Life Sciences Commons^™

The Pho1;2a'-M1.1 Allele Of Phosphate1 Conditions Misregulation Of The Phosphorus Starvation Response In Maize (Zea Mays Ssp. Mays L.), Ana Laura Alonso-Nieves, M. Nancy Salazar-Vidal, J. Vladimir Torres-Rodríguez, Leonardo M. Pérez-Vázquez, Julio A. Massange-Sánchez, C. Stewart Gillmor, Ruairidh J. H. Sawers

Center for Plant Science Innovation: Faculty and Staff Publications

Plant PHO1 proteins play a central role in the translocation and sensing of inorganic phosphate. The maize (Zea mays ssp. mays) genome encodes two co-orthologs of the Arabidopsis PHO1 gene, designated ZmPho1;2a and ZmPho1;2b. Here, we report the characterization of the transposon footprint allele Zmpho1;2a'-m1.1, which we refer to hereafter as pho1;2a. The pho1;2a allele is a stable derivative formed by excision of an Activator transposable element from the ZmPho1;2a gene. The pho1;2a allele contains an 8-bp insertion at the point of transposon excision that disrupts the reading frame and is predicted to …

An Epigenetic Breeding System In Soybean For Increased Yield And Stability, Sunil K. Kenchanmane Raju, Mon-Ray Shao, Robersy Sanchez, Ying-Zhi Xu, Ajay Sandhu, George L. Graef, Sally A. Mackenzie

Department of Agronomy and Horticulture: Faculty Publications

Epigenetic variation has been associated with a wide range of adaptive phenotypes in plants, but there exist few direct means for exploiting this variation. RNAi suppression of the plant-specific gene, MutS HOMOLOG1 (MSH1), in multiple plant species produces a range of developmental changes accompanied by modulation of defence, phytohormone and abiotic stress response pathways along with methylome repatterning. This msh1-conditioned developmental reprogramming is retained independent of transgene segregation, giving rise to transgene-null ‘memory’ effects. An isogenic memory line crossed to wild type produces progeny families displaying increased variation in adaptive traits that respond to selection. This study …

Transcriptional Reprogramming Of Legume Genomes: Perspective And Challenges Associated With Single-Cell And Single Cell-Type Approaches During Nodule Development, Marc Libault

Department of Agronomy and Horticulture: Faculty Publications

Transcriptomic approaches revealed thousands of genes differentially or specifically expressed during nodulation, a biological process resulting from the symbiosis between leguminous plant roots and rhizobia, atmospheric nitrogen-fixing symbiotic bacteria. Ultimately, nodulation will lead to the development of a new root organ, the nodule. Through functional genomic studies, plant transcriptomes have been used by scientists to reveal plant genes potentially controlling nodulation. However, it is important to acknowledge that the physiology, transcriptomic programs, and biochemical properties of the plant cells involved in nodulation are continuously regulated. They also differ between the different cell-types composing the nodules. To generate a more accurate …

Stress-Responsive Pathways And Small Rna Changes Distinguish Variable Developmental Phenotypes Caused By Msh1 Loss, Mon-Ray Shao, Sunil Kumar Kenchanmane Raju, John D. Laurie, Robersy Sanchez, Sally A. Mackenzie

Department of Agronomy and Horticulture: Faculty Publications

Background: Proper regulation of nuclear-encoded, organelle-targeted genes is crucial for plastid and mitochondrial function. Among these genes, MutS Homolog 1 (MSH1) is notable for generating an assortment of mutant phenotypes with varying degrees of penetrance and pleiotropy. Stronger phenotypes have been connected to stress tolerance and epigenetic changes, and in Arabidopsis T-DNA mutants, two generations of homozygosity with the msh1 insertion are required before severe phenotypes begin to emerge. These observations prompted us to examine how msh1 mutants contrast according to generation and phenotype by profiling their respective transcriptomes and small RNA populations.

Results: Using RNA-seq, we analyze …

Transcriptome Profiling Of Buffalograss Challenged With The Leaf Spot Pathogen Curvularia Inaequalis, Bimal S. Amaradasa, Keenan Amundsen

Department of Plant Pathology: Faculty Publications

Buffalograss (Bouteloua dactyloides) is a low maintenance U. S. native turfgrass species with exceptional drought, heat, and cold tolerance. Leaf spot caused by Curvularia inaequalis negatively impacts buffalograss visual quality. Two leaf spot susceptible and two resistant buffalograss lines were challenged with C. inaequalis. Samples were collected from treated and untreated leaves when susceptible lines showed symptoms. Transcriptome sequencing was done and differentially expressed genes were identified. Approximately 27 million raw sequencing reads were produced per sample. More than 86% of the sequencing reads mapped to an existing buffalograss reference transcriptome. De novo assembly of unmapped reads …

Transcriptome Profiling Of Kentucky Bluegrass (Poa Pratensis L.) Accessions In Response To Salt Stress, Shaun B. Bushman, Keenan L. Amundsen, Scott E. Warnke, Joseph G. Robins, Paul G. Johnson

Department of Agronomy and Horticulture: Faculty Publications

Background: Kentucky bluegrass (Poa pratensis L.) is a prominent turfgrass in the cool-season regions, but it is sensitive to salt stress. Previously, a relatively salt tolerant Kentucky bluegrass accession was identified that maintained green color under consistent salt applications. In this study, a transcriptome study between the tolerant (PI 372742) accession and a salt susceptible (PI 368233) accession was conducted, under control and salt treatments, and in shoot and root tissues.

Results: Sample replicates grouped tightly by tissue and treatment, and fewer differentially expressed transcripts were detected in the tolerant PI 372742 samples compared to the susceptible …

Identification Of Differentially Expressed Genes Between Sorghum Genotypes With Contrasting Nitrogen Stress Tolerance By Genome-Wide Transcriptional Profiling, Malleswari Gelli, Yongchao Duo, Anji Reddy Konda, Chi Zhang, David R. Holding, Ismail M. Dweikat

Department of Agronomy and Horticulture: Faculty Publications

Background: Sorghum is an important cereal crop, which requires large quantities of nitrogen fertilizer for achieving commercial yields. Identification of the genes responsible for low-N tolerance in sorghum will facilitate understanding of the molecular mechanisms of low-N tolerance, and also facilitate the genetic improvement of sorghum through marker-assisted selection or gene transformation. In this study we compared the transcriptomes of root tissues from seven sorghum genotypes having differential response to low-N stress.

Results: Illumina RNA-sequencing detected several common differentially expressed genes (DEGs) between four low-N tolerant sorghum genotypes (San Chi San, China17, KS78 and high-NUE bulk) and three …

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 and Staff 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 …

Transcriptome Analysis Of Two Buffalograss Cultivars, Michael Wachholtz, Tiffany Heng-Moss, Paul Twigg, Lisa Baird, Guoqing Lu, Keenan Amundsen

Department of Agronomy and Horticulture: Faculty Publications

Background: Buffalograss [Buchloë dactyloides (Nutt.) Engel. syn. Bouteloua dactyloides (Nutt.) Columbus] is a United States native turfgrass species that requires less irrigation, fungicides and pesticides compared to more commonly used turfgrass species. In areas where water is limited, interest in this grass species for lawns is increasing. While several buffalograss cultivars have been developed through buffalograss breeding, the timeframe for new cultivar development is long and is limited by a lack of useful genetic resources. Two high throughput next-generation sequencing techniques were used to increase the genomic resources available for buffalograss.

Results: Total RNA was extracted and …

High-Throughput Transcriptome Sequencing For Snp And Gene Discovery In A Moth, Nicholas J. Miller, Jing Sun, Thomas W. Sappington

Department of Entomology: Faculty Publications

The western bean cutworm, Striacosta albicosta (Smith) (Leptidoptera: Noctuidae) is a pest of corn (Zea mays L.) and dry beans that underwent a dramatic range expansion in North America during the first decade of the 21st century. Research into the population genetics of this species has been hindered by a lack of genetic markers. The transcriptome of adult male S. albicosta was partially sequenced using Illumina sequencing-by-synthesis. Assembly of the sequence reads yielded 16,847 transcript sequences, of which 6,631 could be assigned a putative function. A search for single nucleotide polymorphisms (SNPs) identified 2,487 candidate SNPs distributed among 1,265 …

Transcriptome And Gene Expression Analysis In Cold-Acclimated Guayule (Parthenium Argentatum) Rubber-Producing Tissue, Grisel Ponciano, Colleen M. Mcmahan, Wenshuang Xie, Gerard R. Lazo, Terry A. Coffelt, Jillian Collins-Silva, Aise Nural-Taban, Martin Gollery, David K. Shintani, Maureen C. Whalen

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Natural rubber biosynthesis in guayule (Parthenium argentatum Gray) is associated with moderately cold night temperatures. To begin to dissect the molecular events triggered by cold temperatures that govern rubber synthesis induction in guayule, the transcriptome of bark tissue, where rubber is produced, was investigated. A total of 11,748 quality expressed sequence tags (ESTs) were obtained. The vast majority of ESTs encoded proteins that are similar to stress-related proteins, whereas those encoding rubber biosynthesis- related proteins comprised just over one percent of the ESTs. Sequence information derived from the ESTs was used to design primers for quantitative analysis of the …