Genetics Has Enabled the Improvement of Breeding Strategies: Single-Cell Analysis, Epigenetics, cis-Regulation and Gene Editing to Exploit Genetic Variants Underlying Phenotypes

The study of genetics seeks to understand the molecular relationships that ensure the proper patterning of gene expression necessary for plant development and its responses to the environment that determine crop performance. Improvements in molecular genetics, biotechnology, and a deeper understanding of gene expression have given breeders access to major sources of phenotypic novelty in plants and allowed them to accelerate genetic gains by breeding locally adapted crops. Advances in genetics, and more recently the edition of epigenetic marks, cis-regulatory elements and gene editing have gained significant importance in crop breeding. Single-cell level studies have helped to elucidate cell heterogeneity and intercellular regulation in key tissues, enabling a more precise comprehension of the effects of plant developmental processes on phenotypes. The aim of this review is to highlight how genetic knowledge has fostered progress in crop improvement and selection. After a summary of the historical use of genetics in breeding strategies over the past 100 years, we discuss how the latest technological developments in genetics can be leveraged in complex quantitative trait improvement. Recent progress in single-cell analyses allow us to identify the subtle relationship between the genomic blueprint and cellular diversity, connecting this cellular genetic heterogeneity of a plant to specific phenotypes, that would be otherwise overlooked when using bulk cell analyses. High-throughput access to numerous epigenetic marks has also opened up new opportunities and challenges for crop genetic improvement. This progress has led to a better understanding of the role of cis-regulatory elements in determining some aspects of crop performance. Here we also discuss whether it is possible to leverage reliable variations in these regions in crop breeding, using targeted selection to manipulate traits in a wide range of crops. Finally, we outline advances in gene editing tools in crop improvement, and discuss how these could be implemented to accelerate breeding for crops adapted to new environments.