Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa

Abstract

BackgroundThe Multinational Brassica rapa Genome Sequencing Project (BrGSP) has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa. An integrated linkage map between the amphidiploid B. napus and diploid B. rapa will facilitate the rapid transfer of these valuable resources from B. rapa to B. napus (Oilseed rape, Canola).ResultsIn this study, we identified over 23,000 simple sequence repeats (SSRs) from 536 sequenced BACs. 890 SSR markers (designated as BrGMS) were developed and used for the construction of an integrated linkage map for the A genome in B. rapa and B. napus. Two hundred and nineteen BrGMS markers were integrated to an existing B. napus linkage map (BnaNZDH). Among these mapped BrGMS markers, 168 were only distributed on the A genome linkage groups (LGs), 18 distrubuted both on the A and C genome LGs, and 33 only distributed on the C genome LGs. Most of the A genome LGs in B. napus were collinear with the homoeologous LGs in B. rapa, although minor inversions or rearrangements occurred on A2 and A9. The mapping of these BAC-specific SSR markers enabled assignment of 161 sequenced B. rapa BACs, as well as the associated BAC contigs to the A genome LGs of B. napus.ConclusionThe genetic mapping of SSR markers derived from sequenced BACs in B. rapa enabled direct links to be established between the B. napus linkage map and a B. rapa physical map, and thus the assignment of B. rapa BACs and the associated BAC contigs to the B. napus linkage map. This integrated genetic linkage map will facilitate exploitation of the B. rapa annotated genomic resources for gene tagging and map-based cloning in B. napus, and for comparative analysis of the A genome within Brassica species.

Identification of a major QTL for silique length and seed weight in oilseed rape (Brassica napus L.)

“…wisc.edu/research/maps/ssrs.html). The second group of SSR markers was developed from publicly available Brassica sequences by our laboratory (Cheng et al 2009;Fan et al 2010;Li et al 2011;Xu et al 2010;Wang et al 2011). PCR reactions were performed as previously described (Cheng et al 2009).…”

“…A genetic map containing 289 loci was constructed, which covered a total length of 1,381.3 cM of the B. napus genome and has an average distance of 4.8 cM between adjacent loci. All the loci were assigned to the 19 B. napus linkage groups (LGs), which were designated as A1-A10 corresponding to the A genome and C1-C9 corresponding to the C genome by aligning the markers to the previously published linkage maps (Lowe et al 2004;Piquemal et al 2005;Suwabe et al 2006;Cheng et al 2009;Li et al 2011;Xu et al 2010). Segregation distortion of each locus was estimated by the goodness-of-fit test, 77 loci (26.6%) showed distorted segregation (P \ 0.05).…”

Identification of quantitative trait loci associated with oil content and development of near isogenic lines for stableqOC-A10inBrasscia napusL.

“…In our study, most markers used to construct genetic linkage map were previously developed by our lab (Cheng et al 2009;Xu et al 2010;Li et al 2011;Wang et al 2012). Recently, our markers were applied in two studies on QTL mapping for oil content (Sun et al 2012;Wang et al 2013).…”

“…One group was developed by our group, prefixed by "BnEMS", "BnGMS", "BrGMS", and "BoGMS" (Cheng et al 2009;Xu et al 2010;Li et al 2011;Wang et al 2012). The other group was obtained from the previously published studies, prefixed by "Ra", "Ol", "Na", and "Ni" (Lagercrantz et al 1993;Lowe et al 2002Lowe et al , 2004; http://ukcrop.net/ace/ search/BrassicaDB), "BRAS" and "CB" (Piquemal et al 2005), "sN", "sR", and "sS" (http://brassica.agr.gc.ca/ index_e.shtml), "BRMS" (Suwabe et al 2002), "BN" (Kresovich et al 1995;Szewc-McFadden et al 1996), "nia", and "cnu" (Choi et al 2007) and "FITO" (http:// www.osbornlab.agronomy.wisc.edu/research/maps/ssrs.…”

The identification of quantitative trait loci that control the paternal inheritance of a mitochondrial plasmid in rapeseed (<i>Brassica napus </i>L.)

“…(Kresovich et al, 1995;Szewc-McFadden et al, 1996); BnEMS/BnGMS/BoGMS/BrGMS (Cheng et al, 2009;Fan et al, 2010;Li et al, 2010;Xu et al, 2010); BRAS (Piquemal et al, 2005); BRMS (Suwabe et al, 2006); CB (Piquemal et al, 2005;Radoev et al, 2008); FITO (Iniguez-Luy et al, 2008); KBr (Hatakeyama et al, 2010;Kakizaki et al, 2011); MD/MR (Radoev et al, 2008) and Na/Ni/Ol (Piquemal et al, 2005;Radoev et al, 2008).…”