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Decoding the molecular basis of blue grain color codominance in Qingke: Integrative analysis of RNA-seq, DNA
Hongyan Li1, Youhua Yao1, Yongmei Cui1
1Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China; Qinghai Key Laboratory of Hulless Barley Genetics and Breeding/Qinghai Subcenter of National Hulless Barley Improvement/Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China.
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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