Genetic Diversity and Population Structure Analysis of Citrus Germplasm By SNP Markers

The phylogenetic origin of some secondary species in Citrus and important cultivars resulting from sexual crosses remains unclear. The aim of this project was to study the genetic diversity, population structure and phylogenetic origin of some important citrus cultivars. A total of 1536 single nucleotide polymorphism (SNP) markers were analyzed for a collection of 80 accessions from the Florida Citrus Arboretum, Winter Haven, FL, including citrons, mandarins, pummelos, papedas, trifoliate oranges, kumquats and other Citrus relatives. Genetic diversity statistics were calculated for each SNP, the entire population, specified groups, and each accession, respectively. Phylogenetic relationships among the 80 accessions were determined by neighbor-joining trees. The STRUCTURE detected five basic populations and revealed C. maxima introgressions in several recent-selected mandarin cultivars. Inferred admixture structures of many secondary citrus species and important varieties were consistent with their previous hypothesized origins. The phylogenetic tree data combined with the STRUCTURE results may be useful to solve many phylogenetic questions in Citrus.