Decoding the molecular basis of blue grain color codominance in Qingke: Integrative analysis of RNA-seq, DNA methylation, and miRNA-seq.

Hongyan Li; Youhua Yao; Yongmei Cui; Xin Li; Xiaohua Yao; Kunlun Wu

doi:10.1016/j.ygeno.2026.111294

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Decoding the molecular basis of blue grain color codominance in Qingke: Integrative analysis of RNA-seq, DNA methylation, and miRNA-seq.

Hongyan Li·Youhua Yao·Yongmei Cui·Xin Li·Xiaohua Yao·Kunlun Wu

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Abstract

The grains on single spike of the F1 generation from the cross between blue- and white-grained Qingke (Hordeum vulgare L. var. nudum Hook. f.) are randomly distributed in blue and white colors. This study integrated data from RNA-seq, DNA methylation, and miRNA-seq to analyze this trait. The results showed that the HvF3'5'H gene is likely central to the development of this codominant phenotype. Through cross-validation of three omics approaches, it was found that the HvMYB gene targeted by miR858-z, as well as the WRKY24 and At3g44326 genes targeted by novel-m0152-5p, novel-m0153-5p, and novel-m0154-5p, are correlated with DNA methylation. qRT-PCR analysis confirmed that the four aforementioned genes exhibited variety-specific and developmental stage-specific expression patterns. This study dissects the regulatory network underlying the codominant blue and white grain color divergence on a single Qingke spike from a multi-omics perspective.

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DNA Methylation MicroRNAs Hordeum RNA-Seq Pigmentation Plant Proteins Gene Expression Regulation, Plant Codominance of blue and white grain colors DNA methylation RNA-seq miRNA-seq Journal Article

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Hongyan Li, Youhua Yao, Yongmei Cui, Xin Li, Xiaohua Yao, Kunlun Wu. 2026-07-16. Decoding the molecular basis of blue grain color codominance in Qingke: Integrative analysis of RNA-seq, DNA methylation, and miRNA-seq.. https://doi.org/10.1016/j.ygeno.2026.111294

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