Location: Plant, Soil and Nutrition Research
Project Number: 8062-21000-052-004-A
Project Type: Cooperative Agreement
Start Date: Sep 1, 2023
End Date: Aug 31, 2024
Objective:
The proposed work is a joint effort to develop genomic and bioinformatics approaches to accelerate the breeding of crops and to discover genetic mechanisms across the grasses that can be used to enhance the sustainability of maize by improving nutrient recycling.
The two goals are:
1. Leverage knowledge developed in crops and model systems to create functionally based genomic selection models that work across species and
2. Identify genes and regulation patterns that will enable maize production to be more sustainable.
a. Develop transferable DNA level models that predict gene expression and protein activities.
b. Develop systems for plant breeders and geneticists to deploy haplotype and gene activity models across species.
c. Identify the genes and regulatory patterns used by maize and maize’s related grasses to adapt to temperature extremes.
d. Identify the genes and regulatory patterns used by maize and maize’s related grasses to recycle nutrients.
Approach:
1. Genomic datasets will be generated for maize and other grasses under a wide range of abiotic conditions and tissues. These will be integrated with and compared to other plant datasets to train machine learning models that accurately predict RNA expression and protein levels.
2. Software systems will be developed to efficiently share genomic haplotypes and inferences of gene activity levels to plant geneticists and breeders. This will involve developing webservices (e.g., Genomics Breeder Workbench), databases (e.g., PHG – Practical Haplotype Graph), algorithms (e.g., TASSEL), and breeder/geneticist accessible software libraries (e.g., rPHG, rTASSEL, BioKotlin).
3. The project of identifying the genes for enhancing temperature adaptation and nutrient recycling will be comprised of the following:
a. Thirty public sector research groups across the country are part of the U.S. Genomes To Field (G2F) Initiative, an experiment looking at Genotype by Environment to understand how maize genetics interacts with its environment.
This project uses genomics to sequence and profile the germplasm in this national experiment and participates in high intensity phenotypic evaluation and analysis to understand how the environment interacts with genetics.
b. Cold tolerance genes and regulation patterns will be identified in Tripsacum dactyloides and other grasses through genetic mapping, cross speciation comparative mapping, and RNA and protein profiling. Hypotheses will be tested by editing or transgenics in maize.
c. Perennial grasses naturally recycle nitrogen, phosphorus, and enhance soil carbon. The nutrient recycling genes and regulation patterns will be identified in perennial grasses through genetic mapping, cross speciation comparative mapping, and RNA and protein profiling. Hypotheses will be tested by editing or transgenics in maize.
