Open Access

ARTICLE

Genome-Wide Scanning Analysis for MYB and MADS in Hydrangea macrophylla and the Inflorescence Type Related Candidate Genes Expression Analysis

Qunlu Liu^1,#, Fiza Liaquat^1,2,#, Qiqi Tang¹, Jun Yang^3,4, Shuai Qiu⁵, Amber Malik², Kang Ye^3,4, Kai Gao⁵, Jun Qin^3,4,*

1 Department of Landscape Architecture, School of Design, Shanghai Jiao Tong University, Shanghai, 200240, China
2 School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
3 Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
4 Shanghai Engineering Research Center of Urban Tree Ecology and Applications, Shanghai, 200020, China
5 Hangzhou Landscaping Incorporated Company, Hangzhou, 310020, China

* Corresponding Author: Jun Qin. Email:
# These authors contributed equally to this work

(This article belongs to the Special Issue: Nutrient Dynamics in Improving Plant Productivity and Ecosystem Functioning: Adaptation and Resource Conservation)

Phyton-International Journal of Experimental Botany 2025, 94(11), 3539-3562. https://doi.org/10.32604/phyton.2025.071989

Received 17 August 2025; Accepted 20 October 2025; Issue published 01 December 2025

Abstract

Hydrangea macrophylla is a popular ornamental shrub with a lot of economic and aesthetic value. It is known for its different flower shapes (lacecap and mophead) and the way its flowers change color depending on the pH of the soil. Even though it is important for gardening, we still don’t know much about the molecular processes that lead to flower growth. The purpose of this study was to find and study SNP-related genes and transcription factors that are connected to the growth of H. macrophylla flowers. Genome-wide SNP analysis identified 11 SNPs associated with MYB transcription factors and 10 SNPs linked to a MADS-box SEP1 gene, highlighting their potential role in inflorescence-type regulation. These SNPs provide genomic resources for functional validation and marker-assisted breeding in Hydrangea macrophylla. We found the MYB and MADS-box gene families, which are important for pigmentation and flower organ identity, through an analysis of the transcriptome and gene expression. The MYB family has 73 1R-MYBs, 105 R2R3-MYBs, and 4 3R-MYBs. The MADS-box family had 42 Type I (M-type) members and 36 Type II (MIKC-type) members. Motif and phylogenetic analysis showed that certain domains were preserved. For example, R2R3-MYBs and MIKC-type MADS genes are grouped with Arabidopsis orthologs, which suggests that their functions are also preserved. There was a clear link between the greatest expression of MADS-box genes and the distinct phases of floral bud differentiation. Some MYB genes, on the other hand, showed alternative expression patterns that may help petals or sepals develop. qRT-PCR validation of representative MYB and MADS-box genes corroborated the transcriptome-based expression profiles, supporting their role in flower development and inflorescence-type regulation.

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