Construction and analysis of a high-density genetic linkage map in cabbage (Brassica oleracea L. var. capitata)

Abstract

BackgroundBrassica oleracea encompass a family of vegetables and cabbage that are among the most widely cultivated crops. In 2009, the B. oleracea Genome Sequencing Project was launched using next generation sequencing technology. None of the available maps were detailed enough to anchor the sequence scaffolds for the Genome Sequencing Project. This report describes the development of a large number of SSR and SNP markers from the whole genome shotgun sequence data of B. oleracea, and the construction of a high-density genetic linkage map using a double haploid mapping population.ResultsThe B. oleracea high-density genetic linkage map that was constructed includes 1,227 markers in nine linkage groups spanning a total of 1197.9 cM with an average of 0.98 cM between adjacent loci. There were 602 SSR markers and 625 SNP markers on the map. The chromosome with the highest number of markers (186) was C03, and the chromosome with smallest number of markers (99) was C09.ConclusionsThis first high-density map allowed the assembled scaffolds to be anchored to pseudochromosomes. The map also provides useful information for positional cloning, molecular breeding, and integration of information of genes and traits in B. oleracea. All the markers on the map will be transferable and could be used for the construction of other genetic maps.

Transcriptome sequencing of two parental lines of cabbage (Brassica oleracea L. var. capitata L.) and construction of an EST-based genetic map

“…Earlier studies demonstrated that AG/CT and AAG/CTT were the predominant di- and trinucleotide SSR motifs, respectively, in plant dicot ESTs [2,14,50,51,53,54], which is similar to our observation. These findings suggest that AG and AAG motifs can be considered common features of EST-SSRs in dicot plants.…”

“…The occurrences of segregation distortion have been observed in Brassica species which showed a number of distorted markers mapped on the genetic map [14,20,28]. In this study, we assigned all but 7 of the 271 polymorphic markers to linkage groups.…”

Comparison of Positions of QTLs Conferring Resistance to <i>Xanthomonas campestris</i> pv. <i>campestris</i> in <i>Brassica oleracea</i>

“…The map length of 1099.4 cM was similar to the map length, 1112, 1048, and 1197.9 cM of [22,28,35], respectively, and longer than the map lengths, 891.4, 320.5, 928.7 cM of [18,19,27], respectively. In our map, the average interval between markers was 6.1 cM, indicating that the length and marker distribution of our map were suitable for QTL analysis of Xcc resistance.…”

“…The linkage map included 155 SSR and 26 CAPS markers ( Table 4). To align our map to the internationally accepted Brassica map, we used pW, pX, CB, BRMS, BoGMS and BoSF, markers reported by [22][23][24]26,29,34].…”

In-depth analysis of internal control genes for quantitative real-time PCR in Brassica oleracea var. botrytis

“…botrytis) is an important vegetable crop in the genus Brassica. The whole genome of B. oleracea was recently sequenced, and there is increasing interest in the functional genomics of cauliflower (Wang et al, 2012). In the present study, we aimed to assess the most suitable reference gene(s) for qRT-PCR gene expression studies in Brassica oleracea L. var.…”