Genome-wide Association Study of Biological Shape Based on Elliptic Fourier Analysis: A Case Study in Rice Grain Shape Variation

摘要

Cultivars of a crop species sometimes show large infraspecific morphological variability in the organs or parts of a plant of interest to humans. The Genome-wide association study (GWAS) based on elliptic Fourier analysis is suited for the genetic dissection of infraspecific shape variation. In this chapter, a series of analyses are described for GWAS of biological shape based on elliptic Fourier analysis, using rice grain shape data as an example. Genotype data of 3,183 SNPs was used and grain shape data of 77 elliptic Fourier descriptors collected for 179 accessions from a world rice collection. Scores of the first three principal components of elliptic Fourier descriptors were used as grain shape phenotypes. In the rice accession, there was a subpopulation structure, among which the grain shape was differentiated. In GWAS, a Bayesian regression model was employed to estimate subpopulation structure effects and effects of all genome-wide SNPs simultaneously. In the first principal component, which accounted for the length-to-width ratio of the grain, two strong associations were detected on chromosome 3 and 5 at the locations that were close to known grain shape genes, GS3 and qSW5. In the second and third principal components, each of which explained minor (less than 2%) shape variation, relatively strong associations were found at several SNPs. These SNPs may be closely linked to genes controlling grain shape variation. The rice dataset and R scripts used in the analysis described in this chapter are available at http://lbm.ab.a.u-tokyo.ac.jp/ ~iwata/gwashape/.