Plant Breeding and Genetics Commons^™

Cdc5, A Dna Binding Protein, Positively Regulates Posttranscriptional Processing And/Or Transcription Of Primary Microrna Transcripts, Shuxin Zhang, Meng Xie, Guodong Ren, Bin Yu

Center for Plant Science Innovation: Faculty Publications

CDC5 is a MYB-related protein that exists in plants, animals, and fungi. In Arabidopsis, CDC5 regulates both growth and immunity through unknown mechanisms. Here, we show that CDC5 from Arabidopsis positively regulates the accumulation of microRNAs (miRNAs), which control many biological processes including development and adaptations to environments in plants. CDC5 interacts with both the promoters of genes encoding miRNAs (MIR) and the DNA-dependent RNA polymerase II. As a consequence, lack of CDC5 reduces the occupancy of polymerase II at MIR promoters, as well as MIR promoter activities. In addition, CDC5 is associated with the DICER–LIKE1 complex, …

Comparative Studies Of Differential Gene Calling Using Rna-Seq Data, Ximeng Zheng, Etsuko N. Moriyama

Center for Plant Science Innovation: Faculty Publications

Background: With its massive amount of data, gene-expression profiling by RNA-Seq has many advantanges compared with microarray experiments. RNA-Seq analysis, however, is fundamentally different from microarray data analysis. Techniques developed for analyzing microarray data thus cannot be directly applicable for the digital gene expression data. Several statistical methods have been developed for identifying differentially expressed genes specifically from RNA-Seq data over the past few years.
Results: In this study, we examined the performance of differential gene-calling methods using RNA-Seq data in practical situations. We focused on two representative methods: one parametric method, DESeq, and one nonparametric method, NOISeq. …

A Novel Function Prediction Approach Using Protein Overlap Networks, Shide Liang, Dandan Zheng, Daron M. Standley, Huarong Guo, Chi Zhang

Center for Plant Science Innovation: Faculty Publications

Background: Construction of a reliable network remains the bottleneck for network-based protein function prediction. We built an artificial network model called protein overlap network (PON) for the entire genome of yeast, fly, worm, and human, respectively. Each node of the network represents a protein, and two proteins are connected if they share a domain according to InterPro database.
Results: The function of a protein can be predicted by counting the occurrence frequency of GO (gene ontology) terms associated with domains of direct neighbors. The average success rate and coverage were 34.3% and 43.9%, respectively, for the test genomes, …

A Thraustochytrid Diacylglycerol Acyltransferase 2 With Broad Substrate Specificity Strongly Increases Oleic Acid Content In Engineered Arabidopsis Thaliana Seeds, Chunyu Zhang, Umidjon Iskandarov, Elliott T. Klotz, Robyn L. Stevens, Rebecca E. Cahoon, Tara J. Nazarenus, Suzette L. Pereira, Edgar B. Cahoon

Center for Plant Science Innovation: Faculty Publications

Diacylglycerol acyltransferase (DGAT) catalyses the last step in acyl-CoA-dependent triacylglycerol (TAG) biosynthesis and is an important determinant of cellular oil content and quality. In this study, a gene, designated TaDGAT2, encoding a type 2 DGAT (DGAT2)-related enzyme was identified from the oleaginous marine protist Thraustochytrium aureum. The deduced TaDGAT2 sequence contains a ~460 amino acid domain most closely related to DGAT2s from Dictyostelium sp. (45–50% identity). Recombinant TaDGAT2 restored TAG biosynthesis to the Saccharomyces cerevisiae H1246 TAG-deficient mutant, and microsomes from the complemented mutant displayed DGAT activity with C16 and C18 saturated and unsaturated fatty acyl-CoA and diacylglycerol …

Identification Of Sources Of Resistance To Damping-Off And Early Root/Hypocotyl Damage From Rhizoctonia Solani In Common Bean (Phaseolus Vulgaris L.), P. A. Peña, James R, Steadman, Kent M. Eskridge, Carlos A. Urrea

Panhandle Research and Extension Center

Rhizoctonia solani causes economically important root and hypocotyl diseases in common bean throughout the world. Root health is a vital factor in plant development and root diseases would negatively influence water and nutrient uptake as well as cause direct stand reduction and root rot damage to the crop. An efficient common bean screening method to evaluate damping-off and early root/ hypocotyl damage from R. solani was developed and used to identify dry bean lines with levels of resistance to this disease. Two sets of 163 and 111 lines previously evaluated for drought tolerance in Nebraska and Puerto Rico were evaluated …

Fuzzy Clustering Of Cpp Family In Plants With Evolution And Interaction Analyses, Tao Lu, Yongchao Dou, Chi Zhang

Center for Plant Science Innovation: Faculty Publications

Background: Transcription factors have been studied intensively because they play an important role in gene expression regulation. However, the transcription factors in the CPP family (cystein-rich polycomb-like protein), compared with other transcription factor families, have not received sufficient attention, despite their wide prevalence in a broad spectrum of species, from plants to animals. The total number of known CPP transcription factors in plants is 111 from 16 plants, but only 2 of them have been studied so far, namely TSO1 and CPP1 in Arabidopsis thaliana and soybean, respectively.
Methods: In this work, to study their functions, we applied …

Sorghum Transformation: Overview And Utility, Tejinder Kumar, Arlene Howe, Shirley Sato, Ismail M. Dweikat, Tom E. Clemente

Department of Agronomy and Horticulture: Faculty Publications

Over the past decade genomics resources available for sorghum have rapidly expanded (Paterson Int J Plant Genomics 2008:6, 2008), these resources, coupled with the recent completion of the genome sequence which is relatively small in size (730 Mb) (Paterson et al. Nature 457:551–556, 2009) makes sorghum a rather attractive species to study. Moreover, the USDA germplasm system maintains 42,614 accessions, of which more than 800 exotic landraces have been converted to day length-insensitive lines to facilitate their use in breeding programs. In addition, a set of EMS mutation stocks developed by the USDA Plant Stress and Germplasm Development Unit in …

Germinación In Vitro De Laelia Speciosa (Kunth) Schltr., Una Herramienta Para Su Conservación Ex Situ, María Ascención Aguilar-Morales, Ana Laura López-Escamilla

Estudios científicos en el estado de Hidalgo y zonas aledañas

Dentro de la familia Orchideaceae, Laelia speciosa (Kunth) Schltr. es probablemente la orquídea más explotada en México, por lo que es importante establecer estrategias de conservación. El objetivo del presente trabajo fue determinar el mejor medio de cultivo para la germinación in vitro de semillas. Cápsulas maduras e inmaduras de L. speciosa, fueron colectadas en la Reserva de la Biosfera Barranca de Metztitlán, Hidalgo, México y las semillas se sembraron en condiciones in vitro en cuatro tratamientos: Murashige y Skoog (MS) (1962) al 100%; MS al 50%; Knudson C (KC) (1946) al 50% y KC al 100%. A los …

Nutrient Contents, Color, Texture, And Sensory Evaluation Of 12 Arkansas Grown Soybean Cultivars In Canned Products, Quyen Nguyen, Navam Hettiarachchy, Srinivas J. Rayaprolu

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

Soybean was introduced in the U.S. in the 1800s, and it has been proven to have several health benefits. New cultivars of soybeans with varying hull colors have been developed using plantbreeding technology. Canning is one of the effective processing methods to extend the shelf life of products. However, very little information is available on canned soybeans. This research studied the composition of 12 soybean cultivars including two cultivars with brown seed coat (R08-4014 and R09-349), three cultivars with black seed coat (R07-1927, R07-10396, and R09-345), and seven regular cultivars with yellow seed coat (R05-1772, R05-4969, R07-2001, R08-4005, R08- 4006, …

Evaluation Of Cover Crops In High Tunnel Vegetable Rotation, Tyler A. Patrick, Neal Mays, Jason Mcafee, Curt R. Rom

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

Organic vegetable production within high tunnels allows for an extended growing season, crop protection, and environmental control. The USDA National Organic Program (NOP) standards mandate evidence that the soil has been maintained and improved over the course of production. Previous studies have indicated the potential of cover crops for reducing competitive vegetation, and improving soil quality, thus resulting in greater plant growth, nutrient uptake, and yield. However, there has been limited work in the confines of high tunnels as part of a tunnel-system rotation. Ten nitrogen-fixing and ten non-legume cover crops were established under a high tunnel and evaluated for …

Characterization Of Seediness Attributes Of Blackberry Genotypes, Bethany Sebesta, John R. Clark, Renee T. Threlfall, Luke R. Howard

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

Fresh market blackberries can feel “seedy” when consumed. This “seediness” is associated with the presence of pyrenes which are comprised of a single seed enclosed in an endocarp. Small pyrene size  (<3 mg) is preferred in both fresh-market and processed blackberry products. Yet, the proportion of pyrene weight to total berry weight can be more important than pyrene size. The objective of this study was to determine and compare descriptive sensory analysis and pyrene characteristics of blackberry genotypes from the University of Arkansas System Division of Agriculture blackberry breeding program. Panelists were trained according to Spectrum® methods and evaluated 20 genotypes for overall seediness. Pyrene characteristics, including weight and dimension, were measured for 22 genotypes. Seven of the 22 genotypes had an individual pyrene weight of 3 mg or less. Pyrene weight to berry weight ratio ranged from 2.7% (‘Tupy’) to 5.4% (‘Prime-Ark® 45’). ‘Tupy’ had low individual pyrene weights and a low ratio, which are most likely factors that contribute to its widespread acceptance by consumers. Pyrene weight to berry weight ratio was positively correlated to descriptive overall seediness (r = 0.70) but not to number of pyrenes/berry. Therefore, finding a desirable pyrene weight to berry weight ratio is integral to decreasing perceived seediness in the development of new blackberry cultivars.

Sugar-Enhanced And Synergistic Sweet Corn Cultivar Evaluation For Northern Indiana, 2012, Elizabeth Maynard

Purdue Fruit and Vegetable Research Reports

Indiana growers harvested sweet corn for fresh market sales from 5,800 acres in 2011, with an average yield of 67 cwt/acre (159 crates or 3.3 tons per acre) and a total value of $17.9 million (USDA NASS, 2012). Indiana ranked 15th among states for production of fresh market sweet corn and produced about 1.3% of the nation’s total in 2011. The 2007 USDA Ag Census reported 603 Indiana farms producing sweet corn for fresh markets and 51 farms selling to processors. Sweet corn fields for fresh market sales are located throughout the state. In northern Indiana, bicolor corn is most …

Supersweet Sweet Corn Cultivar Evaluation For Northern Indiana, 2012, Elizabeth Maynard

Purdue Fruit and Vegetable Research Reports

Indiana growers harvested sweet corn for fresh market sales from 5,800 acres in 2011, with an average yield of 67 cwt/acre (159 crates or 3.3 tons per acre) and a total value of $17.9 million (USDA NASS, 2012). Indiana ranked 15th among states for production of fresh market sweet corn and produced about 1.3% of the nation’s total in 2011. The 2007 USDA Ag Census reported 603 Indiana farms producing sweet corn for fresh markets and 51 farms selling to processors. Sweet corn fields for fresh market sales are located throughout the state. In northern Indiana, bicolor corn is most …

Supersweet Sweet Corn Cultivar Evaluation For Northern Indiana, 2012, Elizabeth Maynard

Midwest Vegetable Trial Reports

Indiana growers harvested sweet corn for fresh market sales from 5,800 acres in 2011, with an average yield of 67 cwt/acre (159 crates or 3.3 tons per acre) and a total value of $17.9 million (USDA NASS, 2012). Indiana ranked 15th among states for production of fresh market sweet corn and produced about 1.3% of the nation’s total in 2011. The 2007 USDA Ag Census reported 603 Indiana farms producing sweet corn for fresh markets and 51 farms selling to processors. Sweet corn fields for fresh market sales are located throughout the state. In northern Indiana, bicolor corn is most …

Sugar-Enhanced And Synergistic Sweet Corn Cultivar Evaluation For Northern Indiana, 2012, Elizabeth Maynard

Midwest Vegetable Trial Reports

Indiana growers harvested sweet corn for fresh market sales from 5,800 acres in 2011, with an average yield of 67 cwt/acre (159 crates or 3.3 tons per acre) and a total value of $17.9 million (USDA NASS, 2012). Indiana ranked 15th among states for production of fresh market sweet corn and produced about 1.3% of the nation’s total in 2011. The 2007 USDA Ag Census reported 603 Indiana farms producing sweet corn for fresh markets and 51 farms selling to processors. Sweet corn fields for fresh market sales are located throughout the state. In northern Indiana, bicolor corn is most …

A Study Of The Genes Tfl1 And Lfy As Agents In The Divergent Evolution Of The Plant Species Arabidopsis Thaliana And Carica Papaya, Ryan Lockard

Honors Program Theses

The long term goals of this study are to: (1) To determine if the genes TFLI and LFY perform any role in the divergent evolution and development of these two plant species; (2) If so, begin to assess whether the homologs' functional divergence is a result of gene regulation, protein function, both, or some different genetic mechanism altogether. These goals will be accomplished by genetically transforming Arabidopsis thaliana plants containing TFLI and LFY knockout mutations (those genes removed) with the homologous genes from Carica papaya in order to compare differences in development between the plants resulting from the influence of …

Breeding For Modified Seed Composition In Soybean: Selection Of Genotypes, Yield Stability, And Environmental Effects, Luciano Miguel Jaureguy

Graduate Theses and Dissertations

The development of cultivars with modified seed composition represents an excellent alternative to cope with the world's need for more nutritious food. Understanding the genetic and environmental factors controlling crop seed quality traits is of crucial importance for such an endeavor. The objectives of this study were: a) to evaluate the efficiency of phenotype and marker-assisted selection for low stachyose and low phytate soybean breeding lines, and their yield stability, b) to study the effect of management practices planting date and delayed harvest on soybean seed composition, and c) to study the potential association between soil properties and leaf chemical …

Taxonomy And Dna Barcoding In The Genus Manfreda (Salisb.) Asparagaceae, William David Ritchie

Graduate Theses and Dissertations

The genus Manfreda Salisb. of Asparagaceae is a genus of potential horticultural interest and is currently subject to breeding efforts at the University of Arkansas. A lack of taxonomic clarity however undermines the classification of potential inter - and intrageneric hybrids. The study aims to assess existing species delimitation within the genus Manfreda employing morphology while investigating the potential utility of Consortium for the Barcode of Life Plant (CBOL) DNA Barcodes for identification of specific taxa and an External Transcribed Spacer (ETS) - Internal Transcribed Spacer (ITS) DNA barcode for developed hybridized taxa.

Observation of 855 herbarium specimens facilitated phylogenetic …

Evaluation Of The Recombination Efficiencies Of Flp Proteins, Linh Duy Nguyen

Graduate Theses and Dissertations

Site-specific recombination systems are powerful tools for genetic modification. They have been used to integrate a transgene into a pre-defined locus and to remove marker genes from a transgene locus. Two of the most widely used site-specific recombination systems in plants are the Cre/lox system from the bacteriophage P1 and the FLP/FRT system from the yeast Saccharomyces cerevisiae. The Cre/lox system is well-characterized and is the first choice in application of site-specific recombination system. However, some applications such as marker-free site-specific gene integration require the use of two recombination systems. In addition, the availability of alternative recombination systems can offer …

Fuzzy Clustering Of Cpp Family In Plants With Evolution And Interaction Analyses, Tao Lu, Yongchao Dou, Chi Zhang

Center for Plant Science Innovation: Faculty Publications

Background: Transcription factors have been studied intensively because they play an important role in gene expression regulation. However, the transcription factors in the CPP family (cystein-rich polycomb-like protein), compared with other transcription factor families, have not received sufficient attention, despite their wide prevalence in a broad spectrum of species, from plants to animals. The total number of known CPP transcription factors in plants is 111 from 16 plants, but only 2 of them have been studied so far, namely TSO1 and CPP1 in Arabidopsis thaliana and soybean, respectively.

Methods: In this work, to study their functions, we applied …