Progress 10/01/12 to 09/30/13
Outputs
Progress Report Objectives (from AD-416): Determine the molecular mechanisms by which plants perceive and respond to developmental, biotic and abiotic signals throughout the life cycle to enhance the quality and production efficiency of agriculturally important crops. Approach (from AD-416): A combination of modern molecular, genetic, genomic, proteomic and bioinformatic approaches will be used to address this multifaceted problem. Particular emphasis will be placed on identifying signaling components, regulatory genes and transcriptional networks involved in controlling plant responses to developmental, biotic and abiotic signals. Genes that respond to light under control of the phytochrome photosensory system will be identified and the regulatory mechanisms defined. Genes involved in regulating the circadian clock will be identified and functionally defined. Genes controlling vegetative and reproductive development will be identified and characterized. Plant hormone function in mediating growth and developmental responses will be explored. Genes involved in plant responses to biotic and abiotic challenges will be identified and characterized. On an ongoing basis, cutting-edge strategies and technologies in areas such as targeted reverse-genetic gene disruption, high-density microarray analysis, and biocomputational approaches, will be assimilated and will be identified and characterized. These accomplishments relate to the parent project, 5335-21000-032-00D, in connecting networks between growth and environmental response. ARS scientists made significant advances in identifying components of the regulatory networks involved in how plants grow and perceive their environment. They identified a key modifier of fruit patterning activity in Arabidopsis. They also identified stem cell signaling proteins in the rice (Oryza sativa) genomic sequence database, as well as in the maize genome sequence database. Another key accomplishment was the first comprehensive analysis of circadian clock-driven gene expression in maize and detailed analysis of genes that regulate flowering time in maize. The circadian clock analysis is also being carried out under drought conditions. A third key accomplishment was the discovery of gene(s) that regulate maize growth and respond to the environment. A fourth accomplishment is progress in characterizing a pollen specific transcription factor. Plants that are mutant in this gene have reduced seed set, implicating this transcription factor in controlling processes required for correct double fertilization. A fifth accomplishment was progress in understanding of the virulence mechanisms of bacteria that infect plants and the innate mechanisms in disease resistance. A final accomplishment was a detailed understanding of the role of phytocrome and interacting partners in seedling emergence. The overall impact of these many accomplishments is that a number of novel regulatory genes that affect plant biomass and yield were identified and their functions analyzed, benefiting agriculture by facilitating the characterization and manipulation of related genes in many crop plant species.
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Progress 10/01/11 to 09/30/12
Outputs
Progress Report Objectives (from AD-416): Determine the molecular mechanisms by which plants perceive and respond to developmental, biotic and abiotic signals throughout the life cycle to enhance the quality and production efficiency of agriculturally important crops. Approach (from AD-416): A combination of modern molecular, genetic, genomic, proteomic and bioinformatic approaches will be used to address this multifaceted problem. Particular emphasis will be placed on identifying signaling components, regulatory genes and transcriptional networks involved in controlling plant responses to developmental, biotic and abiotic signals. Genes that respond to light under control of the phytochrome photosensory system will be identified and the regulatory mechanisms defined. Genes involved in regulating the circadian clock will be identified and functionally defined. Genes controlling vegetative and reproductive development will be identified and characterized. Plant hormone function in mediating growth and developmental responses will be explored. Genes involved in plant responses to biotic and abiotic challenges will be identified and characterized. On an ongoing basis, cutting-edge strategies and technologies in areas such as targeted reverse-genetic gene disruption, high-density microarray analysis, and biocomputational approaches, will be assimilated and will be identified and characterized. Formerly 5335-21000-027-03S (1/10). BSL-1; 7/1/10. Documents SCA with UC Berkeley. ARS scientists at Albany, California, collaborated with scientists from University of California Berkeley to carry out studies aimed at determining the function of plant genes. They showed that overexpression of PTEN, a protein and lipid phosphatase, caused disturbed lipid signaling and excessive autophagy in pollen tubes, which led to gametophytic male sterility. Another group developed a high-throughput quantitative membrane-based yeast-two hybrid system, providing a genomics- era platform for the analysis of protein-protein interactions. Further, they described new virulence strategies employed by bacterial type III secreted effectors to manipulate plant defense mechanisms. A third group demonstrated that the small signaling molecule CLE8 regulates embryo and endosperm development. This lab showed that CLE8 activity promotes overall seed size, and thus may be targeted to improve plant yield. A fourth group cloned and characterized a kinase that regulates leaf growth and reproductive development. Using microarray-based expression profiling, a fifth group has defined a core set of genes, regulated by the phytochrome (phy)-PIF transcription-factor signaling pathway, that respond rapidly and reciprocally to light and shade, in emergent seedlings and vegetative-canopy-exposed plants, respectively. These genes are enriched for transcription-factor-encoding loci, providing targets for manipulating light-shade-modulated sculpturing of vegetational architecture, of potential relevance to biofuel production. The sixth lab identified mutations in the maize homologs of Gigantea, an important protein for regulating flowering time and the circadian clock. Finally, the seventh group discovered that small RNAs regulate levels of disease resistance loci in Solanaceous species.
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Progress 10/01/10 to 09/30/11
Outputs
Progress Report Objectives (from AD-416) Determine the molecular mechanisms by which plants perceive and respond to developmental, biotic and abiotic signals throughout the life cycle to enhance the quality and production efficiency of agriculturally important crops. Approach (from AD-416) A combination of modern molecular, genetic, genomic, proteomic and bioinformatic approaches will be used to address this multifaceted problem. Particular emphasis will be placed on identifying signaling components, regulatory genes and transcriptional networks involved in controlling plant responses to developmental, biotic and abiotic signals. Genes that respond to light under control of the phytochrome photosensory system will be identified and the regulatory mechanisms defined. Genes involved in regulating the circadian clock will be identified and functionally defined. Genes controlling vegetative and reproductive development will be identified and characterized. Plant hormone function in mediating growth and developmental responses will be explored. Genes involved in plant responses to biotic and abiotic challenges will be identified and characterized. On an ongoing basis, cutting-edge strategies and technologies in areas such as targeted reverse-genetic gene disruption, high-density microarray analysis, and biocomputational approaches, will be assimilated and will be identified and characterized. ARS scientists in collaboration with scientists of UC Berkeley increased our knowledge of how plant genes function. They showed that the Anaphase- Promoting Complex (APC), previously known to have a role in protein degradation, also regulates transcription of a cell cycle gene, and that this regulation, which is mediated by microRNAs, is important for pollen development. They published a comprehensive analysis of CLV3-related CLE polypeptide signaling gene expression and over-expression activity in Arabidopsis vegetative and reproductive development. This work indicated that many plant developmental and/or physiological processes may be regulated by CLE-mediated intercellular signaling. Scientists also discovered that a number of diverse signaling pathways appear to converge on the Phytochrome-Interacting Factor (PIF) family of bHLH transcription factors as intermediates in the transduction process. The list of pathways includes ethylene signaling, thus expanding the scope of the concept further. Another group developed maize mutants that accelerate flowering time and shorten plant stature, demonstrating that the circadian clock regulates these important aspects of maize development. They established that the rapid flowering of Arabidopsis plants induced by high temperature is a response specifically to the high temperature during the last half of the day. These findings are relevant to the effect of global climate change on plant development. Another group identified a gene that regulates glucose levels in maize cell walls. Plants carrying a mutation in the gene have higher glucose in adult leaves and improved saccharification, which makes a better lignocellulosic biofuel. Finally, ARS scientists discovered that disease resistance loci in the Solanaceous species, such as potato and tomato, are targeted by small RNAs. The small RNAs modulate the level of expression of these expanded gene families.
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Progress 10/01/09 to 09/30/10
Outputs
Progress Report Objectives (from AD-416) Determine the molecular mechanisms by which plants perceive and respond to developmental, biotic and abiotic signals throughout the life cycle to enhance the quality and production efficiency of agriculturally important crops. Approach (from AD-416) A combination of modern molecular, genetic, genomic, proteomic and bioinformatic approaches will be used to address this multifaceted problem. Particular emphasis will be placed on identifying signaling components, regulatory genes and transcriptional networks involved in controlling plant responses to developmental, biotic and abiotic signals. Genes that respond to light under control of the phytochrome photosensory system will be identified and the regulatory mechanisms defined. Genes involved in regulating the circadian clock will be identified and functionally defined. Genes controlling vegetative and reproductive development will be identified and characterized. Plant hormone function in mediating growth and developmental responses will be explored. Genes involved in plant responses to biotic and abiotic challenges will be identified and characterized. On an ongoing basis, cutting-edge strategies and technologies in areas such as targeted reverse-genetic gene disruption, high-density microarray analysis, and biocomputational approaches, will be assimilated and will be identified and characterized. Formerly 5335-21000-027-03S (1/10). Documents SCA with UC Berkeley. This is a new project that replaced 5335-21000-027-03-S which is continuing and expanding upon the work of the former projects 5335-21430- 007-00D, 5335-22000-007-00D, and 5335-21000-026, -027, -028, -027, -029, - 030 and -031-00D ARS scientist demonstrated that the BOP1 and BOP2 regulatory proteins control leaf formation by suppressing KNOX1 and YABBY transcription factor activity at the base of the organ. Results were reported in the peer-reviewed journal Genes & Development (Ron, M. et al. 2010. Genes & Dev 24: 1010-1021). ARS scientist identified a maize mutant with increased glucan in the cell wall, an impediment to plant feedstocks and identified the tasselsheath4 gene that regulates leaf size which is critical for improving biofeedstocks. Research results were published in six publications. ARS scientist demonstrated that mutants without normal circadian rhythms could not distinguish between moderate and warm temperatures and that maize genes with expression regulated by the circadian clock is integral to maize photosynthesis, carbohydrate metabolism, cell wall synthesis, and phytohormone production. Research results published in Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 463:763-768. Demonstrated that ARS scientist analyzed plants regenerated from calluses and showed that site specific integration mediated by the Bxb1 recombination system occurred at a ~10% frequency. This is practical for commercial developers to obtain site-specifically integrated transgenes, and will help speed the development of more precisely engineered transgenic varieties. Research results were published in The phiC31 Recombinase Demonstrates Heritable Passage of Site-specific Genomic Excision in Arabidopsis. BioMed Central (BMC)Biotechnology. Available:doi:10.1186/1472-6750-10-17. An ARS scientist concluding 10 years of research on the function of the ACC synthase enzymes encoded by 9 genes in Arabidopsis. The results revealed a critical role for ACC and were published in A Combinatorial Interplay Among the 1-Aminocyclopropane-1-carboxylate Isoforms Regulates Ethylene Biosynthesis in Arabidopsis thaliana. Genetics. doi:10. 1534/genetics.109.107102 An ARS scientist investigated the functional and evolutionary properties of three pathogen disease resistance loci of wild Solanum species using comparative genomics. Results were published Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs. Genome Research. 19:42-56 and Inferred origin of several Native American potatoes from the Pacific Northwest using SSR markers. Euphytica. 174:15- 29. Research at the PGEC provides an essential knowledge base for biotechnology's impact on agriculture. The knowledge has moved from determining the function of single genes to elucidation of entire networks. This information can be used to understand the function of developmental processes in crop processes. Monitoring of activities is carried out by weekly seminars and monthly meetings.
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Progress 10/01/08 to 09/30/09
Outputs
Progress Report Objectives (from AD-416) Determine the molecular mechanisms by which plants perceive and respond to developmental, biotic and abiotic signals throughout the life cycle to enhance the quality and production efficiency of agriculturally important crops. Approach (from AD-416) A combination of modern molecular, genetic, genomic, proteomic and bioinformatic approaches will be used to address this multifaceted problem. Particular emphasis will be placed on identifying signaling components, regulatory genes and transcriptional networks involved in controlling plant responses to developmental, biotic and abiotic signals. Genes that respond to light under control of the phytochrome photosensory system will be identified and the regulatory mechanisms defined. Genes involved in regulating the circadian clock will be identified and functionally defined. Genes controlling vegetative and reproductive development will be identified and characterized. Plant hormone function in mediating growth and developmental responses will be explored. Genes involved in plant responses to biotic and abiotic challenges will be identified and characterized. On an ongoing basis, cutting-edge strategies and technologies in areas such as targeted reverse-genetic gene disruption, high-density microarray analysis, and biocomputational approaches, will be assimilated and will be identified and characterized. Documents SCA with UC Berkeley. Significant Activities that Support Special Target Populations An ARS scientist determined the expression patterns of 24 members of the CLE family of putative signaling molecules throughout Arabidopsis development. She found that most Arabidopsis tissues express multiple CLE genes during the life cycle, and detected dynamic CLE gene expression patterns during developmental processes such as lateral root initiation, stamen maturation and fruit formation. An ARS scientist determined that the hormone gibberellin is directly regulated by the KNOTTED1 transcription factor and that the regulatory sequences of the GA-2-oxidase gene are conserved in the grasses. She has also identified a number of other direct targets using chromatin sequencing. An ARS scientist identified a substantial number of maize transcripts under circadian regulation and discovered several likely maize clock components. Microarray analysis showed 10% of maize transcripts exhibit a circadian rhythm; a clear illustration of the maize circadian oscillator�s broad transcriptional regulatory purview. An ARS scientist showed that mutants which carry truncated versions of a protein disulfide isomerase have embryo sac maturation and disrupted pollen tube guidance, whereas gene knockouts in this gene had no effect.. An ARS scientist analyzed plants regenerated from calluses generated in FY08 and showed that site specific integration mediated by the Bxb1 recombination system occurred at a ~10% frequency. This is practical for commercial developers to obtain site-specifically integrated transgenes, and will help speed the development of more precisely engineered transgenic varieties. An ARS scientist has discovered a novel complexity in phytochrome (phy)- mediated light signaling, whereby bHLH signaling partners function as transcription factors in regulating early gene-expression, but as direct feedback modulators of phy-protein abundance in regulating later visible seedling morphogenesis. An ARS scientist is concluding 10 years of research on the function of the ACC synthase enzymes encoded by 9 genes in Arabidopsis. The results have revealed a critical role for ACC and is soon to be published. An ARS scientist investigated the functional and evolutionary properties of three pathogen disease resistance loci of wild Solanum species using comparative genomics. Research at the PGEC provides an essential knowledge base for biotechnology's impact on agriculture. The knowledge has moved from determining the function of single genes to elucidation of entire networks. This information can be used to understand the function of developmental processes in crop processes. Monitoring of activities is carried out by weekly seminars and monthly meetings.
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