Decipher the Fate of Introgressions from wild relatives in the wheat genome – DeFI-Wheat

The demographic increase estimated for the next 50 years will induce a simultaneous growth in the world cereal demand for feeding as well as for non-food uses. In addition, there will be a decrease of agricultural land areas, especially in the developing countries. Agriculture will also have to increasingly face ecological constraints using less fertilizers, herbicides, pesticides and water as well as novel environmental conditions (drought and heat stresses) resulting from climate changes. Thus, to meet human needs by 2050, cereal production will have to be significantly improved in the next decades but taking into account the context of a sustainable agriculture.
One way to face this challenge is to better manage and exploit the available genetic resources, which remain largely underexploited although extensive in cereals. Since the 1960s, disease resistance genes have been massively introduced in the allo-hexaploid bread wheat genome (Triticum aestivum; 2n = 6x = 42; genome AABBDD) using numerous sources of wild species. One of the most famous example of these introgressions is the introduction of a rust-resistance locus (Lr37/Yr17/Sr38) on wheat chromosome 2A (2A/2N translocation) and an eyespot resistance gene (Pch1) on wheat chromosome 7D (7D/7Dv translocation) coming from the tetraploid wild species Aegilops ventricosa (DvDvNN).
Introduction of these alien fragments occurs through the formation of crossing-overs (COs; reciprocal exchanges of DNA fragments between chromosomes) between the related but not homologous (thus called homoeologous) chromosomes from the wild species and those of wheat. However, COs between homoeologous chromosomes is an extremely rare event and once introduced, COs are blocked in introgressions preventing thus further reduction of their size. The reasons of this clamping remains elusive explaining why breeders are reluctant in using wild species in their breeding schemes because introgression of beneficial traits often leads to a simultaneous introduction of deleterious traits (yield loss, lodging…) following linkage drag that cannot be broken.
DeFI-Wheat proposes to solve this riddle to give breeders a helping hand for a better management of useful introgressions in wheat. The project will focus the analyses on two well-known introgressions derived from Ae. ventricosa (2A/2N and 7D/7Dv introgressions) in the variety Renan. DeFI-Wheat relies on three main hypotheses that may explain why recombination is blocked within introgressions: (1) a lack of synapsis between the introgressed segments and the corresponding homoeologous regions from wheat; (2) a reduction of the number of DSBs that initiate COs within the two introgressions; (3) a different and constraining epigenetic landscape compared to the wild-type within introgressions preventing efficient recombination.
To validate one or several of these hypotheses, the project will be structured into three interconnected work packages (WP) with different tasks that will constitute the deliverables of the project. WP1 will evaluate the ability of the two introgressions in Renan to efficiently synapse with the corresponding homoeologous regions from Chinese Spring. This will be based on improved cytogenetic approaches using relevant antibodies (designed against ASY1 and ZYP1) and sets of unique probes specific to the two introgressions. WP2 will draw the profile of DSBs along the two introgressions using ChIP-Seq of the DSB-associated-protein DMC1, a technology that was already successfully applied to wheat which warrants the success of the capture. WP3 will enlighten the epigenetic pattern within introgressions using isolated-4n-meiocytes (from early Leptotene, before DSB formation, to late prophase I) and original adapted strategies (ATAC-Seq, ChIP-Seq)
DeFI-Wheat will therefore generate fundamental knowledge for a better control and mastering of recombination in wheat and to better and fully exploit available genetic diversity of wheat rela