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A Genome-Wide Survey Of Highly Expressed Non-Coding Rnas And Biological Validation Of Selected Candidates In Agrobacterium Tumefaciens, Keunsub Lee, Xiaoqiu Huang, Chichun Yang, Danny Lee, Kan Nobuta, Jian-Bing Fan, Kan Wang 2016 Iowa State University

A Genome-Wide Survey Of Highly Expressed Non-Coding Rnas And Biological Validation Of Selected Candidates In Agrobacterium Tumefaciens, Keunsub Lee, Xiaoqiu Huang, Chichun Yang, Danny Lee, Kan Nobuta, Jian-Bing Fan, Kan Wang

Xiaoqiu Huang

Agrobacterium tumefaciens is a plant pathogen that has the natural ability of delivering and integrating a piece of its own DNA into plant genome. Although bacterial non-coding RNAs (ncRNAs) have been shown to regulate various biological processes including virulence, we have limited knowledge of how Agrobacterium ncRNAs regulate this unique inter-Kingdom gene transfer. Using whole transcriptome sequencing and an ncRNA search algorithm developed for this work, we identified 475 highly expressed candidate ncRNAs from A. tumefaciens C58, including 101 trans-encoded small RNAs (sRNAs), 354 antisense RNAs (asRNAs), 20 5′ untranslated region (UTR) leaders including a RNA thermosensor and 6 ...


Horizontal Transfer Generates Genetic Variation In An Asexual Pathogen, Xiaoqiu Huang 2016 Iowa State University

Horizontal Transfer Generates Genetic Variation In An Asexual Pathogen, Xiaoqiu Huang

Xiaoqiu Huang

There are major gaps in the understanding of how genetic variation is generated in the asexual pathogen Verticillium dahliae. On the one hand, V. dahliae is a haploid organism that reproduces clonally. On the other hand, single-nucleotide polymorphisms and chromosomal rearrangements were found between V. dahliae strains. Lineage-specific (LS) regions comprising about 5% of the genome are highly variable between V. dahliae strains. Nonetheless, it is unknown whether horizontal gene transfer plays a major role in generating genetic variation in V. dahliae. Here, we analyzed a previously sequenced V. dahliae population of nine strains from various geographical locations and hosts ...


Identification Of Highly Variable Supernumerary Chromosome Segments In An Asexual Pathogen, Xiaoqiu Huang, Anindya Das, Binod B. Sahu, Subodh K. Srivastava, Leonor F. S. Leandro, Kerry O'Donnell, Madan K. Bhattacharyya 2016 Iowa State University

Identification Of Highly Variable Supernumerary Chromosome Segments In An Asexual Pathogen, Xiaoqiu Huang, Anindya Das, Binod B. Sahu, Subodh K. Srivastava, Leonor F. S. Leandro, Kerry O'Donnell, Madan K. Bhattacharyya

Xiaoqiu Huang

Supernumerary chromosome segments are known to harbor different transposons from their essential counterparts. The aim of this study was to investigate the role of transposons in the origin and evolution of supernumerary segments in the asexual fungal pathogen Fusarium virguliforme. We compared the genomes of 11 isolates comprising six Fusarium species that cause soybean sudden death syndrome (SDS) or bean root rot (BRR), and identified significant levels of genetic variation in A+T-rich repeat blocks of the essential chromosomes and in A+T-neutral regions of the supernumerary segments. The A+T-rich repeat blocks in the essential chromosomes were highly variable ...


Resistant Starch: Promise For Improving Human Health, Diane F. Birt, Terri D. Boylston, Suzanne Hendrich, Jay-Lin Jane, James Hollis, Li Li, John F. McClelland, Samuel Moore, Gregory J. Phillips, Matthew James Rowling, Kevin Schalinske, Marvin Paul Scott, Elizabeth M. Whitley 2016 Iowa State University

Resistant Starch: Promise For Improving Human Health, Diane F. Birt, Terri D. Boylston, Suzanne Hendrich, Jay-Lin Jane, James Hollis, Li Li, John F. Mcclelland, Samuel Moore, Gregory J. Phillips, Matthew James Rowling, Kevin Schalinske, Marvin Paul Scott, Elizabeth M. Whitley

Kevin Schalinske

Ongoing research to develop digestion-resistant starch for human health promotion integrates the disciplines of starch chemistry, agronomy, analytical chemistry, food science, nutrition, pathology, and microbiology. The objectives of this research include identifying components of starch structure that confer digestion resistance, developing novel plants and starches, and modifying foods to incorporate these starches. Furthermore, recent and ongoing studies address the impact of digestion-resistant starches on the prevention and control of chronic human diseases, including diabetes, colon cancer, and obesity. This review provides a transdisciplinary overview of this field, including a description of types of resistant starches; factors in plants that affect ...


Mapping Of Iron And Zinc Quantitative Trait Loci In Soybean For Association To Iron Deficiency Chlorosis Resistance, Keith E. King, Gregory A. Peiffer, Manju B. Reddy, Nick Lauter, Shun Fu Lin, Silvia R. Cianzio, Randy C. Shoemaker 2016 Iowa State University

Mapping Of Iron And Zinc Quantitative Trait Loci In Soybean For Association To Iron Deficiency Chlorosis Resistance, Keith E. King, Gregory A. Peiffer, Manju B. Reddy, Nick Lauter, Shun Fu Lin, Silvia R. Cianzio, Randy C. Shoemaker

Manju B. Reddy

Iron deficiency chlorosis (IDC) in soybean results in yield losses or in extreme cases death. Breeding for resistance has shown limited success with no cultivar having complete resistance. Mineral content of the soybean could be an indicator of the ability of the plant to withstand the effects of IDC. Iron (Fe) and zinc (Zn) concentration was examined in soybean seed and leaves. SSR, RFLP, and BARCSOYSSR markers were used to construct a linkage map used for mapping of Fe and Zn concentrations. The QTL analysis for the combined data identified one major QTL for seed Fe accumulation on chromosome 20 ...


Oxalate And Phytate Of Soy Foods, Ismail A. Al-Wahsh, Harry T. Horner, Reid G. Palmer, Manju B. Reddy, Linda K. Massey 2016 Washington State University

Oxalate And Phytate Of Soy Foods, Ismail A. Al-Wahsh, Harry T. Horner, Reid G. Palmer, Manju B. Reddy, Linda K. Massey

Manju B. Reddy

The consumption of foods made from soybeans is increasing because of their desirable nutritional value. However, some soy foods contain high concentrations of oxalate and/or phytate. Oxalate is a component of calcium oxalate kidney stones, whereas phytate is an inhibitor of calcium kidney stone formation. Thirty tested commercial soy foods exhibited ranges of 0.02−2.06 mg oxalate/g and 0.80−18.79 mg phytate/g. Commercial soy foods contained 2−58 mg of total oxalate per serving and 76−528 mg phytate per serving. Eighteen of 19 tofu brands and two soymilk brands contained less than ...


Iron Bioavailability Of Hemoglobin From Soy Root Nodules Using A Caco-2 Cell Culture Model, Amy K. Proulx, Manju B. Reddy 2016 Iowa State University

Iron Bioavailability Of Hemoglobin From Soy Root Nodules Using A Caco-2 Cell Culture Model, Amy K. Proulx, Manju B. Reddy

Manju B. Reddy

Heme iron has been identified in many plant sourcesmost commonly in the root nodules of leguminous plants, such as soy. Our objective was to test the effectiveness of soy root nodule (SRN) and purified soy hemoglobin (LHb) in improving iron bioavailability using an in vitro Caco-2 cell model, with ferritin response as the bioavailability index. We assessed bioavailability of iron from LHb (either partially purified (LHbA) or purified (LHbD)) with and without food matrix and compared it with that from bovine hemoglobin (BHb), ferrous sulfate (FeSO4), or SRN. Bioavailability of each treatment was normalized to 100% of the FeSO4 treatment ...


Fermentation And Lactic Acid Addition Enhance Iron Bioavailability Of Maize, Amy K. Proulx, Manju B. Reddy 2016 Iowa State University

Fermentation And Lactic Acid Addition Enhance Iron Bioavailability Of Maize, Amy K. Proulx, Manju B. Reddy

Manju B. Reddy

Maize is one of the most important cereal crops for human consumption, yet it is of concern due to its low iron bioavailability. The objective of this study was to determine the effects of processing on iron bioavailability in common maize products and elucidate better processing techniques for enhancing iron bioavailability. Maize products were processed to represent different processing techniques: heating (porridge), fermentation (ogi), nixtamalization (tortillas), and decortication (arepas). Iron and phytate contents were evaluated. Iron bioavailability was assessed using the Caco-2 cell model. Phytate content of maize products was significantly reduced by decortication (25.6%, p ) 0.003) and ...


Resistant Starch: Promise For Improving Human Health, Diane F. Birt, Terri D. Boylston, Suzanne Hendrich, Jay-Lin Jane, James Hollis, Li Li, John F. McClelland, Samuel Moore, Gregory J. Phillips, Matthew James Rowling, Kevin Schalinske, Marvin Paul Scott, Elizabeth M. Whitley 2016 Iowa State University

Resistant Starch: Promise For Improving Human Health, Diane F. Birt, Terri D. Boylston, Suzanne Hendrich, Jay-Lin Jane, James Hollis, Li Li, John F. Mcclelland, Samuel Moore, Gregory J. Phillips, Matthew James Rowling, Kevin Schalinske, Marvin Paul Scott, Elizabeth M. Whitley

Suzanne Hendrich

Ongoing research to develop digestion-resistant starch for human health promotion integrates the disciplines of starch chemistry, agronomy, analytical chemistry, food science, nutrition, pathology, and microbiology. The objectives of this research include identifying components of starch structure that confer digestion resistance, developing novel plants and starches, and modifying foods to incorporate these starches. Furthermore, recent and ongoing studies address the impact of digestion-resistant starches on the prevention and control of chronic human diseases, including diabetes, colon cancer, and obesity. This review provides a transdisciplinary overview of this field, including a description of types of resistant starches; factors in plants that affect ...


Resistant Starch: Promise For Improving Human Health, Diane F. Birt, Terri D. Boylston, Suzanne Hendrich, Jay-Lin Jane, James Hollis, Li Li, John F. McClelland, Samuel Moore, Gregory J. Phillips, Matthew James Rowling, Kevin Schalinske, Marvin Paul Scott, Elizabeth M. Whitley 2016 Iowa State University

Resistant Starch: Promise For Improving Human Health, Diane F. Birt, Terri D. Boylston, Suzanne Hendrich, Jay-Lin Jane, James Hollis, Li Li, John F. Mcclelland, Samuel Moore, Gregory J. Phillips, Matthew James Rowling, Kevin Schalinske, Marvin Paul Scott, Elizabeth M. Whitley

Diane F. Birt

Ongoing research to develop digestion-resistant starch for human health promotion integrates the disciplines of starch chemistry, agronomy, analytical chemistry, food science, nutrition, pathology, and microbiology. The objectives of this research include identifying components of starch structure that confer digestion resistance, developing novel plants and starches, and modifying foods to incorporate these starches. Furthermore, recent and ongoing studies address the impact of digestion-resistant starches on the prevention and control of chronic human diseases, including diabetes, colon cancer, and obesity. This review provides a transdisciplinary overview of this field, including a description of types of resistant starches; factors in plants that affect ...


Orm Expression Alters Sphingolipid Homeostasis And Differentially Affects Ceramide Synthase Activity, Athen N. Kimberlin, Gongshe Han, Kyle D. Luttgeharm, Ming Chen, Rebecca E. Cahoon, Julie M. Stone, Jonathan E. Markham, Teresa M. Dunn, Edgar B. Cahoon 2016 University of Nebraska - Lincoln

Orm Expression Alters Sphingolipid Homeostasis And Differentially Affects Ceramide Synthase Activity, Athen N. Kimberlin, Gongshe Han, Kyle D. Luttgeharm, Ming Chen, Rebecca E. Cahoon, Julie M. Stone, Jonathan E. Markham, Teresa M. Dunn, Edgar B. Cahoon

Faculty Publications from the Center for Plant Science Innovation

Sphingolipid synthesis is tightly regulated in eukaryotes. This regulation in plants ensures sufficient sphingolipids to support growth while limiting the accumulation of sphingolipid metabolites that induce programmed cell death. Serine palmitoyltransferase (SPT) catalyzes the first step in sphingolipid biosynthesis and is considered the primary sphingolipid homeostatic regulatory point. In this report, Arabidopsis (Arabidopsis thaliana) putative SPT regulatory proteins, orosomucoidlike proteins AtORM1 and AtORM2, were found to interact physically with Arabidopsis SPT and to suppress SPT activity when coexpressed with Arabidopsis SPT subunits long-chain base1 (LCB1) and LCB2 and the small subunit of SPT in a yeast (Saccharomyces cerevisiae) SPT-deficient mutant ...


Transcriptome Response Of Cassava Leaves Under Natural Shade, Zehong Ding, Yang Zhang, Yi Xiao, Fangfang Liu, Minghui Wang, Xinguang Zhu, Peng Liu, Qi Sun, Wenquan Wang, Ming Peng, Tom Brutnell, Pinghua Li 2016 Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, Hainan

Transcriptome Response Of Cassava Leaves Under Natural Shade, Zehong Ding, Yang Zhang, Yi Xiao, Fangfang Liu, Minghui Wang, Xinguang Zhu, Peng Liu, Qi Sun, Wenquan Wang, Ming Peng, Tom Brutnell, Pinghua Li

Faculty Publications from the Center for Plant Science Innovation

Cassava is an important staple crop in tropical and sub-tropical areas. As a common farming practice, cassava is usually cultivated intercropping with other crops and subjected to various degrees of shading, which causes reduced productivity. Herein, a comparative transcriptomic analysis was performed on a series of developmental cassava leaves under both full sunlight and natural shade conditions. Gene expression profiles of these two conditions exhibited similar developmental transitions, e.g. genes related to cell wall and basic cellular metabolism were highly expressed in immature leaves, genes involved in lipid metabolism and tetrapyrrole synthesis were highly expressed during the transition stages ...


Nanocomposite Adhesive Of English Ivy (Hedera Helix): Bioproduction, Nanoparticle Isolation, And Molecular Analysis, Jason Neil Burris 2016 University of Tennessee, Knoxville

Nanocomposite Adhesive Of English Ivy (Hedera Helix): Bioproduction, Nanoparticle Isolation, And Molecular Analysis, Jason Neil Burris

Doctoral Dissertations

English ivy naturally produces organic nanoparticles from its adventitious root hairs, and possesses characteristics that may allow them to replace metal-based nanoparticles in common applications, such as sunscreen. At the onset of the research, it was hypothesized that a physical mechanism of attachment, similar to the gecko footpad, was used to generate the adhesive force for attachment; however, through the results obtained from recent work, it is clear that a biochemical mechanism is involved in the generation of the strength of adhesion. Therefore, the goal of this research was to provide a better understanding of the genetic basis of nanoparticle ...


Comparative Evolutionary Analysis Of Organellar Genomic Diversity In Green Plants, Weishu Fan 2016 University of Nebraska - Lincoln

Comparative Evolutionary Analysis Of Organellar Genomic Diversity In Green Plants, Weishu Fan

Theses, Dissertations, and Student Research in Agronomy and Horticulture

The mitochondrial genome (mitogenome) and plastid genome (plastome) of plants vary immensely in genome size and gene content. They have also developed several eccentric features, such as the preference for horizontal gene transfer of mitochondrial genes, the reduction of the plastome in non-photosynthetic plants, and variable amounts of RNA editing affecting both genomes. Different organismal lifestyles can partially account for the highly diverse organellar genomes across the tree of green plants. For example, endosymbiotic and parasitic lifestyles can dramatically affect the genomic architectures of plant mitochondria and plastids. In this study, the organellar genomes of several green plants with atypical ...


Reducing Pollen Dispersal Using Forest Windbreaks, Carol Auer, Thomas Meyer, Vernie Sagun 2016 University of Connecticut - Storrs

Reducing Pollen Dispersal Using Forest Windbreaks, Carol Auer, Thomas Meyer, Vernie Sagun

Plant Science Articles

The adoption of genetically engineered (GE) crops has created a demand for practical methods to mitigate pollen dispersal and gene flow. The goal of this project was to measure the ability of a narrow forest windbreak to reduce downwind pollen fluxes from switchgrass (Panicum virgatum L.), a North American grass and model biofuels feedstock. Switchgrass fields were established in two identical plots where one had a forest windbreak and the other was in an open (control) site. Switchgrass reproduction, pollen dispersal, wind speed, and wind direction were measured over two years. Daily release of switchgrass pollen peaked at 11:00-13 ...


Distribution Of Genomic Variation In The Usda Soybean Germplasm Collection And Relationship With Phenotypic Variation, Nonoy Batiller Bandillo 2016 University of Nebraska-Lincoln

Distribution Of Genomic Variation In The Usda Soybean Germplasm Collection And Relationship With Phenotypic Variation, Nonoy Batiller Bandillo

Theses, Dissertations, and Student Research in Agronomy and Horticulture

The USDA Soybean Germplasm Collection harbors a large stock of genetic diversity with potential to accelerate soybean cultivar development. The extent and nature of favorable alleles contained in the collection are not well known nor is the distribution of genetic variation and how it relates to phenotypic variation. The genotyping of the entire USDA Soybean Germplasm Collection marked the beginning of a systematic exploration of genetic diversity for genetic research and breeding. In this research, we conducted the first comprehensive analysis of population structure on the collection of ~14,400 soybean accessions [Glycine max (L.) Merr. and G. soja Siebold ...


Rna-Seq Based Analysis Of Population Structure Within The Maize Inbred B73, Zhikai Liang, James C. Schnable 2016 University of Nebraska-Lincoln

Rna-Seq Based Analysis Of Population Structure Within The Maize Inbred B73, Zhikai Liang, James C. Schnable

Faculty Publications from the Center for Plant Science Innovation

Recent reports have shown than many identically named genetic lines used in research around the world actually contain large amounts of uncharacterized genetic variation as a result of cross contamination of stocks, unintentional crossing, residual heterozygosity within original stocks, or de novo mutation. 27 public, large scale, RNA-seq datasets from 20 independent research groups around the world were used to assess variation within the maize (Zea mays ssp. mays) inbred B73, a four decade old variety which served as the reference genotype for the original maize genome sequencing project and is widely used in genetic, genomic, and phenotypic research. Several ...


Dawn Or Doom: The Risks And Rewards Of Emerging Technologies, Diana Hancock, Steve Tally, Gerry McCartney, Michele Arthur 2016 Purdue University

Dawn Or Doom: The Risks And Rewards Of Emerging Technologies, Diana Hancock, Steve Tally, Gerry Mccartney, Michele Arthur

Purdue P-12 Networking Summit & Poster Session

Dawn or Doom is a free and open to the public conference at Purdue where we focus on benefits and risks surrounding some of the technologies that are both the most disruptive to current practices and being adopted the fastest. A collection of Purdue faculty experts and some outside speakers showcase their many perspectives related to this technology explosion, explore conditions that will foster innovation and investment into the next generation, and address the big-picture issues where both optimism and pessimism are warranted.


Identification Of Candidate Genes Underlying An Iron Efficiency Quantitative Trait Locus In Soybean, Gregory A. Peiffer, Keith E. King, Andrew J. Severin, Gregory D. May, Silvia R. Cianzio, Shun Fu Lin, Nicholas C. Lauter, Randy C. Shoemaker 2016 Iowa State University

Identification Of Candidate Genes Underlying An Iron Efficiency Quantitative Trait Locus In Soybean, Gregory A. Peiffer, Keith E. King, Andrew J. Severin, Gregory D. May, Silvia R. Cianzio, Shun Fu Lin, Nicholas C. Lauter, Randy C. Shoemaker

Andrew Severin

Prevalent on calcareous soils in the United States and abroad, iron deficiency is among the most common and severe nutritional stresses in plants. In soybean (Glycine max) commercial plantings, the identification and use of iron-efficient genotypes has proven to be the best form of managing this soil-related plant stress. Previous studies conducted in soybean identified a significant iron efficiency quantitative trait locus (QTL) explaining more than 70% of the phenotypic variation for the trait. In this research, we identified candidate genes underlying this QTL through molecular breeding, mapping, and transcriptome sequencing. Introgression mapping was performed using two related near-isogenic lines ...


A Brief History Of Corn: Looking Back To Move Forward, Jon Derek Pruitt 2016 University of Nebraska-Lincoln

A Brief History Of Corn: Looking Back To Move Forward, Jon Derek Pruitt

Doctoral Documents from Doctor of Plant Health Program

Maize was domesticated from teosinte in Mexico some 7,000 to 10,000 years ago and quickly spread through the Americas. It has become one of the most important crops at a local and global level. Two types, Northern Flint corn and Southern Dent corns provided the basis of the genetic background of modern maize hybrids. The development of hybrids, first double-cross and later single-cross hybrids, along with a transition to high input farming provided huge yield increases, which have continued to improve with improving technology.

Increase in maize production also caused a rise in Western corn Rootworm (Diabrotica virgifera ...


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