van Nocker lab

390 Plant and Soil Sciences

Michigan State University

Research Interest - Plant Developmental Genetics

email Steve van Nocker

Plant Growth and Development (PLB/HRT865) will be offered again in Fall 2010.

Research Interests - Plant Developmental Genetics

What are the underlying genetic mechanisms that determine plant form, and how are these controlled? What are the key genes that influence agriculturally important traits such as flowering?  What parallels exist between plant and human development, and can studies in plants shed light on issues such as cancer and stem cell biology?

Current Projects:

Exploiting chromatin landmarks to characterize complex plant genomes. Progress is the science of genomics is no longer limited by the technologies that obtain genomic DNA sequence, but rather by the ability to interpret this information and uncover biologically relevant features of the genome.  In addition, DNA sequence is only one component of the information content of the genome.  Additional information - called epigenetic information - is encoded partly by the proteinaceous matrix called chromatin in which the DNA is packaged.  Specific modifications to the histone proteins, which make up the bulk of chromatin, are closely associated with the characteristics of the genes to which they are affixed.  The objective of this project is to evaluate novel approaches to facilitate sequence analysis of gene-rich regions in plants with complex genomes, identify chromatin landmarks useful for genome annotation, and identify polymorphic sequences most useful for genetic map construction, utilizing a wild apple species as a reference.  The project is expected to help uncover how epigenetic information is linked to gene activity, add accuracy to annotation efforts, and uncover cryptic and previously unanticipated features of the genome. (11/09 Now recruiting for two postdoctoral positions and a PhD student)

Transcriptional memory and epigenetic mechanisms. As an organism develops, cells may proliferate to maintain a pool of stem cells, or differentiate to form specialized tissues. We are studying the mechanisms by which states of gene activity are propagated within and across mitotic boundaries, specifically in relation to chromatin-associated proteins and modifications of DNA and histones at specific genetic sites. In Arabidopsis, we identified a class of protein required for maintaining transcriptional activity of a subset of developmental regulatory genes by counteracting the repressive activity of the so-called Polycomb-group proteins. As part of this project, we recently published the first genome-wide map of transcriptional-activating chromatin modifications in a plant genome (Oh et al 2008). This project also involves gene mapping and cloning, identification of unknown, related proteins through purification and mass spectrometry.

Flowering. Plants have evolved an enormous diversity of strategies to flower at the time of year best suited to their reproduction. Most have intricate mechanisms to perceive daylength and temperature, which are superimposed onto an endogenous flowering program. We are using genetic and molecular techniques to elucidate the networks of gene expression involved in triggering flowering in plants, using Arabidopsis as a model. We are focusing on vernalization (acceleration of flowering by cold) which, in Arabidopsis, results in the downregulation of the FLC/MAF family of MADS-box flowering-inhibitor genes. This project involves genetic screens, mapping, gene cloning, and analyses of genetic interactions. For more information on the genetic mechanisms of flowering, see our review (van Nocker and Ek-Ramos 2004).

Juvenility and inflorescence architecture in Malus (apple). We are also studying flowering in the cultivated apple (Malus x domestica). The commercial apple industry is limited by various flowering-related problems, including lack of flowering in alternate years (biennial bearing) and overcropping. The goal of this project is to identify genes and genetic loci that influence flowering-related traits, especially juvenility and inflorescence architecture, in apple. This work involves the evaluation of the diversity in flowering traits seen in nature in Malus species, the genetic mapping of these traits (QTL analysis), and evaluating evolutionary conservation of the function of flowering genes known in other species. (11/09 Now recruiting for PhD student position)

Fruit abscission. We are taking a multifaceted approach to understand fruit abscission in the cultivated apple, with the goal of developing tools and providing the basis for efficient production practices to control fruit retention and drop. To map early molecular events in abscission layer activation, we are analyzing global profiles of gene activity during natural and chemically promoted abscission. These studies can be used as a blueprint to develop new strategies for fruit thinning and retention. We are also cataloging natural variation in fruit abscission-related traits among cultivated varieties and wild species of apple (see our recent publication in the journal Euphytica; Sun et al 2008). This is the first step in a long-term project to construct linkage maps revealing genetic loci that influence these traits. Such maps can be utilized for gene identification and the breeding of novel cultivars with abscission-related characteristics naturally optimized for 21st-century production technologies. (11/09 Now recruiting for PhD student position)

Selected Recent Publications:

Two postdoctoral positions are now available (see below).

Assistantships now available for PhD graduate students for the projects below through the Program in Genetics, Cell and Molecular Biology, Plant Breeding/Genetics/Biotechnology, or Horticulture

To facilitate application, first send an email describing interests, goals and background to Steve van Nocker (vannocke@msu.edu).