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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #349105

Research Project: Genomic Approaches and Genetic Resources for Improving Rice Yield and Grain Quality

Location: Dale Bumpers National Rice Research Center

Title: Dissection of genetic architecture of grain chalk using NIR spectroscopy

Author
item Barnaby, Jinyoung
item Huggins, Trevis
item Lee, Hoonsoo - Us Forest Service (FS)
item Oh, Mirae - Us Forest Service (FS)
item Mcclung, Anna
item Mcclung, Anna
item Pinson, Shannon
item Tarpley, Lee - Texas A&M University
item Kim, Moon
item Edwards, Jeremy

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 1/19/2018
Publication Date: 10/1/2018
Citation: Barnaby, J.Y., Huggins, T.D., Lee, H., Oh, M., McClung, A.M., Pinson, S.R., Tarpley, L., Kim, M.S., Edwards, J. 2018. Dissection of genetic architecture of grain chalk using NIR spectroscopy. Rice Technical Working Group Meeting Proceedings. February 19-22, 2018, San Diego, California. Electronic Publication.

Interpretive Summary:

Technical Abstract: Chalk is a major quality characteristic that causes grain breakage during milling and loss of crop value. In this study, we sought to elucidate the quantitatively inherited grain chalk trait in rice and to conduct genome-wide association mapping to identify SNPs and candidate genes associated with grain chalk. Whole grain rice (dehulled rough rice) of the USDA mini-core collection rice germplasm grown in AR (2009 and 2010) and TX (2008) was evaluated using a high throughput phenotyping tool, hyperspectral imaging system. This diversity panel has approximately 220 varieties originating from around the world, includes representatives of the five subpopulations of O. sativa, and has an associated genomic dataset of 3.3 million SNP markers. Our results showed that a wavelength range of 600-700 nm of visible NIR (VisNIR) spectroscopy was significantly associated with the grain chalk phenotype, and further identified several chalk related genes, i.e. phosphatase protein, serine/threonine kinase, phospholipase, glycosyl hydrolase family proteins, that were identified previously, as well as other novel genes. Furthermore, quantification of the chalk trait using this imaging system was validated using a bi-parental mapping population segregating for grain chalk. These results indicate the value of using hyperspectral imaging as a means of non-destructive high throughput phenotyping for rice grain chalk and suggest the possibility of using this method for other physicochemical grain properties.