ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Development and EvoDevo
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1674383
Integrative GWAS and Transcriptomic Analyses Reveal Regulatory Genes Controlling Shoot Branching in Sunflower
Provisionally accepted
Yiyi Sun1Yanwen Wang1Jingyan Bai1Jiatong Guo1Guiting Li2Xiaojie Yang2Qiuzhen Tian2Yingying Huang2Shuping Lv2
Hengchun Cao2*Lingyun Liu1*- 1Henan University, Kaifeng, China
- 2Henan Academy of Agricultural Sciences (HNAAS), Zhengzhou, China
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Abstract Shoot branching plays a crucial role in shaping plant architecture, influencing both yield potential and ornamental qualities in sunflower (Helianthus annuus L.), but the genetic mechanisms underlying this trait are still not well understood. To investigate this, we performed a genome-wide association study (GWAS) using 82 sunflower accessions with diverse branching phenotypes and identified 62 significant single-nucleotide polymorphisms (SNPs). Of these, sixty SNPs clustered within a 12.40–17.13 Mb region on chromosome 10. Linkage disequilibrium (LD) block analysis delineated this region, containing 113 genes. Integration of transcriptomic analysis of shoot apical meristems of both branched and unbranched lines revealed 12 differentially expressed genes (DEGs) within the GWAS interval, including two long non-coding RNAs (lncRNAs) that demonstrated significant co-expression with several protein-coding candidates. Notably, one gene (HanXRQr2_Chr10g0423211) harbored a nonsynonymous SNP and displayed moderate differences in expression. Tissue-specific RNA-seq and qRT-PCR confirmed the involvement of these 13 genes in branching regulation. Overall, this study advances our understanding of the genetic mechanisms controlling shoot branching in sunflower and highlights candidate genes for targeted breeding to enhance plant architecture.
Keywords: sunflower, shoot branching, plant architecture, GWAS, transcriptome analysis
Received: 28 Jul 2025; Accepted: 05 Sep 2025.
Copyright: © 2025 Sun, Wang, Bai, Guo, Li, Yang, Tian, Huang, Lv, Cao and Liu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Hengchun Cao, Henan Academy of Agricultural Sciences (HNAAS), Zhengzhou, China
Lingyun Liu, Henan University, Kaifeng, China
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