Performing Department
(N/A)
Non Technical Summary
Many crops, including maize, sorghum, and many millets, occur in a sub-family of grasses called the Panicoideae. All panicoids share a floral trait that constrains their potential productivity. Grass flowers occur in structures called spikelets. Panicoideae spikelets contain two flowers, but usually only one flower (the upper flower) is fertile and produces a grain after pollination. This is because the floral organs (called carpels) that go on to form the grain are suppressed in lower flowers, leading to sterile flowers. Thus, potential crop productivity is constrained by carpel suppression. In this era of genome engineering, carpel suppression genes could be transformative targets for genome editing and yield improvement. However, only a few genes are known to regulate carpel suppression in maize and its relatives. Furthermore, how these genes interact in pathways, and whether these genes have conserved functions in many grass species remains unknown. Here, we will (1) expand the list of genes with known roles in carpel suppression, (2) determine how carpel suppression genes are ordered into genetic networks and pathways in maize, and (3) test the hypothesis that a common genetic mechanism regulates carpel suppression in the Panicoideae. To achieve these objectives, we will use state-of-the-art methods in genetics, genomics, computer vision, and quantitative phenotyping.This project will provide fundamental knowledge for ensuring resilient and prosperous agricultural systems in the U.S. Carpel suppression genes represent promising targets to increase yield in maize, an important crop in the U.S., and in its climate resilient relatives in the Panicoideae. Our results will represent an important first step in determining the genetic architecture of carpel suppression and will allow us to evaluate the potential for the genes we identify to affect productivity in maize and the model panicoid Setaria viridis at small scales. Given the relative ease of genome editing in many grasses, the discoveries we make can be translated to other crops, to be rigorously evaluated in yield trials. There is a growing interest worldwide in climate- resilient panicoid crops, including sorghum and proso millet. However, while many millets are drought, salt and heat tolerant, most are not high-yielding, and have not been subject to the intensive breeding that has so dramatically improved U.S. maize yield in the 20th century. Selective breeding, together with targeted modifications to key developmental genes, such as carpel suppression genes, could dramatically accelerate yield improvements. Thus, identifying the genes that control panicoid crop productivity could accelerate the production of high-yielding, climate-resilient crops that would enhance the long-term sustainability of U.S. food production systems.
Animal Health Component
0%
Research Effort Categories
Basic
100%
Applied
(N/A)
Developmental
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Goals / Objectives
Carpel suppression occurs in at least half of every flower produced by grasses in the Panicoideae subfamily, which includes maize and the climate-resilient millets. Carpel suppression limits potential grain production and crop yield. Therefore, carpel suppression genes represent promising genome editing targets to increase yield in panicoid crops. The major goal of this project is to identify genes that regulate carpel suppression in maize and its relatives in the Panicoideae, and to determine how these genes are ordered into genetic pathways. To achieve this goal, we will (Objective 1) determine the genetic underpinnings of carpel suppression, and dramatically increase the number of known maize carpel suppression genes; (Objective 2) determine interactions between genetic pathways regulating carpel suppression in maize; and (Objective 3) determine the roles for homologs of maize carpel suppression genes in setaria. This project will also contribute to agricultural education, by training postdoctoral researchers, and at least two undergraduate researchers in fundamental research of the genetics of carpel suppression.In Objective 1, we will use bulked segregant analysis coupled to high-throughput sequencing to map the genes underlying 40 carpel suppression mutants, and quantify their morphological phenotypes. Depending on our mapping and phenotyping results, we will clone a subset of these mutant genes. This objective is expected to involve all participants, to start immediately, and be completed in the first half of the second year of the project period.In Objective 2 we will (1) order select carpel suppression genes into genetic pathways; (2) define the genetic modules and pathways regulating carpel suppression; and (3) identify carpel suppression gene candidates that can be explored in crop improvement efforts. To achieve these sub-objectives, we will perform three sets of experiments: (1) phytohormone rescue experiments, (2) phytohormone and sugar measurements, and (3) transcriptomics experiments. This objective is expected to involve the postdocs, undergraduates, collaborators, and the PD. Experiments associated with this objective will start in the first year, and be completed in the second year of the project period.In Objective 3, we will test the hypothesis that carpel suppression is mediated by homologous genes across the panicoids. To do this, we will make and characterize mutants of maize carpel suppression gene homologs using CRISPR-Cas9 genome editing in setaria, which is distantly related to maize. This objective is expected to involve the postdocs, undergraduates, collaborators, and the PD. Experiments associated with this objective will start immediately, and be completed by the end of the project period.
Project Methods
In Objective 1, we will use a protocol that we optimized for using high-throughput sequencing to identify the chromosomal locations of carpel suppression genes disrupted in 38 genetic mutants. For select mutants, we will go on to identify the precise genes disruptions that are causing the mutant phenotypes using standard map-based cloning and reverse genetics methods. In Objective 2, we will perform phytohormone rescue experiments, phytohormone measurements and transcriptomics using standard methods and data analysis protocols. In addition to bulk transcriptomics approach, we will use emerging single cell technologies to expand the resolution of our analysis to the scale of individual cells within developing inflorescences. In Objective 3, we will use CRISPR-Cas9 genome editing to generate genetic mutants in the panicoid model species Setaria viridis. These mutants will be characterized using transcriptomics, network analysis, and X-ray uCT. Expert collaborators have been identified that will be assisting us with any methods outside of our lab's direct realms of expertise.Efforts to publicize our results and to deliver science-based knowledge will include presentations at seminars and scientific conferences; publishing scientific papers; classroom teaching on genetics and plant biology in the PD's classes. The project will be evaluated according to milestones successfully reached. These milestones include (1) determining the map intervals of focal maize genes; (2) generating mutants in Setaria viridis (3) acquiring and releasing quantitative phenotypic data in maize and Setaria viridis; (4) generating, analyzing, and releasing transcriptomic data for maize and Setaria viridis; and (5) generating and releasing a curated list of putative carpel suppression genes with conserved roles in the Panicoideae. In addition, success will be indicated by successful publication of scientific papers.