USING SYSTEMS BIOLOGY APPROACHES TO UNDERSTAND THE TRANSCRIPTIONAL REGULATION UNDERLYING PLANT DEFENSE AND GROWTH

Plant complex traits are controlled by multi-layer of dynamic and complicated gene networks regulated at different levels. To better inform crop breeding to promote desired traits, a comprehensive and fundamental understanding of their genetic basis is much needed. With the rapid developments of omics planforms and next generation sequencing technology, we now have large-scale data from genome, epigenome, transcriptome, metabolome, and others for the crop plants. Integration of those multiple omics data together with computational approaches led to the establishment of a novel science known as system biology. Research described in this thesis used system biology approaches to dissect complex crop traits such as disease response of tomato (Chapter2 and Chapter3) and the heterosis of nitrogen use efficiency of maize (Chapter4).

Plant disease response is an elaborate, multilayered complex trait involving several lines of defense signaling. In the past decades, progress in molecular analyses of plant immune system has revealed key elements of a complex response network in Arabidopsis, a model species. Histone modifications, a type of epigenetic regulation, have emerged as key modulators that regulate defense responses, while our understanding of the role of histone-modifying enzymes in this process is still in its infancy. Here, we described the immune function of two histone methyltransferases SDG33 and SDG34 in tomato. We found the single mutants in sdg33 and sdg34 showed increased susceptibility to hemibiotrophic bacterial pathogen Pseudomonas syringae whereas the double mutant sdg33sdg34 is comparable to wild type. Using RNA-seq and histone ChIP-seq approaches, we investigated the possible underlying mechanisms and found that the expression of a set of immune-related genes is misregulated by P. syringae only in the single mutants but not in the double mutant. Integrating with epigenomic data, we found that the misexpression of those SDG33/SDG34 dependent immune-response genes was associated with altered histone methylation status in the single mutant. Intriguingly, the double mutant also showed altered histone methylation but unaffected gene expression, suggesting a compensating regulatory mechanism at play. The function of SDG33 and SDG34 in immune response seems to be specific for the pathogen, as the double mutants exhibited enhanced resistance the single mutants showed no altered responses when treated with necrotrophic fungal pathogen Botrytis cinerea. Network analysis found the most regulatory gene by B. cinerea in a SDG33/SDG34 dependent manner have been implicated in biotic stress response such as ERF4, TOPLESS, PUB23 and RCD1. Comparing the immune response of double mutant against P. syringae and B. cinerea, we found that the disease related genes are only mis-regulated in the interaction of B. cinerea treatment not in the P. syringae treatment, which could be the reason of enhanced resistance to B. cinerea but not for P. syringae in the double mutants. In summary, we found the histone methyltransferases SDG33 and SDG34 has different functions in the immune response against P. syringae and B. cinerea, which might be direct or indirect relevant to the histone methylation level of the expression of downstream immune related gene.

In addition to biotic stress, another complex trait studied in this thesis is the heterosis of nitrogen use efficiency (NUE) in Maize. NUE is another complex trait associated with multiple physiological processes including N sensing, uptake, assimilation, transport, and storage. Heterosis refers to a phenomenon where the progeny generated by crossing two different cultivars of the same species exhibit superior fitness than the inbred parents. Even though, heterosis has been exploited to improve complex traits including NUE, the underlying molecular mechanisms is not completely understood. Here, we analyzed N-responsive transcriptomes and physiological traits of a panel of six maize hybrids and their corresponding inbreds grown in the field at two different N levels. We observed diverse levels of trait heterosis that are dependent on the N conditions and organ types. We discovered dramatic pattern shift of beyond-parental-range gene expression in hybrids in response to varying N levels. We identified through integrative analyses a set of genes whose expression heterosis are quantitatively correlated to trait heterosis. These genes are involved in response to stimulus, photosynthesis, and N metabolism, and likely mediate the heterosis phenotype of N-use and growth traits in maize. In summary, our integrated analysis provided insights into the mechanistic basis of the heterosis of NUE. 

Together, applying systems and functional genomics approaches to investigate important agricultural traits could lead to a comprehensive understanding of plant complex traits to inform future engineering and breeding for better crops.