Location: Plant Gene Expression Center2013 Annual Report
1a. Objectives (from AD-416):
Objective 1 : Utilize RNAseq profiling to characterize an age dependent and species-independent “meristem maturation clock”. Using gradually maturing shoot apices and deep RNA seq, we will construct a shoot maturation atlas for Solanaceae (potato and tomato) and grasses species of (maize and Brachypodium). Apices at 4-6 time points, starting with dissected embryos (in grasses, many embryos contain several leaves) or germinating seedlings and ending at transition to flowering, will be collected at regular intervals. The dynamic changes in gene expression will be used to construct a “meristem maturation clock” comprised of universal and species specific markers. Objective 2 : Utilize RNAseq and “meristem maturation clocks” to characterize the state of lateral shoots with different fates. We will collect axillary shoot apices of equivalent state as the shoots in aim 1 for RNA seq analysis. We will compare 1) lower and upper nodes that make the same terminal organs (inflorescence) either slowly or shortly after initiation (tomato and Brachypodium) 2) lower and upper nodes that make different terminal organs; potato – forming stolons or vegetative lateral branches or maize - forming tillers (that will have a terminal tassel) or axillary shoots with a terminal ear. These shoots will be compared with each other, and with samples collected from the different stages of the primary shoot (aim 1). Objective 3 : Determine the contribution of the miR156 pathway to the “shoot maturation clock” and to the fate of lateral meristems. Compare “young” and “old” primary apices and side shoots of Cg/35S:miR156 plants with same age WT apices. Classify genes with age-dependent expression dynamics as miR156 dependent and miR156 independent. Objective 4 : Compare the consequences of targeted manipulation of age dependent programs by “universal” and species-specific factors. Can we specifically modify primary and side shoots? Can we use it to alter overall plant architecture in a favorable way? Using the expression atlas, promoters of genes with specific types of expression will be selected. These will include genes with specific age dependent gradients (increasing and decreasing), differential activation in primary and lateral shoots, and age dependent expression in lateral shoots. We will use these and “general” promoters as means to specifically modify shoot architecture and composition for tailoring of economically useful traits. We will explore the roles of factors of the miR156 pathway as well as miR156-independent factors, both “universal” and species-specific. We will monitor shoot architecture, productivity and composition of the classical plant products (fruits, grains tubers) as well as potentially novel products (hay and biofule raw materials).
1b. Approach (from AD-416):
Carry out high throughput RNA sequencing analysis on main shoots and lateral shoots of maize and potato in wild-type and Corngrass overexpressing lines during a developmental time course. Identify genes that are expressed at specific stages and obtain their promoters to make transgenic plants.
3. Progress Report:
The work relates to the parent project Objective 2 given the enormous importance of Corngrass in regualting plant architecture. RNAseq was carried out on Brachypodium, Switchgrass and maize that overexpressed miR156 and control plants. miR156 maintains plants in a juvenile state, thus a comparison can be made between juvenile and adult plants across grass species. Although over 1000 genes are differentially expressed between the juvenile and adult state for each species, only 20 or so are in common. This small number may be due to the fact that we rely on synteny to identify the orthologs and the genome for switchgrass is incomplete and difficult to work with.