Life Sciences Commons^™

Molecular Approaches In The Analysis Of Red Clover Rhizobium Symbiosis, Randy D. Dinkins, L. Koch, M. L. Sullivan, H. Zhu

IGC Proceedings (1997-2023)

Red clover (Trifolium pratense L.) is an important forage and pasture legume grown throughout temperate regions. Because it can form a symbiotic relationship with rhizobium, it is able to fix atmospheric nitrogen. Due to the high cost of nitrogen fertilizers, pasture legumes have been increasingly important in forage production settings. Red clover has not been a model legume primarily due to selfincompatibility and the associated high level of genomic heterozygosity, therefore it has not been a significant contributor in molecular or genetic studies and basic information on red clover legume/rhizobium symbiosis is lacking. Using recently annotated genomic resources, RNA-seq …

Beta-Carbonic Anhydrase Gene Expression Levels Change Depending On The Drought Severity In Both The Leaves And Roots Of Arabidopsis Thaliana, Sertan Çevi̇k, Oğuzhan Kurt, Ayşi̇n Güzel Değer, Ferit Kocaçinar, Rıza Bi̇nzet

Turkish Journal of Botany

In this study, it was aimed to determine the relationship between β carbonic anhydrase (βCA) gene expression levels and drought stress severity. For this purpose, the expression levels of six βCA genes in the roots and leaves of Arabidopsis thaliana were investigated under mild, moderate, and severe drought conditions. In addition, changes in the biomass, leaf water content, photosynthetic efficiency, CA enzyme activity, free proline content, and lipid peroxidation were also determined. The results showed that all of the β CA gene expression levels and CA enzyme activity increased in the leaf under mild drought conditions; however, the expression levels …

Genome-Wide Identification Of Qtls Associated With Iron Deficiency Tolerance In Soybean Reveals Gata12 As The Integrator Of Iron Signaling In Roots, Amir Maqbool, Ahmet Şahi̇n, Allah Bakhsh, Emre Aksoy

Turkish Journal of Botany

Iron (Fe) is an essential micronutrient required for plant growth and development. However, its deficiency causes substantial yield losses, particularly in alkaline soils. Soybean (Glycine max) serves as an ideal model to study Fe deficiency chlorosis (IDC) due to its inefficient Fe uptake from the soil. Although the quantitative trait loci (QTL) associated with IDC tolerance were determined in soybean, the specific genes within these QTL regions remain unidentified. In this study, it was aimed to identify and analyze the expression levels of genes present in IDC-responsive soybean QTL under Fe deficiency. Through this investigation, 6593 genes were identified within …

Unraveling Prevalence And Effects Of Deleterious Mutations In Maize Elite Lines Across Decades Of Modern Breeding, Shichao Sun, Baobao Wang, Changyu Li, Gen Xu, Jinliang Yang, Matthew B. Hufford, Jeffrey Ross-Ibarra, Haiyang Wang, Li Wang

Department of Agronomy and Horticulture: Faculty Publications

Future breeding is likely to involve the detection and removal of deleterious alleles, which are mutations that negatively affect crop fitness. However, little is known about the prevalence of such mutations and their effects on phenotypic traits in the context of modern crop breeding. To address this, we examined the number and frequency of deleterious mutations in 350 elite maize inbred lines developed over the past few decades in China and the United States. Our findings reveal an accumulation of weakly deleterious mutations and a decrease in strongly deleterious mutations, indicating the dominant effects of genetic drift and purifying selection …

Light Intensity Is Positively Correlated With The Synthesis Of Condensed Tannins In Lotus Corniculatus, Sergio Arcioni, T. Bovone, F. Damiani, F. Paolocci

IGC Proceedings (1997-2023)

The importance of Condensed Tannins (CT) in forage legumes has been well documented in several studies. The role of plant genetics in this field is the acquisition of competences in order to be able to modulate CT synthesis in leaves of these species. The role of light has been investigated in this work on the increase of condensed tannin levels in leaves of two contrasting genotypes of birdsfoot trefoil (Lotus corniculatus).

Physiological And Transcriptomic Responses Of Two Artemisia Californica Populations To Drought: Implications For Restoring Drought-Resilient Native Communities, Hagop S. Atamian Dr., Jennifer L. Funk

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

As climate change brings drier and more variable rainfall patterns to many arid and semi-arid regions, land managers must re-assemble appropriate plant communities for these conditions. Transcriptome sequencing can elucidate the molecular mechanisms underlying plant responses to changing environmental conditions, potentially enhancing our ability to screen suitable genotypes and species for restoration. We examined physiological and morphological traits and transcriptome sequences of coastal and inland populations of California sagebrush (Artemisia californica), a critical shrub used to restore coastal sage scrub vegetation communities, grown under low and high rainfall environments. The populations are located approximately 36 km apart but …

The Investigation Of Flowering Control In Late/Rare Flowering Lolium Perenne, S. Byrne, I. S. Donnison, L. J. Mur, E. Guiney

IGC Proceedings (1997-2023)

Flowering in Lolium perenne (perennial ryegrass) results in reduced digestibility and its inhibition would enhance forage quality. Flowering regulation has been well studied in Arabidopsis thaliana (Simpson and Dean, 2002) and orthologs of Arabidopsis flowering genes underlying heading date Quantitative Trait Loci (QTL) have been identified in rice (Yano, M et al., 2000). However it is not clear yet how universally applicable such studies are to Lolium. The project goals are to characterise the gene expression profiles of late/rare flowering L. perenne plants to determine factors affecting flowering and to map the genes involved in the flowering process. Initial …

Boron Toxicity Induces Sulfate Transporters At Transcriptional Level In Arabidopsis Thaliana, Ceyhun Kayihan, Emre Aksoy, Su Naz Mutlu

Turkish Journal of Botany

Plants activate glutathione (GSH)-dependent detoxification pathways at biochemical and molecular levels under boron (B) toxicity. Sulfate uptake and transport are necessary for GSH biosynthesis in plants. Therefore, the transcriptional regulation of some sulfate transporters was determined in this study to clarify the importance of these transporters in leaf and root tissues of Arabidopsis thaliana under toxic B conditions. The expression level of SULTR1;3 was dramatically increased in leaf and root tissues under moderate and severe toxic B conditions, suggesting source-to-sink sulfate translocation under B toxicity. Stable expression levels of SULTR2;1, SULTR2;2, and low SULTR3;5 expression might restrict the sulfate movement …

Mapk-Mediated Transcription Factor Gatad Contributes To Cry1ac Resistance In Diamondback Moth By Reducing Pxmalp Expression, Le Guo, Zhouqiang Cheng, Jianying Qin, Dan Sun, Shaoli Wang, Qingjun Wu, Neil Crickmore, Xuguo Zhou, Alejandra Bravo, Mario Soberón, Zhaojiang Guo, Youjun Zhang

Entomology Faculty Publications

The benefits of biopesticides and transgenic crops based on the insecticidal Cry-toxins from Bacillus thuringiensis (Bt) are considerably threatened by insect resistance evolution, thus, deciphering the molecular mechanisms underlying insect resistance to Bt products is of great significance to their sustainable utilization. Previously, we have demonstrated that the down-regulation of PxmALP in a strain of Plutella xylostella (L.) highly resistant to the Bt Cry1Ac toxin was due to a hormone-activated MAPK signaling pathway and contributed to the resistance phenotype. However, the underlying transcriptional regulatory mechanism remains enigmatic. Here, we report that the PxGATAd transcription factor (TF) is responsible for the …

Identification And Characterization Of A Long Fruit Mutant In Cucumis Sativus L., Yajing Hu, Xiaojing Dong, Yana Zhang, Rui Tang, Jiali Li, Chenxing Cao, Chunhua Chen, Zhonghai Ren, Lina Wang

Turkish Journal of Botany

A long fruit (lf) mutant was obtained from the cucumber inbred line 'SN5' by ethyl methanesulfonate (EMS)-mediated mutagenesis. We found that plant height and internode length of lf were significantly decreased, while leaf area was significantly increased in comparison to wild type (WT) plants. Higher carbohydrate level, together with lower chlorophyll content and photosynthetic parameters, was revealed in lf leaves than those of WT. Longer fruits, as well as enhanced fruit quality, were observed for mutant plants in comparison to WT, and the difference in fruit length was continuously increased with the development of fruits. ELISA and real-time PCR analyses …

Biological Interactions In Grassland Soils And Productivity, R. Cook, R. D. Bardgett, W. R. Eason, L. Skøt, K. J. Webb

IGC Proceedings (1997-2023)

This paper describes research on interactions between grassland plant species and soil microorganisms. Both parasitic and symbiotic microorganisms modify nutrient transfers between plants and soil. Experiments are described in which nematode infection of clover increased nitrogen transfer to companion ryegrass plants. Infection of clover enhanced activity of soil bacterial and fungal communities. Legume genotypes differing only in responses to symbionts (rhizobium and arbuscular mycorrhizal fungi) and pathogens are being developed for studies of gene expression during establishing and functional symbioses. Such plants can be used in experiments as defined perturbations that will provide information on the interactions and functions of …

Genetic Resistance To The Downy Mildew Pathogen And Breeding Towards Durable Disease Management In Spinach, Bazgha Zia

Graduate Theses and Dissertations

Spinach (Spinacia oleracea) is a self-pollinated, dioecious winter crop. Prevalent challenges to the production of spinach include disease pressure imposed by downy mildew, which is caused by Peronospora effusa (=P. farinosa f. sp. spinaciae [Pfs]). A total of 19 new races of P. effusa have emerged, imposing serious challenges to the disease management in spinach production. Accordingly, this study was designed to explore the genetic components for establishing the basis of durable disease resistance development against the downy mildew pathogen (P. effusa 13) in spinach, through the use of various genome engineering approaches.

Our results have led (Chapter 2) to …

Physiological And Molecular Responses Of Eurythermal And Stenothermal Populations Of Zostera Marina L (Eelgrass) To Climate Change, Carmen C. Zayas-Santiago

OES Theses and Dissertations

As CO₂ levels in Earth’s atmosphere and oceans steadily rise, varying organismal responses may produce ecological losers and winners. Increased ocean CO₂ can enhance seagrass productivity and thermal tolerance, providing some compensation for climate warming. However, the consistency of this CO₂ effect across populations of cosmopolitan species such as Zostera marina L. (eelgrass) remains largely unknown. This study analyzed whole-plant performance metabolic profiles and gene expression patterns of distinct eelgrass populations in response to CO₂ enrichment. Populations were transplanted from Nisqually Landing and Dumas Bay, two cold water environments in Puget Sound, WA (USA) that rarely …

Elevated Atmospheric Co2 Concentration Triggers Redistribution Of Nitrogen To Promote Tillering In Rice, Juan Zhou, Yingbo Gao, Junpeng Wang, Chang Liu, Zi Wang, Minjia Lv, Xiaoxiang Zhang, Yong Zhou, Guichun Dong, Yulong Wang, Jianye Huang, Dafeng Hui, Zefeng Yang, Youli Yao

Biology Faculty Research

Elevated atmospheric CO₂ concentration (eCO₂) often reduces nitrogen (N) content in rice plants and stimulates tillering. However, there is a general consensus that reduced N would constrain rice tillering. To resolve this contradiction, we investigated N distribution and transcriptomic changes in different rice plant organs after subjecting them to eCO₂ and different N application rates. Our results showed that eCO₂ significantly promoted rice tillers (by 0.6, 1.1, 1.7, and 2.1 tillers/plant at 0, 75, 150, and 225 kg N ha⁻¹ N application rates, respectively) and more tillers were produced under higher N application rates, …

The Ear Motif In The Arabidopsis Mads Transcription Factor Agamous-Like 15 Is Not Necessary To Promote Somatic Embryogenesis, Sanjay Joshi, Christian Keller, Sharyn E. Perry

Plant and Soil Sciences Faculty Publications

AGAMOUS-like 15 (AGL15) is a member of the MADS domain family of transcription factors (TFs) that can directly induce and repress target gene expression, and for which promotion of somatic embryogenesis (SE) is positively correlated with accumulation. An ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motif of form LxLxL within the carboxyl-terminal domain of AGL15 was shown to be involved in repression of gene expression. Here, we examine whether AGL15′s ability to repress gene expression is needed to promote SE. While a form of AGL15 where the LxLxL is changed to AxAxA can still promote SE, another form with a …

Low‐Temperature Tolerance Related Cbf And Fructosyltrans Ferase Genes In Forage Grasses, H. Hisano, K. Tamura, M. Yoshida, A. Kanazawa, T. Yamada

IGC Proceedings (1997-2023)

No abstract provided.

Poplar Allene Oxide Synthase 1 Gene Promoter Drives Rapid And Localized Expression By Wounding, Bin Lei, Christopher J. Frost, Tao Xu, Joshua Herr, John E. Carlson, Haiying Liang

Department of Plant Pathology: Faculty Publications

Promoters play critical roles in controlling the transcription of genes and are important as tools to drive heterologous expression for biotechnological applications. In addition to core transcription factor-binding motifs that assist in the binding of RNA polymerases, there are specific nucleotide sequences in a promoter region to allow regulation of gene expression. The allene oxide synthase (AOS) gene family are cytochrome P450s that are responsive to a variety of environmental stress, making them good candidates for the discovery of inducible promoters. Populus AOS homologs separate phylogenetically into two clades. Based on the 19 promoter motifs with significant abundance differences between …

Synergism And Antagonism In Plant Acclimation To Abiotic Stress Combinations, Karl-Josef Dietz

Turkish Journal of Botany

Acclimation of plants to their environment involves mechanisms at all molecular levels and only the complete temporal and spatial pattern adequately describes the acclimation state. The diversity of physiological states realized in plants increases by the essentially infinite combinations of abiotic and biotic stresses, considering duration, impact order, and strength. The interference between stressors involves phenomena of synergism, antagonism, and indifference. This review exemplarily sketches principles of interference considering posttranslational modifications, the formation of molecular assemblies in regulosomes, the regulation of gene expression, and the vast number of other posttranscriptional controls e.g., in RNA processing and recruitment to ribosomes. Small …

A Transcriptional Regulatory Network Of Rsv3-Mediated Extreme Resistance Against Soybean Mosaic Virus, Lindsay C. Demers, Neelam R. Redekar, Aardra Kachroo, Sue A. Tolin, Song Li, M. A. Saghai Maroof

Plant Pathology Faculty Publications

Resistance genes are an effective means for disease control in plants. They predominantly function by inducing a hypersensitive reaction, which results in localized cell death restricting pathogen spread. Some resistance genes elicit an atypical response, termed extreme resistance, where resistance is not associated with a hypersensitive reaction and its standard defense responses. Unlike hypersensitive reaction, the molecular regulatory mechanism(s) underlying extreme resistance is largely unexplored. One of the few known, naturally occurring, instances of extreme resistance is resistance derived from the soybean Rsv3 gene, which confers resistance against the most virulent Soybean mosaic virus strains. To discern the regulatory mechanism …

Characterization Of The Transcriptional Divergence Between The Subspecies Of Cultivated Rice (Oryza Sativa), Malachy T. Campbell, Qian Du, Kan Li, Sandeep Sharma, Chi Zhang, Harkamal Walia

Agronomy & Horticulture -- Faculty Publications

Background: Cultivated rice consists of two subspecies, Indica and Japonica, that exhibit well-characterized differences at the morphological and genetic levels. However, the differences between these subspecies at the transcriptome level remains largely unexamined. Here, we provide a comprehensive characterization of transcriptome divergence and cis-regulatory variation within rice using transcriptome data from 91 accessions from a rice diversity panel (RDP1).

Results: The transcriptomes of the two subspecies of rice are highly divergent. Japonica have significantly lower expression and genetic diversity relative to Indica, which is likely a consequence of a population bottleneck during Japonica domestication. We leveraged high-density genotypic data and …

Effect Of Fungicide Pretreatment On Lipid Peroxidation, Antioxidant Enzyme Systems And Proline Accumulation In Tomato (Lycopersicon Esculentum Mill.) Leaves Under High Temperature Stress, Eli̇f Yüzbaşioğlu

Turkish Journal of Botany

The aim of the present study was to determine the effect of high temperature stress (HT) and to evaluate the protective role of fungicide pretreatment against HT stress in tomato leaves. The oxidative stress was triggered under HT stress through an increase in the content of malondialdehyde (MDA) and hydrogen peroxide (H2O2). Also, it caused a decline in photosynthetic pigments and enhanced the proline in tomato. However, the activities of catalase (CAT; EC 1.11.1.6), peroxidase (POX; EC 1.11.1.7), and glutathione S-transferase (GST; EC.2.5.1.18), as well as ascorbate-glutathione cycle enzymes (APX, EC 1.11.1.11, DHAR, EC 1.8.5.1, MDHAR EC 1.6.5.4, GR; EC …

Dehydrins: An Overview Of Current Approaches And Advancement, Nesli̇han Saruhan Güler, Rabi̇ye Terzi̇

Turkish Journal of Botany

Since plants are exposed to diverse environmental stresses in their natural area, numerous reviews have demonstrated many aspects of dehydrins (DHNs), including structural and functional dynamics, and multiple roles such as membrane protection, cryoprotection of enzymes, chaperone feature, and protection from reactive oxygen species. In this review, we have focused on new information, and other promising and emerging topics of DHNs in plants. This review outlines particularly the potential regulatory mechanisms of DHNs associated with stress tolerance and the role of DHNs in morphological responses of the plants exposed to environmental stresses. Besides the discussion of the signaling pathways involved …

Interspecific Gene Flow Potentiates Adaptive Evolution In A Hybrid Zone Formed Between Pinus Strobiformis And Pinus Flexilis, Mitra Menon

Theses and Dissertations

Species range margins are often characterised by high degrees of habitat fragmentation resulting in low genetic diversity and higher gene flow from populations at the core of the species range. Interspecific gene flow from a closely related species with abutting range margins can increase standing genetic diversity and generate novel allelic combinations thereby alleviating limits to adaptive evolution in range margin populations. Hybridization driven interspecific gene flow has played a key role in the demographic history of several conifer due to their life history characteristics such as weak crossability barriers and long generation times. Nevertheless, demonstrating whether introgression is adaptive …

Substantial Contribution Of Genetic Variation In The Expression Of Transcription Factors To Phenotypic Variation Revealed By Erd-Gwas, Hung-Ying Lin, Qiang Liu, Xiao Li, Jinliang Yang, Sanzhen Liu, Yinlian Huang, Michael J. Scanlon, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

Background: There are significant limitations in existing methods for the genome-wide identification of genes whose expression patterns affect traits.

Results: The transcriptomes of five tissues from 27 genetically diverse maize inbred lines were deeply sequenced to identify genes exhibiting high and low levels of expression variation across tissues or genotypes. Transcription factors are enriched among genes with the most variation in expression across tissues, as well as among genes with higher-than-median levels of variation in expression across genotypes. In contrast, transcription factors are depleted among genes whose expression is either highly stable or highly variable across genotypes. We developed a …

Characterization And Tissue-Specific As Well As Heat-Stress Expression Analysis Of Cbl-Interacting Protein Kinase Genes In Dimocarpus Longan Lour, Wei Zheng, Xueming Dong, Xuefei Yu, Qiuying Zhang

Turkish Journal of Botany

The CBL-interacting protein kinase (CIPK) gene family plays important roles in plant growth, development, and responses to abiotic stresses. To date, the CIPKs have been extensively identified and characterized in various plants. However, there have been few studies on CIPKs in Dimocarpus longan Lour (D. longan). In this study we identified eight putative CIPKs in D. longan (DlCIPKs) according to RNA-seq data. The physicochemical properties, subcellular localization, conserved motifs, phylogenetic relationships, glycosylation and phosphorylation sites, and gene ontology annotation were analyzed using bioinformatics tools. The tissue-specific and heat-stress-responsive expressions were systematically investigated as well. Ten motifs widely maintained by DlCIPKs …

Regulation Of Boron Toxicity Responses Via Glutathione-Dependent Detoxification Pathways At Biochemical And Molecular Levels In Arabidopsis Thaliana, Doğa Seli̇n Kayihan, Ceyhun Kayihan, Yelda Özden Çi̇ftçi̇

Turkish Journal of Botany

The fine-tuned regulation of the Halliwell-Asada cycle (ascorbate-glutathione pathway) in Arabidopsis thaliana under boron (B) toxicity was shown in our previous report. In this study, we investigated the expression levels of some members of the glutathione S-transferase (GST) superfamily, such as phi (GSTF2, GSTF6, GSTF7, and GSTF8), tau (GSTU19), and zeta (GSTZ1) classes in Arabidopsis thaliana that were exposed to 1 mM boric acid (1B) and 3 mM boric acid (3B). Additionally, the expression levels of genes for glutathione (GSH) and phytochelatin biosynthesis as well as miR169 and miR156 were evaluated in Arabidopsis thaliana exposed to 1B and 3B. Moreover, …

Variations In Ethylene Sensitivity Among Mungbean [Vigna Radiata (L.) Wilczek] Genotypes Exposed To Drought And Waterlogging Stresses, Susheel Kumar Raina, Nikhil Raskar, Lalitkumar Aher, Ajay Kumar Singh, Dhammaprakash Pandhari Wankhede, Jagadish Rane, Paramjit Singh Minhas

Turkish Journal of Botany

Ethylene is an important phytohormone that regulates several aspects of plant development including those crucial for drought tolerance. The main aim of the present work was to investigate variability in ethylene sensitivity of mungbeans to seed germination, waterlogging, and leaf senescence, and the underlying transcriptional regulation of ethylene biosynthetic/responsive genes. Significant variation was observed for silver-nitrate-mediated germination inhibition and flooding stress tolerance among the mungbean genotypes. Genotypes with differential ethylene sensitivity (IC-325817 and IC-325756) revealed variable leaf senescence rates upon exposure to exogenously supplied ethephon. Drought induced significant upregulation of VrACS7 and VrERF genes in the more sensitive genotype, implicating …

Suberin Biosynthesis And Deposition In The Wound-Healing Potato (Solanum Tuberosum L.) Tuber Model, Kathlyn Natalie Woolfson

Electronic Thesis and Dissertation Repository

Suberin is a heteropolymer comprising a cell wall-bound poly(phenolic) domain (SPPD) covalently linked to a poly(aliphatic) domain (SPAD) that is deposited between the cell wall and plasma membrane. Potato tuber skin contains suberin to protect against water loss and microbial infection. Wounding triggers suberin biosynthesis in usually non-suberized tuber parenchyma, providing a model system to study suberin production. Spatial and temporal coordination of SPPD and SPAD-related metabolism are required for suberization, as the former is produced soon after wounding, and the latter is synthesized later into wound-healing. Many steps involved in suberin biosynthesis remain uncharacterized, and the mechanism(s) that regulate …

Developmental Variation In Fruit Polyphenol Content And Related Gene Expression Of A Red-Fruited Versus A White-Fruited Fragraria Vesca Genotype, Sutapa Roy, Sanjay Singh, Douglas D. Archbold

Horticulture Faculty Publications

Two cultivars of F. vesca, red-fruited Baron Solemacher (BS) and white-fruited Pineapple Crush (PC), were studied to compare and contrast the quantitative accumulation of major polyphenols and related biosynthetic pathway gene expression patterns during fruit development and ripening. Developing PC fruit showed higher levels of hydroxycinnamic acids in green stages and a greater accumulation of ellagitannins in ripe fruit in comparison to BS. In addition to anthocyanin, red BS fruit had greater levels of flavan-3-ols when ripe than PC. Expression patterns of key structural genes and transcription factors of the phenylpropanoid/flavonoid biosynthetic pathway, an abscisic acid (ABA) biosynthetic gene, …

Transcriptome Analysis Of Root Development In Wheat Triticum Aestivum Using High Throughtput Sequencing Technologies, Ghana Challa

Electronic Theses and Dissertations

Root provides plant water, nutrients and anchorage from soil. Most our knowledge of molecular mechanisms of root development is from the dicot model plant Arabidopsis, but very few studies have done in monocot crop systems like rice, maize, and wheat. We are studying very short root (VSR) phenotype in wheat, and lack of a sequenced reference genome in wheat prompted us to sequence and assemble the root transcriptome of the reference cultivar Chinese Spring (CS). A root transcriptome was assembled from the sequenced reads generated from root tip and the mature root tissues of CS. Approximately 169 million reads were …