Simple Sequence Repeat-Based Comparative Genomics Between Brassica rapa and Arabidopsis thaliana: The Genetic Origin of Clubroot Resistance

Abstract

An SSR-based linkage map was constructed in Brassica rapa. It includes 113 SSR, 87 RFLP, and 62 RAPD markers. It consists of 10 linkage groups with a total distance of 1005.5 cM and an average distance of 3.7 cM. SSRs are distributed throughout the linkage groups at an average of 8.7 cM. Synteny between B. rapa and a model plant, Arabidopsis thaliana, was analyzed. A number of small genomic segments of A. thaliana were scattered throughout an entire B. rapa linkage map. This points out the complex genomic rearrangements during the course of evolution in Cruciferae. A 282.5-cM region in the B. rapa map was in synteny with A. thaliana. Of the three QTL (Crr1, Crr2, and Crr4) for clubroot resistance identified, synteny analysis revealed that two major QTL regions, Crr1 and Crr2, overlapped in a small region of Arabidopsis chromosome 4. This region belongs to one of the disease-resistance gene clusters (MRCs) in the A. thaliana genome. These results suggest that the resistance genes for clubroot originated from a member of the MRCs in a common ancestral genome and subsequently were distributed to the different regions they now inhabit in the process of evolution.

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).…”

“…Many comparative genetic mapping studies between Brassica species and A. thaliana have highlighted the complexity of the Brassica genome with its extensive replicated nature, as well as frequent appearance of chromosomal rearrangements (Kim et al 2009, Parkin et al 2005, Suwabe et al 2006. In the present study, comparison of B. rapa map with A. thaliana using 147 UGMS and SSR markers loci revealed majority large syntenic regions showing consistency with previously reported syntenic regions (Choi et al 2007, Iniguez-Luy et al 2009, Kim et al 2009, Li et al 2009, Suwabe et al 2006. However, we could not detect all the previously reported conserved chromosomal segments in B. rapa genome due to the lack of molecular markers.…”

“…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).…”

“…LGs were designated as A1-A10 according to international unified Brassica LG nomenclature based on multiple anchor markers mapped on each LG (referred to as R by Choi et al 2007, Suwabe et al 2006 or A by Kim et al 2009). 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.…”