18-BTT EAGER: Controlling meiotic recombination in crops by manipulating DNA methylation

This consortium plans to develop highly innovative strategies to stimulate recombination in genomic regions that are normally refractory to genetic variation in key crop species. Developing ways to increase recombination rates in genome areas of low recombination will contribute to more efficient breeding. The outcome will allow reducing the time required to develop new elite germplasm and enable rapid introgression of desirable genes from diverse sources to facilitate developing more robust crops that will exhibit superior productivity in sustainable ways and be better suited to deal with the challenges arising from the climate change. The goal of this project is to gain an understanding of how DNA methylation influences the meiotic recombination landscape in plants. Meiotic recombination is initiated by the formation of numerous programmed double-strand breaks in chromosomal DNA, a small proportion of which are processed to form crossovers. Thus, genetic variation generated by a single round of meiotic recombination is limited. Furthermore, the distribution of crossovers in plants with large genomes, which include most crops, is highly biased towards the ends of chromosomes. As a result, extensive interstitial and centromere proximal chromosome regions rarely recombine. Yet, these large genome areas contain roughly one-fifth of the genes in maize and even larger gene fractions in some other crops, which presents a serious impediment to plant breeding. Recent studies indicate that DNA methylation is a critical factor shaping crossover landscapes. However, the exact relationship between recombination and DNA methylation is not understood. This project seeks to elucidate how DNA methylation affects recombination patterns at the mechanistic level and lay foundations for methods to control crossover landscapes in crops by altering DNA methylation. The study will be conducted in maize and Brassica rapa, to explore the behavior of both monocot and dicot genomes. To elucidate the effect of DNA methylation on meiotic recombination, a protocol to transiently alter DNA methylation patterns in meiosis will be developed. The chemically demethylated plants and selected mutants defective in DNA methylation will be used to determine which steps and processes of meiosis are altered by DNA methylation. It will be also established which specific aspect of DNA methylation affects crossover landscape.

The goal of this project is to gain an understanding of how DNA methylation influences the meiotic recombination landscape in crops and to develop an efficient method for modulating the distribution of recombination events by manipulating DNA methylation levels during meiosis. Meiotic recombination is the main generator of genetic variation in plants. It underpins the breeding programs essential to deliver rapid improvements in crops required to ensure future food security. Meiotic recombination is initiated by the formation of numerous programmed double-strand breaks (DSBs) in chromosomal DNA, a small proportion of which are processed to form crossovers (COs). Thus, genetic variation generated by a single round of meiotic recombination is limited. Furthermore, the distribution of COs in plants with large genomes, which include most crops, is highly biased towards the ends of chromosomes. As a result, extensive interstitial and centromere-proximal chromosome regions rarely recombine. Yet, these large genome areas contain roughly one-fifth of the genes in maize and even larger gene fractions in some other crops. Hence, it would invaluable to develop methods to manipulate CO patterning and increase recombination in interstitial/proximal chromosome regions. Recent work by us and others indicates that DNA methylation is a critical factor shaping CO landscapes. Our studies found an increase in COs as well as CO redistribution from chromosome ends to pericentromeric regions in the maize DNA methylation deficient mutant zmet2. Thus, altering CO locations across the genome may be achieved by modulating DNA methylation patterns.
This project will (i) develop methods to transiently alter DNA methylation patterns in meiosis, and (ii) gain the understanding of how exactly DNA methylation affects CO distribution at the mechanistic level and which specific aspects of DNA methylation are responsible for shaping CO landscapes. We will use maize and Brassica rapa.

Ensuring Food Security over the forthcoming years is one of the main challenges for society. Different factors like population growth and climate change will increase the necessity of sustained improvements in food production (by 2050 it is predicted that food production will have to be increased by at least 50%). Crop breeding would have to improve to deliver the required yields. Molecular plant breeding has transformed the available options for plant breeders in recent years. Nonetheless, crop breeding is highly dependent of meiotic recombination to generate genetic variation through the formation of crossovers (COs). This consortium plans to develop highly innovative strategies to stimulate recombination in genomic regions that are normally refractory to genetic variation in key crop species. In large-genome plants, COs tend to favor locations close to chromosome ends, resulting in large pericentromeric sections of chromosomes being CO-depleted In maize, one-third of the genome and one-fifth of genes are in the pericentromeric regions, which show on average 20-fold less recombination than the more-highly recombining distal chromosome regions. In wheat and barley, the fractions of the affected genes are even higher. This situation presents a serious impediment to plant breeding. Developing ways to increase recombination rates in genome areas of low recombination will contribute to more efficient breeding. The outcome will allow reducing the time required to develop new elite germplasm and enable rapid introgression of desirable genes from diverse sources to facilitate developing more robust crops that will exhibit superior productivity in sustainable ways and be better suited to deal with the challenges arising from the climate change.