State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095, Jiangsu Province, China.
Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, China.
Plant Cell Rep. 2024 Mar 6;43(4):84. doi: 10.1007/s00299-024-03172-4.
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.
通过 GWAS 阐明了菊花开花时间的动态遗传结构。在稳定的 QTN 和 QEI 周围鉴定了 36 个已知基因和 14 个候选基因，其中 ERF-1 较为突出。开花时间（FT）适应是菊花（一种多用途观赏植物）的主要育种目标之一。为了揭示菊花 FT 的动态遗传结构，在 2 种环境下对 169 个品系的 10 个 FT 相关性状进行了表型研究。5 个非条件 FT 性状（萌芽（FBD）、可见着色（VC）、早开（EO）、盛开（OF）和衰败期（DP）的广义遗传力范围为 56.93-84.26%，高于 5 个衍生条件 FT 性状的遗传力（38.51-75.13%）。OF_EO 和 DP_OF 的表型变异系数相对较大，范围为 30.59-36.17%。基于 375865 个 SNPs，应用压缩方差分量混合线性模型 3VmrMLM 进行多基因全基因组关联研究（GWAS）。结果，在单环境分析中，119 个 QTN 与非条件 FT 性状有关，67 个 QTN 与环境互作（QEIs）有关。对于条件性状，在单环境分析中检测到 343 个 QTN，在多环境分析中检测到 119 个 QTN 和 83 个 QEIs。在稳定 QTN 和 QEI 周围的基因中，有 36 个是拟南芥和其他植物中已知 FT 基因的同源物；通过结合转录组学数据和功能注释，挖掘出 14 个候选基因，包括 ERF-1、ACA10 和 FOP1。此外，ERF-1 的单倍型分析揭示了具有极端 FBD 的 6 个优秀品系。我们的研究结果有助于了解 FT 的动态遗传结构，并为未来的菊花分子育种计划提供有价值的资源。
