Browsing by Author "Suren, Haktan"

Now showing 1 - 8 of 8
  • Thumbnail Image
    Architecture and Evolution of Xylem-related Gene Coexpression Networks in Poplars
    Suren, Haktan (Virginia Tech, 2013-02-14)
    With the advent of sequencing technologies, a variety of methods have been available day by day. Each of these methods have helped scientists to for a deeper understanding of the biological function and evolutionary constraints on the relevant genes, which can be gained through the use of modern computational approaches. Numerous approaches have being developed to advance these goals, and interaction network mapping is one of them. This method has been employed to study a variety of organisms to illustrate shared (conserved) or individual (unique) properties, and is mainly based on identifying and visualizing modules of co-expressed genes. As being a very strong candidate for such tools, co-expression gene network was used in this study to indentify the genes in wood formation of Populus trichocarpa with the help of the other novel bioinformatics tools such as Gene Ontology and Cytoscape. In order to booster the accuracy of the findings, we have combined it with an evolutionary approach, synonymous and non-synonymous ratio (dN/dS) of the proteins to show the selective patterns of the genes in a comparative fashion between woody and non-woody plants. This thesis is proposed to help plant scientists to gain insights into the genes that are involved in wood formation. By taking advantage of the computational studies have been done on this paper, one can validate the experiments along with reducing the cumbersomeness of the lab trials on the topic of wood formation in plants
  • Thumbnail Image
    Differential roles of melatonin in plant-host resistance and pathogen suppression in cucurbits
    Mandal, Mihir Kumar; Suren, Haktan; Ward, Brian; Boroujerdi, Arezue; Kousik, Chandrasekar (2018-10)
    Since the 1950s, research on the animal neurohormone, melatonin, has focused on its multiregulatory effect on patients suffering from insomnia, cancer, and Alzheimer's disease. In plants, melatonin plays major role in plant growth and development, and is inducible in response to diverse biotic and abiotic stresses. However, studies on the direct role of melatonin in disease suppression and as a signaling molecule in host-pathogen defense mechanism are lacking. This study provides insight on the predicted biosynthetic pathway of melatonin in watermelon (Citrullus lanatus), and how application of melatonin, an environmental-friendly immune inducer, can boost plant immunity and suppress pathogen growth where fungicide resistance and lack of genetic resistance are major problems. We evaluated the effect of spray-applied melatonin and also transformed watermelon plants with the melatonin biosynthetic gene SNAT (serotonin N-acetyltransferase) to determine the role of melatonin in plant defense. Increased melatonin levels in plants were found to boost resistance against the foliar pathogen Podosphaera xanthii (powdery mildew), and the soil-borne oomycete Phytophthora capsici in watermelon and other cucurbits. Further, transcriptomic data on melatonin-sprayed (1mmol/L) watermelon leaves suggest that melatonin alters the expression of genes involved in both PAMP-mediated (pathogen-associated molecular pattern) and ETI-mediated (effector-triggered immunity) defenses. Twenty-seven upregulated genes were associated with constitutive defense as well as initial priming of the melatonin-induced plant resistance response. Our results indicate that developing strategies to increase melatonin levels in specialty crops such as watermelon can lead to resistance against diverse filamentous pathogens.
  • Thumbnail Image
    Elucidation of resistance signaling and identification of powdery mildew resistant mapping loci (ClaPMR2) during watermelon-Podosphaera xanthii interaction using RNA-Seq and whole-genome resequencing approach
    Mandal, Mihir Kumar; Suren, Haktan; Kousik, Chandrasekar (2020-08-20)
    Watermelon is an important vegetable crop and is widely cultivated in USA with an approximate global production of >100 million tons. Powdery mildew (PM) caused by Podosphaera xanthii is a major production-limiting factor on watermelon and other cucurbits. Numerous PM and multiple disease resistant (MDR) watermelon germplasm lines have been developed by the USDA in Charleston, SC. To gain a better understanding of the innate and activated molecular defense mechanisms involved during compatible and incompatible PM-watermelon interactions, we inoculated PM susceptible (USVL677-PMS) and resistant (USVL531-MDR) watermelon plants with 10(5) conidia ml(-1) of P. xanthii. RNA-seq profiling was done on leaf samples collected at 0, 1, 3, and 8 days post inoculation (DPI). A total of 2,566 unique differentially expressed genes (DEGs) were identified between compatible and incompatible interactions with P. xanthii. The compatible interactions resulted in distinct plant gene activation (>twofold unique transcripts, 335:191:1762
  • Thumbnail Image
    Evidence for extensive heterotrophic metabolism, antioxidant action, and associated regulatory events during winter hardening in Sitka spruce
    Collakova, Eva; Klumas, Curtis; Suren, Haktan; Myers, Elijah; Heath, Lenwood S.; Holliday, Jason A.; Grene, Ruth (2013-04-30)
    Background Cold acclimation in woody perennials is a metabolically intensive process, but coincides with environmental conditions that are not conducive to the generation of energy through photosynthesis. While the negative effects of low temperatures on the photosynthetic apparatus during winter have been well studied, less is known about how this is reflected at the level of gene and metabolite expression, nor how the plant generates primary metabolites needed for adaptive processes during autumn. Results The MapMan tool revealed enrichment of the expression of genes related to mitochondrial function, antioxidant and associated regulatory activity, while changes in metabolite levels over the time course were consistent with the gene expression patterns observed. Genes related to thylakoid function were down-regulated as expected, with the exception of plastid targeted specific antioxidant gene products such as thylakoid-bound ascorbate peroxidase, components of the reactive oxygen species scavenging cycle, and the plastid terminal oxidase. In contrast, the conventional and alternative mitochondrial electron transport chains, the tricarboxylic acid cycle, and redox-associated proteins providing reactive oxygen species scavenging generated by electron transport chains functioning at low temperatures were all active. Conclusions A regulatory mechanism linking thylakoid-bound ascorbate peroxidase action with “chloroplast dormancy” is proposed. Most importantly, the energy and substrates required for the substantial metabolic remodeling that is a hallmark of freezing acclimation could be provided by heterotrophic metabolism.
  • Thumbnail Image
    Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa
    Guerra, Fernando P.; Suren, Haktan; Holliday, Jason A.; Richards, James H.; Fiehn, Oliver; Famula, Randi; Stanton, Brian J.; Shuren, Richard; Sykes, Robert; Davis, Mark F.; Neale, David B. (2019-11-20)
    Background Populus trichocarpa is an important forest tree species for the generation of lignocellulosic ethanol. Understanding the genomic basis of biomass production and chemical composition of wood is fundamental in supporting genetic improvement programs. Considerable variation has been observed in this species for complex traits related to growth, phenology, ecophysiology and wood chemistry. Those traits are influenced by both polygenic control and environmental effects, and their genome architecture and regulation are only partially understood. Genome wide association studies (GWAS) represent an approach to advance that aim using thousands of single nucleotide polymorphisms (SNPs). Genotyping using exome capture methodologies represent an efficient approach to identify specific functional regions of genomes underlying phenotypic variation. Results We identified 813 K SNPs, which were utilized for genotyping 461 P. trichocarpa clones, representing 101 provenances collected from Oregon and Washington, and established in California. A GWAS performed on 20 traits, considering single SNP-marker tests identified a variable number of significant SNPs (p-value < 6.1479E-8) in association with diameter, height, leaf carbon and nitrogen contents, and δ15N. The number of significant SNPs ranged from 2 to 220 per trait. Additionally, multiple-marker analyses by sliding-windows tests detected between 6 and 192 significant windows for the analyzed traits. The significant SNPs resided within genes that encode proteins belonging to different functional classes as such protein synthesis, energy/metabolism and DNA/RNA metabolism, among others. Conclusions SNP-markers within genes associated with traits of importance for biomass production were detected. They contribute to characterize the genomic architecture of P. trichocarpa biomass required to support the development and application of marker breeding technologies.
  • Thumbnail Image
    Mining and visualization of microarray and metabolomic data reveal extensive cell wall remodeling during winter hardening in Sitka spruce (Picea sitchensis)
    Grene, Ruth; Klumas, Curtis; Suren, Haktan; Yang, Kuan; Collakova, Eva; Myers, Elijah; Heath, Lenwood S.; Holliday, Jason A. (Frontiers, 2012)
    Microarray gene expression profiling is a powerful technique to understand complex developmental processes, but making biologically meaningful inferences from such studies has always been challenging. We previously reported a microarray study of the freezing acclimation period in Sitka spruce (Picea sitchensis) in which a large number of candidate genes for climatic adaptation were identified. In the current paper, we apply additional systems biology tools to these data to further probe changes in the levels of genes and metabolites and activities of associated pathways that regulate this complex developmental transition. One aspect of this adaptive process that is not well understood is the role of the cell wall. Our data suggest coordinated metabolic and signaling responses leading to cell wall remodeling. Co-expression of genes encoding proteins associated with biosynthesis of structural and non-structural cell wall carbohydrates was observed, which may be regulated by ethylene signaling components. At the same time, numerous genes, whose products are putatively localized to the endomembrane system and involved in both the synthesis and trafficking of cell wall carbohydrates, were up-regulated. Taken together, these results suggest a link between ethylene signaling and biosynthesis, and targeting of cell wall related gene products during the period of winter hardening. Automated Layout Pipeline for Inferred NEtworks (ALPINE), an in-house plugin for the Cytoscape visualization environment that utilizes the existing GeneMANIA and Mosaic plugins, together with the use of visualization tools, provided images of proposed signaling processes that became active over the time course of winter hardening, particularly at later time points in the process. The resulting visualizations have the potential to reveal novel, hypothesis generating, gene association patterns in the context of targeted subcellular location.
  • Thumbnail Image
    Phenotypic and Genomic Local Adaptation across Latitude and Altitude in Populus trichocarpa
    Zhang, Man; Suren, Haktan; Holliday, Jason A. (Oxford University Press, 2019-07-10)
    Local adaptation to climate allows plants to cope with temporally and spatially heterogeneous environments, and parallel phenotypic clines provide a natural experiment to uncover the genomic architecture of adaptation. Though extensive effort has been made to investigate the genomic basis of local adaptation to climate across the latitudinal range of tree species, less is known for altitudinal clines. We used exome capture to genotype 451 Populus trichocarpa genotypes across altitudinal and latitudinal gradients spanning the natural species range, and phenotyped these trees for a variety of adaptive traits in two common gardens. We observed clinal variation in phenotypic traits across the two transects,which indicates climate-driven selection, and coupled gene-based genotype–phenotype and genotype–environment association scans to identify imprints of climatic adaptation on the genome. Although many of the phenotype-and climate-associated genes were unique to one transect, we found evidence of parallelism between latitude and altitude, as well as significant convergence when we compared our outlier genes with those putatively involved in climatic adaptation in two gymnosperm species. These results suggest that not only genomic constraint during adaptation to similar environmental gradients in poplar but also different environmental contexts, spatial scale, and perhaps redundant function among potentially adaptive genes and polymorphisms lead to divergent adaptive architectures.
  • Thumbnail Image
    Sequence capture as a tool to understand the genomic basis for adaptation in angiosperm and gymnosperm trees
    Suren, Haktan (Virginia Tech, 2017-06-21)
    Forest trees represent a unique group of organisms combined with ecological and economic importance. Owing to their random mating system and widespread geographical distribution, they harbor abundance genetic variation both within and among populations. Despite their importance, research in forest trees has been underrepresented majorly due to their large and complex genome and scarce funding. However, recent climate change and other associated problems such as insect outbreaks, diseases and stress related damages have urged scientists to focus more on trees. Furthermore, the advent in high-throughput sequencing technologies have allowed trees to be sequenced and used as reference genome, which provided deeper understanding between genotype and environment. Whole genome sequencing is still not possible for organisms having large genomes including most tree species, and it is still not feasible economically for population genomic studies which require sequencing hundreds of samples. To get around this problem, genomic reduction is required. Sequence capture has been one of the genomic reduction techniques enabled studying the subset of the DNA of interest. In this paper, our primary goal is to outline challenges, provide guidance about the utility of sequence capture in trees, and to leverage such data in genome-wide association analyses to find the genetic variants that underlie complex, adaptive traits in spruce and pine, as well as poplar. Results of this research will facilitate bridging the genomic information gap between trees and other organisms. Moreover, it will provide better understanding how genetic variation governs phenotype in trees, which will facilitate both marker assisted selection for improved traits as well as provide guidance to determine forest management strategies for reforestation to mitigate the effects of climate change.