Periodic Reporting for period 3 - EPICROP (Dissecting epistasis for enhanced crop productivity)
Período documentado: 2022-08-01 hasta 2024-01-31
A frontier in genetics is to understand how complex genotypes translate into quantitative trait variation. In breeding, gene mutations can have beneficial effects in one genotype but cause detrimental outcomes when introduced into a distinct genotype, which is due to interactions with mutations in the new genotypic context. Such genetic interactions are also known as epistasis and represent a hurdle for targeted trait breeding in plants and animals because the consequences are often impossible to predict. With this EPICROP project, we aim at better understanding the molecular principles of genetic interactions in crops and at revealing hidden mutations that arose during domestication and modulate flowering traits in the model crop tomato. For this, we investigate the interplay of genes that regulate the activity of plant stem cells, which give rise to all above-ground tissues and eventually flowers and fruits. We focus on a group of interacting regulatory genes to study how genetic interactions affect the dynamics of gene expression during stem cell development. We then harness the obtained molecular principles to modulate stem cell development and flower production. In a second aim, we use genome editing to uncover how mutations are modified in diverse tomato varieties and reveal genes that changed during domestication and breeding for adaptations in flowering. The outcome of this project will advance our understanding of genetic interactions in crops and may outline novel strategies for predictable trait breeding for bringing more resilience and sustainability into our agricultural production systems.
During the course of this project, my team revealed that genetic suppression of a beneficial flowering mutation is due to gene loss of a closely related paralog during tomato domestication. We now exploit this newly-identified genetic relationship by base editing to generate more compact and faster flowering tomato varieties.
In addition, we established a novel tomato variety for higher-throughput genome editing experiments. In collaboration with the group of Michael Schatz (Johns Hopkins University, USA), we generated a chromosome-level genome assembly for a rapid-cycling tomato genotype and optimized strategies for genome editing (Alonge et al., 2021, bioRxiv). We expect that this genotype and the genomic resources will be a foundation for future genome-scale editing experiments in the model crop tomato.
In addition, we established a novel tomato variety for higher-throughput genome editing experiments. In collaboration with the group of Michael Schatz (Johns Hopkins University, USA), we generated a chromosome-level genome assembly for a rapid-cycling tomato genotype and optimized strategies for genome editing (Alonge et al., 2021, bioRxiv). We expect that this genotype and the genomic resources will be a foundation for future genome-scale editing experiments in the model crop tomato.
A major innovative aspect of the EPICROP project is the integration of genetic and genomic analyses with advanced genome editing approaches to decipher the genetic diversity that evolved during crop domestication and breeding.
We characterized an example of genetic suppression of a flowering mutation that depends on the loss of a paralogous gene during tomato domestication. This example highlights how hidden genetic variants affect trait variation during domestication and breeding, and emphasizes the need for a better understanding of genetic interactions for predictable crop improvement.
Furthermore, we established a novel experimental genotype, which nearly doubles the number of generations per year, and new genomic resources for future genome-wide editing and functional genomics experiments in tomato. This approach also outlines strategies for rapidly generating diverse personalized reference systems in other species.
We characterized an example of genetic suppression of a flowering mutation that depends on the loss of a paralogous gene during tomato domestication. This example highlights how hidden genetic variants affect trait variation during domestication and breeding, and emphasizes the need for a better understanding of genetic interactions for predictable crop improvement.
Furthermore, we established a novel experimental genotype, which nearly doubles the number of generations per year, and new genomic resources for future genome-wide editing and functional genomics experiments in tomato. This approach also outlines strategies for rapidly generating diverse personalized reference systems in other species.