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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Research Project #434556

Research Project: Mapping Crop Genome Functions for Biology-Enabled Germplasm Improvement

Location: Plant, Soil and Nutrition Research

Project Number: 8062-21000-044-00-D
Project Type: In-House Appropriated

Start Date: Apr 4, 2018
End Date: Apr 3, 2023

Objective 1: Apply comparative genomic, genetic, and molecular approaches to the dissection of complex traits and the understanding of genome functions; develop and implement new standards for the management and analysis of plant genomic, genetic and phenotypic information; and dissect gene networks associated with programming crop plant development and adaptation to environment (GxE). Sub-objective 1.A: Reference genomic resources will be generated to target support four crop communities. The achievement of this objective will generate information management resources for maize (Zea mays), sorghum (Sorghum bicolor), grapevine (Vitis vinifera), and rice (Oryza sativa). Sub-objective 1.B: Develop functional and comparative genomics resources for plant reference genomes. The achievement of this objective will expand the Gramene databases to encompass reference genomes of at least 75 unique plant species. Sub-objective 1.C: Develop functional networks for crop and model species. Through achieving this objective, an integrated genetics, transcriptomics, and molecular interaction data will be generated to define regulatory networks that influence plant traits through effects on developmental morphology (architecture) and response to environment. Objective 2: Accelerate sorghum trait analysis, germplasm analysis, genetic studies, and breeding by acquiring, integrating, and providing open access to sorghum genome sequences and annotations, germplasm diversity information, trait mapping information, and phenotype information in a sorghum crop genome database system, with an initial emphasis on sugarcane aphid resistance.

The future of crop breeding will increasingly rely on strategies that combine genetic resources with rapidly advancing tools and knowledge in genomics, trait mapping, high-throughput phenotyping, and genome-editing. Yet, major challenges remain in translating vast amounts of data into useable biological models and building scalable information systems to enable researchers and breeders to contribute to and exploit these future technologies. To meet these challenges, this project will engage several strategic initiatives and collaborations that produce new genomics data, cyberinfrastructure, and hypothesis-based research. The first objective will generate new genomics datasets among four crop groups: sorghum, maize, rice and grapevine. Objective 1.A will produce a minimum of 30 high-quality reference genome assemblies, transcriptomes, and corresponding annotations. In maize and sorghum, we will also generate ENCODE-type molecular data sets to study the relationships between chromatin structure, gene expression, and phenotype. In sorghum and grapevine, we will sequence disease resistance genes across key germplasms that target critically important pests/pathogens. To enable sharing of reproducible workflows and promote interoperability, computational work will be performed using the recently developed SciApps cyberinfrastructure. In Objective 1.B, genomics data will be further disseminated via Gramene/Ensembl to support genome stewardship, comparative and pan-genomics analysis (in 2-3 crop groups), and display of ENCODE-type and publicly archived variation/genotype data. This platform will enable researchers to evaluate structural variation within crop clades and use conservation profiles to evaluate candidate genes. In Objective 1.C, we will continue several hypothesis-based studies of gene regulatory networks that underlie yield components influenced by morphological development and nutrient and stress response/adaptation. These projects combine forward and reverse genetics with transcriptional profiling, fluorescence in situ sequencing, and yeast-based molecular interaction assays to elucidate regulatory pathways that control plant traits. We will continue to use sorghum EMS mutagenized lines to dissect pathways underlying inflorescence architecture and the multi-seeded trait. Research in nitrogen use efficiency will be continued using maize and Arabidopsis as models. Objective 2 focuses on development of the new sorghum genomics and genetics portal to serve scientists and breeders working on grain sorghum improvement. Goals include initial release of Sorghum Base as a comparative functional genomics resource, with future development of infrastructure to support phenotypic data and genomics-enabled germplasm improvement. A critical component of this plan includes sorghum community engagement. The products of these two objectives will include well-characterized germplasm and the associated genotypic and phenotypic characterization of complex agronomic traits, which will enable genomic-assisted breeding and novel approaches for understanding the genetic architecture of traits critical to US agriculture.