Location: Plant, Soil and Nutrition Research
Project Number: 8062-21000-050-043-A
Project Type: Cooperative Agreement
Start Date: Jul 1, 2025
End Date: Jun 30, 2026
Objective:
Center and Agency mission critical research focuses on generating and analyzing genome information for the sake of developing insights into the genetic basis of plant disease (including citrus greening disease also known as HLB), nutritional quality for humans (vitamins A, C, and folate), and optimal yield and quality. Data is utilized by plant producers, breeders and seed companies in the development and production of optimized fruit, vegetable and grain crops supporting farmers, processors and US consumers. Large amounts of DNA genome sequence, epigenome, transcriptome, proteome and additional genomics and phenotype data requires specialized computational infrastructure and skills. The Cooperator is known world-wide for skills in analysis of plant genomes, development of pan-genomes and developing functional insights from genome data. These analytical tools are necessary to enable ARS scientists in understanding target biological processes and the development of molecular tools that enable breeders to select improved varieties that will keep US growers and downstream product chain participants economically competitive in producing healthy and nutritious food for US consumers and for export markets. This agreement will support mission critical research on citrus ($3 billion), tomato ($3 billion), brassicas (broccoli $1 billion, cauliflower $0.3 billion), beans ($1 billion) and maize ($70 billion).
Approach:
ARS performs controlled studies in field and greenhouse settings to create plant tissues that can be analyzed for genome content and activity associated with positive crop traits including yield, quality, nutrient content, and disease resistance (e.g. HLB). Cooperator has a history of working closely with ARS to generate and analyze DNA sequence and proteome data that can be used to 1) link DNA sequences and/or gene/protein abundance to targeted traits; 2) identify genes and genetic variants that facilitate positive trait outcomes; 3) survey and analyze crop genomes to identify useful varieties to be used in breeding for target traits; 4) analyze pathogen (HLB) genomes to identify targets for control/eradication; and 5) identify and develop molecular tools and signatures that can be exploited for crop improvement. Specific analyses the Cooperator can perform includes construction of complete genome sequences, development of pan-genomes, complex multi-genome alignments, gene annotation and identification of alternate transcripts, and QTLs/eQTLs. Analyzed data leads to genetic targets for mission critical crop improvement objectives across multiple CRIS projects.