*3.5. GWAS and Mining of Genes Controlling Plant Architecture*

Combining the data concerning 191,417 high-quality SNPs and the data of the nine phenotypic traits in EN2019 and EN2020, we performed a GWAS via the cMLM method of GAPIT software and the cMLM and MLM methods of TASSEL software, with the PC matrix and kinship matrix serving as covariates. When the significance threshold was <sup>1</sup> × <sup>10</sup><sup>−</sup>3, 281 SNPs associated with each trait and corresponding PVE values were obtained. According to the data in Tables S4–S16, GAPIT software revealed 113 SNPs associated with plant architecture in EN2019 and 93 SNPs in EN2020, and the PVE values ranged from 24.06% to 44.46% in EN2019 and from 25.20% to 44.48% in EN2020. The cMLM model of TASSEL software revealed 35 SNPs associated with plant architecture in EN2019 and 40 SNPs in EN2020, and the PVE values ranged from 23.33% to 49.63% in EN2019 and from 22.37% to 59.73% in EN2020.

Among the identified SNPs, 18 were detected by GAPIT. 5\_\_55325230, 5\_\_55325289 and 10\_\_268875261 were associated with plant height in EN2019 and EN2020; 27\_\_13304666 was associated with stem diameter in EN2019 and EN2020; 9\_193339518 was associated with primary branch diameter in EN2019 and EN2020. Eight SNPs (17\_\_232431589, 27\_\_194241646, 27\_\_194241707, 17\_\_46614191, 8\_\_66464970, 27\_\_55624912, 27\_\_112009133 and 14\_\_58564373) were associated with number of leaf nodes and total number of lateral buds in EN2019. Five SNPs (3\_\_163391415, 25\_\_13632558, 25\_\_13632658, 22\_\_108888654

and 7\_\_185418131) were associated with number of leaf nodes and total number of lateral buds in EN2020. According to the cMLM model of TASSEL, the same 10 SNPs were detected: 23\_\_171200599 was associated with plant height in EN2019 and EN2020, 8 SNPs (11\_\_125802422, 17\_\_280870788, 21\_\_242369101, 24\_\_15091361, 23\_\_293787130, 23\_\_293967285, 23\_\_294075102 and 23\_\_308947968) were associated with number of leaf nodes and total number of lateral buds in EN2019, and 9\_\_215337463 was associated with number of leaf nodes and total number of lateral buds in EN2020. Additionally, 19\_\_104723464 was associated with number of lateral flower buds in EN2020. According to the MLM method of TASSEL, 23\_\_171200599 was also associated with plant height in EN2020; 11\_\_125802422 was associated with total number of lateral buds in EN2019; 17\_\_280870788 was associated with number of leaf nodes in EN2019; 21\_\_242369101, 24\_\_15091361, 23\_\_293787130, 23\_\_293967285, 23\_\_294075102 and 23\_\_308947968 were associated with the number of leaf nodes and total number of lateral buds in EN2019; 9\_\_215337463 was associated with number of leaf nodes in EN2020.

After comparing genes related to SNP loci of three models, the cMLM model of TASSEL software was chosen finally. Combining the annotation of TAIR, candidate genes are shown in Table 3, and the Manhattan plots of cMLM model of TASSEL can be found in supplementary file S1. We identified four candidate genes: *phyB*, *BRH1*, *CPC* and *bZIP16*.

**Table 3.** List of SNP sites, candidate genes, and functional annotation for selected architectural traits in spray cut chrysanthemums identified with cMLM model of TASSEL.

