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ARS Home » Southeast Area » Stoneville, Mississippi » Genomics and Bioinformatics Research » Research » Research Project #441416

Research Project: Genomic Selection is Looming: Building a Robust Genotype-to-Phenotype Platform to Revolutionize Public Cotton Breeding

Location: Genomics and Bioinformatics Research

Project Number: 6066-21310-006-019-I
Project Type: Interagency Reimbursable Agreement

Start Date: Dec 15, 2021
End Date: Dec 14, 2025

Our long-term goal is to enable genetic and phenotypic technology-directed breeding of upland cotton (Gossypium hirsutum L.) in public breeding programs. The overarching goal of this project is to facilitate collaboration between public upland cotton breeding programs by doing the groundwork to develop the necessary practical tools required to deploy genome-assisted selection for desirable traits. Overall, we hope to increase accessibility and usefulness of existing resources by filling in the gaps left behind during the growth of cotton genomics to breeding applications. The specific objectives of this project are: 1) Develop a standardized, publicly available, shared system to evaluate haplotypes via low-cost, high-throughput, genotyping in cultivated upland cotton by synthesizing existing information regarding genetic diversity and trait architecture. 2) Implement a standardized phenotyping database and integrated informatics system for public cotton breeding programs based on the common Breeding API (BrAPI) language. 3) Initiate and test genome-assisted selection in multiple public cotton breeding programs to develop recommendations and procedures for public breeders

Initially in Objective 1, all public data sources of genomic information and trait localization efforts (in the form of quantitative trait loci and genome wide association studies) will be assimilated and integrated into a joint data set. This information will be referenced to the most applicable current reference to evaluate haplotype blocks and their relationship to trait locations; which will be used to inform overlap with single nucleotide polymorphism data on current genotyping platforms. These integrated data sets will be used to inform development of a new genotyping platform which will be cost effective enough to apply at scale in breeding programs. In Objective 2, we will work with Washington State University (WSU) and Breeding Insight (BI); which are both developing Breeding API (BrAPI) enabled systems for collecting phenotyping information for breeding programs. BrAPI will allow for direct communication and this proposal will enable building supporting tools and training systems for breeders to select which interface they prefer and information can be assimilated and shared across the WSU and BI platforms in the background. In this proposal we will congregate the 3 public breeding programs of focus here and get them working on one of those systems as well as importing historical data. We will also collaborate with the other ARS groups as well as any public groups that which to participate to develop an ontologies list of traits being collected and the associated methods for collection to represent the initial phenotypic trait lists to populate the databases for data collection. In Objective 3, we will utilize the systems developed in Objective 2 as well as the genotyping platform developed in Objective 1; to test and initiate implementation of genomic selection in 2 public breeding programs and a specific trait mapping project in the remaining program which focuses on high-throughput phenotyping.