Genetic architecture and genomic prediction of plant height-related traits in chrysanthemum

Abstract

Plant height (PH) is a crucial trait determining plant architecture in chrysanthemum. To better understand the genetic basis of PH, we investigated the variations of PH, internode number (IN), internode length (IL), and stem diameter (SD) in a panel of 200 cut chrysanthemum accessions. Based on 330 710 high-quality SNPs generated by genotyping by sequencing, a total of 42 associations were identified via a genome-wide association study (GWAS), and 16 genomic regions covering 2.57 Mb of the whole genome were detected through selective sweep analysis. In addition, two SNPs, Chr1_339370594 and Chr18_230810045, respectively associated with PH and SD, overlapped with the selective sweep regions from F_ST and π ratios. Moreover, candidate genes involved in hormones, growth, transcriptional regulation, and metabolic processes were highlighted based on the annotation of homologous genes in Arabidopsis and transcriptomes in chrysanthemum. Finally, genomic selection for four PH-related traits was performed using a ridge regression best linear unbiased predictor model (rrBLUP) and six marker sets. The marker set constituting the top 1000 most significant SNPs identified via GWAS showed higher predictabilities for the four PH-related traits, ranging from 0.94 to 0.97. These findings improve our knowledge of the genetic basis of PH and provide valuable markers that could be applied in chrysanthemum genomic selection breeding programs.

Acknowledgements

We wish to thank the high-performance computing platform of Bioinformatics Center, Nanjing Agricultural University for pro-viding data analysis platform services. This work was finan-cially supported by the National Natural Science Foundation of China (32171857), China Agriculture Research System (CARS-23-A18), Jiangsu Agriculture Science and Technology Innovation Fund (CX(21)2004), and the Priority Academic Program Develop-ment of Jiangsu Higher Education Institutions.

Author contributions

F.Z. and J.S. conceived and designed the study. F.C., W.F., and Z.G. provided the materials. X.Z. and F.J. performed the field experiments. X.Z. and J.S. analyzed the data and finalized the manuscript. Y.H. and Y.L. prepared the tables and references. F.Z., Z.W., and J.J. revised the article. All authors have read and approved the final manuscript.

Data availability

The GBS data used in this study have been deposited in the National Center of Biotechnology Information Sequence Read Archive (SRA) under BioProject accession number PRJNA1004079. The data supporting this work are available in the paper and its supplementary information files. The data generated and the ana-lytical results of the study are available from the corresponding author upon request.

Conflict of interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Supplementary data

Supplementary data is available at Horticulture Research online.

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