CoPIs: Changbin Chen (University of Minnesota), Shahryar Kianian (North Dakota State University), Jarek Pillardy (Cornell University) and Ernest Retzel (National Center for Genome Resources)
The goal of this project is to generate the first comprehensive, high-density map of recombination in maize. Recombination is the main source of genetic variation in higher eukaryotes; it facilitates adaptation, purges deleterious mutations from genomes and populations, and is a major determinant of genome architecture. In addition, recombination is utilized as an unparalleled instrument of plant breeding. However, despite its importance, little is known about factors that affect the distribution of recombination events in plants and other higher eukaryotes. To understand where recombination takes place in the maize genome, the project will (1) map the distribution of meiotic double-strand breaks (DSBs) that initiate meiotic recombination using a novel chromatin immunoprecipitation-sequencing approach; (2) map at very high-resolution crossover (CO) and some non-crossover (NCO) recombination products for maize chromosome 9; (3) examine CO rates at several selected locations outside chromosome 9; and (4) relate maps of DSB and CO distribution will be related to local genome features, including the presence of expressed genes, chromatin modification patterns, repetitive DNA elements, and specific DNA sequence motifs. Elucidating the DSB and CO distribution patterns, and identifying factors that affect them, will have tremendous implications for the understanding how the genome is shaped by recombination as well as have practical importance for plant breeding.
Meiotic recombination generates the variation on which breeders apply selection. This research will provide breeders with information on linkage drag when introducing traits from unimproved genetic backgrounds, on how many plants are required to find segregants with desirable gene combinations, and how to develop more efficient breeding methods with smaller populations and faster breeding cycles. About one-fifth of maize genes are located in regions of highly reduced recombination rates. Developing ways to increase recombination in these regions will allow utilizing higher numbers of allele combinations in maize breeding programs, leading to more efficient breeding. This understanding will be transferable to other crop plants with similar patterns of recombination (e.g. wheat). A number of activities to enhance training of students and young scientists are an inherent part of this project, including summer internship programs targeting minority-serving and small liberal art colleges and universities. Results of this project will be available on the project website (www.rec_hotspots.org) and deposited into public repositories, including GenBank, GEO, MaizeGDB, and the NCGR database.