**1. Introduction**

Chrysanthemum (*Chrysanthemum morifolium* Ramat.) is one of the four most popular cut flowers worldwide and is an important component in the floral industry [1]. Branching is one of the most important agricultural traits of chrysanthemum, playing an important role in morphological formation, and affecting ornamental quality and economic value. Operations involving decapitation and/or removal of lateral buds constitute nearly 1/3 of production costs [2]. The growth and development of chrysanthemum are largely affected by various environmental factors. As a quantitative trait controlled by multiple genes, branching is affected by both the environment and the genetic background [3,4], and the underlying molecular mechanism that governs branching still needs to be elucidated.

Shoot branching is controlled by various hormone signaling pathways, including auxin, strigolactones (SLs), cytokinins (CKs) and brassinosteroids (BRs) [5]. Apical dominance is a universal phenomenon in plants and is mainly maintained by auxin. According to the auxin canalization model, auxin can act as a second messenger to regulate downstream signals or functions [6]. Moreover, auxin acts upstream of SLs and CKs, which promote and inhibit shoot branching, respectively. The biosynthesis of CKs is repressed by auxin, as the key CK biosynthesis-related enzyme Isopentenyltransferase (IPT) is downregulated by auxin [7,8]. The biosynthesis of SLs is activated by auxin, as the key SL biosynthesis-related genes *carotenoid cleavage dioxygenase*7 (*CCD7*) and *carotenoid cleavage dioxygenase8* (*CCD8*) are upregulated by auxin [9]. Through the BR signaling component

**Citation:** Sun, D.; Zhang, L.; Su, J.; Yu, Q.; Zhang, J.; Fang, W.; Wang, H.; Guan, Z.; Chen, F.; Song, A. Genetic Diversity and Genome-Wide Association Study of Architectural Traits of Spray Cut Chrysanthemum Varieties. *Horticulturae* **2022**, *8*, 458. https://doi.org/10.3390/ horticulturae8050458

Academic Editor: Luigi De Bellis

Received: 26 April 2022 Accepted: 18 May 2022 Published: 19 May 2022

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brassinazole-resistant1 (BZR1), BRs can promote increased tillering in rice [10] and bud outgrowth of tomato [11]. Sugars are a major source of carbon and energy in plants. A recent study indicated that sugars can promote initial bud outgrowth and downregulate the expression levels of *BRANCHED1* (*BRC1*) [12]. However, the gene regulatory network governing plant architecture still needs to be elucidated, and new key genes and pathways need to be identified for continued research.

The environment also plays an important role in determining plant architecture [13]. Treatments involving drought, heat and drought plus heat were shown to reduce the shoot outgrowth of *Pinus edulis* [14]. Leaf distribution, branch distribution and canopy photosynthetic rate were also influenced by temperature in potato [15]. Light is a pivotal environmental factor that influences the growth of shoots, and increasing light intensity can promote the growth of branches in herbaceous and tree species [16–18]. Nitrogen is an important nutrient element in the soil and can alter the amino acid content and influence the branch growth of plants [19]. *TaNAC2-5A* is a nitrate-inducible gene and can increase tiller numbers and spikelet numbers of wheat [20]. Various environmental factors influence the architecture of plants, which reflects their adaptation and evolution.

Genome-wide association studies (GWASs) are efficient tools to exploit complex genetic mechanisms through associations of agronomic traits with single-nucleotide polymorphisms (SNPs) within a group of individuals or natural inbred lines [21,22]. For chrysanthemum, GWASs have been used to identify genes related to waterlogging resistance and flower color [23–25], providing a reference for transgenic breeding. GWASs have also been used to identify key regulatory genes controlling plant architecture. In *Brassica napus*, plant height, branch initiation height and branch number have been used to identify functional loci [26–29]. In rice, plant height, tillering, and panicle morphology were examined, and the gibberellic acid (GA) signaling-related gene *OsSPY* was found to be associated with semidwarfism and small panicles [30]. However, no architecture-related research has been conducted in spray cut chrysanthemum, and the molecular mechanism controlling architecture still needs to be elucidated.

In this study, we performed phenotypic measurements and a statistical analysis on nine architectural traits of 195 spray cut chrysanthemum varieties in two continuous years (2019 and 2020). Because the environments of these two years were different, we defined the environment in 2019 as EN2019 and the environment in 2020 as EN2020. The effect of different environmental factors, variation and relationships of different traits and cluster analysis of all spray cut chrysanthemum were analyzed. GWAS was also performed to find latent functional genes controlling architectural traits in chrysanthemums.

#### **2. Materials and Methods**
