Maize DNA-sequencing strategies and genome organization

A large amount of repetitive DNA complicates the assembly of the maize genome sequence. Genome-filtration techniques, such as methylation-filtration and high-CoT separation, enrich gene sequences in genomic libraries. These methods may provide a low-cost alternative to whole-genome sequencing for maize and other complex genomes.     

Maize centromeric chromatin scales with changes in genome size

Centromeres are defined by the location of Centromeric Histone H3 (CENP-A/CENH3) which interacts with DNA to define the locations and sizes of functional centromeres. An analysis of 26 maize genomes including 110 fully assembled centromeric regions revealed positive relationships between centromere size and genome size. These effects are independent of variation in the amounts of the major centromeric satellite sequence CentC. We also backcrossed known centromeres into two different lines with larger genomes and observed consistent increases in functional centromere sizes for multiple centromeres. Although changes in centromere size involve changes in bound CENH3, we could not mimic the effect by overexpressing CENH3 by threefold. Literature from other fields demonstrate that changes in genome size affect protein levels, organelle size and cell size. Our data demonstrate that centromere size is among these scalable features, and that multiple limiting factors together contribute to a stable centromere size equilibrium.     

Maize genome structure variation: interplay between retrotransposon polymorphisms and genic recombination

Although maize (Zea mays) retrotransposons are recombinationally inert, the highly polymorphic structure of maize haplotypes raises questions regarding the local effect of intergenic retrotransposons on recombination. To examine this effect, we compared recombination in the same genetic interval with and without a large retrotransposon cluster. We used three different bz1 locus haplotypes, McC, B73, and W22, in the same genetic background. We analyzed recombination between the bz1 and stc1 markers in heterozygotes that differ by the presence and absence of a 26-kb intergenic retrotransposon cluster. To facilitate the genetic screen, we used Ds and Ac markers that allowed us to identify recombinants by their seed pigmentation. We sequenced 239 recombination junctions and assigned them to a single nucleotide polymorphism-delimited interval in the region. The genetic distance between the markers was twofold smaller in the presence of the retrotransposon cluster. The reduction was seen in bz1 and stc1, but no recombination occurred in the highly polymorphic intergenic region of either heterozygote. Recombination within genes shuffled flanking retrotransposon clusters, creating new chimeric haplotypes and either contracting or expanding the physical distance between markers. Our findings imply that haplotype structure will profoundly affect the correlation between genetic and physical distance for the same interval in maize.     

Maize plants prime anti-herbivore responses by the memorizing and recalling of airborne information in their genome

Intact maize plants prime for defensive action against herbivory in response to herbivore-induced plant volatiles (HIPVs) emitted from caterpillar-infested conspecific plants. The recent research showed that the primed defense in receiver plants that had been exposed to HIPVs was maintained for at least 5 d after exposure. Herbivory triggered the receiver plants to enhance the expression of a defense gene for trypsin inhibitor (TI). At the upstream sequence of a TI gene, non-methylated cytosine residues were observed in the genome of HIPV-exposed plants more frequently than in that of healthy plant volatile-exposed plants. These findings provide an innovative mechanism for the memory of HIPV-mediated habituation for plant defense. This mechanism and further innovations for priming of defenses via plant communications will contribute to the development of plant volatile-based pest management methods in agriculture and horticulture.     

Maize ATR safeguards genome stability during kernel development to prevent early endosperm endocycle onset and cell death

The ataxia-telangiectasia mutated (ATM) and ATM and Rad3-related (ATR) kinases coordinate the DNA damage response. The roles described for Arabidopsis thaliana ATR and ATM are assumed to be conserved over other plant species, but molecular evidence is scarce. Here, we demonstrate that the functions of ATR and ATM are only partially conserved between Arabidopsis and maize (Zea mays). In both species, ATR and ATM play a key role in DNA repair and cell cycle checkpoint activation, but whereas Arabidopsis plants do not suffer from the absence of ATR under control growth conditions, maize mutant plants accumulate replication defects, likely due to their large genome size. Moreover, contrarily to Arabidopsis, maize ATM deficiency does not trigger meiotic defects, whereas the ATR kinase appears to be crucial for the maternal fertility. Strikingly, ATR is required to repress premature endocycle onset and cell death in the maize endosperm. Its absence results in a reduction of kernel size, protein and starch content, and a stochastic death of kernels, a process being counteracted by ATM. Additionally, while Arabidopsis atr atm double mutants are viable, no such mutants could be obtained for maize. Therefore, our data highlight that the mechanisms maintaining genome integrity may be more important for vegetative and reproductive development than previously anticipated.

Differently from Arabidopsis, ATR activity in maize plays an essential role under control growth conditions, ensuring genome stability during kernel Development.     

Membranes in motion

The Keystone Symposium on the Molecular Basis for Biological Membrane Organization and Dynamics held in January this year offered new insights into the molecular machines at work in cells. Topics included the machinery responsible for the dynamic shape of organelles, the budding and fusion of vesicular carriers, and the intricate sorting systems that ensure the correct delivery of cellular components.     

Theory in motion

Modeling studies are now a significant part of mainstream research in motor control. Novel and classical modeling techniques used in recent work on small and large motor systems illustrate the different roles that models play in furthering our understanding of motor systems. The models presented reveal single neuron short-term memory, unexpected effects of reciprocal inhibition and methods for decoding activity in large populations of neurons.