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

• Published in: Journal of Integrative Agriculture Vol. 20; no. 11; pp. 2900 - 2913
• Main Authors: HU, Fu-chu, CHEN, Zhe, WANG, Xiang-he, WANG, Jia-bao, FAN, Hong-yan, QIN, Yong-hua, ZHAO, Jie-tang, HU, Gui-bing
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01.11.2021; 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; 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%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%Environment and Plant Protection Institute,Chinese Academy of Tropical Agricultural Sciences,Haikou 571101,P.R.China%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; Elsevier
• Subjects: dwarf-related traits; genotyping-by-sequencing (GBS); Litchi chinensis; QTL analysis; SNP genetic map; QTL analysis; Litchi chinensis; dwarf-related traits; genotyping-by-sequencing (GBS); SNP genetic map
• ISSN: 2095-3119; 2352-3425
• DOI: 10.1016/S2095-3119(20)63387-1

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 3027 SNP markers with a total length of 1711.97 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.