Homoeologous exchanges as drivers for innovation in Brassica napus – EDIn

Structural variation is a major driver of genetic diversity and an important substrate for species adaptation and selection. Understanding the relationships between structural variants and functional innovations thus represents a major issue to be addressed. In allopolyploid species, which are common in angiosperms and particularly widespread in crops, exchanges between homeologous chromosomes (i.e. between constituent subgenomes), called HEs for homoeologous exchanges, represent a major source of structural variants. However, we still know little about the genome-wide distribution and resulting functional diversity generated by these variants even though they may have played a prominant role in the evolutionary success of allopolyploidy in plants. In the EDIn project, we will develop an integrated set of analyses to advance knowledge on the causes and consequences of HEs, from the mechanisms responsible for their formation to their effects on gene and genome expression, on chromatin dynamics and plant phenotypic variation in oilseed rape, Brassica napus. Based on highly original plant material specifically designed to promote HE, combined with state-of-the-art multi-omics approaches, our project will address fundamental questions in the context of the allotetraploidy of the B. napus crop genome. EDIn is composed of three main workpackages. WP1 aims to profile the products of inter-homoeologue recombination at very high resolution and build a predictive model of their occurrence, which would be useful in breeding for managing introgressions in crop x wild relative hybrids. WP2 aims to evaluate the global consequences of HEs on gene expression at genome-scale but also at population level. In particular, it will make it possible to characterise the impact of HE on gene regulation networks, which would represent the first in-depth analysis for an allopolyploid crop. WP3 aims to establish the causality of specific HEs by developing an original genetic association study, and to characterize their impact on the reorganisation of the genomic and epigenomic landscapes. In a highly original manner, WP3 will study the changes in the epigenome and the reorganisation of chromatin that introgression of alien chromatin originating from a HE can cause. Our results should therefore prove fruitful in developing useful knowledge and operational strategies for the improvement and diversification of allopolyploid crops, in particular for the management of their genetic diversity or associated genetic resources. This research will be conducted by a consortium of renowned scientists who bring highly complementary expertise, know-how and/or facilities, allowing a more complete understanding of the impact of HEs on the functioning of the allopolyploid genome. One original aspects of this consortium is its direct link to higher education, which represents an excellent opportunity to teach students about the socio-economic impact of public research and train future researchers in the field of recombination, genomics, epigenetics, chromatin organisation and dynamics, for plant breeding.