Epigenomic variation in maize
Geneticists study the basis of heritable variation within species. Most heritable differences can be attributed to sequence differences among different individuals that segregate in Mendelian fashion. However, there is also evidence for heritable variation that cannot be attributed to sequence variation. This epigenetic variation can be encoded by differences in the modifications to DNA or histones. One well-characterized example is DNA methylation. In most cases, DNA methylation is correlated with reduced gene expression or activity levels for a particular region of the genome. It is important to understand the relative contribution and role of epigenetic variation to understand how information is passed from parents to off-spring.
Matthew Vaughn (University of Texas at Austin) and I have a National Science Foundation Plant Genome Program grant to study epigenomic variation in maize. We are comparing the genomic distribution of several chromatin modifications in a variety of maize genotypes. Further information on this project can be found on the Maize epigenomic variation project website.
The genome of many plant species is a mosaic of genes and repetitive elements. Most of these repetitive elements are derived from different types of transposable elements. The exact types and locations of transposons present in genomes varies widely between species and even between individuals of the same species. Genomes have developed a variety of mechanisms to suppress transposon movement and to mitigate the influence of transposon on genes. Maize provides a good system for studying how transposons and genes interact. Over 80% of the maize genome is derived from transposons and most genes have transposons located very nearby. We are studying how the genome uses chromatin modifications to separate genes and transposons. In addition, we are attempting to determine how transposons might create new regulatory information that can influence expression of genes.
Evolution of gene expression responses
Plants are sessile organisms that must respond to environmental changes in order to survive. In order to produce enough food for a growing population in a changing climate it will be important for scientists to understand the mechanisms that plants use to tolerate abiotic stress. Changes in gene expression levels are one mechanism that plants use to respond to environmental stress. We are studying natural variation in responses to abiotic stress to probe the evolution and mechanisms of gene expression responses to abiotic stress. We seek to understand how genes acquire, or lose, specific gene expression responses. By understanding how certain alleles respond to environmental stress we might be able to engineer plants with improved responses to environmental stresses such as extreme temperatures or drought.
Environmentally induced epigenetic variation
One particularly intriguing aspect of epigenetic variation is the potential for instability in the system. While genetic variation is generally stable and has quite predictable patterns of inheritance, epigenetic variation can be quite unstable and may be influenced by environmental differences. This creates the potential for the environment to affect information that may be passed on to off-spring. We have studied DNA methylation patterns in plants subjected to environmental stress and tissue culture (in collaboration with Shawn Kaeppler at the University of Wisconsin-Madison). We found little evidence for changes in DNA methylation in most conditions but did find a number of genomic regions with altered DNA methylation following tissue culture.
Integrative genomics in maize
Genomic studies have the potential to characterize differences in sequence or gene expression across the whole genome. There is great potential to harness genomic datasets to develop models to explain and predict phenotypic variation. In collaboration with Chad Myers (University of Minnesota) we have been developing co-expression networks based on gene expression profiles of different genotypes or developmental stages. Our goal is to develop models that integrate gene expression profiles and genetic variation data to explain phenotypic differences. This project will develop computation resources to assist with the characterization of QTL and breeding efforts for a variety of traits.
Imprinted gene expression in maize
Most plant and animal species require contributions of genetic material from both a maternal and paternal parent. While the genetic material contributed by the two parents can be very similar there are some regions that are differently marked, or imprinted, based upon which parent it was inherited from. This imprinting results in differential expression of two alleles depending upon their parent-of-origin. The majority of imprinting documented in plant species occurs in endosperm tissue. The maize seed includes a large, persistent endosperm and provides a useful model system for studying imprinting. My group documented imprinting at the Mez1 locus of maize. We characterized several chromatin modifications associated with imprinting and have studied the effects of transposable elements on imprinting. Current efforts have focused on genome-wide analysis of parent-of-origin effects on the maize transcriptome.
Gene expression in hybrids and heterosis
Heterosis, or hybrid vigor, refers to the phenomena in which hybrid off-spring exhibits phenotypic characteristics that are superior to either parent. This genetic phenomenon has a substantial impact upon human agriculture practices and is widely used in many crop species despite a complete lack of an understanding of its molecular basis. During the course of a series of studies on allelic variation among maize lines and the prevalence of cis- and trans-regulatory variation, we gathered gene expression profiles for a series of inbred and hybrid maize lines. While there is extensive variation in gene expression levels among maize genotypes, most hybrids express genes at the mid-parent level or within the range of the parents. It is quite rare to observe hybrid gene expression levels that are outside of the parental range of expression for that gene. Recent studies have focused on further defining the phenomena of heterosis and developing detailed information for a variety of phenotypes in many different hybrids.
Structural genomic variation
While many biologists tend to think of individuals within a species as having very similar genomes there is growing evidence for major differences in the structure of genomes in different individuals of the same species. This structural genomic variation includes insertion/deletions, inversions and translocations. The insertion/deletions include examples of copy number variation (CNV) where different individuals possess different copy numbers for the same sequence and presence-absence variation (PAV) where some individuals contain a sequence while others lack this sequence. In collaboration with Patrick Schnable Iowa State University) and Jeffrey Jeddeloh (Roche NimbleGen) we have used comparative genomic hybridization (CGH) to study structural variation among maize inbreds. There are numerous examples of CNV and PAV among different maize genotypes. Current efforts are focused on understanding the contributions of these CNV and PAV to phenotypic diversity in maize.
Effects of aneuploidy on gene expression patterns
It is well known that aneuploidy often results in a phenotypic syndrome. However, the exact process through which altered copy number of sequences leads to phenotypic changes has not been well characterized in plant or animal systems. We used a segmental aneuploidy that is trisomic for most of the short arm of maize chromosome 5 to profile how aneuploidy affects the transcriptome. These studies found evidence that aneuploidy may interfere with proper developmental timing of gene expression. Several genes were found that exhibit ectopic expression in tissues where they are normally silent.