The goal of this project was to illuminate the mechanisms controlling distribution of recombination events in maize, a model species as well as a major crop.  Meiotic recombination is a process in which two parental chromosomes, one from the father and the other one from the mother, exchange parts during sexual reproduction.  Recombination creates new genetic variation in the progeny, which facilitates adaptation to new environments and purges detrimental mutations from genomes and populations.  Thus, meiotic recombination is one of the main forces behind species evolution.  In addition, it is utilized as an unparalleled instrument of plant and animal breeding.  However, despite their importance, recombination events are not evenly distributed along chromosomes.  In plants with large and complex genomes, such maize and the majority of other crops, they are predominantly located at chromosome ends, leaving large regions in the middle of chromosomes devoid of recombination.  Such distribution pattern creates major impediment to breeding, since the recombination-poor chromosome segments contain a significant fraction of genes.  

This project sought to elucidate why recombination takes place in specific sites in the genome and understand how the locations of these sites are affected by genetic and epigenetic factors.  With artificial intelligence approaches, we found that the genome sites where meiotic recombination takes place exhibit specific chromatin characteristics that are distinct from those of the genome at large.  Interestingly, different sets of chromatin features promote the initiation of meiotic recombination, which occurs by programmed formation of breaks in DNA, versus the repair of these breaks to form reciprocal exchanges of chromosome segment called crossovers.  We also developed a method to track the progression of crossover intermediates and discovered that the patterns of crossover distribution are decided at multiple steps during the progression of the recombination pathway.  We found that DNA methylation is the key factor controlling whether meiotic DNA breaks are repaired as crossovers.  Reducing genome-wide DNA methylation levels opens up to crossover formation chromosome regions that are normally crossover deprived.  Furthermore, we developed a computer algorithm that can very precisely identify crossover sites by taking into account the local DNA methylation levels and presence of nucleosomes.  This algorithm performs equally well across different plant species, suggesting conservation of characteristics that affect crossover distribution.  Finally, we also found that although the distribution of crossovers produced in males and females is similar at the chromosome-wide scale, there are several differences between the sexes in microscale.  

Understanding the mechanism controlling the distribution of recombination events will facilitate development of methods to increase recombination in the low-recombination regions of chromosomes.  Such methods will allow breeders to create novel combinations of genes that are located in these regions, and help them produce superior crop varieties.  To facilitate translation of results of this project into technologies useful for plant breeding, we formed a strategic partnership with Meiogenix Inc, a biotech startup focused on developing tools for targeting recombination to specific chromosome regions in yeast and plants.  We collaborated with Meiogenix include in their technology portfolio methods to boost crossovers by altering DNA methylation levels.  As another avenue of translating the knowledge on recombination into plant breeding practice, we conducted a simulation study to examine how altering CO patterns can affect selection gain.  Within the scope of the projects, we operated a Science Undergraduate Minority Mentoring Internship and Training (SUMMIT) program, which each year sponsored four 10-week internships for undergraduate students from groups underrepresented in biological sciences.  

Last Modified: 11/03/2022
Modified by: Wojciech P Pawlowski