Exploring the genome sequence of diploid potatoes and dissecting the genetic architecture of agronomical traits using phenomics

Potato (Solanum tuberosum L.) is crucial for global food security. However, potato improvement needs to unleash more breeding potential to sustain a growing population while facing the challenges of climate change. Researchers are focusing on diploid potatoes to overcome the slow progress and low genetic gains associated with tetraploid varieties. Understanding the genetic diversity, domestication history, and mitochondrial genome of diploid potatoes is essential for effective breeding. This thesis provides an in-depth analysis of diploid potatoes. Chapter 2 reviews their potential for breeding. Subsequent chapters explore the genome and population structure of diploid potatoes, mitochondrial genome characterization, and phenotypic analysis of a segregating F2 population. Using resequencing data from 367 accessions, I mapped genomic variations and identified 232 domestication sweeps. This research confirmed S. candolleanum as the ancestor of landraces and pinpointed genes affecting tuber dormancy and other traits. Chapter 4 examines the mitochondrial genomes of 39 diploid potatoes, revealing variations linked to evolutionary differences and cytoplasmic male sterility. Chapter 5 focuses on phenotyping a segregating population, using image-based and 3D technologies to track growth and identify 691 bins associated with 203 traits. This led to the discovery of candidate genes related to tuber yield and quality. Overall, this thesis sheds light on potato domestication, highlights key candidate genes, and demonstrates the potential of advanced phenotyping techniques. This promises to accelerate the pace and precision of potato breeding programs, thereby paving the way for the development of superior potato varieties tailored to meet evolving agricultural needs and ensure global food security.