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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

2009 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
Previously simple-sequence-repeat (SSR) markers were developed and used to evaluate the genetic diversity in 380 sexually-derived accessions in the citrus variety collection (CVC) and resulted in designating a core collection containing the majority of the genetic diversity. The core collection has been flagged in GRIN. Information regarding the primers developed is posted at . Perform genetic analysis of citrus, citrus relatives, and date palms accessions received materials. In June 2009 we initiated a project in which an undergraduate student will use SSR markers to analyze 53 samples from new germplasm received as seed and putatively related accessions to assess uniqueness and prioritize accessions for addition to the protected collection. Aid in the evaluation, selection, improvement and utilization of germplasm by use of molecular markers and/or sequence analyses. Sequence data from a nuclear gene was obtained to better understand the phylogeny of citrus relatives in relation to their roles as possible alternative hosts of HLB, sources of disease resistance and the possibility of identifying new tolerant rootstocks. We selected 61 species from 35 Rutaceae genera and sequenced a 1 Kb fragment of a nuclear gene, malate dehydrogenase. The region of this house-keeping gene included in the analysis has both introns and exons. Introns were rich in parsimony informative characters. The phylogenetic information generated provides a source of SNP markers and aids in a better understanding of the relationships among the different accessions studied. Parsimony analysis showed that several of the major genera of the subfamily Aurantioideae formed distinct clades with excellent bootstrap support. Aurantioideae formed a monophyletic group as expected. Most genera identified by Swingle and Reece (1967) based on morphological characters are in agreement with the sequence data generated in this study. However, the position of the clades in the parsimony phylogram do not reflect the phylogeny implied by the taxonomic classification of the most widely accepted system of Swingle and Reece. A revision of the tribes and subtribes may be essential to incorporate the recent molecular data generated by this study and other studies based on chloroplast sequences. Rutaceous plants collected from huanglongbing infested areas of Florida were tested for the presence of Candidatus Liberibacter asiaticus by quantitative PCR of the plant samples. The information generated will be useful in formulating guidelines for preventing the spread of HLB. ADODR monitored activities by meetings, site visits, e-mail correspondence, and phone calls.

4. Accomplishments

Last Modified: 06/24/2017
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