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Article|14 Nov 2023|OPEN
Genetic architecture and genomic prediction of plant height-related traits in chrysanthemum
Xuefeng Zhang1,2 ,† , Jiangshuo Su1,2 ,† , Feifei Jia1 , Yuhua He1,2 , Yuan Liao1,2 , Zhenxing Wang1,2 , Jiafu Jiang1,2 , Zhiyong Guan1,2 , Weimin Fang1,2 , Fadi Chen1,2 , Fei Zhang,1,2 ,
1State 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, Nanjing 210095, China
2Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing 210014, China
*Corresponding author. E-mail: zhangfei@njau.edu.cn
Both authors contributed equally to the study.

Horticulture Research 11,
Article number: uhad236 (2024)
doi: https://doi.org/10.1093/hr/uhad236
Views: 19

Received: 08 May 2023
Accepted: 06 Nov 2023
Published online: 14 Nov 2023

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 FST 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.