Siela N. Maximova - US grants

Apple trees do not reproduce true-to-type from seed. Instead, desirable cultivars are propagated by grafting vegetative material onto suitable rootstocks. Rootstocks can alter scion traits of importance to agriculture, including fruit size, flowering timing, the number of flowers and fruits produced, drought tolerance, disease resistance, cold tolerance, and tree stature. In effect, the traits of genetically identical apple cultivar scions can be very different depending on the rootstock to which they are grafted. This project harnesses this phenomenon to identify genes in apple trees that are involved in controlling agriculturally important traits. The central hypothesis driving this research is that scions grafted to different rootstocks have different overall patterns of gene activity, and that these differences in gene activity play a role in determining the trait differences between the trees. Global gene expression patterns in "Gala" cultivar scions grafted to a series of different rootstocks will be compared. Genes whose expression level is rootstock-dependent will be identified (at least 500 unique genes). A DNA microarray comprised of the differentially expressed genes will be developed and used to survey a large number of scion/rootstock combinations in order to associate the expression of particular genes with particular traits.

This project will result in the identification of genes whose activity depends on the identity of the rootstock. The sequences of these genes will be made public though databases including GenBank (http://www.ncbi.nlm.nih.gov/) and the Genome Database for Rosaceae (http://www.genome.clemson.edu/gdr/). The results of the microarray experiments will be made available to the public though GEO database (http://www.ncbi.nlm.nih.gov/geo/). The sequence and microarray data will be made publicly available through the GEO database as soon as the first manuscript describing the results is accepted for journal publication, and will remain accessible after the completion of the project into the foreseeable future. The microarrays themselves will be made available at cost to other non-profit research groups. The broader impacts of this work include minority undergraduate student summer training through the SROP program (http://www.cic.uiuc.edu/programs/SROP/). Each summer, two or three underrepresented undergraduates will be given the opportunity to participate in the project. In addition, one or more graduate students will receive training in genomics research and undergraduates will be engaged in research related to this project during the academic year. The results of this project may also be useful for the development of gene activity markers that could be used in apple breeding programs to try to predict the traits of a tree early on in its development.

This NSF award by the Biotechnology, Biochemical and Biomass Engineering program supports work to develop low-cost bioreactor systems that will enhance the ability to utilize tissue culture to improve agricultural plant productivity. In addition to the typical paradigm of optimizing the chemical and environmental conditions within the bioreactor, this research seeks to demonstrate the ability to control plant development using transcriptional factors that control the expression of multiple genes. These transcriptional factors will be delivered to the plant tissues using Agrobacterium, a bacteria that has been developed to transiently deliver DNA to cultured plant tissues (developed with previous NSF support; BCS-0003926). The genes associated with plant embryo formation will be identified by examining patterns of gene expression during somatic embryogenesis. The concept of inducing embryo formation will be implemented using Cacao, the source of chocolate, due to its commercial (and social) value. In addition to providing an instructional case study that demonstrates the use of interdisciplinary principles of bioreactor design and molecular biology, the effort will produce thousands of fungal resistant plants that will be distributed to smallholder farmers in South America. In addition, the low-cost bioreactor technology has potential applications to a broad range of food and biomass crops.

The 20th Penn State plant Biology Symposium will focus on the important topic of "Plant Stress-Omics in a Changing Climate". Plenary sessions are focused on water and salinity, atmosphere (temperature, CO2, ozone), biotic/abiotic interactions and the use of novel tools. The conference is held at Penn State University, University Park takes place May 13-16, 2015. There will be two formal poster and two short talk sessions to feature research from talented junior scientists. The conference includes an impressive cadre of US and international speakers. The organizing committee and speaker list seems balanced in terms of broadening participation.

The workshop addresses an important topic in Plant Biology, namely how plants deal with increasing environmental stresses. Particularly noteworthy is a planned workshop preceding the meeting to provide training in novel mass spectrometric methods. These methods are necessary to determine metabolomics changes in response to various environmental stresses. The meeting is an ideal forum for students and postdocs to identify future mentors, and for established scientists to forge meaningful collaborations.

The human population is projected to grow to 9.6 billion by 2050, requiring a 50% increase in food and fiber production. A major constraint to this goal is crop losses due to microbial plant diseases which destroy approximately 15% of the world's total crop production every year. Advances in the science of plant disease control are needed to reduce crop losses to disease. Plant genomes encode thousands of genes involved in disease resistance, called the plant immune system. For some crops, modern science has made rapid progress in identifying disease resistance genes and using them in plant breeding, but for others such as long-lived tree crops, it is much more difficult to make rapid progress. This project will explore the plant immune system via a comprehensive study of the genes important for disease resistance to key pathogens of an important crop, cacao, which is the source of chocolate, and an important cash crop for millions of farmers in developing countries. The methods, tools and knowledge gained will be directly applicable to discovery of genes underlying important traits in other crops, especially trees and many perennial grasses. In addition to contributing to building a global partnership in reaching the goals of feeding a growing population sustainably, this project will involve students and young scientists in the US and in developing countries though international exchanges and collaborations.

This project will establish a new approach for use with perennial crop plants to identify candidate loci for disease resistance using a model tree crop, Theobroma cacao (the chocolate tree). Whole genome re-sequencing and transcriptome sequencing of a core collection of highly diverse cacao genotypes will provide the genetic information necessary to drive the discovery of genes critical for pathogen resistance. Functional analysis of these genes will test their role in resistance and set the stage for future translation of these basic findings to guiding more efficient breeding programs utilizing a wider array of genetic diversity. Importantly, the methods, tools, and knowledge gained will be directly applicable to discovery of genes underlying important traits in other crops, especially heterozygous perennials such as trees and many grasses which are not particularly amenable to approaches developed for the major annual crops such as corn and soybean. The basic evolutionary and functional principles that will be discovered can be generalized to most if not all crop plants. To promote and build genomics research capacity in developing countries and to promote inter-disciplinary cross-training the project will support scientific exchanges between project members and foreign collaborators, through postdoctoral, graduate and undergraduate student training at multiple institutions and will involve students from minority serving institutions. The results of this study will be made publicly available through electronic resources and publications.