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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #370670

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: Differentiating sub-population, production environment and grain chalk by hyperspectral imaging

item Barnaby, Jinyoung
item Huggins, Trevis
item LEE, HOONSOO - Chungnam National University
item McClung, Anna
item Pinson, Shannon
item OH, MIRAE - National Institute Of Animal Science
item Bauchan, Gary
item TARPLEY, LEE - Texas A&M University
item LEE, KANGJIN - National Institute Of Horticultural & Herbal Science (NIHHS)
item Kim, Moon
item Edwards, Jeremy

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 12/4/2019
Publication Date: 1/6/2021
Citation: Barnaby, J.Y., Huggins, T.D., Lee, H., McClung, A.M., Pinson, S.R., Oh, M., Bauchan, G.R., Tarpley, L., Lee, K., Kim, M.S., Edwards, J. 2021. Differentiating sub-population, production environment and grain chalk by hyperspectral imaging. Proceedings of 38th Rice Technical Working Group Meeting, February 24-27, 2020, Orange Beach, Alabama. p 177. Electronic Publication.

Interpretive Summary:

Technical Abstract: Rice grain quality influences crop value and is important to growers, millers, and processors as well as consumers. Grain quality in rice is determined by multiple factors including starch composition, cooking quality, and grain size, shape, and translucency (chalky appearance). High grain chalk causes grain breakage during milling and loss of crop value impacting domestic and export markets. Molecular markers are sought as tools for marker-assisted selection (MAS) in rice breeding for traits like grain quality that are complex, difficult to phenotype and are influenced by the environment. Furthermore, Genome-Wide Association mapping Studies (GWAS) have been used in rice to map a wide range of traits. One of the bottlenecks, however, in mapping of genes for grain quality traits is the intensive labor, time, and expense required to phenotype the diversity of physicochemical traits impacting rice quality. High throughput Vis/NIR spectroscopy phenotyping is a rapid analytical tool that assesses samples by utilizing visible and invisible regions of the spectrum. The aim of this study was to determine if Vis/NIR hyperspectral imaging of whole grain rice can discern differences in rice sub-population structure and production environment, as well as grain quality traits. Whole grain (brown) rice samples from the USDA mini-core collection grown in multiple locations were evaluated using hyperspectral imaging and compared with results from standard grain quality phenotyping. Loci associated with hyperspectral values were mapped in the mini-core with 3.2 million SNPs in a genome-wide association study (GWAS). Our results show that visible and near infra-red (Vis/NIR) spectroscopy can classify rice according to sub-population and production environment based on differences in physicochemical properties. The 702-900 nm range of the NIR spectrum was associated with the undesirable chalky grain trait. GWAS revealed that grain chalk and hyperspectral variation share genomic regions containing several plausible candidate genes for grain chalkiness. Hyperspectral quantification of grain chalk was validated using a segregating bi-parental mapping population. These results indicate that Vis/NIR can be used for non-destructive high throughput phenotyping of grain chalk and, potentially, other grain quality properties.