Comparative mapping of Brassica juncea and Arabidopsis thaliana using Intron Polymorphism (IP) markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genomes

Background: Extensive mapping efforts are currently underway for the establishment of comparative genomics between the model plant, Arabidopsis thaliana and various Brassica species. Most of these studies have deployed RFLP markers, the use of which is a laborious and time-consuming process. We therefore tested the efficacy of PCR-based Intron Polymorphism (IP) markers to analyze genome-wide synteny between the oilseed crop, Brassica juncea (AABB genome) and A. thaliana and analyzed the arrangement of 24 (previously described) genomic block segments in the A, B and C Brassica genomes to study the evolutionary events contributing to karyotype variations in the three diploid Brassica genomes. Results: IP markers were highly efficient and generated easily discernable polymorphisms on agarose gels. Comparative analysis of the segmental organization of the A and B genomes of B. juncea (present study) with the A and B genomes of B. napus and B. nigra respectively (described earlier), revealed a high degree of colinearity suggesting minimal macro-level changes after polyploidization. The ancestral block arrangements that remained unaltered during evolution and the karyotype rearrangements that originated in the Oleracea lineage after its divergence from Rapa lineage were identified. Genomic rearrangements leading to the gain or loss of one chromosome each between the A-B and A-C lineages were deciphered. Complete homoeology in terms of block organization was found between three linkage groups (LG) each for the A-B and A-C genomes. Based on the homoeology shared between the A, B and C genomes, a new nomenclature for the B genome LGs was assigned to establish uniformity in the international Brassica LG nomenclature code. Conclusion: IP markers were highly effective in generating comparative relationships between Arabidopsis and various Brassica species. Comparative genomics between the three Brassica lineages established the major rearrangements, translocations and fusions pivotal to karyotype diversification between the A, B and C genomes of Brassica species. The inter-relationships established between the Brassica lineages vis-à-vis Arabidopsis would facilitate the identification and isolation of candidate genes contributing to traits of agronomic value in crop Brassicas and the development of unified tools for Brassica genomics

Comparative mapping of <it>Brassica juncea </it>and <it>Arabidopsis thaliana </it>using Intron Polymorphism (IP) markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genomes

Abstract Background Extensive mapping efforts are currently underway for the establishment of comparative genomics between the model plant, Arabidopsis thaliana and various Brassica species. Most of these studies have deployed RFLP markers, the use of which is a laborious and time-consuming process. We therefore tested the efficacy of PCR-based Intron Polymorphism (IP) markers to analyze genome-wide synteny between the oilseed crop, Brassica juncea (AABB genome) and A. thaliana and analyzed the arrangement of 24 (previously described) genomic block segments in the A, B and C Brassica genomes to study the evolutionary events contributing to karyotype variations in the three diploid Brassica genomes. Results IP markers were highly efficient and generated easily discernable polymorphisms on agarose gels. Comparative analysis of the segmental organization of the A and B genomes of B. juncea (present study) with the A and B genomes of B. napus and B. nigra respectively (described earlier), revealed a high degree of colinearity suggesting minimal macro-level changes after polyploidization. The ancestral block arrangements that remained unaltered during evolution and the karyotype rearrangements that originated in the Oleracea lineage after its divergence from Rapa lineage were identified. Genomic rearrangements leading to the gain or loss of one chromosome each between the A-B and A-C lineages were deciphered. Complete homoeology in terms of block organization was found between three linkage groups (LG) each for the A-B and A-C genomes. Based on the homoeology shared between the A, B and C genomes, a new nomenclature for the B genome LGs was assigned to establish uniformity in the international Brassica LG nomenclature code. Conclusion IP markers were highly effective in generating comparative relationships between Arabidopsis and various Brassica species. Comparative genomics between the three Brassica lineages established the major rearrangements, translocations and fusions pivotal to karyotype diversification between the A, B and C genomes of Brassica species. The inter-relationships established between the Brassica lineages vis-à-vis Arabidopsis would facilitate the identification and isolation of candidate genes contributing to traits of agronomic value in crop Brassicas and the development of unified tools for Brassica genomics.</p

Genetic map of showing three linkage groups of the B genome (B6, B7 and B8)

The corresponding nomenclature followed earlier for the B genome of (with a prefix J) [11] and (with a prefix G) [18] is given in parentheses. This new nomenclature for the B genome linkage groups has been designated based on the comparative homoeology discerned between the A, B and C genomes in this study. Each genetic locus bears the name of the At () gene and the colour code of the At chromosome from which it is derived. At loci in italics represent the RFLP probes mapped earlier [11]. Loci marked with an asterisk (*) are derived from multicopy At genes [28]. Loci in black represent markers of the framework map [11]. The organization of the LGs based on the genomic blocks identified by Schranz et al. [15] has been represented on the left of each linkage group. The genomic blocks have been coloured differently based on the five At chromosomes from which they originate. Single copy At loci from different blocks mapped as unique insertions are shown in lower case on the right of each genomic block.<p><b>Copyright information:</b></p><p>Taken from "Comparative mapping of and using Intron Polymorphism (IP) markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genomes"</p><p>http://www.biomedcentral.com/1471-2164/9/113</p><p>BMC Genomics 2008;9():113-113.</p><p>Published online 3 Mar 2008</p><p>PMCID:PMC2277410.</p><p></p

Genetic map of showing five linkage groups of the B genome (B1, B2, B3, B4 and B5)

The corresponding nomenclature followed earlier for the B genome of (with a prefix J) [11] and (with a prefix G) [18] is given in parentheses. This new nomenclature for the B genome linkage groups has been designated based on the comparative homoeology discerned between the A, B and C genomes in this study. Each genetic locus bears the name of the At () gene and the colour code of the At chromosome from which it is derived. At loci in italics represent the RFLP probes mapped earlier [11]. Loci marked with an asterisk (*) are derived from multicopy At genes [28]. Loci in black represent markers of the framework map [11]. The organization of the LGs based on the genomic blocks identified by Schranz et al. [15] has been represented on the left of each linkage group. The genomic blocks have been coloured differently based on the five At chromosomes from which they originate. Single copy At loci from different blocks mapped as unique insertions are shown in lower case on the right of each genomic block.<p><b>Copyright information:</b></p><p>Taken from "Comparative mapping of and using Intron Polymorphism (IP) markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genomes"</p><p>http://www.biomedcentral.com/1471-2164/9/113</p><p>BMC Genomics 2008;9():113-113.</p><p>Published online 3 Mar 2008</p><p>PMCID:PMC2277410.</p><p></p

Comparative block arrangement in (a) the A genome of (A1–A10; present study) and (N1–N10) 16 and (b) the B genome of (B1–B8; present study) and (G1–G8) 18

Blocks identified in only one of the two studies being compared have been highlighted by a grey background. Based on the non-rearranged blocks that flank the centromere in the AK (ancestral karyotype) and At (), the putative centromeric location (represented by solid circles) has been highlighted for the linkage groups wherever possible. New blocks proposed in the present study not shown earlier by Schranz et al. [15] have been marked with an asterisk (*). Blocks with markers from the loci (pericentromeric regions of At) not defined by Schranz et al. [15] have been marked with a question mark (?). Blocks placed within brackets represent insertions within a bigger block.<p><b>Copyright information:</b></p><p>Taken from "Comparative mapping of and using Intron Polymorphism (IP) markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genomes"</p><p>http://www.biomedcentral.com/1471-2164/9/113</p><p>BMC Genomics 2008;9():113-113.</p><p>Published online 3 Mar 2008</p><p>PMCID:PMC2277410.</p><p></p

The block arrangements in the A and B genomes are based on the consensus block arrangement of the A genomes of (A1–A10; present study) and (N1–N10) 16 and the B genomes of (B1–B8; present study) and (G1–G8) 18

The C genome is based on the map (N11–N19) [16]. The original nomenclature of the 2 LGs of the C genome (N16 and N17) and all the LGs of the B genome (G1–G8) have been shown in parentheses with the re-designated nomenclature. Certain single gene insertions were considered as putative blocks (marked with asterisk) if a similar block was found present at the corresponding region in the homoeologous chromosome. Filled bars represent the common blocks shared between all the three members of the group. Large gaps (≥10 cM regions devoid of any markers) in the LGs have been depicted by hatched boxes. Arrows represent the orientation of the gene order (within the block) with respect to the corresponding regions in At.<p><b>Copyright information:</b></p><p>Taken from "Comparative mapping of and using Intron Polymorphism (IP) markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genomes"</p><p>http://www.biomedcentral.com/1471-2164/9/113</p><p>BMC Genomics 2008;9():113-113.</p><p>Published online 3 Mar 2008</p><p>PMCID:PMC2277410.</p><p></p

Molecular mapping reveals two independent loci conferring resistance to Albugo candida in the east European germplasm of oilseed mustard Brassica juncea

White rust caused by Albugo candida (Pers.) Kuntze is a major disease of the oilseed mustard Brassica juncea. Almost all the released varieties of B. juncea in India are highly susceptible to the disease. This causes major yield losses. Hence, there is an urgent need to identify genes for resistance to white rust and transfer these to the existing commercial varieties through marker-assisted breeding. While the germplasm belonging to the Indian gene pool is highly susceptible to the disease, the east European germplasm of B. juncea is highly resistant. In the present study, we have tagged two independent loci governing resistance to A. candida race 2V in two east European lines, Heera and Donskaja-IV. Two doubled haploid populations were used; the first population was derived from a cross between Varuna (susceptible Indian type) and Heera (partially resistant east European line) and the second from a cross between TM-4 (susceptible Indian type) and Donskaja-IV (fully resistant east European line). In both the resistant lines, a single major locus was identified to confer resistance to white rust. In Heera, the resistance locus AcB1-A4.1 was mapped to linkage group A4, while in Donskaja-IV, the resistant locus AcB1-A5.1 was mapped to linkage group A5. In both the cases, closely linked flanking markers were developed based on synteny between Arabidopsis and B. juncea. These flanking markers will assist introgression of resistance-conferring loci in the susceptible varieties