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United States Department of Agriculture

Agricultural Research Service

Title: What phylogeny and gene genealogy analyses reveal about homoplasy in citrus microsatellite alleles

Authors
item Barkley, Noelle
item Krueger, Robert
item Federici, Claire - UNIVERSITY OF CALIFORNIA
item Roose, Mikeal - UNIVERSITY OF CALIFORNIA

Submitted to: Plant Systematics and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 30, 2009
Publication Date: July 28, 2009
Repository URL: http://hdl.handle.net/10113/44172
Citation: Barkley, N.L., Krueger, R., Federici, C.T., Roose, M.L. 2009. What phylogeny and gene genealogy analyses reveal about homoplasy in citrus microsatellite alleles. Plant Systematics and Evolution. 282:71-86.

Interpretive Summary: Simple Sequence Repeat (SSR) markers are widely used for genetic diversity and parentage analysis. There are two main models (infinite alleles and stepwise mutation) used to analyze SSR data both with different assumptions. The underlying assumptions of these models are based on how the SSR alleles are changing. Allele size alone can not provide any information to allow one to decipher how these repeat elements evolve and change. This can only be accomplished by sequencing the alleles and analyzing the data to discover if the mechanism of change is consistent with the infinite alleles or the stepwise mutation model. The main goal of this work was to determine which model would be most appropriate for analyzing citrus SSR alleles. Additionally, homoplasy in which alleles are identical in state but not identical by descent has been reported to be a problem in SSR marker analysis. Therefore, this study aimed to determine the level of homoplasy that occurred in SSR alleles from three genera; Citrus, Fortunella, and Poncirus.

Technical Abstract: Sixty-five microsatellite alleles from three Simple Sequence Repeat (SSR) loci (cAGG9, CCT01 and GT03) of various Citrus, Fortunella or Poncirus accessions were cloned and sequenced to determine their mode of evolution. This data was used to assess sequence variation by calculating the average number of different nucleotides per site between sequences which ranged from 0.00730 for marker cAGG9 to 0.01624 for marker CCT01 with a mean of 0.01324. Sequences for each marker were aligned and subsequently used to determine relationships between alleles of different taxa via parsimony. Very few parsimony informative characters were detected for markers cAGG9 and CCT01 even with the inclusion of accessions from two genera related to Citrus (Fortunella and Poncirus). Allelic size variation at each SSR marker examined was due to changes in repeat length with one exception. Gaps occurred 3.73 times more frequently than base substitutions for marker cAGG9; however, for markers GT03 and CCT01 the gaps occurred only 1.53 and 1.1 times more than base substitutions, respectively. Point mutations were detected in various alleles in the microsatellite region and the region flanking the microsatellite, but no insertion/deletion (indels) mutations were detected in the flanking sequence of the microsatellite. Several of the point mutations were found to be genus, species or allele specific and some mutations in the flanking region were informative about the inferred evolutionary relationships among alleles. Overall, a few cases of apparent homoplasy were observed where the core microsatellite repeat was changed, causing alleles of the same size class to be identical in state but not identical by descent.

Last Modified: 11/27/2014
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