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Article|01 Jun 2021|OPEN
Identification of the PmWEEP locus controlling weeping traits in Prunus mume through an integrated genome-wide association study and quantitative trait locus mapping
Xiaokang Zhuo1,2, Tangchun Zheng2,1,, Suzhen Li1,2, Zhiyong Zhang1,2, Man Zhang2, Yichi Zhang1,2, Sagheer Ahmad 1,2, Lidan Sun1,2, Jia Wang2, Tangren Cheng2 & Qixiang Zhang2,1,
1Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083 Beijing, China
2Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083 Beijing, China

Horticulture Research 8,
Article number: 131 (2021)
doi: 10.1038/hortres.2021.131
Views: 148

Received: 20 Aug 2020
Revised: 20 Jan 2021
Accepted: 07 Apr 2021
Published online: 01 Jun 2021


Weeping Prunus mume (mei) has long been cultivated in East Asia for its specific ornamental value. However, little is known about the regulatory mechanism of the weeping trait in mei, which limits molecular breeding for the improvement of weeping-type cultivars. Here, we quantified the weeping trait in mei using nested phenotyping of 214 accessions and 342 F1 hybrids. Two major associated loci were identified from the genome-wide association study (GWAS), which was conducted using 3,014,409 single nucleotide polymorphisms (SNPs) derived from resequencing, and 8 QTLs and 55 epistatic loci were identified from QTL mapping using 7,545 specific lengths amplified fragment (SLAF) markers. Notably, an overlapping PmWEEP major QTL was fine mapped within a 0.29 Mb region on chromosome 7 (Pa7), and a core SNP locus closely associated with the weeping trait was screened and validated. Furthermore, a total of 22 genes in the PmWEEP QTL region were expressed in weeping or upright mei based on RNA-seq analysis. Among them, only a novel gene (Pm024213) containing a thioredoxin (Trx) domain was found to be close to the core SNP and specifically expressed in buds and branches of weeping mei. Co-expression analysis of Pm024213 showed that most of the related genes were involved in auxin and lignin biosynthesis. These findings provide insights into the regulatory mechanism of the weeping trait and effective molecular markers for molecular-assisted breeding in Prunus mume.