Development and genetic mapping of microsatellite markers from genome survey sequences in Brassica napus

Abstract

Microsatellite or simple sequence repeat (SSR) markers are routinely used for tagging genes and assessing genetic diversity. In spite of their importance, there are limited numbers of SSR markers available for Brassica crops. A total of 627 new SSR markers (designated BnGMS) were developed based on publicly available genome survey sequences and used to survey polymorphisms among six B. napus cultivars that serve as parents for established populations. Among these SSR markers, 591 (94.3%) successfully amplified at least one fragment and 434 (73.4%) detected polymorphism among the six B. napus cultivars. No correlation was observed between SSR motifs, repeat number or repeat length with polymorphism levels. A linkage map was constructed using 163 newly developed BnGMS marker loci and anchored with 164 public SSRs in a doubled haploid population. These new markers are evenly distributed over all linkage groups (LGs). Given that the majority of these SSRs are derived from bacterial artificial chromosome (BAC) end sequences, they will be useful in the assignment of their cognate BACs to LGs and facilitate the integration of physical maps with genetic maps for genome sequencing in B. napus.

Repeated Polyploidy Drove Different Levels of Crossover Suppression between Homoeologous Chromosomes inBrassica napusAllohaploids

“…We confirmed the position of GMs185 (Cheng et al, 2009) within this interval by selective genetic mapping, as detailed in Supplemental Data Set 1 online. PCR and electrophoresis were performed using the same protocols as described by Foisset et al (1996) and Delourme et al (2006).…”

“…Eight molecular markers (see details in Supplemental Data Set 1 online) were selected from published genetic maps (Delourme et al, , 2008Liu et al, 2006;Cheng et al, 2009) to span the region within which PrBn was mapped as a QTL (Liu et al, 2006). We confirmed the position of GMs185 (Cheng et al, 2009) within this interval by selective genetic mapping, as detailed in Supplemental Data Set 1 online.…”

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

“…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).…”

Identification of a microsatellite marker linked to the fertility-restoring gene for a polima cytoplasmic male-sterile line in Brassica napus L.

“…The initial process of developing SSR primer sequence was tedious and costly because it is a DNA sequencing based marker; nonetheless, lots of genome sequences and expressed sequence tags (ESTs) have been released online, which results in a few SSR markers successfully developed and used in rapeseed genetic and breeding research programs (Lowe et al, 2004;Piquemal et al, 2005;Cheng et al, 2009). However, there is no SSR marker reported to associate with Rfp gene.…”