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ARS Home » Midwest Area » St. Paul, Minnesota » Cereal Disease Lab » Research » Publications at this Location » Publication #331472
Title: Gene evolutionary trajectories and GC patterns driven by recombination in Zea mays

Author
item SUNDARARAJAN, ANITHA - Desiderio Finamore Veterinary Research Institute (FEPAGRO)
item DUKOWIC-SCHULZE, STEFANIE - University Of Minnesota
item KWICKLIS, MADELINE - Desiderio Finamore Veterinary Research Institute (FEPAGRO)
item ENGSTROM, KAYLA - Desiderio Finamore Veterinary Research Institute (FEPAGRO)
item GARCIA, NATHAN - Desiderio Finamore Veterinary Research Institute (FEPAGRO)
item OVIEDO, OLIVER - Desiderio Finamore Veterinary Research Institute (FEPAGRO)
item RAMARAJ, THIRUVARANGAN - Desiderio Finamore Veterinary Research Institute (FEPAGRO)
item GONZALES, MICHAEL - Desiderio Finamore Veterinary Research Institute (FEPAGRO)
item HE, YAN - Cornell University
item MINGHUI, WANG - Cornell University
item SUN, QI - Cornell University
item PILLARDY, JAROSLAW - Desiderio Finamore Veterinary Research Institute (FEPAGRO)
item Kianian, Shahryar
item PAWLOWSKI, WOJCIECH - Desiderio Finamore Veterinary Research Institute (FEPAGRO)
item CHEN, CHANGBIN - University Of Minnesota
item MUDGE, JOANN - Desiderio Finamore Veterinary Research Institute (FEPAGRO)

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/15/2016
Publication Date: 9/22/2016
Citation: Sundararajan, A., Dukowic-Schulze, S., Kwicklis, M., Engstrom, K., Garcia, N., Oviedo, O., Ramaraj, T., Gonzales, M., He, Y., Minghui, W., Sun, Q., Pillardy, J., Kianian, S., Pawlowski, W., Chen, C., Mudge, J. 2016. Gene evolutionary trajectories and GC patterns driven by recombination in Zea mays. Frontiers in Plant Science. doi: 10.3389/fpls.2016.01433.

Interpretive Summary: In eukaryotes, meiotic exchange of genetic information, or recombination, between homologous chromosomes is a critical step in generating genetic diversity required for adaptation. Recombination is also a crucial tool in plant improvement efforts. Local genome architecture is sculpted by the recombination process, and genome architecture, in turn, drives recombination. This interplay helps to create variability in genomic space, defining relatively stable and plastic genomic regions. This fluctuation in genomic stability is critical for balancing adaptation and stability on the phenotypic level. Here we explore the relationship between recombination and genomic GC patterns by comparing GC gene content at each of the three codon positions to instances of a variable GC-rich motif that underlies double strand break (DSB) hotspots and to meiocyte-specific gene expression. Our data suggests a strong link between the GC-rich motif underlying DSB hotspots and high GC genes.

Technical Abstract: Recombination occurring during meiosis is critical for creating genetic variation and plays an essential role in plant evolution. In addition to creating novel gene combinations, recombination can affect genome structure through altering GC patterns. In maize (Zea mays) and other grasses, another intriguing GC pattern exists. Maize genes show a bimodal GC content distribution that has been attributed to nucleotide bias in the third, or wobble, position of the codon. Recombination may be an underlying driving force given that recombination sites are often associated with high GC content. Here we explore the relationship between recombination and genomic GC patterns by comparing GC gene content at each of the three codon positions (GC1, GC2, and GC3, collectively termed GCx) to instances of a variable GC-rich motif that underlies double strand break (DSB) hotspots and to meiocyte-specific gene expression. Surprisingly, GCx bimodality in maize cannot be fully explained by the codon wobble hypothesis. High GCx genes show a strong overlap with the DSB hotspot motif, possibly providing a mechanism for the high evolutionary rates seen in these genes. On the other hand, genes that are turned on in meiosis (early prophase I) are biased against both high GCx genes and genes with the DSB hotspot motif, possibly allowing important meiotic genes to avoid DSBs. Our data suggests a strong link between the GC-rich motif underlying DSB hotspots and high GCx genes.