Comparison of shape quantification methods for genomic prediction, and genome-wide association study of sorghum seed morphology

Lisa Sakamoto, Hiromi Kajiya-Kanegae, Koji Noshita, Hideki Takanashi, Masaaki Kobayashi, Toru Kudo, Kentaro Yano, Tsuyoshi Tokunaga, Nobuhiro Tsutsumi, Hiroyoshi Iwata

Research output: Contribution to journalArticle

Abstract

Seed shape is an important agronomic trait with continuous variation among genotypes. Therefore, the quantitative evaluation of this variation is highly important. Among geometric morphometrics methods, elliptic Fourier analysis and semi-landmark analysis are often used for the quantification of biological shape variations. Elliptic Fourier analysis is an approximation method to treat contours as a waveform. Semi-landmark analysis is a method of superimposed points in which the differences of multiple contour positions are minimized. However, no detailed comparison of these methods has been undertaken. Moreover, these shape descriptors vary when the scale and direction of the contour and the starting point of the contour trace change. Thus, these methods should be compared with respect to the standardization of the scale and direction of the contour and the starting point of the contour trace. In the present study, we evaluated seed shape variations in a sorghum (Sorghum bicolor Moench) germplasm collection to analyze the association between shape variations and genome-wide single-nucleotide polymorphisms by genomic prediction (GP) and genome-wide association studies (GWAS). In our analysis, we used all possible combinations of three shape description methods and eight standardization procedures for the scale and direction of the contour as well as the starting point of the contour trace; these combinations were compared in terms of GP accuracy and the GWAS results. We compared the shape description methods (elliptic Fourier descriptors and the coordinates of superposed pseudo-landmark points) and found that principal component analysis of their quantitative descriptors yielded similar results. Different scaling and direction standardization procedures caused differences in the principal component scores, average shape, and the results of GP and GWAS.

Original languageEnglish
Article numbere0224695
JournalPloS one
Volume14
Issue number11
DOIs
Publication statusPublished - Jan 1 2019

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Sorghum
Genome-Wide Association Study
Sorghum (Poaceae)
Seed
Seeds
Genes
Standardization
genomics
prediction
Fourier analysis
seeds
standardization
Polymorphism
methodology
Fourier Analysis
Principal component analysis
Nucleotides
genome-wide association study
Direction compound
germplasm conservation

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

Comparison of shape quantification methods for genomic prediction, and genome-wide association study of sorghum seed morphology. / Sakamoto, Lisa; Kajiya-Kanegae, Hiromi; Noshita, Koji; Takanashi, Hideki; Kobayashi, Masaaki; Kudo, Toru; Yano, Kentaro; Tokunaga, Tsuyoshi; Tsutsumi, Nobuhiro; Iwata, Hiroyoshi.

In: PloS one, Vol. 14, No. 11, e0224695, 01.01.2019.

Research output: Contribution to journalArticle

Sakamoto, L, Kajiya-Kanegae, H, Noshita, K, Takanashi, H, Kobayashi, M, Kudo, T, Yano, K, Tokunaga, T, Tsutsumi, N & Iwata, H 2019, 'Comparison of shape quantification methods for genomic prediction, and genome-wide association study of sorghum seed morphology', PloS one, vol. 14, no. 11, e0224695. https://doi.org/10.1371/journal.pone.0224695
Sakamoto, Lisa ; Kajiya-Kanegae, Hiromi ; Noshita, Koji ; Takanashi, Hideki ; Kobayashi, Masaaki ; Kudo, Toru ; Yano, Kentaro ; Tokunaga, Tsuyoshi ; Tsutsumi, Nobuhiro ; Iwata, Hiroyoshi. / Comparison of shape quantification methods for genomic prediction, and genome-wide association study of sorghum seed morphology. In: PloS one. 2019 ; Vol. 14, No. 11.
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