Here is a talk I presented at the European Cytogenetics Association ECA course in March 2026. Below is also an AI-generated summary of my points. Acknowledgements and references are on the slides. The Powerpoint file is 80Mb in size, and slides can be edited and used (CC-BY).

The talk explains how cytogenomics—the study of chromosomes, genomes, and their evolution—underpins advances in plant and animal breeding, agricultural productivity, and biodiversity conservation. It combines classical cytogenetics with modern DNA sequencing, genome assemblies, and molecular tools.

1. Cytogenomics in Crop Evolution and Breeding
   Polyploidy and genome evolution

Many crops (e.g., wheat, oats, Brassica, banana) are polyploids, containing multiple chromosome sets.
Polyploidy drives speciation, genome diversification, and the emergence of novel traits.
Whole-genome duplications and chromosomal rearrangements (e.g., fusions, translocations, nesting) are major evolutionary forces.

Examples

Wheat: well‐studied A, B, D genome origins, hybridization with wild relatives, introgression of disease-resistance genes.
Banana & Ensete: extensive chromosomal rearrangements across diploid and triploid cultivars.
Brassica A, B, C genomes: transposon-based genome differentiation; identification of translocations.

3. Cytogenetics for Breeding New Traits
   Alien introgression

Wild species are used to introduce resistance genes into crops (e.g., wheat streak mosaic virus resistance from Thinopyrum).
Hybridization followed by backcrossing transfers valuable chromosome segments.

Somatic hybridization (cell fusion)

E.g., Nicotiana somatic hybrids combining disease resistance from different species.

Massive oligonucleotide probe sets

Large, chromosome-specific probe libraries enable high-resolution FISH mapping, particularly in complex or polyploid genomes (oat, Brassica, Urochloa).

4. Genome Composition and Repetitive DNA

Plant genomes contain large proportions of repetitive sequences (up to 87% in Avena longiglumis).
Transposable elements (copia, gypsy), tandem repeats, rDNA arrays, and structural repeats shape genome architecture.
Difficulty of assembling rDNA arrays and centromere regions is highlighted.

5. High-Resolution Genomics
   Long-read sequencing (Nanopore, PacBio)

Enables complete chloroplast genomes, mitochondrial genome reconstruction, and chromosome-level assemblies.
Reveals:

heteroplasmy,
NUMTs (nuclear mitochondrial transfers),
complex repeat-mediated restructuring.

Large genome studies

Avena longiglumis: 3.85 Gb genome shows massive repeat expansion and uniform genome enlargement compared to rice and Brachypodium.
Comparative genomics shows unexpected patterns of distal translocations, unlike wheat.

6. Applications Beyond Crops
   Livestock genomics

Sheep pangenome studies reveal structural variants linked to traits such as fat-tail morphology.
Chromosomal mapping of organellar sequences in animals.

7. Biodiversity, Agriculture, and Sustainability
   Contribution of genetics & agriculture

Increased yields (~1% per year for 60 years).
Food production improved via genetics and agronomy, not more land or labour.

Challenges
Agriculture has:

degraded land,
overused water,
increased pollution,
accelerated climate change,
reduced biodiversity.

Current priorities
Since population growth has slowed (except in Africa), the goal is to increase agricultural sustainability, conserving biodiversity while maintaining productivity.

8. The Seven F’s of Farming
   Agriculture provides:
   Food, Feed, Fuel, Fibre, Feedstock, Flowers, Pharmaceuticals
   Special case:

Ensete ventricosum in Ethiopia: both a staple food and major medicinal plant.

9. Future Directions

Integrating AI, genomics, phenomics, and cytogenetics to identify minor-effect genes and epistatic interactions.
Using biodiversity and genomic knowledge to build climate-resilient, disease-resistant, sustainable crops.
Cytogenomics remains central to understanding genomes and enabling targeted breeding.