Characterization and comparison of gene-based simple sequence repeats across Brassica species

Abstract

Simple sequence repeats (SSRs) are important components of eukaryotic genomes and may play an important role in regulating gene expression. However, the characteristics of genic SSRs and the effect of interspecific hybridization and polyploidization on genic SSRs seem not to have received desired attention in terms of scientific investigations. To determine the features of genic SSRs and elucidate their role in polyploidization process of the Brassica family, we identified SSRs in Plant Genome Database-assembled unique transcripts (PUTs) of Brassica species. A higher density of SSRs and a greater number of compound motif SSRs and mononucleotide motif types with large average number of repeats were detected in allotetraploid Brassica napus than in the diploid parental species (Brassica rapa and Brassica oleracea). In addition, a greater proportion of SSR-PUTs were found to be associated with the stress response and developmental processes in B. napus than in the parents. A negative correlation between the repeat number and the motif type and the total length, and a positive correlation between the repeat number and the total length of SSRs were observed. PUT-SSR might be generated from A/T-rich regions. The successful development of 123 pairs of SSR primers for Brassica PUTs showed that SSR-PUTs could be exploited as gene-based SSR functional markers for application in Brassica breeding. These results indicate that interspecific hybridization and polyploidization could trigger the amplification of SSRs, and long SSRs might become shorter to enable the plant to adapt to environmental and artificial selection.

Evolutionary Dynamics of Microsatellite Distribution in Plants: Insight from the Comparison of Sequenced Brassica, Arabidopsis and Other Angiosperm Species

“…This was consistent with previous findings: the frequencies of microsatellites in the transcribed sequences/unigenes of A. thaliana , B. rapa and B. oleracea were lower than that of B. napus [14], [26]; the duplicated genes in Arabidopsis typically contained a higher frequency of microsatellites [10]. These results strongly suggested that polyploidy may lead to the slight increase in the frequency of microsatellites in the coding sequences, which may be advantageous for evolution because microsatellites in coding sequences can be directly linked to gene function, providing a basis for quick adaptations to environmental changes [1], [4], [27].…”

“…The current investigation also revealed several constant microsatellite characteristics in plant evolution, as the observed high level of consistency among all the species investigated in this and other studies [8], [9], [14], [15], [25], [45], [57], [58], [59] was not likely a chance event. First, trinucleotide repeat microsatellites were dominant in coding sequences (Figure 3; Table 3), which is undoubtedly caused by the triplet nature of codons [4].…”

“…High similarity was also observed for several characteristics of microsatellites investigated in the EST sequences of three Brassica genus species [45] and in the genomic sequences of two O. sativa subspecies [46]. However, for the species of different genera, families, orders and classes (e.g., Brassica vs. Arabidopsis , Brassicaceae vs. Caricaceae , Brassicales vs Fabales and Monocotyledoneae vs. Dicotyledoneae ), the differences in their microsatellite characteristics usually become larger (Table 2, 3, 5; Table S2–3C).…”

Development and Characterization of EST-SSR Markers in Taxodium ‘zhongshansa’

“…A potential explanation for the high ratio of mononucleotide SSR loci in this study was that mononucleotide SSRs would be amplified rapidly after interspecific hybridization (Gao et al 2011). The repeat units of 10, 5, 11, and 6 about SSR sequences account 69.73 % of the total SSRs, thus a rough trend could be discerned where the size of SSRs mainly ranged from 10 to 18 bp (Table 2).…”

RNA-seq based SNPs in some agronomically important oleiferous lines of Brassica rapaand their use for genome-wide linkage mapping and specific-region fine mapping

“…Markers obtained from the gene space of a species, are most informative. EST-cDNA probes [14,41], genic SSRs [42,43], intron polymorphism (IP) markers [15,43] and InDels (Sequence Tagged Sites, STS) [44], have all been successfully used for comparative mapping and studying genomic synteny amongst the Brassica species belonging to the U’s triangle [9]. …”