Abstract
A significant fraction of the nuclear DNA of all eukaryotes is comprised of simple sequence repeats (SSRs). Although these sequences are widely used for studying genetic variation, linkage mapping and evolution, little attention had been paid to the chromosomal distribution and cytogenetic diversity of these sequences. In this paper, we report the distribution characterization of mono-, di-, and tri-nucleotide SSRs in Brassica rapa ssp. chinensis. Fluorescence in situ hybridization was used to characterize the cytogenetic diversity of SSRs among morphotypes of B. rapa ssp. chinensis. The proportion of different SSR motifs varied among morphotypes of B. rapa ssp. chinensis, with tri-nucleotide SSRs being more prevalent in the genome of B. rapa ssp. chinensis. We determined the chromosomal locations of mono-, di-, and tri-nucleotide repeat loci. The results showed that the chromosomal distribution of SSRs in the different morphotypes is non-random and motif-dependent, and allowed us to characterize the relative variability in terms of SSR numbers and similar chromosomal distributions in centromeric/peri-centromeric heterochromatin. The differences between SSR repeats with respect to abundance and distribution indicate that SSRs are a driving force in the genomic evolution of B. rapa species. Our results provide a comprehensive view of the SSR sequence distribution and evolution for comparison among morphotypes B. rapa ssp. chinensis.
Highlights
Simple sequence repeats (SSRs), known as microsatellites, are composed of 1–6 nucleotide motifs that are repeated in tandem and are widely and non-randomly distributed in 100–1000s of copies in the genomes of both monocots and dicots (Tautz and Renz, 1984; Toth et al, 2000; Mortimer et al, 2005; Lawson and Zhang, 2006; Hong et al, 2007)
We demonstrated that: (1) not all of the simple sequence repeats (SSRs)-based probes produced fluorescence in situ hybridization (FISH) signals on all B. rapa ssp. chinensis chromosomes; (2) some SSR signal intensity did not show a relationship to the abundance in the genome database; (3) the distributional patterns of SSR signals depended on the SSR motif used and the species analyzed; and (4) differences in SSR abundance and density were shown within and between genomes
Differences were observed in the abundance and localization of motifs between the different B. rapa ssp. chinensis morphotypes, a general distribution pattern emerged
Summary
Simple sequence repeats (SSRs), known as microsatellites, are composed of 1–6 nucleotide motifs that are repeated in tandem and are widely and non-randomly distributed in 100–1000s of copies in the genomes of both monocots and dicots (Tautz and Renz, 1984; Toth et al, 2000; Mortimer et al, 2005; Lawson and Zhang, 2006; Hong et al, 2007). Li et al (2004) reviewed that SSRs in different positions in a gene can play important roles in regulating its expression and determining the function of its products. The accumulated evidence indicates that SSRs play an important role in chromatin organization, regulation of gene activity (Nagaki et al, 2004), recombination, DNA replication, the cell cycle, the mismatch DNA repair system (Li et al, 2002), and protein coding regions (Sonah et al, 2011)
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