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Elucidating Melatonin-Mediated Distinct Mechanistic Of Specific Gene Expression Of Coriander (Coriandrum Sativum L.) Under Chromium Stress, Arwa Abdulkreem Al-Huqail, Suliman Mohammed Suliman Alghanem, Haifa Abdulaziz Sakit Alhaithloul, Nayab Naeem, Wajiha Sarfraz, Noreen Khalid, Baber Ali

Turkish Journal of Agriculture and Forestry

The current investigation demonstrates that the application of MEL (0, 1 and 2 µmol L−1) mitigates the effects of Cr stress 0 (no Cr), 50 and 100 mg kg−1 on coriander (Coriandrum sativum L.) plants. Results from the present study showed that the increasing levels of Cr concentration in the soil induced a significant decrease in shoot length, root length, shoot fresh weight, root fresh weight, shoot dry weight, root dry weight, chlorophyll-a, chlorophyll-b, total chlorophyll, carotenoid contents, net photosynthesis, transpiration rate and stomatal conductance by 36%, 24%, 17%, 64%, 27%, 23%, 19%, 29%, 36%, 18%, 73%, 83% and 43% …

Expression Of The Genes (Cbf2, Cbf4, Nced1, Myb14, Pld) During Acclimation And De-Acclimation In Dormant Buds Of Chambourcin And 3309 C Grapevine Accessions, Di̇lek Karataş, Hüseyi̇n Karataş

Turkish Journal of Agriculture and Forestry

Deacclimatization results in a loss of bud cold-hardiness whereas cold acclimation results in an increase in it. The regulation of the buds’ cold acclimation and deacclimation in woody plants are poorly understood. This study indicated that differential gene expression during acclimation and transition of the buds from acclimation to deacclimation in the light of dormancy and bud water content. One-year-old vine latent bus of cv. Chambourcin vines and 3309 C (Vitis riparia x Vitis rupestris) were used for the analyses. Five genes (CBF2, CBF4, NCED1, MYB14, and PLD) were selected for quantitative real-time PCR. Quantitative real-time PCR was applied to …

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 …

Assessment Of Drought Stress Responsive Genes Expression Profiles And Proline Accumulation In A Diverse Set Of Grapevine Rootstocks, Canan Yüksel Özmen, Funda Yilmaz Baydu, Mohammad Hasanzadeh, Mert Öktem, Günseli̇ Babaoğlu, Umut Ki̇bar, Saber Delpasand Khabbazi, Kemal Kazan, Ali̇ Ergül

Turkish Journal of Agriculture and Forestry

In order to study plant responses to drought stress, it is important to have markers for such responses. This issue has been a challenge for decades and numerous traits have been used for this purpose. In the current study, the influence of drought stress on proline biosynthesis, leaf water potential, and also gene expression levels of 10 genes probably involved in drought stress response regulation pathways were investigated. Also, all experiments were performed in both root and leaf tissues of studied rootstocks to investigate the response of plant tissues which is more suitable for the assessment of possible markers. As …

Evaluation Of Gene Expression Levels In Grapevine Cultivars After Erysphe Necator Andmethyl Jasmonate Treatments, Nur Arslan, Murat Akkurt

Turkish Journal of Agriculture and Forestry

Powdery mildew (PM - Eryshpe necator) is one of the most important diseases threatening the world of viticulture. This study determined that the gene expression levels of Myc2, WRKY1, and DHN1a in Boğazkere (V. vinifera L. PM susceptible), Cabernet Sauvignon (V. vinifera L. PM susceptible), Kishmish Vatkana (V. vinifera L. PM tolerant), and Regent (V. vinifera L. PM tolerant) cultivars after PM and PM-Methyl jasmonate (MeJa) treatments by real-time polymerase chain reaction (RT-PCR). The susceptible and tolerant cultivars that were compared in the study were inoculated with PM which was taken from the natural environment and was sprayed with 50 …

Crosstalk Between Flowering And Cold Tolerance Genes In Almonds (Amygdalus Spp.), Başak Özdemi̇r, Fatma Yeşi̇m Okay, Gölge Sarikamiş, Canan Yüksel Özmen, Umut Ki̇bar, Ali̇ Ergül

Turkish Journal of Agriculture and Forestry

Almond production is usually affected by late spring frosts. Late flowering is an important trait in almond production in order to avoid frost damage. Breeding for late flowering has always been an important objective in almond breeding programs. Utilising molecular approaches may guide and accelerate breeding programs. In the present study, the expressions of the Prunus persica FLOWERING LOCUS T (PpFT) and Prunus armeniaca SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (PabSOC1) genes known as floral integrators that promote flowering in plants were determined in almonds (Amygdalus spp.). Frost tolerance is another important trait in almond production. Almond accessions may vary in …

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 …

Exogenous Cysteine Alleviates Mercury Stress By Promoting Antioxidant Defence In Maize(Zea Mays L.) Seedlings, Ferhunde Aysi̇n, Aykut Karaman, Asli Yilmaz, Özkan Aksakal, Ebru Gezgi̇nci̇oğlu, Sakineh Mohammadi Kohnehshahri

Turkish Journal of Agriculture and Forestry

Mercury (Hg) is one of the most important environmental pollutants that negatively affects plant growth and development. Cysteine (Cys) plays an important role in plant response to various environmental stress factors. In the present study, the alleviation of Hg stress through exogenous Cys treatment to maize seedlings was evaluated. For this purpose, a hydroponic experiment was set up to investigate the effect of HgCI2 (100 μM) and in combination with Cys (200 μM) on plant growth, total chlorophyll content, reactive oxygen species, antioxidant enzyme activities, and mRNA expression levels of some antioxidant genes in maize seedlings. The results showed that …

Estimation And Testing Of Gene Expression Heterosis, Tieming Ji, Peng Liu, Dan Nettleton

Dan Nettleton

Heterosis, also known as the hybrid vigor, occurs when the mean phenotype of hybrid offspring is superior to that of its two inbred parents. The heterosis phenomenon is extensively utilized in agriculture though the molecular basis is still unknown. In an effort to understand phenotypic heterosis at the molecular level, researchers have begun to compare expression levels of thousands of genes between parental inbred lines and their hybrid offspring to search for evidence of gene expression heterosis. Standard statistical approaches for separately analyzing expression data for each gene can produce biased and highly variable estimates and unreliable tests of heterosis. …

Genome-Wide Identification And Molecular Characterization Of Citrus Unshiu Wrkytranscription Factors In Satsuma Mandarin: Clues For Putative Involvement In Cell Growth,Fruit Ripening, And Stress Response, Mariem Ayadi, Rim Mzid, Rayda Ben Ayed, Najla Kharrat, Henda Merchaoui, Ahmed Rebai, Mohsen Hanana

Turkish Journal of Agriculture and Forestry

WRKY transcription factors, being involved in several biological roles, stimulus signaling, and stress response, could be interesting candidates to prospect, particularly in the Citrus unshiu (Satsuma mandarin) genome. Our approach, mainly based on computational analyses, led to the identification of 51 CiuWRKYs followed by their molecular characterization. Syntenic relationship analysis showed significant bias towards sweet orange and Arabidopsis chromosomes. Analyses of promoter region showed that CiuWRKY1 modulates gene transcription through W-box site targeting. The deduced CiuWRKY1 protein was moderately hydrophobic. A comparative in silico analysis among Arabidopsis thaliana and Citrus sinensis WRKYs allowed us to designate orthologous genes. Lacking available …

Enhancing Resolution Of Natural Methylome Reprogramming Behavior In Plants, Robersy Sanchez, Xiaodong Yang, Hardik Kundariya, Jose R. Barreras, Yashitola Wamboldt, Sally A. Mackenzie

Department of Agronomy and Horticulture: Faculty Publications

We have developed a novel methylome analysis procedure, Methyl-IT, based on information thermodynamics and signal detection. Methylation analysis involves a signal detection problem, and the method was designed to discriminate methylation regulatory signal from background noise induced by thermal fluctuations. Comparison with three commonly used programs and various available datasets to furnish a comparative measure of resolution by each method is included. To confirm results, methylation analysis was integrated with RNAseq and network enrichment analyses. Methyl-IT enhances resolution of genome methylation behavior to reveal network-associated responses, offering resolution of gene pathway influences not attainable with previous methods.

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

Department of Agronomy and Horticulture: Faculty Publications

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 …

66th National Poultry Breeder Roundtable Poster_Jibin Zhang.Pdf, Jibin Zhang, Carl J. Schmidt, Susan J. Lamont

Jibin Zhang

Pag 2017 Poster _ Jibin Zhang.Pdf, Jibin Zhang, Michael G. Kaiser, Melissa S. Herrmann, Rodrigo A. Gallardo, David A. Bunn, Terra R. Kelly, Jack C. M. Dekkers, Huaijun Zhou, Susan J. Lamont

Jibin Zhang

Differential Expression Of Cyb5a In Chinese And European Pig Breeds Due To Genetic Variations In The Promoter Region..Pdf, Ying Bai, Jibin Zhang, Y Xue, Yl Peng, Gang Chen, Meiying Fang

Jibin Zhang

Physiological Characteristics, Antioxidant Enzyme Activities, And Gene Expression In 2 Spring Canola (Brassica Napus L.) Cultivars Under Drought Stress Conditions, Seyed Mohammad Hosseini, Tahereh Hasanloo, Saeed Mohammadi

Turkish Journal of Agriculture and Forestry

This study examined the influence of drought stress during the flowering stage of 2 canola cultivars on some physiological characteristics, antioxidant activities, and gene expression of antioxidant enzymes. Significant differences were observed among interactions of cultivars and levels of drought stress in total shoot dry material, relative water content percentage, proline, carbohydrates, gene expression, and activities of antioxidant enzymes. Moreover, a significant positive correlation was indicated between shoot dry materials with relative water content percentage, sucrose, catalase activity, ascorbate peroxidase activity, and cytosolic ascorbate peroxidase relative gene expression ratio. Antioxidant enzymatic activity and the association between gene transcript levels and …

Psim24 Is A Novel Versatile Gene Expression Vector For Transient Assays As Well As Stable Expression Of Foreign Genes In Plants, Dipak K. Sahoo, Nrisingha Dey, Indu B. Maiti

Kentucky Tobacco Research and Development Center Faculty Publications

We have constructed a small and highly efficient binary Ti vector pSiM24 for plant transformation with maximum efficacy. In the pSiM24 vector, the size of the backbone of the early binary vector pKYLXM24 (GenBank Accession No. HM036220; a derivative of pKYLX71) was reduced from 12.8 kb to 7.1 kb. The binary vector pSiM24 is composed of the following genetic elements: left and right T-DNA borders, a modified full-length transcript promoter (M24) of Mirabilis mosaic virus with duplicated enhancer domains, three multiple cloning sites, a 3'rbcsE9 terminator, replication functions for Escherichia coli (ColE1) and Agrobacterium tumefaciens (pRK2-OriV) and the replicase trfA …

Jibin Zhang's Ppt For Midwest Meeting.Pdf, Jibin Zhang, Yeunsu Suh, Young Min Choi, Michael E. Davis, Kichoon Lee

Jibin Zhang

Gene Set Testing To Characterize Multivariately Differentially Expressed Genes, John R. Stevens, S. Clay Isom

Conference on Applied Statistics in Agriculture

In a gene expression experiment (using oligo array, RNA-Seq, or other platform), researchers typically seek to characterize di erentially expressed genes based on common gene function or pathway involve-ment. The eld of gene set testing provides numerous characterization methods, some of which have proven to be more valid and powerful than others. These existing gene set testing methods focus on experimental designs where there is a single null hypothesis (usually involving association with a continuous or categorical phenotype) for each gene. Increasingly common experimental designs lead to multiple null hypotheses for each gene, and the characterization of these multivariately di …

Microarray Analysis Of Late Response To Boron Toxicity In Barley (Hordeum Vulgare L.) Leaves, Mehmet Tufan Öz, Remzi̇ye Yilmaz, Füsun Eyi̇doğan, Leo De Graaff, Meral Yücel, Hüseyi̇n Avni̇ Öktem

Turkish Journal of Agriculture and Forestry

DNA microarrays, being high-density and high-throughput, allow quantitative analyses of thousands of genes and their expression patterns in parallel. In this study, Barley1 GeneChip was used to investigate transcriptome changes associated with boron (B) toxicity in a sensitive barley cultivar (Hordeum vulgare L. cv. Hamidiye). Eight-day-old aseptically grown seedlings were subjected to 5 or 10 mM boric acid (B(OH)_3) treatments for 5 days and expression profiles were determined with DNA microarrays using total RNA from leaf tissues. Among the 22,840 transcripts - each represented with a probe set on the GeneChip - 19,424 probe sets showed intensity values greater than …

Dynamic Clustering Of Cell-Cycle Microarray Data, Lingling An, R. W. Doerge

Conference on Applied Statistics in Agriculture

The cell cycle is a crucial series of events that are repeated over time, allowing the cell to grow, duplicate, and split. Cell-cycle systems play an important role in cancer and other biological processes. Using gene expression data gained from microarray technology it is possible to group or cluster genes that are involved in the cell-cycle for the purpose of exploring their functional co-regulation. Typically, the goal of clustering methods as applied to gene expression data is to place genes with similar expression patterns or profiles into the same group or cluster for the purpose of inferring the function of …

Genetic Mapping Of Gene Expression Levels: Expression Level Polymorphism Analysis For Dissecting Regulatory Networks Of Plant Disease Resistance, Kyunga Kim, Marilyn A. L. West, Richard W. Michelmore, Dina A. St. Clair, R. W. Doerge

Conference on Applied Statistics in Agriculture

The genetic basis of inherited traits has been studied through di erent approaches in many areas of science. Examples include quantitative trait locus (QTL) analysis and mutant analysis in genetics, genome sequencing and gene expression analysis in genomics. Each of these approaches is used for the investigation of complex traits, such as disease resistance, but also provides knowledge on components of complex biological systems. We introduce a novel functional genomics approach that integrates two areas, genetics and genomics, by applying QTL analysis to quantitative di erences in the mRNA abundance of trait-related genes. This approach allows comprehensive dissection of regulatory …

In Situ Localisation Of Axi 1 (Auxin Independent) Gene In Rhizobium Leguminosarum Inoculated Root Tips Of Pea Plants, Yeşi̇m Yalçin Mendi̇, Katharina Pawlowski, Seli̇m Çeti̇ner

Turkish Journal of Agriculture and Forestry

Axi 1 is the only characterized auxin independent gene in tobacco plants. In this study, the effect of axi 1 gene on cortical cell division during different stages of nitrogen fixation and on the role of polar auxin transport were investigated. Root and nodule samples were taken from pea seedlings 24 hours, 48 hours, 6 days and 10 days after inoculation with R. leguminosarum PRE strain. Using in situ hybridisation, the location of the axi 1 gene expression in root and nodule tissues was identified. The results showed that in root tissues inoculated with Rhizobia, the axi 1 gene is …