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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.

Panjabi P, Jagannath A, Bisht NC, Padmaja KL, Sharma S, Gupta V, Pradhan AK, Pental D - BMC Genomics (2008)

Bottom Line: Complete homoeology in terms of block organization was found between three linkage groups (LG) each for the A-B and A-C genomes.IP markers were highly effective in generating comparative relationships between Arabidopsis and various 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India. ppriyagen@yahoo.com

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.

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The block arrangements in the A and B genomes are based on the consensus block arrangement of the A genomes of B. juncea (A1–A10; present study) and B. napus (N1–N10) [16] and the B genomes of B. juncea (B1–B8; present study) and B. nigra (G1–G8) [18]. The C genome is based on the B. napus 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.
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Figure 7: The block arrangements in the A and B genomes are based on the consensus block arrangement of the A genomes of B. juncea (A1–A10; present study) and B. napus (N1–N10) [16] and the B genomes of B. juncea (B1–B8; present study) and B. nigra (G1–G8) [18]. The C genome is based on the B. napus 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.

Mentions: Considerable homoeology has been reported between the LGs of the A and C genomes [16]. With the mapping information for the B genome derived from the present study, we were able to compare the block-based architecture of the LGs of the three diploid Brassicas to understand the extent of homoeology shared between the three genomes. This analysis provided insights into the prominent rearrangements that shaped the three genomes and also identified those ancestral blocks which remained unaltered in all the three diploid Brassica genomes. For this comparative study, the RFLP loci of the C genome of B. napus [16] were converted to their corresponding At loci (Additional file 4). Figure 7 provides an overall view of the homoeology between the three genomes.


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.

Panjabi P, Jagannath A, Bisht NC, Padmaja KL, Sharma S, Gupta V, Pradhan AK, Pental D - BMC Genomics (2008)

The block arrangements in the A and B genomes are based on the consensus block arrangement of the A genomes of B. juncea (A1–A10; present study) and B. napus (N1–N10) [16] and the B genomes of B. juncea (B1–B8; present study) and B. nigra (G1–G8) [18]. The C genome is based on the B. napus 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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2277410&req=5

Figure 7: The block arrangements in the A and B genomes are based on the consensus block arrangement of the A genomes of B. juncea (A1–A10; present study) and B. napus (N1–N10) [16] and the B genomes of B. juncea (B1–B8; present study) and B. nigra (G1–G8) [18]. The C genome is based on the B. napus 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.
Mentions: Considerable homoeology has been reported between the LGs of the A and C genomes [16]. With the mapping information for the B genome derived from the present study, we were able to compare the block-based architecture of the LGs of the three diploid Brassicas to understand the extent of homoeology shared between the three genomes. This analysis provided insights into the prominent rearrangements that shaped the three genomes and also identified those ancestral blocks which remained unaltered in all the three diploid Brassica genomes. For this comparative study, the RFLP loci of the C genome of B. napus [16] were converted to their corresponding At loci (Additional file 4). Figure 7 provides an overall view of the homoeology between the three genomes.

Bottom Line: Complete homoeology in terms of block organization was found between three linkage groups (LG) each for the A-B and A-C genomes.IP markers were highly effective in generating comparative relationships between Arabidopsis and various 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India. ppriyagen@yahoo.com

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.

Show MeSH