Characteristics of Microsatellites in Brassica rapa Genome and their Potential Utilization for Comparative Genomics in Cruciferae

Abstract

We evaluated the nature of microsatellites in Brassica rapa in order to develop an informative and reliable DNA marker system for Brassica genetic analysis. Microsatellites were isolated by hybridization screening of an unconcentrated small-insert genomic library using triand dinucleotide probes. Of 45,000 clones screened, 210 had repeat sequences, in which 228 microsatellites were identified. The most frequent microsatellite motif was (GA) n at a frequency of one every 4.8 × 10 5 bp, followed by (CAA) n at one every 5.0 × 10 5 bp. The frequency of the tri-and dinucleotide microsatellites throughout the B. rapa genome was estimated to be one every 120 Kb. The number of repeats and the polymorphism information content of the dinucleotide microsatellites were higher than those of the trinucleotide microsatellites. More than 90 % of the primer pairs successfully amplified the corresponding microsatellite regions in other Brassica species. Furthermore, a considerable portion of them could be used in other Cruciferous species, 78.5 % in Raphanus sativus, 68.6 % in Sinapis alba and 39.8 % in Arabidopsis thaliana. Based on these results, we concluded that B. rapa microsatellites have a high potential for the development of DNA markers that could contribute to the genetic analysis of Brassica and other Cruciferae.

Simple Sequence Repeat-Based Comparative Genomics Between Brassica rapa and Arabidopsis thaliana: The Genetic Origin of Clubroot Resistance

“…One of the most conspicuous characteristics of the present map is the mapping of the 113 SSR markers. As indicated in the human linkage map (Dib et al 1996), SSR markers have certain outstanding characteristics: (i) a codominant nature of high information value on genetic analysis; (ii) most can detect a single locus, while RFLP probes have a tendency to detect more than one locus in Brassica; (iii) SSR loci are well conserved among various B. rapa accessions, and most can be applied to related species such as B. oleracea, B. napus, and A. thalinana with high accuracy (Suwabe et al 2002(Suwabe et al , 2004; and (iv) their genotype can be detected by a simple PCR technique. That is, in Brassica, SSR markers make it possible to carry out accurate genetic analysis with a simple technique, and moreover, the correspondence of the linkage groups and/or the linkage segments in the different maps can be compared with great clarity.…”

“…Molecular markers: Complete information on the SSR markers is described in Suwabe et al (2002Suwabe et al ( , 2004. A total of 343 SSR markers were used for the construction of the map.…”

“…The methodology for claiming homologous SSR loci was the following: (i) upper and lower nucleotide sequences flanking the SSR were aligned independently, because repeat numbers of SSRs differ greatly between B. rapa and A. thaliana (Suwabe et al 2004), (ii) the results of each alignment for an SSR locus were compared, and (iii) SSR loci with a consistent homology of flanking upper and lower regions were realigned with the entire nucleotide sequences of SSR loci to calculate a homology value. We regarded as homologous SSR loci that had flanking upper and lower genomic regions assigned to the same region in the A. thaliana genome with a threshold value of E , 10 ÿ10 .…”

Identification of quantitative trait loci controlling late bolting in Chinese cabbage (Brassica rapa L.) parental line Nou 6 gou

“…The DNA markers used in the study were 43 simple sequence repeat (SSR) markers (prefix BRMS) reported by Suwabe et al (2002Suwabe et al ( , 2004Suwabe et al ( , 2006, 30 SSR markers (prefixes Na, Ni, Ol and Ra) reported by Lowe et al (2004), 99 SSR markers (prefix KBr) reported by Hatakeyama et al (2010), 14 ESTbased SSR markers (prefix BRE) developed by Abe et al (unpublished data), and 7 SSR markers (prefix ENA or EJU) reported by Choi et al (2007). For genotyping the S locus, we amplified S locus glycoprotein by using primer pairs reported by Nishio et al (1996).…”

Mapping QTLs for mineral accumulation and shoot dry biomass under different Zn nutritional conditions in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

“…A total of 205 SSR markers derived from B. rapa, B. nigra, B. oleracea and B. napus (Lowe et al 2004;Ge et al 2005;Suwabe et al 2002Suwabe et al , 2004Suwabe et al , 2006Kim et al 2006;Choi et al 2007;T. Osborn, personal communication;G.…”