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United States Department of Agriculture

Agricultural Research Service

Research Project: Use of Molecular Markers to Determine Genetic Relationships of Citrus and Citrus Relatives

Location: National Clonal Germplasm Repository for Citrus & Dates

2008 Annual Report


1a.Objectives (from AD-416)
Provide expertise in the area of genetic analysis of germplasm of citrus, citrus relatives, and date palm. This supports the mission to collect, evaluate, and distribute germplasm of citrus, citrus relatives, and date palm.


1b.Approach (from AD-416)
Use molecular markers and gene sequence information to characterize citrus, citrus relatives, and date palm accessions to help identify redundancies and gaps in the collection, screen potential new accessions, and identify important regulatory genes of metabolic pathways. Documents SCA with UC Riverside. Replaces 5310-21000-008-03S (4/08). FORMERLY 5310-21000-008-12S (8/08).


3.Progress Report

This research has involved evaluation of the genetic diversity present in the citrus variety collection.

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. Phylogenetic analysis identified groups corresponding to mandarins, pummelos, citron, and some citrus relatives, but some accessions appear to be incorrectly classified. Trees derived from sequences of the different genes are not congruent, indicating that evolutionary patterns may be complex. This preliminary research suggests that this may be a powerful method to determine ancestry. ADODR monitored activities by meetings and site visits.


Last Modified: 8/27/2014
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