ARS | Publication request: Phylogenetic analysis of Citrus based on sequences of six nuclear genes

Submitted to: Plant and Animal Genome VX Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: October 16, 2007
Publication Date: N/A

Technical Abstract: Citrus has a long history of cultivation. The phylogenetic relationships between the different cultivars of citrus are not clearly understood because of hybridization, nucellar embryony and somatic mutations. Earlier studies on citrus taxonomy and phylogeny were based on isozymes analyses, microsatellite and RAPD data. We have sequenced about 1 Kb gene fragments from six nuclear genes of 33 citrus and related accessions. The study included 4 citrons, 4 limes, 1 lemon, 7 mandarins, 2 sour oranges, 1 sweet orange, 1 tangor, 3 pummelos, 2 papedas, 2 trifoliates, 1 kumquat, 1 Microcitrus, 4 citrus relatives belonging to the sub-tribes Citrinae and Balsamocitrinae. The citrus accessions selected for the study were representatives from a core collection selected based on SSR marker analysis and included several known hybrids. Several of the cultivars had a high level of heterozygosity. The heterozygous accessions were resolved using the software PHASE and/or by cloning and sequencing. Haplotype information was generated and used for phylogenetic studies using PAUP and Mr. Bayes analysis. Two of the six phylogenetic trees had polytomies reflecting uncertainty about relationships. Coalescence simulations using Mesquite were done to test whether hybridization or the sorting of ancestral polymorphisms best explains incongruence seen between several loci for alleles from some accessions. The possible ancestry of the accessions in the study was inferred based on the different kinds of analyses done. Relationships among haplotypes from various accessions provide new depth to knowledge about relationships among citrus taxa.