Plant Breeding and Genetics Commons^™

High Occurrence Of Functional New Chimeric Genes In Survey Of Rice Chromosome 3 Short Arm Genome Sequences, Chengjun Zhang, Jun Wang, Nicholas C. Marowsky, Manyuan Long, Rod A. Wing, Chuanzhu Fan

Biological Sciences Faculty Research Publications

In an effort to identify newly evolved genes in rice,we searched the genomes of Asian-cultivated rice Oryza sativa ssp. japonica and its wild progenitors, looking for lineage-specific genes. Using genome pairwise comparison of approximately 20-Mb DNA sequences from the chromosome 3 short arm (Chr3s) in six rice species, O. sativa, O. nivara, O. rufipogon, O. glaberrima, O. barthii, and O. punctata, combined with synonymous substitution rate tests and other evidence, we were able to identify potential recently duplicated genes, which evolved within the last 1 Myr. We identified 28 functional O. sativa genes, which …

Landscape Features Impact On Soil Available Water, Corn Biomass, And Gene Expression During The Late Vegetative Stage, Stephanie Hansen, Sharon A. Clay, David E. Clay, C. Gregg Carlson, Graig Reicks, Youssef Jarachi, David Horvath

Agronomy, Horticulture and Plant Science Faculty Publications

Crop yields at summit positions of rolling landscapes often are lower than backslope yields. The differences in plant response may be the result of many different factors. We examined corn (Zea mays L.) plant productivity, gene expression, soil water, and nutrient availability in two landscape positions located in historically high (backslope) and moderate (summit and shoulder) yielding zones to gain insight into plant response differences. Growth characteristics, gene expression, and soil parameters (water and N and P content) were determined at the V12 growth stage of corn. At tassel, plant biomass, N content, ¹³C isotope discrimination (Δ), and …

Morphological And Molecular Taxonomic Identification And Phylogenetics Of Criconematoidea, Marco Cordero

Graduate Theses and Dissertations

The superfamily Criconematoidea has been studied since 1886. It is composed of two families: Criconematidae (subfam. Criconematinae, Hemicycliophorinae) and Tylenchulidae (subfam. Tylenchulinae, Paratylenchinae and Tylenchocriconematinae). Multiple species in genera have been identified and differences and similarities have been found. Species belonging to genera Mesocriconema and Criconemoides show very few differences making their identification difficult. Seventy two populations were studied. They were collected in Arkansas and/or received from the following states: California, Florida, Kansas, Missouri, North Carolina and Tennessee. Populations of the following species were identified: Mesocriconema curvatum, M. kirjanovae, M. onoense, M. ornatum, M. sphaerocephala, M. surinamense, M. vadense, M. …

Final Evaluation Of The North East Agricultural Region (Near) Strategy, Andrew Blake, Don Burnside, Vicki Williams

All other publications

No abstract provided.

Genetic Diversity Of Seed Dormancy And Molecular Evolution Of Weedy Red Rice, Te Ming Tseng

Graduate Theses and Dissertations

Rice is the grain with the third-highest global production. In the US, Arkansas is the largest rice producing state; however, an estimated 62% of the rice fields in the state are infested with red rice, and can cause up to 80% yield reduction in rice. Among its weedy traits, seed dormancy plays an important role in its persistence, and helps red rice escape weed management techniques thereby increasing the red rice soil seedbank. Red rice also has the potential to hybridize among themselves and with cultivated rice, thus resulting in diverse phenotypes and genotypes. In this study we measured variation …

Squash Variety Trials Summer 2012, Rebecca Brown

University of Rhode Island Vegetable Production Research Reports

Variety trials of summer squashes and zucchini conducted in Kingston, RI, USA.

Leek Variety Trials, 2012, Rebecca Brown, Noah Leclaire-Conway

University of Rhode Island Vegetable Production Research Reports

Variety trial of leek varieties conducted at Kingston, RI, in 2012.

Melon Variety Trials, 2012, Rebecca Brown

University of Rhode Island Vegetable Production Research Reports

Melon variety trial conducted at Kingston, RI, in summer of 2012.

Onion Variety Trials, 2012, Rebecca Brown, Noah Leclaire-Conway

University of Rhode Island Vegetable Production Research Reports

No abstract provided.

Cucumber Variety Trials 2012, Rebecca Brown

University of Rhode Island Vegetable Production Research Reports

Slicing and pickling cucumber variety trials conducted at Kingston, RI, during the summer of 2012.

Pseudomonas Hopu1 Modulates Plant Immune Receptor Levels By Blocking The Interaction Of Their Mrnas With Grp7, Valerie Nicaise, Anna Joe, Byeong-Ryool Jeong, Christin Korneli, Freddy Boutrot, Isa Westedt, Dorothee Staiger, James R. Alfano, Cyril Zipfel

Center for Plant Science Innovation: Faculty Publications

Pathogens target important components of host immunity to cause disease. The Pseudomonas syringae type III-secreted effector HopU1 is a mono-ADP-ribosyltransferase required for full virulence on Arabidopsis thaliana. HopU1 targets several RNA-binding proteins including GRP7, whose role in immunity is still unclear. Here, we show that GRP7 associates with translational components, as well as with the pattern recognition receptors FLS2 and EFR. Moreover, GRP7 binds specifically FLS2 and EFR transcripts in vivo through its RNA recognition motif. HopU1 does not affect the protein–protein associations between GRP7, FLS2 and translational components. Instead, HopU1 blocks the interaction between GRP7 and FLS2 and …

Small Interfering Rna–Mediated Translation Repression Alters Ribosome Sensitivity To Inhibition By Cycloheximide In Chlamydomonas Reinhardtii, Xinrong Ma, Eun-Jeong Kim, Insun Kook, Fangrui Ma, Adam Voshall, Etsuko N. Moriyama, Heriberto D. Cerutti

Center for Plant Science Innovation: Faculty Publications

Small RNAs (sRNAs; approximately 20 to 30 nucleotides in length) play important roles in gene regulation as well as in defense responses against transposons and viruses in eukaryotes. Their biogenesis and modes of action have attracted great attention in recent years. However, many aspects of sRNA function, such as the mechanism(s) of translation repression at postinitiation steps, remain poorly characterized. In the unicellular green alga Chlamydomonas reinhardtii, sRNAs derived from genomeintegrated inverted repeat transgenes, perfectly complementary to the 39 untranslated region of a target transcript, can inhibit protein synthesis without or with only minimal mRNA destabilization. Here, we report …

Complementarity To An Mirna Seed Region Is Sufficient To Induce Moderate Repression Of A Target Transcript In The Unicellular Green Alga Chlamydomonas Reinhardtii, Tomohito Yamasaki, Adam Voshall, Eun-Jeong Kim, Etsuko N. Moriyama, Heriberto Cerutti, Takeshi Ohama

Center for Plant Science Innovation: Faculty Publications

MicroRNAs (miRNAs) are 20–24 nt noncoding RNAs that play important regulatory roles in a broad range of eukaryotes by pairing with mRNAs to direct post-transcriptional repression. The mechanistic details of miRNA-mediated post-transcriptional regulation have been well documented in multicellular model organisms. However, this process remains poorly studied in algae such as Chlamydomonas reinhardtii, and specific features of miRNA biogenesis, target mRNA recognition and subsequent silencing are not well understood. In this study, we report on the characterization of a Chlamydomonas miRNA, cre-miR1174.2, , which is processed from a near-perfect hairpin RNA. Using Gaussia luciferase (gluc) reporter genes, …

Camelina Seed Transcriptome: A Tool For Meal And Oil Improvement And Translational Research, Huu T. Nguyen, Jillian E. Silva, Ram Podicheti, Jason Macrander, Wenyu Yang, Tara J. Nazarenus, Jeong-Won Nam, Jan G. Jaworski, Chaofu Lu, Brian E. Scheffler, Keithanne Mockaitis, Edgar B. Cahoon

Center for Plant Science Innovation: Faculty Publications

Camelina (Camelina sativa), a Brassicaceae oilseed, has received recent interest as a biofuel crop and production platform for industrial oils. Limiting wider production of camelina for these uses is the need to improve the quality and content of the seed protein-rich meal and oil, which is enriched in oxidatively unstable polyunsaturated fatty acids that are deleterious for biodiesel. To identify candidate genes for meal and oil quality improvement, a transcriptome reference was built from 2047 Sanger ESTs and more than 2 million 454-derived sequence reads, representing genes expressed in developing camelina seeds. The transcriptome of approximately 60K transcripts …

Comparative Analyses Of Two Geraniaceae Transcriptomes Using Next-Generation Sequencing, Jinxin Zhang, Tracey A. Ruhlman, Jeffrey P. Mower, Robert K. Jansen

Center for Plant Science Innovation: Faculty Publications

Background: Organelle genomes of Geraniaceae exhibit several unusual evolutionary phenomena compared to other angiosperm families including accelerated nucleotide substitution rates, widespread gene loss, reduced RNA editing, and extensive genomic rearrangements. Since most organelle-encoded proteins function in multi-subunit complexes that also contain nuclear-encoded proteins, it is likely that the atypical organellar phenomena affect the evolution of nuclear genes encoding organellar proteins. To begin to unravel the complex co-evolutionary interplay between organellar and nuclear genomes in this family, we sequenced nuclear transcriptomes of two species, Geranium maderense and Pelargonium x hortorum.

Results: Normalized cDNA libraries of G. maderense and …

Arabidopsis 56–Amino Acid Serine Palmitoyltransferase- Interacting Proteins Stimulate Sphingolipid Synthesis, Are Essential, And Affect Mycotoxin Sensitivity, Athen N. Kimberlin, Saurav Majumder, Gongshe Han, Ming Chen, Rebecca E. Cahoon, Julie M. Stone, Teresa M. Dunn, Edgar B. Cahoon

Center for Plant Science Innovation: Faculty Publications

Maintenance of sphingolipid homeostasis is critical for cell growth and programmed cell death (PCD). Serine palmitoyltransferase (SPT), composed of LCB₁ and LCB₂ subunits, catalyzes the primary regulatory point for sphingolipid synthesis. Small subunits of SPT (ssSPT) that strongly stimulate SPT activity have been identified in mammals, but the role of ssSPT in eukaryotic cells is unclear. Candidate Arabidopsis thaliana ssSPTs, ssSPTa and ssSPTb, were identified and characterized. Expression of these 56–amino acid polypeptides in a Saccharomyces cerevisiae SPT null mutant stimulated SPT activity from the Arabidopsis LCB₁/LCB₂ heterodimer by >100-fold through physical interaction with LCB …

Pseudomonas Syringae Pv. Syringae Uses Proteasome Inhibitor Syringolin A To Colonize From Wound Infection Sites, Johana C. Misas-Villamil, Izabella Kolodziejek, Emerson Crabill, Farnusch Kaschani, Sherry Niessen, Takayuki Shindo, Markus Kaiser, James R. Alfano, Renier A. L. Van De Hoorn

Center for Plant Science Innovation: Faculty Publications

Infection of plants by bacterial leaf pathogens at wound sites is common in nature. Plants defend wound sites to prevent pathogen invasion, but several pathogens can overcome spatial restriction and enter leaf tissues. The molecular mechanisms used by pathogens to suppress containment at wound infection sites are poorly understood. Here, we studied Pseudomonas syringae strains causing brown spot on bean and blossom blight on pear. These strains exist as epiphytes that can cause disease upon wounding caused by hail, sand storms and frost. We demonstrate that these strains overcome spatial restriction at wound sites by producing syringolin A (SylA), a …

Functional Modeling Identifies Paralogous Solanesyl-Diphosphate Synthases That Assemble The Side Chain Of Plastoquinone-9 In Plastids, Anna Block, Rikard Fristedt, Sara Rogers, Jyothi Kumar, Brian Barnes, Joshua Barnes, Christian Elowsky, Yashitola Wamboldt, Sally Ann Mackenzie, Kevin Redding, Sabeeha S. Merchant, Gilles J. Basset

Center for Plant Science Innovation: Faculty Publications

Background: Plastid isoforms of solanesyl-diphosphate synthase catalyze the elongation of the prenyl side chain of plastoquinone-9.

Results: Corresponding mutants display lower levels of plastoquinone-9 and plastochromanol-8 and display intact levels of vitamin E.

Conclusion: Plastochromanol-8 originates from a subfraction of non-photoactive plastoquinol-9 and is not essential for seed longevity.

Significance: Viable plastoquinone-9 mutants are invaluable tools for understanding plastid metabolism.

Mutational Analyses Of A Fork Head Associated Domain Protein, Dawdle, In Arabidopsis Thaliana, Lakshmi Ayiloor Narayanan, Dipaloke Mukherjee, Shuxin Zhang, Bin Yu, David Chevalier

Center for Plant Science Innovation: Faculty Publications

DAWDLE (DDL) gene encodes a protein that contains an N-terminal arginine-rich domain and a C-terminal Fork Head Associated (FHA) domain in Arabidopsis thaliana. DDL protein is believed to function in microRNA biogenesis by mediating the recruitment of pri-microRNA to DICER-LIKE 1 and also stabilizing the microRNA. The aim of this study was to conduct a structure-function analysis to identify the regions in DDL that are of functional significance. Targeted Induced Local Lesions in Genome screen was performed in the Columbia erecta-105 background of Arabidopsis resulting in the identification of eight point mutations spanning DDL. The mutants were characterized by …

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, …