%0 Journal Article
%T Large-scale polymorphism of heterochromatic repeats in the DNA of Arabidopsis thaliana
%A Jerry Davison
%A Anand Tyagi
%A Luca Comai
%J BMC Plant Biology
%D 2007
%I BioMed Central
%R 10.1186/1471-2229-7-44
%X Using geographically separate populations of A. thaliana, we assayed variation in the heterochromatic repeat arrays using two independent methods and identified significant polymorphism among them, with variation by as much as a factor of two in the centromeric 180 bp repeat, in the 45S rDNA arrays and in the Athila retroelements. In the accession with highest genome size as measured by flow cytometry, Loh-0, we found more than a two-fold increase in 5S RNA gene copies relative to Col-0; results from fluorescence in situ hybridization with 5S probes were consistent with the existence of size polymorphism between Loh-0 and Col-0 at the 5S loci. Comparative genomic hybridization results of Loh-0 and Col-0 did not support contiguous variation in copy number of protein-coding genes on the scale needed to explain their observed genome size difference. We developed a computational data model to test whether the variation we measured in the repeat fractions could account for the different genome sizes determined with flow cytometry, and found that this proposed relationship could account for about 50% of the variance in genome size among the accessions.Our analyses are consistent with substantial repeat number polymorphism for 5S and 45S ribosomal genes among accession of A. thaliana. Differences are also suggested for centromeric and pericentromeric repeats. Our analysis also points to the difficulties in measuring the repeated fraction of the genome and suggests that independent validation of genome size should be sought in addition to flow cytometric measurements.The fundamental mechanisms that generate and shape genomic diversity ¨C mutation, recombination, selection and drift ¨C were well known before the genomic era. Despite advances, the variation of a eukaryote species' genome from individual to individual is still not well understood. A significant source of intraspecific diversity, variation in the copy number of genomic elements (Copy Number Variation, CNV) is def
%U http://www.biomedcentral.com/1471-2229/7/44