Almeria, the leading European region in terms of fruits and vegetable production and exportation, is emerging as a prominent innovation hub for greenhouse technology and production. In the field of plant breeding, Almería concentrates a significant portion of the total horticulture seed business activity among the world. Indeed, the most notable Spanish and international companies are based in Almeria, producing novel horticultural varieties through intensive research and development programs. These novel varieties ”made in Almeria” are not only used in this Spanish region but also exported and cultivated in many different greenhouses all over the world. The area of Genetics at the University of Almería is in close collaboration with the seed companies and the productive system of Almería. More precisely, the HORTICULTURAL GENETICS research group accumulates more than 25 years of experience focusing on research and teaching activities in the field of plant biotechnology and breeding. The goal of the present course is to share our theoretical and practical knowledge regarding the biotechnology methods and tools widely used in horticultural crops breeding and production. To do so, our multidisciplinary group encompass the fields of genetics, plant physiology, plant production and food technology allowing us to perform high-throughput plant phenotyping for abiotic and biotic stress tolerance, nutrients, drought and salinity tolerance, and postharvest fruit quality. The phenomics studies are followed by molecular studies through high-throughput genotyping using next-generation sequencing (NGS) technologies and bioinformatics analysis in order to identify plant materials, molecular markers and genes useful for developing novel cultivars in horticultural crops.
- To study the productive system and business model of Almería linked to vegetable breeding programs, throughout site visits to seed companies, seedbeds, field varietal assays, and packing and exportation companies of fresh F&V.
- To teach widely used biotechnology tools employed in vegetable breeding programs, including those focused on postharvest fruit quality, and tolerance to different conditions such as abiotic, nutrition, drought, and biotic stresses.
- To obtain hands-on experience in phenomics, genomics and bioinformatics tools applied to plant breeding by means of laboratory practices and bioinformatics analyses.
Module 1. Breeding for postharvest fruit quality (4 days)
- General introduction.
- Lecture: Quality in fruits and vegetables from physicochemical, nutritional and sensory perspectives.
- Lecture: Physiological parameters involved in fruit ripening and postharvest storage.
- Practice: Evaluation of postharvest quality parameters in different genotypes of fruits and vegetables.
- Lecture: Breeding applied to postharvest quality traits in fruits and vegetables
- Lecture: Development and use of plant mutant resources and TILLING approaches
- Practice: Screening of ethylene insensitive mutants and cultivars in zucchini and watermelon.
- Site visit to LA CAÑA. Identification of fruits and vegetable traits demanded by supermarkets and consumers.
Module 2. Breeding for resistance to abiotic stresses (4 days)
- Lecture: Abiotic stress. Nutritional and salinity assessment.
- Practice: Screening of cultivar and mutant populations for salinity stress tolerance.
- Lecture: Oxidative stress tolerance.
- Practice: Screening of cultivar and mutant populations for oxidative stress tolerance.
- Practice: ROS measurement in different genotypes.
- Technical visit to seedbed company. Development and use of drafting in plant breeding.
Module 3: Breeding for resistance to pests and diseases (4 days)
- Lecture: Plant breeding for plant pests and diseases tolerance.
- Practice: Screening for virosis resistance in cultivar and natural populations. Mechanical and natural virus inoculation using virulent whiteflies.
- Practice: Assessment of ToLCNDV accumulation using qPCR.
- Practice: Symptoms evaluation and molecular basis controlling virus resistance in plants.
- Site visit to MONSANTO.
- Site visit to ENZA ZADEN
Module 4: Application of Genomic and Bioinformatic tools in plant molecular breeding. (4 days)
- Lecture: Introduction to next-generation sequencing, bioinformatics analysis, and omics tools.
- Practice: Utilization and mining of biological sequence databases. Understanding different data formats.
- Lecture: Functional genomics
- Practice: Identification of causal mutations conferring important agronomic traits. SNP calling and filtering.
- Practice: QTL-seq. Identification of QTLs linked to important agronomic traits
- High-throughput plant genotyping: Taq-man, Kaspar y Sequenom.
- Practice: Genetic maps and QTL analysis in segregating populations.
- Practice: genotyping of segregating populations using Taq-man probes.
- Lecture: Bioinformatics pipelines for the analysis of RNA-seq data in the model and non-model plants.
- Practice: Design of a bioinformatics pipeline for the analysis of RNA-seq data: quality filtering, trimming, mapping and differential gene expression. Visualization and interpretation of the obtained results.
The course has a very important practical component. In each module, the professor will explain the theoretical basis and the design of the experiments that will be developed in the practical sessions. In the field trials, students will learn to identify and select agronomic interesting traits, laboratory experiments will improve student skills for the chemical and physical screening of plants, as well as high-throughput plant genotyping. In computer-assisted classes, students will understand the bioinformatic tools for SNPs and mutations identification, QTL analysis, and gene expression studies by using RNAseq.
Professional Visits and Complementary Academic Activities
- Seedbed NATURAL GREEN. El Ejido. Almería. Multiplication of seedlings, and study of grafting methods. Importance of grafts to improve vegetable production under biotic and abiotic stresses.
- Seed company MONSANTO. La Mojonera. Almeria. Demonstration of the biotechnological tools used by the company to improve the genetic resistance of plants: double haploid production through anther “in vitro” culture, phenotyping for resistance to pests and diseases.
- Seed company ENZA ZADEN. Cartagena, Murcia. Visit variety trials of the company's research station, and conducting a tasting of melon, watermelon and squash new varieties.
- Fresh F&V exportation company LA CAÑA. Motril. Granada. Important supplier of fruits and vegetables in Europe. Visit processing and packaging lines of fruits and vegetables, and food quality and safety laboratories. Variety trials of tomato, cucumber, mango, and avocado. Analysis of market and consumer demands.
- Attendance and participation in lecturers and practical classes (40%).
- Reports of lab experiments and site visits to the industry (40%).
- Interactive evaluation of the contents of the course through the Kahhoots test tool (20%).
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