Construction of high-density SNP genetic maps and QTL mapping for dwarf-related traits in Litchi chinensis Sonn

doi:10.1016/S2095-3119(20)63387-1

Journal of Integrative Agriculture ›› 2021, Vol. 20 ›› Issue (11): 2900-2913.DOI: 10.1016/S2095-3119(20)63387-1

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

收稿日期:2020-05-15 出版日期:2021-11-01 发布日期:2021-09-17

Construction of high-density SNP genetic maps and QTL mapping for dwarf-related traits in Litchi chinensis Sonn

HU Fu-chu^{1, 2}, CHEN Zhe², WANG Xiang-he², WANG Jia-bao³, FAN Hong-yan², QIN Yong-hua¹, ZHAO Jie-tang¹, HU Gui-bing¹

¹ State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/College of Horticulture, South China Agricultural University, Guangzhou 510642, P.R.China
² Key Laboratory of Tropical Fruit Tree Biology of Hainan Province/Institute of Tropical Fruit Trees, Hainan Academy of Agricultural Science, Haikou 571100, P.R.China
³ Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, P.R.China

Received:2020-05-15 Online:2021-11-01 Published:2021-09-17
Contact: Correspondence ZHAO Jie-tang, Tel/Fax: +86-20-85280228, E-mail: jtzhao@scau.edu.cn; HU Gui-bing, E-mail: guibing@scau.edu.cn
About author:HU Fu-chu, E-mail: hufuchu@163.com;
Supported by:
This study was funded by the Key-Area of Research and Development Program of Guangdong Province, China (2018B020202011), the National Natural Science Foundation of China (31701885), the China Agriculture Research System of MOF and MARA (CARS-32-05), the State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, China (SKLCUSA-b201716), and the YangFan Innovative & Entrepreneurial Research Team Project, China (2014YT02H013).

摘要/Abstract

摘要：

荔枝在亚热带地区广泛种植，具有重要的经济价值。高密度遗传图谱构建和相关数量性状基因座（QTL）定位是分子标记辅助育种的前提。本研究利用矮化荔枝品种‘紫娘喜’和乔化荔枝品种‘妃子笑’之间的178个子代F₁群体为材料，采用基因分型测序（GBS）技术构建基于单核苷酸多态性（SNP）的高密度连锁图谱。遗传图谱包含3027个SNP标记，分布在15个连锁群上，总的遗传距离为1711.97 cM，平均遗传距离为0.57 cM。基于此高密度遗传图谱和三年的表型分析，共检测到37个QTL与8个矮化性状相关，包括枝梢长度（LNB）、枝梢直径（DNB）、复叶柄长度（LCP）、复叶柄直径（DCP）、节间长度（LI）、叶片长度（LSL）、叶片宽度（WSL）和株高（PH）。这些QTL可以解释8.0％至14.7％（平均= 9.7％）的表型变异。其中，发现几个QTL簇，特别是在LG04和LG11连锁群上，暗示调节荔枝矮化性状的基因可能成簇分布。在这些QTL区间鉴定到126个候选基因，其中55个基因在‘紫娘喜’和‘妃子笑’之间的表达存在差异。这些差异表达基因（DEGs）参与细胞发育、物质运输、信号转导和植物形态发生的调控，可能在调控植物矮化性状中起重要作用。高密度遗传图谱构建及矮化性状相关QTLs分析将为荔枝分子标记辅助育种奠定坚实的基础。

Abstract: Litchi chinensis Sonn is widely cultivated in subtropical regions and has an important economic value. A high-density genetic map is a valuable tool for mapping quantitative trait loci (QTL) and marker-assisted breeding programs. In this study, a single nucleotide polymorphism (SNP)-based high-density linkage map was constructed by a genotyping-by-sequencing (GBS) protocol using an F1 population of 178 progenies between two commercial litchi cultivars, ‘Ziniangxi’ (dwarf) and ‘Feizixiao’ (vigorous). The genetic map consisted of 3 027 SNP markers with a total length of 1 711.97 cM in 15 linkage groups (LGs) and an average marker distance of 0.57 cM. Based on this high-density linkage map and three years of phenotyping, a total of 37 QTLs were detected for eight dwarf-related traits, including length of new branch (LNB), diameter of new branch (DNB), length of common petiole (LCP), diameter of common petiole (DCP), length of internode (LI), length of single leaf (LSL), width of single leaf (WSL), and plant height (PH). These QTLs could explain 8.0 to 14.7% (mean=9.7%) of the phenotypic variation. Among them, several QTL clusters were observed, particularly on LG04 and LG11, which might show enrichment for genes regulating the dwarf-related traits in litchi. There were 126 candidate genes identified within the QTL regions, 55 of which are differentially expressed genes by RNA-seq analysis between ‘Ziniangxi’ and ‘Feizixiao’. These DEGs were found to participate in the regulation of cell development, material transportation, signal transduction, and plant morphogenesis, so they might play important roles in regulating plant dwarf-related traits. The high-density genetic map and QTLs identification related to dwarf traits can provide a valuable genetic resource and a basis for marker-assisted selection and genomic studies of litchi.

Key words: Litchi chinensis , SNP genetic map , dwarf-related traits , QTL analysis , genotyping-by-sequencing (GBS)

. [J]. Journal of Integrative Agriculture, 2021, 20(11): 2900-2913.

HU Fu-chu, CHEN Zhe, WANG Xiang-he, WANG Jia-bao, FAN Hong-yan, QIN Yong-hua, ZHAO Jietang, HU Gui-bing. Construction of high-density SNP genetic maps and QTL mapping for dwarf-related traits in Litchi chinensis Sonn[J]. Journal of Integrative Agriculture, 2021, 20(11): 2900-2913.

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Construction of high-density SNP genetic maps and QTL mapping for dwarf-related traits in Litchi chinensis Sonn

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