ABSTRACT: Research conducted, including the rationale: Weeds reduce yield in soybeans through incompletely defined mechanisms. The effects of weeds on the soybean transcriptome were evaluated in field conditions during four separate gR1.fastqing seasons. Methods: RNASeq data were collected from 6 biological samples of soybeans gR1.fastqing with or without weeds. Weed species and the methods to maintain weed free controls varied between years to mitigate treatment effects and to allow detection of general soybeans weed responses. Key results: Soybean plants were not visibly nutrient or water stressed. We identified 55 consistently down-regulated genes in weedy plots. Many of the down-regulated genes were heat shock genes. Fourteen genes were consistently up-regulated. Several transcription factors including a PHYTOCHROME INTERACTING FACTOR 3-like gene (PIF3) were included among the up-regulated genes. Gene set enrichment analysis indicated roles for increased oxidative stress and jasmonic acid signaling responses during weed stress. Main conclusion: The relationship of this weed-induced PIF3 gene to genes involved in shade avoidance responses in arabidopsis provide evidence that this gene may be important in the response of soybean to weeds. These results suggest the weed-induced PIF3 gene will be a target for manipulating weed tolerance in soybean. Samples were collected from two treatments ("Control" and "Weedy") with six biological replicates (2008, 2009, and twop each for 2010 and 2011) for each treatment.
Project description:Purpose: This study is designed to identify genes and processes that are differentially regulated in corn when it is grown with or without weeds through the entire critical weed free period (to V8) or when weeds were removed early in the critical weed free period (at V4) and the plants were allowed to recover until V8. Methods: Corn was grown as described above in field plots near Brookings SD in 2007 and 2008 and RNA was extracted from the top-most leaf tips from four plants per treatment plot. Unidirectional cDNA illumina sequencing libraries were constructed for each sample (pooled leaf tips from the given plot), and were sequenced (some samples were paired end sequenced and some were single end sequenced - all 100 bases for PE and SE reads), quality trimmed, and analyzed using the Tuxedo suite of programs for SE reads of the forward read libraries for each sample. Results: We identified a small number of genes that were differentially expressed in both years. More importantly, gene set enrichment analysis of the data determined that weeds, when present through the critical weed free period impacted phytochrome signaling, defense responses, photosynthetic processes, oxidative stress responses, and various hormone signaling processes. When weeds were removed at V4 and the plants allowed to recover until V8, the weeds still imprinted impacts on phytochrome signaling, oxidative stress, and defense responses. Thus, it appears that weeds presence through the early portion of the critical weed free period, even after removal, induced processes that reduce corn growth and yield that lasted at least through V8. Conclusions: This study represents the first investigation of the impact of the lasting effects of weeds during the early critical weed free period on the transcriptome of corn, and provides additional data on the impact of weeds through the critical weed free period that augments and confirms much of what was observed in similar microarray studies. Overall design: Experimental Design: Samples all collected at the same developmental stage (V8) from three treatments (control, weedy, and weeds removed followed by recovery), in each of two years (2007 and 2008), with two to three biological replicates of each treatment in each year.
Project description:Cultivated soybean has domesticated in China for a long history, and there are several significant phenotypic differences between wild and cultivated soybeans. Seed of cultivar is generally larger than wild soybean, therefore here we comprehensively analyzed transcriptomes of thirteen soybean accessions seeds including seven wild soybeans and six landraces through applying strand-specific RNA sequencing. Differential expressed genes related seed weight were identified, some of them were known to be associated with seed development in Arabidopsis. Noncoding RNAs are known to play important roles in plant development, and we profiled the expression pattern of long noncoding RNA (lncRNA) in cultivated and wild soybean seeds. We have identified 1,251 long intergenic noncoding RNA, 243 intronic RNA and 81 antisense lncRNA, transcriptional levels of a number of lncRNAs were significantly different between cultivated and wild soybeans, suggesting that lncRNA may be involved in soybean seed development. Overall design: High-depth paired-end RNA-seq from wild and cultivated soybeans
Project description:Background The homeodomain leucine zipper (HD-Zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation of plant growth and response to environmental stresses. Many HD-Zip genes are characterized in Arabidopsis (Arabidopsis thaliana), and members of the family are being investigated for abiotic stress responses in rice (Oryza sativa), maize (Zea mays), poplar (Populus trichocarpa) and cucumber (Cucmis sativus). Findings in these species suggest HD-Zip genes as high priority candidates for crop improvement. Results In this study we have identified members of the HD-Zip gene family in soybean cv. 'Williams 82', and characterized their expression under dehydration and salt stress. Homology searches with BLASTP and Hidden Markov Model guided sequence alignments identified 101 HD-Zip genes in the soybean genome. Phylogeny reconstruction coupled with domain and gene structure analyses using soybean, Arabidopsis, rice, grape (Vitis vinifera), and Medicago truncatula homologues enabled placement of these sequences into four previously described subfamilies. Of the 101 HD-Zip genes identified in soybean, 88 exist as whole-genome duplication-derived gene pairs, indicating high retention of these genes following polyploidy in Glycine ~10 Mya. The HD-Zip genes exhibit ubiquitous expression patterns across 24 conditions that include 17 tissues of soybean. An RNA-Seq experiment performed to study differential gene expression at 0, 1, 6 and 12 hr soybean roots under dehydration and salt stress identified 20 differentially expressed (DE) genes. Several of these DE genes are orthologs of genes previously reported to play a role under abiotic stress, implying conservation of HD-Zip gene functions across species. Screening of HD-Zip promoters identified transcription factor binding sites that are overrepresented in the DE genes under both dehydration and salt stress, providing further support for the role of HD-Zip genes in abiotic stress responses. Conclusions We provide a thorough description of soybean HD-Zip genes, and identify potential candidates with probable roles in dehydration and salt stress. Expression profiles generated for all soybean genes, under dehydration and salt stress, at four time points, will serve as an important resource for the soybean research community, and will aid in understanding plant responses to abiotic stress. We sequenced mRNA from soybean cv. "Williams 82" root samples that includes three control samples (0 hr), and three biological replicates for each of the three time points 1, 6 and 12 hr under dehydration and salt stress
Project description:This study was designed to identify changes in gene expression when corn was placed under various related stresses including being grown with a competing weed (canola) to the V4 or V8 stage, or when 40% shade cloth was present to the V4 or V8 stage, or under low nitrogen (no added nitrogen fertilizer), or under weed/shade free fertilized control conditions. In all 5 treatments and the control, samples were harvested at V8. Mechanisms underlying early season weed stress on crop growth are not well described. Corn vegetative growth and development, yield, and gene expression response to nitrogen (N), light (40% shade), and weed stresses were compared with the response of nonstressed plants. Vegetative parameters, including leaf area and biomass, were measured from V2 toV12 corn stages. Transcriptome (2008) or quantitative Polymerase Chain Reaction (q PCR) (2008/09) analyses examined differential gene expression in stressed versus nonstressed corn at V8. Vegetative parameters were impacted minimally by N stress although grain yield was 40% lower. Shade, present until V2, reduced biomass and leaf area > 50% at V2 and, at V12, recovering plants remained smaller than nonstressed plants. Grain yields of shade-stressed plants were similar to nonstressed controls, unless shade remained until V8. Growth and yield reductions due to weed stress in 2008 were observed when weeds remained until V6. In 2009, weed stress at V2 reduced vegetative growth, and weed stress until V4 or later reduced yield. Principle component analysis of differentially expressed genes indicated that shade and weed stress had more similar gene expression patterns to each other than to nonstressed or low N stressed tissues. Weed-stressed corn had 630 differentially expressed genes compared with the nonstressed control. Of these genes, 259 differed and 82 were shared with shade-stressed plants. Corn grown in N-stressed conditions shared 252 differentially expressed genes with weed-stressed plants. Ontologies associated with light/photosynthesis, energy conversion, and signaling were down-regulated in response to all three stresses. Although shade and weed stress clustered most tightly together, only three ontologies were shared by these stresses, O-methyltransferase activity (lignification processes), Poly U binding activity (post-transcriptional gene regulation), and stomatal movement. Based on both morphologic and genomic observations, results suggest that shade, N, and weed stresses to corn are regulated by both different and overlapping mechanisms. three biological replicates for each treatment and the control were collected and the resulting labeled cDNA was hybridized to the 46,000-element maize microarray chip developed by the University of Arizona using their protocol (International Microarray Workshop Handbook, 2009Gardiner et al. 2005). The hybridization scheme was a dual hybridization using a rolling circle balanced dye swap design. Thus we had thre biological replicates for each growth condition amd two technical replicates for each biological sample.
Project description:Seed germination is important to soybean (Glycine max) growth and development, ultimately affecting soybean yield. A lower seed field emergence has been the main hindrance for breeding soybeans low in phytate. Although this reduction could be overcome by additional breeding and selection, the mechanisms of seed germination in different low phytate mutants remain unknown. In this study, we performed a comparative transcript analysis of two low phytate soybean mutants (TW-1 and TW-1-M), which have the same mutation, a 2 bp deletion in GmMIPS1, but show a significant difference in seed field emergence. Overall design: 18 samples were analyzed in this research, and three replicates were included.
Project description:Soybean is a nutritionally important crop that exhibits reductions in growth and yields under drought stress. To investigate soybean responses during post-drought recovery, a gel-free proteomic technique was used to examine the protein profile. Two-day-old soybeans were stressed with drought for 4 days, recovered for 4 days, and root including hypocotyl was collected under drought and during the recovery stage. Morphological analysis revealed that growth was suppressed under drought stress that recovered following stress removal. Malondialdehyde content was increased under drought stress but returned to normal during the recovery stage. A total of 792 and 888 proteins were identified in control and drought-stressed root including hypocotyl during recovery stage, respectively. Based on the proteomic and cluster analyses, peroxidase and aldehyde dehydrogenase were significantly changed at analyzed time points under drought stress and during recovery. The activity of peroxidase was decreased under drought stress but increased during recovery. The activity of aldehyde dehydrogenase was increased under drought stress but returned to normal during the recovery stage. These results suggest that peroxidase and aldehyde dehydrogenase play key role in post-drought recovery in soybean by scavenging toxic reactive oxygen species and reducing harmful aldehydes load.
Project description:Soybean oil consumption is increasing worldwide and parallels the obesity epidemic in the U.S. Rich in unsaturated fats, especially linoleic acid, soybean oil is assumed to be healthy, and yet it induces obesity, diabetes, insulin resistance and fatty liver in mice. The genetically modified soybean oil Plenish came on the U.S. market in 2014: it is low in linoleic acid and similar to olive oil in fatty acid composition. Here we show that Plenish induces less obesity than conventional soybean oil: metabolomics, proteomics and a transgenic mouse model implicate oxylipin metabolites of omega-6 and omega-3 fatty acids (linoleic and α-linolenic acid, respectively), which are generated by target genes of nuclear receptor HNF4α. While Plenish induces less insulin resistance than conventional soybean oil, it results in hepatomegaly and liver dysfunction as does olive oil. Altering the fatty acid profile of soybeans could help reduce obesity but may also cause liver complications. Overall design: cDNA isolated from livers from WT or α7HMZ mice, were 100bp pair-ended sequenced using Illumina TruSeq RNA Sample Prep v2 Kit
Project description:We examined global gene expression patterns of mouse embryonic stem cells overexpressing EGFP, Nanog wild-type, or Nanog L122A mutants in normal, "-LIF" or "+RA" culture conditions by RNA-seq experiments. In “+RA” culture conditions, the expression patterns of the RA-responsive genes were slightly different in WT transfectants and more different in L122A transfectants compared with EGFP transfectants. These results suggested that L122A transfectants showed partial resistant activity against RA-induced differentiation, which was not found in WT mNANOG transfectants. Examination of 3 different transfectants from mouse embryonic stem cell, RF8 line, in 3 different culture conditions.
Project description:In this study, two small RNA libraries and two degradome libraries were constructed from roots of Al-treated and Al-free Glycine soja seedlings. For miRNA, a total of 7,287,655 and 7,035,914 clean reads in Al-treated and Al-free small RNAs libraries were generated, and 105 known miRNAs ,51 p3/p5 strands of known miRNA and 80 novel miRNAs were identified. Among them, expression of 34 miRNAs was responsive to Al stress. Through degradome sequencing, 82 and 11 genes were identified as tagerts of known and novel miRNAs obtained from this study, respectively. Gene Ontology (GO) annotations of target transcripts indicated that 52 out of 66 targets cleaved by conserved miRNA families may play role in regulation of transcription. sample 1: Examination of small RNA in Al-free wild soybean roots; sampple 2: Examination of small RNA in Al-treated wild soybena roots; sample 3: identification of miRNA targets in Al-free wild soybean roots; sample 4: identification of miRNA targerts in Al-treated wild soybean roots