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ARS Home » Southeast Area » Byron, Georgia » Fruit and Tree Nut Research » Research » Publications at this Location » Publication #352320

Research Project: Breeding Stone Fruit Adapted to the Production Environment of the Southeastern United States

Location: Fruit and Tree Nut Research

Title: Genetic diversity and population structure analysis of citrus germplasm with single nucleotide polymorphism markers

Author
item YU, YUAN - UNIVERSITY OF FLORIDA
item Chen, Chunxian
item HUANG, MING - UNIVERSITY OF FLORIDA
item YU, QIBIN - UNIVERSITY OF FLORIDA
item DU, DONGLIANG - UNIVERSITY OF FLORIDA
item MATTIA, MATTHEW - UNIVERSITY OF FLORIDA
item GMITTER JR., FRED - UNIVERSITY OF FLORIDA

Submitted to: Journal of the American Society for Horticultural Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/26/2018
Publication Date: 8/22/2018
Citation: Yu, Y., Chen, C., Huang, M., Yu, Q., Du, D., Mattia, M.R., Gmitter Jr., F.G. 2018. Genetic diversity and population structure analysis of citrus germplasm with single nucleotide polymorphism markers. Journal of the American Society for Horticultural Science. 143(6):399-408. https://doi.org/10.21273/JASHS04394-18.
DOI: https://doi.org/10.21273/JASHS04394-18

Interpretive Summary: Citrus germplasm collection is a valuable resource for citrus genetic breeding studies and further utilization of the resource requires knowledge of their genotypic and phylogenetic relationships. Diverse citrus genotypes, including citrons, mandarins, pummelos, papedas, trifoliate oranges, kumquats, and Citrus related species, are long collected at Florida Citrus Arboretum, Winter Haven, FL, but have never been genotyped. High-throughput molecular markers were used to genotype these materials and determine their marker fingerprints, genetic diversity, and phylogenetic relationships. The results are useful in further genetic and breeding exploitation of interested genotypes in the collection.

Technical Abstract: Citrus germplasm collections are a valuable resource for citrus genetic breeding studies and further utilization of the resource requires knowledge of their genotypic and phylogenetic relationships. Diverse citrus accessions, including citrons, mandarins, pummelos, papedas, trifoliate oranges, kumquats, and Citrus related species, have been housed at the Florida Citrus Arboretum, Winter Haven, FL, but the accessions in the collection have not been genotyped. In this study, a collection of 80 citrus accessions were genotyped using 1536 single nucleotide polymorphism (SNP) markers, to determine their SNP fingerprints, and thereby to assess genetic diversity, population structure, and phylogenetic relationships. Genetic diversity statistics were calculated for the entire collection, specified groups, each genotype, and each SNP, respectively. Phylogenetic relationships among the 80 accessions were determined by principal component analysis (PCA), principal coordinate analysis (PCoA), and neighbor-joining trees. The STRUCTURE detected five basic groups and revealed C. maxima introgressions in several recently-selected mandarin cultivars. Inferred admixture structures of many secondary citrus species and important varieties were consistent with their previous hypothesized origins. The genotyping data and the phylogenetic results may facilitate further exploitation of interesting genotypes in the collection and additional understanding of phylogenetic relationships in Citrus.