Genotyping the Genebank: towards the genotypic characterization of all accessions in the Plant Germplasm Introduction and Testing Research Unit

Authors: Warburton, Marilyn; Cornwall, Alexander; Coyne, Clarice; Dohle, Sarah; Galewski, Paul; REDDY, UMESH - West Virginia State University; Yu, Long-Xi

Submitted to: ASA-CSSA-SSSA Annual Meeting Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 11/1/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary: There are over 100,000 distinct entries (including lines and populations) of crop species and their related wild relatives in the USDA ARS Plant Germplasm Introduction and Testing Research Unit (PGITRU) in Pullman, Wa. The utility of these entries to plant breeders, geneticists, and farmers in the US and worldwide increases in proportion to the genetic and phenotypic (trait) data available for each entry. Therefore, the scientists of the PGITRU and their collaborators are working to systematically characterize all ~100,000 entries with genetic sequencing data. This is a long-term project, and prioritization of the order in which species and crop groups will be characterized depends on funding source, technical difficulties, and stakeholder input. In the past few years, PGITRU and collaborators have generated large sequencing and genetic marker datasets for groups of genebank entries for the crop species in five curatorial programs. Around 12,000 entries have already been genotyped or are currently in the process, representing an excellent start to our long-term goal. Completed data are made available to the public on the Genetic Resources Information Network (GRIN) Global database, making each of these groups of entries ideal for future genetics and breeding improvement projects for traits of interest to the users.

Technical Abstract: The utility of the genetic diversity contained within the USDA ARS National Plant Germplasm System increases in proportion to the genetic and phenotypic data available for the accessions in the collection. A goal of the Plant Germplasm Introduction and Testing Research Unit (PGITRU) in Pullman, Wa, is the systematic characterization of all ~100,000 accessions in the collections. This is a long-term project, and prioritization of the order in which species and crop groups are characterized will depend on funding source, technical difficulties, and stakeholder input. Because SNPs will be used, species will be extensively genotyped after a genomic sequence is published. Genetically heterogeneous, heterozygous accessions (populations) may be delayed until genotyping advances enable more efficient methods, and minor crops and wild relatives will be genotyped as resources permit. In the past two years, PGITRU and collaborators have generated large SNP datasets for panels of genebank accessions for the crop species in five curatorial programs. The Temperate Forage Legume program and the Alfalfa Genetics program have characterized over 5600 accessions of alfalfa and related Medicago spp.; the Agronomy program has had 865 safflower accessions genotyped and is in the process of genotyping 441 accessions of Indian Ricegrass; the Phaseolus program has genotyped 800 accessions of lima beans; the Horticulture Crops program has had 150 accessions of lettuce genotyped; and the Cool Season Food Legumes program has had ~2500 peas, ~2000 lentil, 424 chickpea and 114 bitter vetch accessions genotyped. Genotyping of these crops has been via Whole Genome sequencing, Genotype By Sequencing and other skim sequencing, DArTag arrays, and Illumina HiSeq sequencing of genic regions. Completed data are made available to the public on the Genetic Resources Information Network (GRIN) Global database, making each of these panels of accessions ideal for future GWAS projects for traits of interest to the users.