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Sekhon R.S.,University of Wisconsin - Madison | Hirsch C.N.,University of Minnesota | Childs K.L.,Michigan State University | Breitzman M.W.,University of Wisconsin - Madison | And 6 more authors.
Plant Physiology | Year: 2014

Seed size is a component of grain yield and an important trait in crop domestication. To understand the mechanisms governing seed size in maize (Zea mays), we examined transcriptional and developmental changes during seed development in populations divergently selected for large and small seed size from Krug, a yellow dent maize cultivar. After 30 cycles of selection, seeds of the large seed population (KLS30) have a 4.7-fold greater weight and a 2.6-fold larger size compared with the small seed population (KSS30). Patterns of seed weight accumulation from the time of pollination through 30 d of grain filling showed an earlier onset, slower rate, and earlier termination of grain filling in KSS30 relative to KLS30. This was further supported by transcriptome patterns in seeds from the populations and derived inbreds. Although the onset of key genes was earlier in small seeds, similar maximum transcription levels were observed in large seeds at later stages, suggesting that functionally weaker alleles, rather than transcript abundance, may be the basis of the slow rate of seed filling in KSS30. Gene coexpression networks identified several known genes controlling cellularization and proliferation as well as novel genes that will be useful candidates for biotechnological approaches aimed at altering seed size in maize and other cereals. © 2014 American Society of Plant Biologists. All rights reserved. Source

Cannon E.K.S.,Iowa State University | Cannon S.B.,Corn Insects and Crop Genetics Research Unit
International Journal of Plant Genomics | Year: 2011

CViT (chromosome visualization tool) is a Perl utility for quickly generating images of features on a whole genome at once. It reads GFF3-formated data representing chromosomes (linkage groups or pseudomolecules) and sets of features on those chromosomes. It can display features on any chromosomal unit system, including genetic (centimorgan), cytological (centiMcClintock), and DNA unit (base-pair) coordinates. CViT has been used to track sequencing progress (status of genome sequencing, location and number of gaps), to visualize BLAST hits on a whole genome view, to associate maps with one another, to locate regions of repeat densities to display syntenic regions, and to visualize centromeres and knobs on chromosomes. Copyright © 2011 Ethalinda K. S. Cannon and Steven B. Cannon. Source

Woody J.L.,Iowa State University | Shoemaker R.C.,Corn Insects and Crop Genetics Research Unit
Frontiers in Genetics | Year: 2011

Genomic architecture appears to be a largely unexplored component of gene expression. That architecture can be related to chromatin domains, transposable element neighborhoods, epigenetic modifications of the genome, and more. Although surely not the end of the story, we are learning that when it comes to gene expression, size is also important. We have been surprised to find that certain patterns of expression, tissue specific versus constitutive, or high expression versus low expression, are often associated with physical attributes of the gene and genome. Multiple studies have shown an inverse relationship between gene expression patterns and various physical parameters of the genome such as intron size, exon size, intron number, and size of intergenic regions. An increase in expression level and breadth often correlates with a decrease in the size of physical attributes of the gene. Three models have been proposed to explain these relationships. Contradictory results were found in several organisms when expression level and expression breadth were analyzed independently. However, when both factors were combined in a single study a novel relationship was revealed. At low levels of expression, an increase in expression breadth correlated with an increase in genic, intergenic, and intragenic sizes. Contrastingly, at high levels of expression, an increase in expression breadth inversely correlated with the size of the gene. In this article we explore the several hypotheses regarding genome physical parameters and gene expression. © 2011 Woody and Shoemaker. Source

Haas B.J.,The Broad Institute of MIT and Harvard | Papanicolaou A.,CSIRO | Yassour M.,The Broad Institute of MIT and Harvard | Yassour M.,Hebrew University of Jerusalem | And 22 more authors.
Nature Protocols | Year: 2013

De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary importance, cancer samples or the microbiome. In this protocol we describe the use of the Trinity platform for de novo transcriptome assembly from RNA-seq data in non-model organisms. We also present Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes. In the procedure, we provide a workflow for genome-independent transcriptome analysis leveraging the Trinity platform. The software, documentation and demonstrations are freely available from http://trinityrnaseq.sourceforge.net. The run time of this protocol is highly dependent on the size and complexity of data to be analyzed. The example data set analyzed in the procedure detailed herein can be processed in less than 5 h. Source

Liu J.-Z.,Iowa State University | Horstman H.D.,Iowa State University | Braun E.,Iowa State University | Graham M.A.,Iowa State University | And 8 more authors.
Plant Physiology | Year: 2011

Mitogen-activated protein kinase (MAPK) cascades play important roles in disease resistance in model plant species such as Arabidopsis (Arabidopsis thaliana) and tobacco (Nicotiana tabacum). However, the importance of MAPK signaling pathways in the disease resistance of crops is still largely uninvestigated. To better understand the role of MAPK signaling pathways in disease resistance in soybean (Glycine max), 13, nine, and 10 genes encoding distinct MAPKs, MAPKKs, and MAPKKKs, respectively, were silenced using virus-induced gene silencing mediated by Bean pod mottle virus. Among the plants silenced for various MAPKs, MAPKKs, and MAPKKKs, those in which GmMAPK4 homologs (GmMPK4s) were silenced displayed strong phenotypes including stunted stature and spontaneous cell death on the leaves and stems, the characteristic hallmarks of activated defense responses. Microarray analysis showed that genes involved in defense responses, such as those in salicylic acid (SA) signaling pathways, were significantly up-regulated in GmMPK4-silenced plants, whereas genes involved in growth and development, such as those in auxin signaling pathways and in cell cycle and proliferation, were significantly downregulated. As expected, SA and hydrogen peroxide accumulation was significantly increased in GmMPK4-silenced plants. Accordingly, GmMPK4-silenced plants were more resistant to downy mildew and Soybean mosaic virus compared with vector control plants. Using bimolecular fluorescence complementation analysis and in vitro kinase assays, we determined that GmMKK1 and GmMKK2 might function upstream of GmMPK4. Taken together, our results indicate that GmMPK4s negatively regulate SA accumulation and defense response but positively regulate plant growth and development, and their functions are conserved across plant species. © 2011 American Society of Plant Biologists. All Rights Reserved. Source

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