Source: COLD SPRING HARBOR LABORATORY ASSOCIATION, INC submitted to
MAIZE EAR DEVELOPMENT, A NEW PATHWAY ACTING THROUGH FASCIATED EAR3
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
NEW
Funding Source
Reporting Frequency
Annual
Accession No.
1008540
Grant No.
2016-67013-24572
Project No.
NY.W-2015-06319
Proposal No.
2015-06319
Multistate No.
(N/A)
Program Code
A1101
Project Start Date
Dec 15, 2015
Project End Date
Dec 14, 2019
Grant Year
2016
Project Director
Jackson, D. P.
Recipient Organization
COLD SPRING HARBOR LABORATORY ASSOCIATION, INC
1 BUNGTOWN RD
COLD SPRING HARBOR,NY 11724-2209
Performing Department
Plant Biology
Non Technical Summary
Cereal crops produce the grain that constitutes the majority of our food and feed, therefore a fundamental understanding of their development has potential to improve agricultural yields. Maize in particular is the most cultivated and productive crop worldwide, and work from many groups has shown that changes in developmental control genes have been important for yield increases. This proposal is about the mechanisms by which plants grow and develop, using pools of stem cells called meristems. These structures are maintained in balance by a feedback loop between the CLAVATA and WUSCHEL genes. The proposal will use genetic and genomic approaches to study a newly identified control gene, FASCIATED EAR3 (FEA3), which codes for a cell surface receptor protein. FEA3 and its predicted ligand are expressed in specific groups of cells in the growing plant, suggesting a fundamentally new pathway in growth regulation in plants.Expected outcomes of this proposal are a deeper understanding of signaling during plant growth, and identification of new variants that could be used to enhance inflorescence size and seed productivity, important traits for food, feed and biomass production. The objectives target the program area priority of the NIFA Growth and Development program by using molecular, biochemical, and cellular approaches to improve plant productivity through studies of plant growth and developmental processes. The genes studied in the proposal could be applied in conventional breeding or in biotechnology approaches to improve crop yields and improve sustainability of US agriculture.
Animal Health Component
10%
Research Effort Categories
Basic
90%
Applied
10%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
20615101050100%
Knowledge Area
206 - Basic Plant Biology;

Subject Of Investigation
1510 - Corn;

Field Of Science
1050 - Developmental biology;
Goals / Objectives
This project will characterize a new plant developmental signaling pathway in maize. Previous work in our lab has identified a morphological mutant of maize called fasciated ear3, in which tassel and ear development is severely compromised. Both structures are enlarged, particularly at the growing tip, or meristem. We identified the underlying gene, and found that it encodes a trans-membrane receptor protein, similar to CLAVATA type receptors that function in stem cell signaling and maintenance. However, our preliminary data suggests that this new gene functions in a different pathway, and the proposed work will characterize this pathway, and understand its role in plant development. They project has three major goalsTo perform a detailed analysis of fea3 mutants, and mutants in its candidate receptor, called FCP1.To find proteins that interact with the FEA3 receptor, using proteomics, and candidate downstream factors, using gene expression profiling.To ask if FEA3 can improve maize seed yields. We have found preliminary data that a weak allele of FEA3 has bigger ears with additional rows of kernels. We will continue to characterize this effect, as well as searching for additional genetic modifiers of FEA3 function in natural populations of maize.
Project Methods
A number of different methods will be used to achieve the project goals, as follows:Aim 1. Detailed analysis of fea3 and Zmfcp1 - mutants and mechanism.We will complete the analysis of expression and genetic interactions. This will include histological and molecular analysis, as well as analysis of developmental analysis of double mutants. In addition, tissue specific gene expression using a trans-activation system will be used to test the new signaling pathway hypothesis.AIM 2. FEA3 interactors and networks. Here we will further investigate the mechanism of FEA3 action, by looking for interactors using proteomics, and mRNAseq transcriptome profiling to find genes that may function in a FEA3 network. These experiments should identify candidate downstream signal transduction components as well as additional genes that function in the control of ear development.Aim 3. Can FEA3 improve crop yield traits? Fasciated mutant ears, such as those produced by fea3 mutants, have low seed yield, because they make too many primordia that are very disorganized, and do not fill properly. However, we found that weak alleles of fea3 make more kernels. We will continue to investigate this phenomenon by breeding the weak alleles into different inbred and hybrid backgrounds and measuring kernel yields. We will also look for second site modifiers of the fea3 mutations by crossing to diverse maize germplasm and looking for enhanced phenotypes. Such enhancer loci will be mapped and molecularly isolated.

Progress 12/15/15 to 12/14/16

Outputs
Target Audience:The target audience for this project will be academic scientists, who are interested in crop genetics, and yield traits, as well as industry scientists and breeders is working to improve productivity in maize and other crops. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?A postdoctoral researcher, Byoung Il Je, is supported by this award and has been trained in maize genetics, biochemistry, and imaging. In addition, a second post doc, Fang Xu, joined our lab last year following her PhD in an Arabidopsis disease resistance lab. Fang is being trained in maize genetics and genomics and developmental biology. How have the results been disseminated to communities of interest?Results from this project have been presented in seminars and posters, as follows: Both post docs presented their data in posters at the Maize Genetic Conference, March 2016. Meetings / Seminars (PI): Results from this project have been presented in invited talks at: The European Maize Conference, Hamburg, Germany (Plenary Speaker), The Arabidopsis Conference, Korea, ComBio, Brisbane, Australia (Plenary Speaker), CSH Asia Conference, Awaji, Japan, Pioneer Conference, Univ. Missouri (Plenary Speaker), and Univ. Indiana, Bloomington. Jackson also organized a Cereal Genomics workshop at CSHL in 2016, and 16 postdoctoral scholars or graduate students were trained in theory and practice of cereal genomes. The workshop was partially supported with a separate award from NIFA. What do you plan to do during the next reporting period to accomplish the goals?The project goals are progressing according to the original plan, no major changes are anticipated.

Impacts
What was accomplished under these goals? a. A comparison of actual accomplishments with the goals established for the reporting period (where the output of the project can be expressed readily in numbers, a computation of the cost per unit of output should be submitted if the information is considered useful); This project aims to study a new plant developmental signaling pathway in maize discovered using a morphological mutant of maize called fasciated ear3 (fea3) in which tassel and ear development is severely compromised. Both structures are enlarged, particularly at the growing tip, or meristem. FEA3 encodes a trans-membrane receptor protein, similar to CLAVATA type receptors that function in stem cell signaling and maintenance. However, our preliminary data suggested that this new gene functions in a different pathway, and the proposed work will characterize this pathway, and understand its role in plant development. They project has three major goals. Progress: 1. To perform a detailed analysis of fea3 mutants, and mutants in its candidate receptor, called FCP1. We have completed our analysis of fea3 mutants as well as mutants in its candidate ligand, FCP1. FEA3 is expressed in a domain of the meristem below WUSCHEL, and FCP1 is expressed in developing primordia suggesting a "new" CLAVATA pathway distinct from the canonical CLV3-CLV1 WUS pathway that has been described in Arabidopsis. We collaborated with the group of Henrik Johnsson (Cambridge lab, UK) to produce a mathematical model to integrate the new CLV pathway with the canonical one. We tested this model using maize transgenic expression of FCP1. We also found that weak fea3 alleles can enhance maize yields, by increasing kernel row number. A paper describing these findings was published in Nature Genetics. We also made a phylogeny of FEA3 related proteins, and found 4 highly similar genes that are also expressed in inflorescences. We have knocked out these genes using CRISPR/Cas9, and will produce homozygous lines to look for phenotypes. 2. To find proteins that interact with the FEA3 receptor, using proteomics, and candidate downstream factors, using gene expression profiling. To further understand FEA3 function, we asked if it can bind FCP1 directly, in a collaboration with the Matsubayashi lab (Univ. Nagoya, Japan). Initial results suggest that FEA3 does not bind FCP1, and therefore it may have a co-receptor. To identify this, as well as other interacting proteins, we made tandem affinity protein (TAP-) tagged versions of FEA3 and transformed into maize. We have confirmed expression of the tagged protein and are backcrossing to fea3 mutants as well as to a proliferative meristem background (branched silkless; Tunicate (bdTu)) for collecting large amounts of meristems. 3. To ask if FEA3 can improve maize seed yields. We confirmed that a weak allele of FEA3 has bigger ears with additional rows of kernels, and found up to 50% increased yield in maize ears in our own (low density) field growing conditions. We are continuing to characterize this effect by initiating proper field yield trials, in collaboration with Dupont Pioneer. We are also searching for genetic modifiers of FEA3 to find other players in this new developmental pathway. We have crossed fea3 to each of the diverse maize NAM founder lines, and screened F2 populations for modified phenotypes. Preliminary results suggest at least 2 lines enhance and one line suppresses fea3, and mapping populations will now be created as a first step to identify the modifier loci. As an alternative approach, we also mutagenized fea3 using EMS, and in a preliminary screen of ~ 300 M2 lines this winter we found two putative modifiers that fully suppress the fea3 phenotype. Additional activity has been to characterize another new maize fasciated mutant, called coryne (crn). This was identified as a transposon insertion in a candidate gene, and we are performing genetic analyses to place it into known fasciated pathways. We also continue to propagate and map additional mutants from EMS screens. b. The reasons for slippage if established goals were not met; So far all project goals are progressing as expected. c. Additional pertinent information including, when appropriate, analysis and explanation of cost overruns or unexpectedly high unit costs. The project is progressing extremely well and there are no issues in meeting the goals in the funding period or with funding.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Somssich, M., Je, BI., Simon, R., Jackson, D. (2016) CLAVATA-WUSCHEL signaling in the shoot meristem. Development. 143(18): 3238-48.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Altpeter, F., Springer, NM., Bartley, LE., Blechl, AE., Brutnell, TP., Citovsky, V., Conrad, LJ., Gelvin, SB., Jackson, D., Kausch, AP., Lemaux, PG., Medford, JI., Orozco-C�rdenas, ML., Tricoli, DM., Van, Eck J., Voytas, DF., Walbot, V., Wang, K., Zhang, ZJ., Stewart, CN Jr. (2016) Advancing crop transformation in the era of genome editing. The Plant Cell, 28 (7): 1510-1520.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Je, BI., Gruel, J., Lee, YK., Bommert, P., Arevalo, ED., Eveland, AL., Wu, Q., Goldshmidt, A., Meeley, R., Bartlett, M., Komatsu, M., Sakai, H., J�nsson, H., Jackson, D. (2016) Signaling from maize organ primordia via FASCIATED EAR3 regulates stem cell proliferation and yield traits. Nature Genetics 48(7):785-91.