Efficient large-scale development of microsatellites for marker and mapping applications in Brassica crop species

Abstract

A set of 398 simple sequence repeat markers (SSRs) have been developed and characterised for use with genetic studies of Brassica species. Small-insert (250-900 bp) genomic libraries from Brassica rapa, B. nigra, B. oleracea and B. napus, highly enriched for dinucleotide and trinucleotide SSR motifs, were constructed. Screening the clones with a mixture of oligonucleotide repeat probes revealed positive hybridisation to between 75% and 90% of the clones. Of these, 1230 were sequenced. Primer pairs were designed for 398 SSR clones, and of these, 270 (67.8%) amplified a PCR product of the expected size in their focal and/or closely related species. A further screen of 138 primers pairs that produced a PCR product in B. napus germplasm found that 86 (62.3%) revealed length polymorphisms within at least one line of a test array representing the four Brassica species. The results of this screen were used to identify 56 SSRs and were combined with 41 SSRs that had previously shown polymorphism between the parents of a B. napus mapping population. These 97 SSR markers were mapped relative to a framework of RFLP markers and detected 136 loci over all 19 linkage groups of the oilseed rape genome.

Development and linkage mapping of unigene-derived microsatellite markers in Brassica rapa L.

“…The marker order in the current map was in general agreement with previously published linkage maps (Kim et al 2009, Lowe et al 2004, Piquemal et al 2005, Suwabe et al 2006. LG A9 (126.2 cM) was the longest, LG A4 (69.2 cM) was the shortest, and the markers density varied across LGs for this map (Table 2).…”

“…The use of previously developed SSRs in our genetic map as anchor markers would also help to identify specific genomic regions in earlier maps for fine mapping, tagging and markerassisted selection of important traits loci/QTL for economically important traits in their studies (Cheng et al 2009, Lowe et al 2004, Piquemal et al 2005, Suwabe et al 2006. We anticipate that by releasing the information provided in this study, our newly developed UGMS markers and linkage map would help to better understand the organization and evolution of Brassica genomes with respect to unigenes, in addition to mapping, tagging and cloning of economically important trait QTL/gene(s) and marker-assisted breeding in Brassica crops.…”

“…Furthermore, 651 previously developed SSR primer pairs were used as potential anchor markers to facilitate crossreferencing with other mapping studies. Primer pairs with the prefix "MB" were developed by Lagercrantz et al (1993), "MR" by Uzunova and Ecke (1999), "BRAS" and "CB" by Piquemal et al (2005), "Ra", "Ol", Na" and "Ni" by Lagercrantz et al (1993) and Lowe et al (2002Lowe et al ( , 2004, "BRMS" by Suwabe et al (2002Suwabe et al ( , 2006, "BrFLC" by Kim et al (2006), "ENA", "nia" and "cnu" by Choi et al (2007) and by Kim et al (2009), "BnGMS" by Cheng et al (2009) and FITO markers were obtained by Iniguez-Luy et al (2008).…”

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.…”

“…The total length of the map is 1,090 cM, which represents on average one marker for every 3.8 cM. By using the 38 SSRs and four ESTPs with known map positions on the common B. rapa reference map (Lowe et al 2004;Kim et al 2006;Suwabe et al 2006;Choi et al 2007), the 10 linkage groups were assigned to their corresponding chromosomes R01-R10 (Fig. 1).…”