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

doi:10.1016/S2095-3119(20)63416-5

Journal of Integrative Agriculture ›› 2021, Vol. 20 ›› Issue (5): 1287-1301.DOI: 10.1016/S2095-3119(20)63416-5

所属专题：园艺-分子生物合辑Horticulture — Genetics · Breeding

收稿日期:2020-01-19 出版日期:2021-05-01 发布日期:2021-04-12

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

YU Chao^1*, WAN Hui-hua^1*, Peter M. BOURKE², CHENG Bi-xuan¹, LUO Le¹, PAN Hui-tang¹, ZHANG Qi-xiang^{1, 3}

¹ Beijing 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, Beijing 100083, P.R.China
² Plant Breeding, Wageningen University & Research, Wageningen 6700 AJ, The Netherlands
³ Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, P.R.China

Received:2020-01-19 Online:2021-05-01 Published:2021-04-12
Contact: Correspondence ZHANG Qi-xiang, Tel/Fax: +86-10-62336321, E-mail: zqxbjfu@126.com
About author:YU Chao, E-mail: yuchao@bjfu.edu.cn; * These authors contributed equally to this study.
Supported by:
This research was supported by grants from the National Natural Science Foundation of China (31600565), the Fundamental Research Funds for the Central Public Welfare Research Institutes, China (ZZ13-YQ-053) and the Special Fund for Beijing Common Construction Project, China. Dr. Peter M. Bourke from Plant Breeding, Wageningen University & Research, The Netherlands, was partly funded through the TKI polyploids project (BO-26.03-009-004 and BO-50-002-022).

摘要/Abstract

摘要：

月季（Rosa cvs.）是世界上最重要的观赏植物之一。现代月季多为四倍体，其减数分裂过程中存在双减数分裂和优先配对，使得传统的连锁分析方法不能适用四倍体月季。因此，四倍体月季遗传图谱的构建工作既迫切又具挑战性。本研究以四倍体月季F1杂交群体为试验材料，通过简化基因组测序的方法构建遗传图谱。共检测到17,382个SNP标记，加上课题组前期开发的440个SSR和AFLP标记，利用GATK中同源四倍体的模型进行基因分型，最终获得6,885个高质量的标记。然后利用polymapR进行遗传连锁分析，构建了四倍体月季的高密度遗传连锁图谱。该图谱包含7个连锁群，6,842个标记，总图距为1,158.90 cM，标记间平均遗传距离为0.18 cM。随后对花瓣数量和花朵直径进行QTL分析，检测到1个与花瓣数量相关的主效QTL (qpnum-3-1)，解释表型变异20.18–22.11%。检测到4个与花朵直径相关的QTLs，连续两年的花朵直径数据检测到1个主效QTL（qfdia-2-2）。本研究为现代月季分子标记辅助育种工作奠定基础，同时为其他同源多倍体的遗传分析提供借鉴。

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.

Key words: rose , tetraploid , genetic linkage map , QTLs

. [J]. Journal of Integrative Agriculture, 2021, 20(5): 1287-1301.

YU Chao, WAN Hui-hua, Peter M. BOURKE, CHENG Bi-xuan, LUO Le, PAN Hui-tang, ZHANG Qi-xiang . High density genetic map and quantitative trait loci (QTLs) associated with petal number and flower diameter identified in tetraploid rose[J]. Journal of Integrative Agriculture, 2021, 20(5): 1287-1301.

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

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