Combined genome-wide association studies and expression quantitative trait locus analysis uncovers a genetic regulatory network of floral organ number in a tree peony (Paeonia suffruticosa Andrews) breeding population

Liping Peng; Yang Li; Wanqing Tan; Shangwei Wu; Qing Hao; Ningning Tong; Zhanying Wang; Zheng'an Liu; Qingyan Shu

doi:10.1093/hr/uhad110

Combined genome-wide association studies and expression quantitative trait locus analysis uncovers a genetic regulatory network of floral organ number in a tree peony (Paeonia suffruticosa Andrews) breeding population

Hortic Res. 2023 Jul 5;10(7):uhad110. doi: 10.1093/hr/uhad110. eCollection 2023 Jul.

Authors

Liping Peng^{1

2}, Yang Li^{1

2}, Wanqing Tan^{1

2

3}, Shangwei Wu^{1

2

3}, Qing Hao⁴, Ningning Tong^{1

2}, Zhanying Wang⁵, Zheng'an Liu^{1

2

3}, Qingyan Shu^{1

2

3}

Affiliations

¹ Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China.
² China National Botanical Garden, Beijing 100093, China.
³ College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China.
⁴ College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China.
⁵ Peony Research Institute, Luoyang Academy of Agricultural and Forestry Sciences, Luoyang 471000, China.

Abstract

Great progress has been made in our understanding of floral organ identity determination and its regulatory network in many species; however, the quantitative genetic basis of floral organ number variation is far less well understood for species-specific traits from the perspective of population variation. Here, using a tree peony (Paeonia suffruticosa Andrews, Paeoniaceae) cultivar population as a model, the phenotypic polymorphism and genetic variation based on genome-wide association studies (GWAS) and expression quantitative trait locus (eQTL) analysis were analyzed. Based on 24 phenotypic traits of 271 representative cultivars, the transcript profiles of 119 cultivars were obtained, which indicated abundant genetic variation in tree peony. In total, 86 GWAS-related cis-eQTLs and 3188 trans-eQTL gene pairs were found to be associated with the numbers of petals, stamens, and carpels. In addition, 19 floral organ number-related hub genes with 121 cis-eQTLs were obtained by weighted gene co-expression network analysis, among which five hub genes belonging to the ABCE genes of the MADS-box family and their spatial-temporal co-expression and regulatory network were constructed. These results not only help our understanding of the genetic basis of floral organ number variation during domestication, but also pave the way to studying the quantitative genetics and evolution of flower organ number and their regulatory network within populations.