overview and classification. Beneficial effects of bacterial biostimulants on crops agronomical traits. Crops quality as affected by bacterial biostimulants application at harvest and during shelf life. Case studies related to vegetable crops treated with bacterial biostimulants.
Exploitation of variability in woody crops (3CFU)
May 2021
AIMS
Understanding of the genetic variability in tree crops
TO BE AQUIRED
Tools for preserving and exploiting the genetic variability in tree crops.
PROGRAMME
I. Phenotipic variability in woody species. BASSI, CIRILLI (1 CFU, 6 h)
Basic elements of sistematic pomology in pome and stone fruits, olive, grape and citrus. Main tools for varietal characterization.
Preserving byodiversity: genetic resources collection. Cultivar evaluation and identification.
Breeding principles: qualitative and quantitative traits. Main breeding goal and selection criteria: yield, quality, resistance to biotic and abiotic stresses.
II. Genotipic variability in woody specie and its exploitation: grape as a case study. DE LORENZIS, FAILLA (1 CFU,6 h)
Grapevines genetic resources for breeding of wine, table grapes and rootstock. Phenotyping. Genetic structure of grapevine germplasm. Grapevine domestication: sylvestris vs sativa. Genetic bases of some phenotypic traits: muscat flavor, color, bunch shape. Phenotyping for rootstock resistance to abiotic stress
III. Sequencing the genome of heterozygous species. POZZI, ROSSINI (1CFU, 6 h)
Application of next generation sequencing in grape. Advanced breeding: marker assisted selection; gene pyramiding; genomic selection. Next generation breeding: use of genome bioediting and biotechnologies in grape.
Genomic approaches for dissection and improvement of fruit quality traits in peach. Introduction to peach and fruit quality traits. Breeding goals and traditional approaches. Genomics tools to support breeding - examples through selected case studies: MAS for a Mendelian trait, markers for maturity date and aroma. Challenges and opportunities: complex traits dissection and improvement - towards genomic selection in peach; phenotyping complex traits - texture.
Senescence and quality of flowers and vegetables exploitation of variability in woody crops (3CFU) Antonio Ferrante
May 2021
AIMS
Description of the internal and external factors that affect the plant and argon development and senescence. Relationship with the quality of produce and strategies for preserving the quality during postharvest life.
TO BE AQUIRED
Understanding the mechanisms behind the senescence processes and tools to delay the senescence preserving the quality of horticultural produce.
PROGRAMME
I. Introduction
The fruit and leaf development and quality changes during ripening and senescene.
II Plant hormones and senescence
Physiological, biochemical, and molecular changes induced by the plant hormones and senescence regulation using the plant hormone inhibitors. Use of biotechnological tools for modifying the quality and produce preservation.
III Technological advanced tools for reducing the senescence.
Use of low temperature, controlled or modified atmosphere for slowing down the degenerative processes associated to produce senescence.
Sustainability in animal production (3CFU)
March-April 2021
AIMS
Understanding the main aspects of sustainability in animal productions and identification of improvement strategies
TO BE AQUIRED
Tools for identifying strategies for improving animal production sustainability.
PROGRAMME
I. Environmental impact of animal productions. Sandrucci, Anna Alfea (0.5 CFU, 3 h)
The challenges of sustainability in animal production. Environmental impact of animal productions: GHG emissions, eutrophication, acidification, land use. Factors influencing environmental impact of animal products
II. Mitigation strategies of environmental impact of animal production. Alberto Tamburini (0.5 CFU,3 h)
Agriculture and Climate Change. Methane and ruminal fermentations. Mitigation potential. Food diet changes drive to mitigation. Milk productivity. Feed rations. Carbon sink. Technology and mitigation.
III. Life Cycle Assessment of environmental impact of animal production chains: methodological approaches and application cases. Luciana Bava (0.5 CFU, 3 h)
Life Cycle assessment: what is it? Life Cycle assessment: example from scientific literature. The phases according to EN ISO 14040. Goal and scope. Functional unit. System boundaries. Allocation. Inventory analysis. Impact assessment. Interpretation. Life Cycle Costing. Social Life Cycle
IV. Sustainable livestock systems in developing countries. Matteo Crovetto (0.5 CFU, 3 h)
Contribute of food of animal origin to human diet in developed and developing countries. Undernourishment in the world. Crop and animal production systems: intensive, semi-intensive, extensive. Mixed and small-scale farms
V. Precision feeding for a sustainable animal husbandry. Luca Rapetti (0.5 CFU, 3 h)
What is the precision feeding? Total mixed ration. E-feeders. Technologies to measure nutritional processes. Environmental impact of N and N metabolism in ruminants. Effect of Precision Feeding management on N excretion and production. The enteric methane. Selected strategies for enteric methane mitigation.
VI. Animal welfare for a sustainable animal husbandry. Silvana Mattiello (0.5 CFU, 3 h)
Definition of animal welfare. Why talking about animal welfare? European approach to the evaluation of
animal welfare: animal-based vs resource-based indicators. New trends: positive welfare and animals’ emotions. New technologies for the evaluation and labelling of animal welfare.
--------------------------------------------------------------------------------------------------
Courses activated in previous academic years
Sustainability in animal production
June 2020
Download the presentations of the course:
Introduction to meta analysis in agricultural and environmental research
Dr. Elena Valkama , visiting professor
(Host: Marco Acutis)
TIME: 14.00 -17:00
ROOM: C21
Via Colombo 62, Milano
Novel strategies to accelerate crop improvement
Prof. José F. Gutierrez-Marcos
(Host: Dr. Laura Rossini)
2020
Lectures from 9.00 until 13.00 on the following dates / rooms:• January 28 - Aula C21
• January 29 - Aula C11
• February 4 - Aula C01
• February 5 - Aula C01
• February 11 - Aula C01
• February 12 - Aula C01
May 2019
Exploitation of variability in woody crops
Exploitation of variability in woody crops
Prof. Daniele Bassi
April 2019
Relationship between senescence and quality of fruit and vegetablesprof. Antonio Ferrante
June 26-28, 2018
From -omics to phenotyping for crop improvement.
Como, October 2-7, 2017
Summer School: Introduction to RAD-seq Data Analysis (Second edition)
Monday, June 27, 2016
Facoltà di Agraria, Aula maggiore – Via Celoria, 2 20133 Milano
June 27th - 28th, 2016
Facoltà di Agraria, Aula maggiore – Via Celoria, 2 20133 Milano
Monday 4th-Friday 8th April, 2016
Aula Maggiore - Via Celoria, 2 (MI)