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United States Department of Agriculture

Agricultural Research Service

Research Project: FUNCTIONAL GENOMICS OF PLANT ARCHITECTURE
2011 Annual Report


1a.Objectives (from AD-416)
1. To identify additional components of the CLAVATA meristem signal transduction pathway. [NP 301, C 4, PS 4A]

2: To characterize the role of microRNAs and their target genes in regulating Arabidopsis shoot meristem activity. [NP 301, C 4, PS 4A]

3: To determine the function of the Arabidopsis BOP1 and BOP2 genes in regulating shoot apical meristem activity and leaf development. [NP 301, C 4, PS 4A]

4: To develop and test hypotheses to determine how knowledge of plant architectural genes in Arabidopsis can be applied to crop plants. [NP 301, C 4, PS 4A]


1b.Approach (from AD-416)
Identify, isolate and characterize genes that regulate plant architecture in model systems and agriculturally important crops by.
1)using a sensitized genetic screen to uncover novel components of the Arabidopsis thaliana CLAVATA stem cell signaling pathway;.
2)determining the role of a small regulatory RNA and its five target genes in regulating stem cell maintenance during development;.
3)analyzing the function of the BOP1 and BOP2 genes in regulating stem cell activity and leaf formation; and.
4)developing and testing hypotheses on how knowledge of plant architectural genes in Arabidopsis can be applied to crop plants through the identification and functional analysis of orthologous genes.


3.Progress Report
The first objective of our project is to identify additional components of the CLAVATA (CLV) signaling pathway. To accomplish this we are focusing on characterizing modifiers of a mutation in ULTRAPETALA1 (ULT1), which affects Arabidopsis stem cell accumulation through a pathway overlapping that of CLV3. We have identified an enhancer of ult1 called kanadi1 (kan1) that affects the patterning, and thus the growth, of leaves and fruits. We have taken the first steps to investigate the ult1 kan1 mutant phenotypes by using genetic analysis to determine whether the known organ patterning control genes SPATULA and ETTIN/ARF3 play roles in conferring the ult1 kan1 defects.

The second objective is to characterize the role of microRNAs (miRNAs) and their target genes in regulating shoot apical meristem activity. To accomplish this we are characterizing a dominant enhancer of the jabba-1D miRNA mutant phenotype that we call JABBA MODIFIER1 (JM1). We have performed light microscopy and scanning electron microscopy on JM1 mutant plants to analyze their shoot apical meristem defects.

The third objective is to determine the function of the Arabidopsis BOP1 and BOP2 genes in regulating shoot apical meristem activity and leaf development. To accomplish this we are focusing on the CLV3-related small signaling proteins CLE5 and CLE6 as targets of BOP1 and BOP2 activity. We have used light microscopy and scanning electron microscopy to determine that plants with significantly reduced CLE5 and CLE6 expression have defects in leaf patterning.

The fourth objective is to develop and test hypotheses to determine how knowledge of plant architectural genes in Arabidopsis can be applied to crop plants. To accomplish this we have identified a putative ortholog of the Arabidopsis CLE5 and CLE6 signaling proteins in the rice (Oryza sativa) genomic sequence database. These results have enabled us to formulate the hypothesis that related CLE genes may act similarly to control leaf development in Arabidopsis and an agriculturally-important crop species.


4.Accomplishments
1. Characterization of CLE signaling gene expression profiles in plant development. This work addresses the question of how widely small signaling molecules may act to regulate biological processes during plant development. ARS scientists in the Plant Gene Expression Center in Albany, California, reported that all Arabidopsis vegetative and reproductive tissues express at least one CLE gene, and that many tissues express multiple CLE genes in overlapping patterns. These data indicate that CLE signaling pathways are likely to play important roles in many biological processes during the plant life cycle. We also generated CLE over-expressing Arabidopsis plants and analyzed their developmental phenotypes, and identified eight total or partial loss-of-function CLE alleles. This accomplishment will facilitate the identification of related genes in crop plants that have similar expression patterns, benefiting agriculture by providing a foundation for linking the genes with key developmental traits that be manipulated to potentially enhance shoot and root growth, promote fertilization, and/or increase yield.

2. Characterization of CLE signaling gene expression profiles in plant embryos. This work addresses the question of how widely small signaling molecules may act to regulate biological processes during plant embryogenesis. ARS scientists in the Plant Gene Expression Center in Albany, California, reported that members of the CLV3-related CLE family of small signaling molecules are expressed in Arabidopsis embryos, where they may control intercellular signaling events during embryo formation. We found that five of the nine CLE genes tested had the same expression pattern in embryos as in seedlings, but that the other four had expression patterns that differed between the two stages. These data suggest that CLE genes are widely recruited to new tissue-specific signaling functions during the course of plant development. This accomplishment will facilitate the identification of related genes in crop plants that have similar expression patterns, providing a foundation for linking the genes with key traits in embryos that can be manipulated to potentially improve seed yield and/or increase germination efficiency.


Review Publications
Jun, J., Fiume, E., Roeder, A.H., Meng, L., Sharma, V.K., Osmont, K.S., Baker, C., Ha, C., Meyerowitz, E.M., Feldman, L.J., Fletcher, J.C. 2010. Comprehensive analysis of CLE polypeptide signaling gene expression and overexpression activity in Arabidopsis. Plant Physiology. 154:1721-1736.

Fiume, E., Monfared, M.M., Jun, J., Fletcher, J.C. 2011. CLE polypeptide signaling gene expression in Arabidopsis embryos. Plant Signaling and Behavior. 6:443-444.

Monfared, M.M., Simon, M.K., Meister, R.J., Roig-Villanova, I., Kooiker, M., Colombo, L., Fletcher, J.C., Gasser, C.S. 2011. Overlapping and antagonistic activities of basic Pentacysteine genes affect a range of developmental processes in Arabidopsis. Plant Journal. 66: 1020-1031.

Last Modified: 12/27/2014
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