New approaches for the analysis and utilization of wheat genetic diversity

Addressing the challenge of food security during the current environmental crisis will necessitate rapidly breeding a new generation of adapted cultivars. Genetic diversity and selection of natural variants are key to advances in breeding. However, there is a need for better tools to predict how natural variation impacts plant performances, to improve the precision and efficiency of gene modification, and transfer from wild relatives to crops. We will focus on wheat, one of the most important staple foods of humanity, and on the broad genetic pool of its wild relatives. Our goals are to develop a computational tool to analyze genetic variation in the genomes of modern and wild wheat and to identify deleterious mutations that impair fitness. We will build genomics tools for effective genotyping of deleterious mutations in classical breeding and we will test their effect on yield. Then, we will use genome editing tools to increase diversity via the precise transfer of genes from the wild into the domestic background and for targeted repair of deleterious mutations towards wheat improvement. We plan to achieve this by developing a machine-learning algorithm to predict the presence of deleterious mutations in whole genomes (WP1). Then, we will test how such mutations can affect crop fitness by designing a genotyping microarray for simple identification of deleterious mutations in segregating populations for use in classical breeding (WP2). We will also harness new breeding technologies to increase the genetic diversity in wheat through the precise transfer of genes or chromosomal segments from close and distant chromosomes of wild relatives to modern wheat and for repairing deleterious mutations through modification of the relevant genes (WP3). This project should provide a new understanding of how genetic diversity affects plant fitness and how better to exploit it in plant breeding. All materials and tools developed through this work will be freely available.