An EST-SSR Linkage Map of Raphanus sativus and Comparative Genomics of the Brassicaceae

Abstract

Raphanus sativus (2n = 2x = 18) is a widely cultivated member of the family Brassicaceae, for which genomic resources are available only to a limited extent in comparison to many other members of the family. To promote more genetic and genomic studies and to enhance breeding programmes of R. sativus, we have prepared genetic resources such as complementary DNA libraries, expressed sequences tags (ESTs), simple sequence repeat (SSR) markers and a genetic linkage map. A total of 26 606 ESTs have been collected from seedlings, roots, leaves, and flowers, and clustered into 10 381 unigenes. Similarities were observed between the expression patterns of transcripts from R. sativus and those from representative members of the genera Arabidopsis and Brassica, indicating their functional relatedness. The EST sequence data were used to design 3800 SSR markers and consequently 630 polymorphic SSR loci and 213 reported marker loci have been mapped onto nine linkage groups, covering 1129.2 cM with an average distance of 1.3 cM between loci. Comparison of the mapped EST-SSR marker positions in R. sativus with the genome sequence of A. thaliana indicated that the Brassicaceae members have evolved from a common ancestor. It appears that genomic fragments corresponding to those of A. thaliana have been doubled and tripled in R. sativus. The genetic map developed here is expected to provide a standard map for the genetics, genomics, and molecular breeding of R. sativus as well as of related species. The resources are available at .

Deciphering the Diploid Ancestral Genome of the MesohexaploidBrassica rapa

“…This association was identified on chromosome Sp2 in S. parvula, albeit with a fragment of block V between L and Q (V/K/L/V'/Q/X) (Dassanayake et al, 2011). The same rearrangement was found on B. rapa chromosomes A02, A06, and A09 ( Figure 5A), B. oleracea (see Supplemental Table 6 online), and radish Shirasawa et al, 2011). We analyzed this chromosome region by performing an interspecies comparison between B. rapa, B. oleracea, S. parvula, A. thaliana, and A. lyrata, with the A. lyrata genome (Hu et al, 2011) serving as a proxy for the ACK genome (n = 8).…”

Progression of DNA Marker and the Next Generation of Crop Development

“…EST-SSR markers could, therefore, be used in related species where information on SSRs or ESTs is limited. These markers can also be used effectively for comparative mapping (Shirasawa et al, 2011;Yu et al, 2004;Varshney et al, 2005;Oliveira et al, 2009). EST-SSRs can be used to produce high quality markers, but they are often less polymorphic than genomic SSRs Aggarwal et al, 2007;Eujayl et al, 2002;Thiel et al, 2003).…”

Development of Est-SSR Markers to Assess Genetic Diversity of Broccoli and Its Related Species

“…SSRs, also known as microsatellites, are tandem repeats of 2-6 bp DNA core sequences that are widely distributed in both non-coding and transcribed sequences, generally known as genomic-SSRs and EST-SSRs, respectively (Shirasawa et al 2011). Genomic SSRs are highly polymorphic and widely distributed throughout the genome (Wang et al 2011).…”

“…EST-SSRs, which located in coding region of the genome, demonstrated some valuable advantages such as they can be rapidly found by electronic sorting and have greater transferability between species than genomic SSR, since genic regions are more conserved among related species (Shirasawa et al 2011;Chen et al 2015). Furthermore, EST-SSRs usually present in gene-rich regions and can be used as anchor markers for comparative mapping and genetic evolutionary studies (Zhou et al 2014).…”