Multi-locus genome-wide association studies reveal the dynamic genetic architecture of flowering time in chrysanthemum

• Published in: Plant cell reports 2024-04, Vol.43 (4), p.84-84, Article 84
• Main Authors: Su, Jiangshuo, Zeng, Junwei, Wang, Siyue, Zhang, Xuefeng, Zhao, Limin, Wen, Shiyun, Zhang, Fei, Jiang, Jiafu, Chen, Fadi
• Format: Article
• Language: English
• Subjects: Annotations; Biomedical and Life Sciences; Biotechnology; Budding; Cell Biology; Coefficient of variation; Flowering; Genes; Genome-wide association studies; Genomes; Haplotypes; Heritability; Life Sciences; Nucleotides; Original Article; Ornamental plants; Phenotypes; Phenotypic variations; Plant Biochemistry; Plant breeding; Plant Sciences; Single-nucleotide polymorphism; Transcriptomics
• ISSN: 0721-7714; 1432-203X
• DOI: 10.1007/s00299-024-03172-4

Key message The dynamic genetic architecture of flowering time in chrysanthemum was elucidated by GWAS. Thirty-six known genes and 14 candidate genes were identified around the stable QTNs and QEIs, among which ERF-1 was highlighted. Flowering time (FT) adaptation is one of the major breeding goals in chrysanthemum, a multipurpose ornamental plant. In order to reveal the dynamic genetic architecture of FT in chrysanthemum, phenotype investigation of ten FT-related traits was conducted on 169 entries in 2 environments. The broad-sense heritability of five non-conditional FT traits, i.e., budding (FBD), visible coloring (VC), early opening (EO), full-bloom (OF) and decay period (DP), ranged from 56.93 to 84.26%, which were higher than that of the five derived conditional FT traits (38.51–75.13%). The phenotypic variation coefficients of OF_EO and DP_OF were relatively large ranging from 30.59 to 36.17%. Based on 375,865 SNPs, the compressed variance component mixed linear model 3VmrMLM was applied for a multi-locus genome-wide association study (GWAS). As a result, 313 quantitative trait nucleotides (QTNs) were identified for the non-conditional FT traits in single-environment analysis, while 119 QTNs and 67 QTN-by-environment interactions (QEIs) were identified in multi-environment analysis. As for the conditional traits, 343 QTNs were detected in single-environment analysis, and 119 QTNs and 83 QEIs were identified in multi- environment analysis. Among the genes around stable QTNs and QEIs, 36 were orthologs of known FT genes in Arabidopsis and other plants; 14 candidates were mined by combining the transcriptomics data and functional annotation, including ERF-1 , ACA10 , and FOP1 . Furthermore, the haplotype analysis of ERF-1 revealed six elite accessions with extreme FBD. Our findings contribute to the understanding of dynamic genetic architecture of FT and provide valuable resources for future chrysanthemum molecular breeding programs.