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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #389811

Research Project: Gene Discovery and Crop Design for Current and New Rice Management Practices and Market Opportunities

Location: Dale Bumpers National Rice Research Center

Title: Unraveling the relationship between phenotype based classification of the oryza rufipogon species complex and genotypic subpopulations

item Eizenga, Georgia
item KIM, HYUN-JUNG - Cornell University
item JUNG, JANELLE - Cornell University
item MCNALLY, KENNETH - International Rice Research Institute
item GREENBERG, ANTHONY - Bayesic Research
item Edwards, Jeremy
item NAREDO, ELIZABETH - International Rice Research Institute
item BANATICLA-HILARIO, CELESTE - International Rice Research Institute
item HARRINGTON, SANDRA - Cornell University
item SHI, YUXIN - Cornell University
item KIMBALL, JENNIFER - University Of Minnesota
item HARPER, LISA - Cornell University
item MCCOUCH, SUSAN - Cornell University

Submitted to: Crop Science Society of America
Publication Type: Abstract Only
Publication Acceptance Date: 11/12/2021
Publication Date: 11/12/2021
Citation: Eizenga, G.C., Kim,H., Jung, J., McNally, K.L., Greenberg, A.J., Edwards, J., Naredo, E.B., Banaticla-Hilario, C.N., Harrington, S.E., Shi, Y., Kimball, J.A., Harper, L.A., McCouch, S.R. 2021. Unraveling the relationship between phenotype based classification of the oryza rufipogon species complex and genotypic subpopulations. Abstract. ASA,CSSA,SSSA International Annual Meeting. Salt Lake City, Utah.

Interpretive Summary:

Technical Abstract: Crop wild relatives represent valuable reservoirs of novel variation for breeding but their populations are threatened in declining natural habitats, are sparsely represented in genebanks, and most are poorly characterized. Here we focus on the wild progenitor of Asian rice (Oryza sativa L.), often referred to as the Oryza rufipogon species complex (ORSC). A collection of 240 diverse ORSC accessions, previously characterized by genotyping-by-sequencing (113,739 SNPs), was phenotyped for 44 traits associated with plant, panicle, and seed morphology in the screenhouse at the International Rice Research Institute, Philippines. These traits included heritable phenotypes often recorded as passport data by genebanks. Over 100 of these ORSC accessions were also phenotyped in the greenhouse for 16 traits at Ithaca, New York and for 18 traits at Stuttgart, Arkansas, USA. We implemented a Bayesian Gaussian mixture model to infer accession groups from a subset of these phenotypic data and ascertained four phenotype-based group assignments. We used concordance between the previously reported six genotypic populations and four phenotype-based groups to identify a suite of phenotypic traits that can reliably differentiate the ORSC populations. We further identified traits, whether measured in the tropics or temperate regions, that can discriminate groups and facilitate genebank management of ORSC collections. Phenotypic groups are loosely associated with life history (perenniality versus annuality) and mating habit (self-versus cross-pollinated), and harbor differing levels of introgression from O. sativa. The six ORSC genetic subpopulations detected among these 240 accessions agreed with the six ORSC genetic subpopulations identified in a collection of 446 diverse ORSC accessions, thus validating our subpopulation designations. These genotypic results suggest accessions from the three geographically isolated subpopulations may harbor the most novel variation useful for rice improvement and disclosing the genetic composition of ancient rice subpopulations.