Plant Breeding and Genetics Commons^™

Summaries Of Arkansas Cotton Research 2018, Fred Bourland

Arkansas Agricultural Experiment Station Research Series

Arkansas ended the 2018 season ranked 5th nationally in harvested acres (480,000 acres), 4th in lint yield (1150 lb/acre), and 4th in total production (1,150,000 bales). The string of consecutive years with good yields is helping to drive the increase in cotton acres. Harvest and ginning capacity is a major limiting factor for acre expansion. Cotton planting intentions for 2019 released in late March are at 580,000 acres, up 20% from the 485,000 acres planted in 2018. This continues to push the ginning capacity of 28 gins in 2018 and on-farm picker capacity to the limit. Optimism for cotton is …

Nature-Guided Synthesis Of Advanced Bio-Lubricants, Trevor Romsdahl, Asghar Shirani, Robert E. Minto, Chunyu Zhang, Edgar B. Cahoon, Kent D. Chapman, Diana Berman

Center for Plant Science Innovation: Faculty Publications

Design of environmentally friendly lubricants derived from renewable resources is highly desirable for many practical applications. Here, Orychophragmus violaceus (Ov) seed oil is found to have superior lubrication properties, and this is based on the unusual structural features of the major lipid species— triacylglycerol (TAG) estolides. Ov TAG estolides contain two non-hydroxylated, glycerol-bound fatty acids (FAs) and one dihydroxylated FA with an estolide branch. Estolide branch chains vary in composition and length, leading to their thermal stability and functional properties. Using this concept, nature-guided estolides of castor oil were synthesized. As predicted, they showed improved lubrication properties similar to Ov …

The Database Of Identified Root-Specific Genes And Their Promoters In Maize, Sorghum, And Soybean, Gleb Moisseyev, Divith Rajagopal, Alix Cui, Kiyoul Park, Edgar B. Cahoon, Chi Zhang

Center for Plant Science Innovation: Faculty Publications

Root genes are essential to plants as they dictate factors such as the strength of the plant, reproductivity success, etc. However, in the status quo, studies on root genes are simply ineffective. To be more specific, currently, there are very few online databases of root genes and promoters, which essentially deters root gene studies from being successful. To fix this problem, our lab constructed and coded an online database that contains information about the roots of maize, soybean, and sorghum. We collected 1200 root genes and assessed the strength and success of a given gene. This online database of these …

B.R. Wells Arkansas Rice Research Studies 2018, R. J. Norman, K. A.K. Moldenhauer

Arkansas Agricultural Experiment Station Research Series

No abstract provided.

Assessing Anthocyanin Biosynthesis In Solanaceae As A Model Pathway For Secondary Metabolism, Zou Li, Trisha Vickrey, Moira G. Mcnally, Shirley J. Sato, Thomas E. Clemente, Jeffrey P. Mower

Center for Plant Science Innovation: Faculty Publications

Solanaceae have played an important role in elucidating how flower color is specified by the flavonoid biosynthesis pathway (FBP), which produces anthocyanins and other secondary metabolites. With well-established reverse genetics tools and rich genomic resources, Solanaceae provide a robust framework to examine the diversification of this well-studied pathway over short evolutionary timescales and to evaluate the predictability of genetic perturbation on pathway flux. Genomes of eight Solanaceae species, nine related asterids, and four rosids were mined to evaluate variation in copy number of the suite of FBP enzymes involved in anthocyanin biosynthesis. Comparison of annotation sources indicated that the NCBI …

Network‐Based Feature Selection Reveals Substructures Of Gene Modules Responding To Salt Stress In Rice, Qian Du, Malachy Campbell, Huihui Yu, Kan Liu, Harkamal Walia, Qi Zhang, Chi Zhang

Center for Plant Science Innovation: Faculty Publications

Rice, an important food resource, is highly sensitive to salt stress, which is directly related to food security. Although many studies have identified physiological mechanisms that confer tolerance to the osmotic effects of salinity, the link between rice genotype and salt tolerance is not very clear yet. Association of gene co‐expression network and rice phenotypic data under stress has penitential to identify stress‐responsive genes, but there is no standard method to associate stress phenotype with gene co‐expression network. A novel method for integration of gene co‐expression network and stress phenotype data was developed to conduct a system analysis to link …

Economic Contribution Of The Agricultural Sector To The Arkansas Economy In 2017, Leah English, Jennie Popp, Wayne Miller

AAES Research Reports and Research Bulletins

Agriculture and associated agricultural activities are major contributors to the Arkansas economy. Agriculture is defined as the sum of agricultural production and processing activities, unless otherwise specified, and includes crop and animal production and processing, agricultural support industries, forestry and forest products, and textile goods. Agriculture contributes to the economy through direct agricultural production and value-added processing, and also leads to economic activity in other parts of the economy. This report is the eleventh in a series of reports examining agriculture’s economic contribution to the Arkansas economy. The total economic contribution of agriculture (direct, indirect, and induced effects) on value …

Qtl × Environment Interactions Underlie Adaptive Divergence In Switchgrass Across A Large Latitudinal Gradient, David B. Lowry, John T. Lovell, Li Zhang, Jason Bonnette, Philip A. Fay, Robert B. Mitchell, John Lloyd-Reilley, Arvid R. Boe, Et. Al

Agronomy, Horticulture and Plant Science Faculty Publications

Local adaptation is the process by which natural selection drives adaptive phenotypic divergence across environmental gradients. Theory suggests that local adaptation results from genetic trade-offs at individual genetic loci, where adaptation to one set of environmental conditions results in a cost to fitness in alternative environments. However, the degree to which there are costs associated with local adaptation is poorly understood because most of these experiments rely on two-site reciprocal transplant experiments. Here, we quantify the benefits and costs of locally adaptive loci across 17° of latitude in a four-grandparent outbred mapping population in outcrossing switchgrass (Panicum virgatum L.), …

Mapping A New Disease Resistance Locus In An F1 Progeny Derived From Two Grape Wild Relatives, Gaurab Bhattarai

Graduate Theses/Dissertations

Linkage maps and quantitative trait loci (QTL) analysis have become essential tools for the positional cloning of agronomically important genes and for marker-assisted breeding. In this study, two North American grape species, Vitis rupestris and Vitis riparia, and their 294 F₁ progeny were used to construct parental linkage maps and to perform QTL analysis for downy mildew resistance. Single nucleotide polymorphism (SNP) discovery was accomplished using genotyping-by-sequencing (GBS) and resulted in 348,888 SNPs. Of these, 11,063 informative SNP markers (3.17% of the original SNP dataset) were derived after filtering for various quality parameters and missing data. A two-way …

Transcriptome And Physiological Analyses For Revealing Genes Involved In Wheat Response To Endoplasmic Reticulum Stress., Xing Yu, Tanchun Wang, Meichen Zhu, Liting Zhang, Fengzhi Zhang, Enen Jing, Yongzhe Ren, Zhiqiang Wang, Zeyu Xin, Tongbao Lin

Touro College of Osteopathic Medicine (Middletown) Publications and Research

BACKGROUND: Wheat production is largely restricted by adverse environmental stresses. Under many undesirable conditions, endoplasmic reticulum (ER) stress can be induced. However, the physiological and molecular responses of wheat to ER stress remain poorly understood. We used dithiothreitol (DTT) and tauroursodeoxycholic acid (TUDCA) to induce or suppress ER stress in wheat cells, respectively, with the aim to reveal the molecular background of ER stress responses using a combined approach of transcriptional profiling and morpho-physiological characterization.

METHODS: To understand the mechanism of wheat response to ER stress, three wheat cultivars were used in our pre-experiments. Among them, the cultivar with a …

Investigating The Connection Between Light, A Circadian Clock, And Pathogenesis In Cercospora Zeae-Maydis, John Byron Ridenour

Graduate Theses and Dissertations

Gray leaf spot is a globally important foliar disease of maize caused by the fungus Cercospora zeae-maydis. In C. zeae-maydis, light is a critical environmental signal linked to pathogenesis and secondary metabolism. However, the mechanisms by which the fungus senses and responds to light are not fully understood. Thus, the overarching goal of this project was to unravel the connection between light and pathogenesis in C. zeae-maydis. The conserved fungal protein White Collar-1 (WC-1), designated Crp1 in C. zeae-maydis, senses light and initiates physiological responses. In fungi, WC-1 functions in the White Collar Complex via interaction with White Collar-2 (WC-2). …

Addressing The Challenges Facing Wheat Production: Nebraska And International Breeding Efforts, Sarah Blecha

Doctor of Plant Health Program: Dissertations and Student Research

Bread wheat, Triticum aestivum L., provides 20 percent of the global daily calorie intake. It is the third most important food crop, after rice and corn. Biotic challenges significantly reduce wheat yield; chemical control can be a solution but can be cost prohibitive for subsistence farmers. For many farmers, genetic resistance to biotic stresses can be the most cost effective solution.

The International Center for Agricultural Research in the Dry Areas (ICARDA) and the Nebraska Small Grains Breeding Program have been addressing these wheat production challenges. ICARDA is part of an international research consortium to increase wheat yield and tolerance …

Gamete Nuclear Migration In Animals And Plants, Umma Fatema, Mohammad F. Ali, Zheng Hu, Anthony J. Clark, Tomokazu Kawashima

Plant and Soil Sciences Faculty Publications

The migration of male and female gamete nuclei to each other in the fertilized egg is a prerequisite for the blending of genetic materials and the initiation of the next generation. Interestingly, many differences have been found in the mechanism of gamete nuclear movement among animals and plants. Female to male gamete nuclear movement in animals and brown algae relies on microtubules. By contrast, in flowering plants, the male gamete nucleus is carried to the female gamete nucleus by the filamentous actin cytoskeleton. As techniques have developed from light, electron, fluorescence, immunofluorescence, and confocal microscopy to live-cell time-lapse imaging using …

Development Of Sheath Blight-Resistant Breeding Lines For Southern U.S. Environments And Morphological And Genetic Survey Of Giant Salvinia Populations In Louisiana And Texas, Dominique Clark Galam

LSU Doctoral Dissertations

The southern US environment is a very conducive environment for agriculture and fisheries. Rice farming, shrimping and water related activities help drive the local economy. However, there are several factors that impede the success of these activities. Sheath blight (SB) disease caused by Rhizoctonia solani is one of the major biotic constraints to high grain yield and quality for most commercial U.S. rice varieties. Although different breeding lines with high levels of "partial resistance" have been developed none has been used directly as a commercial variety. The first research objective of this research was to identify and develop advanced breeding …

Phomopsis Stem Canker Of Sunflower In North America: Correlation With Climate And Solutions Through Breeding And Management, Brent S. Hulke, Samuel G. Markell, Nolan C. Kane, Febina M. Mathew

Agronomy, Horticulture and Plant Science Faculty Publications

Climate change is occurring in the central US and is interacting with agroecological factors to increase biotic stress in sunflower. Certain species of Diaporthe cause Phomopsis stem canker in sunflower and other dicotyledonous weeds and crops. The increase in precipitation already observed in the states of North Dakota, South Dakota, and Minnesota have increased the chances of outbreaks of necrotrophic pathogens, like Diaporthe. We discuss how climate trends, combined with technological, management, and economic interactions, are correlated with increasing incidence of Phomopsis stem canker in these and adjacent areas in North America. Further, we discuss management options and the …

Arkansas Cotton Variety Test 2018, Fred Bourland, A. Beach, C. Kennedy, L. Martin, B. Robertson

Arkansas Agricultural Experiment Station Research Series

The primary goal of the Arkansas Cotton Variety Test is to provide unbiased data regarding the agronomic performance of cotton varieties and advanced breeding lines in the major cotton-growing areas of Arkansas. This information helps seed companies establish marketing strategies and assists producers in choosing varieties to plant. These annual evaluations will then facilitate the inclusion of new, improved genetic material in Arkansas cotton production. Adaptation of varieties is determined by evaluating the lines at five University of Arkansas System Division of Agriculture research sites (Manila, Keiser, Judd Hill, Marianna, and Rohwer). Entries in the 2018 Arkansas Cotton Variety Test …

Pteridium Nuclear Gene Phylogeny, Paul G. Wolf, Carol Rowe, Sylvia Kinosian, Joshua P. Der, Peter J. Lockhart, Lara D. Shepherd, Patricia A. Mclenachan, John A. Thomson

Browse all Datasets

Raw amplicon sequence data and raw reads of from GBS library. Also all code and analyses required to process raw data.

Genetic Analysis Of Drought Tolerance In Rice (Oryza Sativa L.), Uttam Bhattarai

LSU Doctoral Dissertations

Drought is a major challenge in rice production system worldwide. We conducted a phenotypic screening of the USA rice genotypes for drought tolerance and assessed genetic diversity using SSR markers. Identification of QTLs for drought tolerance during both vegetative and reproductive stage was done using genotyping by sequencing (GBS) based saturated SNP linkage map. The rice genotypes Jes, Leah, Roy J, Jazzman, and Madison were found to be drought tolerant. Population structure analysis grouped the USA rice genotypes into California, Louisiana, and Arkansas types. Marker-trait association showed that markers RM570 and RM351 were significantly associated with grain yield, spikelet fertility, …

Global Responses Of Resistant And Susceptible Sorghum (Sorghum Bicolor) To Sugarcane Aphid (Melanaphis Sacchari), Hannah M. Tetreault, Sajjan Grover, Erin Scully, Tammy Gries, Nathan A. Palmer, Gautam Sarath, Joe Louis, Scott E. Sattler

Department of Entomology: Faculty Publications

The sugarcane aphid (Melanaphis sacchari) has emerged as a significant pest for sorghum. The use of sugarcane aphid-resistant sorghum germplasm with integrated pest management strategies appears to be an excellent solution to this problem. In this study, a resistant line (RTx2783) and a susceptible line (A/BCK60) were used to characterize the differences in plant responses to the sugarcane aphid through a series of experiments, which examined global sorghum gene expression, aphid feeding behavior and inheritance of aphid resistance. The global transcriptomic responses to sugarcane aphids in resistant and susceptible plants were identified using RNA-seq and compared to the …

Iris-Eda: An Integrated Rna-Seq Interpretation System For Gene Expression Data Analysis, Brandon Monier, Adam Mcdermaid, Cankun Wang, Jing Zhao, Allison Miller, Anne Fennell, Qin Ma

Agronomy, Horticulture and Plant Science Faculty Publications

Next-Generation Sequencing has made available substantial amounts of large-scale Omics data, providing unprecedented opportunities to understand complex biological systems. Specifically, the value of RNA-Sequencing (RNA-Seq) data has been confirmed in inferring how gene regulatory systems will respond under various conditions (bulk data) or cell types (single-cell data). RNA-Seq can generate genome-scale gene expression profiles that can be further analyzed using correlation analysis, co-expression analysis, clustering, differential gene expression (DGE), among many other studies. While these analyses can provide invaluable information related to gene expression, integration and interpretation of the results can prove challenging. Here we present a tool called IRIS-EDA, …