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United States Department of Agriculture

Agricultural Research Service

Research Project: BIOINFORMATIC METHODS AND TOOLS TO PREDICT SMALL GRAIN FIELD PERFORMANCE

Location: Plant, Soil and Nutrition Research

Title: Whole genome association mapping of grain shape variation among Oryza sativa L. germplasms based on elliptic Fourier analysis

Authors
item Iwata, Hiroyoshi - NARC, JAPAN
item Ebana, Kaworu - NIAS, JAPAN
item Uga, Yusaku - NIAS, JAPAN
item Hayashi, Takeshi - NIAS, JAPAN
item Jannink, Jean-Luc

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 20, 2009
Publication Date: July 31, 2009
Citation: Iwata, H., Ebana, K., Uga, Y., Hayashi, T., Jannink, J. 2009. Whole genome association mapping of grain shape variation among Oryza sativa L. germplasms based on elliptic Fourier analysis. Theoretical and Applied Genetics. 114(8):1437-1449.

Interpretive Summary: Although grain shape is an important cereal breeding target, it has been evaluated using simple measurements, e.g. the length : width ratio. Elliptic Fourier analysis is a method to rapidly and accurately describe any closed contour shape using universal shape descriptors. The descriptors can be further summarized using principal component analysis. A visual interpretation of the analysis can be obtained by observing how changes in each component change the expected grain shape. These analyses were applied to a germplasm collection of Asian cultivated rice. The first principal component accounted for over 90% of the total shape variation and was associated with the length : width ratio of brown rice, consistent with the fact that length : width ratio is the major genetic variation of rice grain shape. Five DNA markers were significantly associated with this component; three might be linked to previously reported QTLs. Visual analysis of allelic effects of significant markers showed that the allele of the Japonica variety “Nipponbare” produced plumper grains in four of five cases. For the second to tenth principal components, varietal effects were significant (P < 0.001), although most accounted for less than 1% of the total shape variation. Association mapping detected at least one QTL in six of these nine components showing that breeding programs can alter subtle but heritable shape characteristics associated with these components.

Technical Abstract: Although grain shape is an important cereal breeding target, it has been evaluated using simple measurements, e.g. the length : width ratio. We used elliptic Fourier analysis to evaluate grain shape variation and conducted whole genome association mapping of grain shape using a germplasm collection of Asian cultivated rice. The first principal component of elliptic Fourier descriptors, accounting for over 90% of the total variation, was associated with the length : width ratio of brown rice. That component was the most significant among the first 10 components: the length : width ratio is the major genetic variation of rice grain shape. Bayesian multilocus association mapping detected five significant markers for this component; three might be linked to previously reported QTLs. Allelic effects of significant markers were visualized using inverse Fourier transformation, showing that the allele of a Japonica variety “Nipponbare” produced plumper grains in four of five significant markers. For the second to tenth principal components, varietal effects were significant (P < 0.001), although most accounted for less than 1% of the total variation in elliptic Fourier descriptors. Association mapping detected at least one QTL in six of these nine components: breeding programs can improve the heritable shape characteristics associated with these components. For association mapping, elliptic Fourier analysis’ accuracy and high throughput are suitable; it is readily applicable to cereal crops because it is not based on rice-specific morphological characteristics but rather on universal shape descriptors that can delineate any closed contour.

Last Modified: 4/19/2014
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