Enhancing the searchability, breeding utility and efficient management of germplasm accessions in the USDA-ARS rice collection

Authors: McClung, Anna; Edwards, Jeremy; Jia, Melissa; Huggins, Trevis; Bockelman, Harold; ALI, LIAKAT - University Of Missouri; Eizenga, Georgia

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/23/2020
Publication Date: 6/29/2020
Citation: McClung, A.M., Edwards, J., Jia, M.H., Huggins, T.D., Bockelman, H.E., Ali, L., Eizenga, G.C. 2020. Enhancing the searchability, breeding utility and efficient management of germplasm accessions in the USDA-ARS rice collection. Crop Science. https://doi.org/10.1002/csc2.20256.
DOI: https://doi.org/10.1002/csc2.20256

Interpretive Summary: Most of the world’s crop plants have a treasure chest of phenotypic and genotypic diversity in seed of historical cultivars that were grown before modern breeding techniques were developed as well as cultivars that are grown in widely different ecosystems. This genetic diversity needs to be preserved for future generations in order to combat the mounting global challenges of climate change, improving crop productivity, increasing crop value, and preserving the sustainability of agriculture. Genebanks were established worldwide to preserve and characterize this diversity so that it can be utilized for crop improvement, both now and for generations to come. Some problems faced by genebank managers include mis-identified cultivars, seed mixtures, redundant accessions and lack of resources to adequately characterize the collection for traits of value. In this study we describe how DNA markers can enhance the efficiency and effectiveness of curation of the 19,000 rice accessions in the USDA-ARS National Small Grains Collection, identified as the “Rice-NSGC”. We developed genetic markers that were discerning of Oryza species and subspecies classification. We also demonstrated DNA markers that are associated with sensory and cooking properties, disease resistance, plant height, and red bran that can be used in the Rice-NSGC to help breeders identify germplasm that would be valuable in development of new cultivars.

Technical Abstract: Genebanks conserve world-wide crop genetic diversity in systematically assembled and maintained ex situ collections to be used by current and future generations of plant breeders to improve the productivity, value, and sustainability of agriculture. The USDA-ARS-National Plant Germplasm System, National Small Grains Collection (NSGC) for rice (Oryza sativa L.), identified as “Rice-NSGC”, was established for this purpose. Some challenges that emerge in managing genebanks include providing sufficient and accurate accession information to facilitate searching of the collection, redundant accessions, seed mixtures, mis-identified accessions, gaps in germplasm diversity, and lack of adequate resources to thoroughly characterize the collection. To address these issues a system was implemented for genotyping the Rice-NSGC with molecular markers, including 11 fingerprint markers (FPM), 1 subspecies marker, and 14 trait specific markers (TSM). Utilizing these markers, accessions were classified by species, O. sativa or O. glaberrima; by subspecies, indica or japonica; by subpopulation aromatic, indica, aus, temperate or tropical japonica; and in many cases, by cultivar. The TSM were used to validate phenotypic data for fragrance, red pericarp color, resistance to rice blast disease, leaf and hull pubescence, apparent amylose content, starch pasting properties and gelatinization temperature, and plant height. Discrepancies between the genotypic and phenotypic data provide useful quality control information for managing the collection, but also may represent opportunities to identify accessions harboring novel alleles for the discrepant trait. Genotyping a panel of rice cultivars important to U.S. breeding programs with the FPM and TSM demonstrated that a small panel of markers is adequate differentiating among important US rice cultivars. This study will be the basis for adding TSM descriptors to the Rice-NSGC database, reducing redundancies, correcting mis-identified accessions, thus increasing the value of the collection for rice breeding programs and provide new opportunities for gene discovery.