Multivariate colorimetric phenotyping reveals genetic loci associated with soybean seed coat pigmentation and epicatechin accumulation.

Abstract

Seed coat pigmentation in soybean is controlled by complex genetic mechanisms involving structural and regulatory genes in the flavonoid biosynthetic pathway. Although brown seed coats are often associated with epicatechin (EC) accumulation, visual classification alone cannot reliably predict EC content. To quantitatively characterize seed coat coloration and its relationship with EC accumulation, we evaluated multivariate colorimetric traits (L*, a*, and b* values in the CIELAB color space) in 235 recombinant inbred lines (RILs) derived from Jinpung (yellow seed coat) and IT109098 (greenish-brown seed coat). Principal component analysis (PCA) of L*, a*, and b* values revealed that genotypes with detectable EC were confined to specific regions of the multivariate color space, indicating that EC accumulation is associated with coordinated color balance rather than overall pigmentation intensity. RILs with high EC content showed significantly lower L* (32.76 ± 2.49) and b* (13.18 ± 2.66) values and higher a* values (5.47 ± 1.31) than those with low EC content. Quantitative trait loci (QTL) mapping identified thirteen loci associated with L*, a*, b*, and principal component scores across chromosomes 01, 05, 06, 08, and 19 A major locus on chromosome 08 near the classical I locus explained a large proportion of phenotypic variance in pigmentation traits. In addition, loci on chromosomes 06 and 19 were associated with integrated color components, suggesting quantitative modulation of EC accumulation. Candidate genes within these regions included flavonoid 3'-hydroxylase and transcription factors such as MYB117 , MYB60 , and TCP5 , supported by sequence variation and differential expression analyses. These findings demonstrate that multivariate colorimetric traits provide a useful phenotyping framework for dissecting seed coat pigmentation and EC accumulation and for pre-selecting high-EC soybean lines. Supplementary information The online version contains supplementary material available at 10.1007/s11032-026-01655-8.

Plant phenotyping relevance

大豆種皮の色をCIELAB色値で定量化し、多変量解析による表現型フレームワークとして遺伝子型・EC蓄積との関連を評価しており、色表現型の取得と解析が研究の中心です。

Code and data availability

The paper reports colorimetric phenotyping (L*, a*, b*), PCA, and QTL mapping of a Jinpung × IT109098 soybean RIL population, but provides no public repository deposit, no author analysis code URL, and no image/sensor data deposit. The Data availability statement only points to the article and its supplementary file, a

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