Genome-Wide Development of Polymorphic SNP Markers and Evaluation of Genetic Diversity of Litchi (Litchi chinensis Sonn.)
Author:
Liu Wei1,
Xiao Zhidan1,
Jiang Nonghui1,
Fan Chao1,
Xiang Xu1
Affiliation:
1. Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
Abstract
Litchi (Litchi chinensis Sonn.) is a highly valuable fruit crop that is widely grown in tropical and subtropical areas of the world. Studying its genetic diversity and population structure is critical for effective conservation and breeding programs. In this study, we developed 150 single-nucleotide polymorphism (SNP) markers that were evenly spaced across litchi genome and applied them to the evaluation of the genetic diversity of 84 litchi accessions, including old cultivars, modern cultivars, hybrids from known parents and wild accessions. Ninety-one SNP markers, showing high levels of polymorphism and high genotyping success rates, were used for further analysis. The newly developed SNP markers captured a relatively higher level of genetic diversity (He = 0.364) in litchi cultivars and could be successfully applied for the identification of synonymous cultivars and hybrids with close genetic backgrounds. Cluster analysis grouped all genotypes into three clusters that showed perfect association with their fruit maturation period, among which wild accessions clustered with their corresponding domesticated cultivars, and hybrids from different parent combinations showed different inheritance tendencies. Our study not only provided a set of efficient SNP markers for future genetic research, but also laid an important foundation for the conservation and genetic breeding of litchi.
Funder
Natural Science Foundation of Guangdong Province
the Key-Area Research and Development Program of Guangdong Province, China
the Key Research and Development Program of Guangzhou City China
the Guangdong Litchi Industry Technology System
the Special Fund for Rural Revitalization Strategy
Science and Technology Planning Project of Guangzhou Municipal Science and Technology Bureau
Subject
Plant Science,Ecology,Ecology, Evolution, Behavior and Systematics
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