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Title: Rice diversity panels available through the genetic stocks oryza collection

item McClung, Anna
item Bernhardt, Lorie
item Edwards, Jeremy
item Eizenga, Georgia

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 1/19/2018
Publication Date: 10/16/2018
Citation: McClung, A.M., Bernhardt, L., Edwards, J., Eizenga, G.C. 2018. Rice diversity panels available through the genetic stocks oryza collection. Rice Technical Working Group Meeting Proceedings. February 19-22, 2018, San Diego, California. p. 80.

Interpretive Summary:

Technical Abstract: The Genetic Stocks Oryza (GSOR) Collection was established in 2004 at the USDA-ARS, Dale Bumpers National Rice Research Center (DBNRRC) located in Stuttgart, AR. The mission of GSOR is to provide unique genetic resources to the rice research community for genetic and genomics related research. GSOR is part of the National Plant Germplasm System (NPGS) and the accessions are maintained and distributed from DBNRRC as long as they are considered of value to researchers and seed supplies are available. The collection includes mutants, mapping populations, and diversity panels. Currently, five diversity panels are available for distribution, with another under development. All of the diversity panels have been created as a means of capturing allelic variability within the scope of the targeted population. Each panel has been created from a single plant, pure seed source of each accession in the set and the panel has been phenotyped and genotyped to varying degrees. Seed is freely available for most accessions, however some have restrictions and/or require a material transfer agreement. The USDA Core Collection was provided to GSOR in 2007 and consists of 1794 global rice varieties representing ~10% of the whole world rice collection that is curated by NPGS. The USDA Core Collection has been genotyped with 72 genetic markers and characterized for over 50 agronomic, biotic stress, and grain quality traits. Images of panicles and whole grain (dehulled) rice are accessible for each accession through the NPGS Germplasm Resource Information Network (GRIN). Within the USDA Core Collection is the Mini-core which is a subset of 217 accessions that represent ~1% of the NPGS rice collection. The Mini-core has been extensively phenotyped and, recently, resequencing of the panel has been completed with the data now available to the public. The USA Rice Pedigree Panel was developed as a result of funding from USDA-NIFA (National Institute of Food and Agriculture) in a collaborative project with Cornell University and it consists of 153 accessions that represent most of the germplasm used in over 100 years of rice breeding in the southern USA. Each accession has been phenotyped for height and heading, and genetically characterized using genotyping-by-sequencing (GBS). High resolution images of the plant at heading, seed and whole grain rice are available through GSOR. The Rice Diversity Panel 1 (RDP1) was developed through funding from the National Science Foundation in a collaborative project with Cornell University. The 423 RDP1 accessions that originate from 79 countries are available through GSOR. The GSOR website provides data on 29 plant, panicle, and seed traits, and 43 genetic markers, as well as, high resolution images of panicles, seed, and whole grain rice of the RDP1 accessions. In addition, allelic data using some 700,000 SNPs is available to the public for this panel. The same 700,000 SNP genotyping platform was used to characterize the Rice Diversity Panel 2 (RDP2) which was developed by the International Rice Research Institute (IRRI), Los Banos, The Philippines. The RDP2 includes 1,445 accessions from 92 countries. The panel was imported into the USA and, through a multi-institutional collaboration, brought through quarantine within two years. Images of the original grain received from IRRI are on the GSOR website. Some of the accessions failed successful grow-out in quarantine facilities and had to be reimported. However, seed production was sufficient for distribution of 873 accessions following quarantine, while 460 accessions were rejuvenated at Stuttgart in the field during 2016 and 2017. For these latter accessions, plant images at heading and phenotypic assessment of six plant traits are available. Soon the DBNRRC will add a new Tropical Japonica Core collection to GSOR. The collection will include some 500 global acces