High density genetic map and quantitative trait loci (QTLs) associated with petal number and flower diameter identified in tetraploid rose

Abstract

Rose is one of the most important ornamental and economic plants in the world. Modern rose cultivars are primarily tetraploid, and during meiosis, they may exhibit double reduction or preferential chromosome pairing. Therefore, the construction of a high density genetic map of tetraploid rose is both challenging and instructive. In this study, a tetraploid rose population was used to conduct a genetic analysis using genome sequencing. A total of 17 382 single nucleotide polymorphism (SNP) markers were selected from 2 308 042 detected SNPs. Combined with 440 previously developed simple sequence repeats (SSR) and amplified fragment length polymorphism (AFLP) markers, a marker dosage of 6 885 high quality markers was successfully assigned by GATK software in the tetraploid model. These markers were used in the construction of a high density genetic map, containing the expected seven linkage groups with 6 842 markers, a total map length of 1 158.9 cM, and an average inter-marker distance of 0.18 cM. Quantitative trait locus (QTL) analysis was subsequently performed to characterize the genetic architecture of petal number and flower diameter. One major QTL (qpnum-3-1) was detected for petal number in three consecutive years, which explained 20.18–22.11% of the variation in petal number. Four QTLs were detected for flower diameter; the main locus, qfdia-2-2, was identified in two consecutive years. Our results will benefit the molecular marker-assisted breeding of modern rose cultivars. In addition, this study provides a guide for the genetic and QTL analysis of autotetraploid plants using sequencing-based genotyping methods.