Limits...
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.

Show MeSH
Major rearrangements between the rapa/oleracea and nigra genomes (a, b) and the rapa and oleracea genomes (c, d). Boxes bearing the same color represent homoeologous blocks while the hatched boxes represent large gaps (≥10 cM regions devoid of any markers). (a) Prominent rearrangements between the A/C and B genomes resulting in altered block arrangement (b) Block organization of one LG of the B genome harbours the blocks from two LGs in the A/C genome explaining the difference of one chromosome between the two genomes (c) B. oleracea genome-specific rearrangements (mainly translocations) after the divergence from the Rapa lineage (d) Block organization of two LGs of the C genome (C8, C9) can be derived from three LGs (A8, A9, A10) of the A genome suggesting that the difference of one chromosome between the A and C genomes could be either due to the gain of one of the these LGs in the Rapa lineage or a reduction of one LG in the oleracea genome.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2277410&req=5

Figure 8: Major rearrangements between the rapa/oleracea and nigra genomes (a, b) and the rapa and oleracea genomes (c, d). Boxes bearing the same color represent homoeologous blocks while the hatched boxes represent large gaps (≥10 cM regions devoid of any markers). (a) Prominent rearrangements between the A/C and B genomes resulting in altered block arrangement (b) Block organization of one LG of the B genome harbours the blocks from two LGs in the A/C genome explaining the difference of one chromosome between the two genomes (c) B. oleracea genome-specific rearrangements (mainly translocations) after the divergence from the Rapa lineage (d) Block organization of two LGs of the C genome (C8, C9) can be derived from three LGs (A8, A9, A10) of the A genome suggesting that the difference of one chromosome between the A and C genomes could be either due to the gain of one of the these LGs in the Rapa lineage or a reduction of one LG in the oleracea genome.

Mentions: All the linkage groups belonging to the three diploid Brassica species could be divided into ten categories or groups (Group1–10) based on the extent of homoeology between them (Figure 7). Group 1 consists of A1/B1–B2/C1. A1 was entirely homoeologous to C1, both being constituted by the block arrangement F-T-U. The F-T-U arrangement was specific to the Rapa/Oleracea lineage. Interestingly, this F-T-U arrangement was found repeated in both the A (A3) and the C (C3) genomes (Group 3, Figure 7) but was absent from the B genome. The linkage group B1 shared the F block with A1/C1 in Group1. Due to the presence of two F blocks in B1, this linkage group also had homoeology with Group 3. B2, which shared the U block with A1 and C1, could also be placed in this group. In Group 2 (A2/B2/C2), A2 and C2 were completely homoeologous, while B2 showed homoeology with A2 and C2 for the block motifs R-W-E-O-P. One inversion in B2 could explain the separation of the E block from the R-W block combination (Figure 8). Group 3 (A3/B1–B3/C3) members shared the common block arrangement R-W-J-I-P-O. B3 was almost entirely composed of this block arrangement, while an additional F-T-U block was present in A3 and C3. Members of Group 4 (A4/B4/C4) shared the block motif J-I-S-N-T. A4 and B4 appeared to be homoeologous along their entire length, while C4 had acquired an additional J block. The presence of two J blocks in C4 was a C genome-specific rearrangement. Due to the presence of an additional J block, C4 has also been placed in group 5. In Group 5 (A5/B5/C4–C5), A5 and B5 were homoeologous along their entire length sharing the block motif J-C-F. C5 shared partial homoeology (blocks F-C) with A5 and B5. The terminal J block present in A5 and B5 was however absent in C5. In Group 6 (A6/B6/C5–C6), A6 and B6 were homoeologous along their entire length sharing the block arrangement C-B-A-V-K-L-Q. One inversion in either of the two genomes could explain the reverse orientation of the blocks constituting the lower segment of A6–B6 (blocks V-K-L-Q). Two C genome LGs (C5 and C6) are also components of this group. C5 shared the A-B-C block arrangement with A6/B6 while C6 was homoeologous for the block arrangement V-K-L-Q with A6/B6. Members of Group 7 (A7/B7/C7) shared homoeology for a large E block while Group 8 (A8/B7/C8) members were homoeologous for blocks A-B-U. Group 9 (A9/C8–C9) had A9 sharing homoeology with C9 for the blocks O-Q-X-H-D-V which constituted the top half of both the linkage groups. The lower segment of A9 shared the block arrangement N-I-H-A with C8. No LG from the B genome seemed to possess any major block homoeologous with A9. Members of group 10 (A10/B8/C9) shared the blocks R-W which constituted a major portion of the linkage group in all 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)

Major rearrangements between the rapa/oleracea and nigra genomes (a, b) and the rapa and oleracea genomes (c, d). Boxes bearing the same color represent homoeologous blocks while the hatched boxes represent large gaps (≥10 cM regions devoid of any markers). (a) Prominent rearrangements between the A/C and B genomes resulting in altered block arrangement (b) Block organization of one LG of the B genome harbours the blocks from two LGs in the A/C genome explaining the difference of one chromosome between the two genomes (c) B. oleracea genome-specific rearrangements (mainly translocations) after the divergence from the Rapa lineage (d) Block organization of two LGs of the C genome (C8, C9) can be derived from three LGs (A8, A9, A10) of the A genome suggesting that the difference of one chromosome between the A and C genomes could be either due to the gain of one of the these LGs in the Rapa lineage or a reduction of one LG in the oleracea genome.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 8: Major rearrangements between the rapa/oleracea and nigra genomes (a, b) and the rapa and oleracea genomes (c, d). Boxes bearing the same color represent homoeologous blocks while the hatched boxes represent large gaps (≥10 cM regions devoid of any markers). (a) Prominent rearrangements between the A/C and B genomes resulting in altered block arrangement (b) Block organization of one LG of the B genome harbours the blocks from two LGs in the A/C genome explaining the difference of one chromosome between the two genomes (c) B. oleracea genome-specific rearrangements (mainly translocations) after the divergence from the Rapa lineage (d) Block organization of two LGs of the C genome (C8, C9) can be derived from three LGs (A8, A9, A10) of the A genome suggesting that the difference of one chromosome between the A and C genomes could be either due to the gain of one of the these LGs in the Rapa lineage or a reduction of one LG in the oleracea genome.
Mentions: All the linkage groups belonging to the three diploid Brassica species could be divided into ten categories or groups (Group1–10) based on the extent of homoeology between them (Figure 7). Group 1 consists of A1/B1–B2/C1. A1 was entirely homoeologous to C1, both being constituted by the block arrangement F-T-U. The F-T-U arrangement was specific to the Rapa/Oleracea lineage. Interestingly, this F-T-U arrangement was found repeated in both the A (A3) and the C (C3) genomes (Group 3, Figure 7) but was absent from the B genome. The linkage group B1 shared the F block with A1/C1 in Group1. Due to the presence of two F blocks in B1, this linkage group also had homoeology with Group 3. B2, which shared the U block with A1 and C1, could also be placed in this group. In Group 2 (A2/B2/C2), A2 and C2 were completely homoeologous, while B2 showed homoeology with A2 and C2 for the block motifs R-W-E-O-P. One inversion in B2 could explain the separation of the E block from the R-W block combination (Figure 8). Group 3 (A3/B1–B3/C3) members shared the common block arrangement R-W-J-I-P-O. B3 was almost entirely composed of this block arrangement, while an additional F-T-U block was present in A3 and C3. Members of Group 4 (A4/B4/C4) shared the block motif J-I-S-N-T. A4 and B4 appeared to be homoeologous along their entire length, while C4 had acquired an additional J block. The presence of two J blocks in C4 was a C genome-specific rearrangement. Due to the presence of an additional J block, C4 has also been placed in group 5. In Group 5 (A5/B5/C4–C5), A5 and B5 were homoeologous along their entire length sharing the block motif J-C-F. C5 shared partial homoeology (blocks F-C) with A5 and B5. The terminal J block present in A5 and B5 was however absent in C5. In Group 6 (A6/B6/C5–C6), A6 and B6 were homoeologous along their entire length sharing the block arrangement C-B-A-V-K-L-Q. One inversion in either of the two genomes could explain the reverse orientation of the blocks constituting the lower segment of A6–B6 (blocks V-K-L-Q). Two C genome LGs (C5 and C6) are also components of this group. C5 shared the A-B-C block arrangement with A6/B6 while C6 was homoeologous for the block arrangement V-K-L-Q with A6/B6. Members of Group 7 (A7/B7/C7) shared homoeology for a large E block while Group 8 (A8/B7/C8) members were homoeologous for blocks A-B-U. Group 9 (A9/C8–C9) had A9 sharing homoeology with C9 for the blocks O-Q-X-H-D-V which constituted the top half of both the linkage groups. The lower segment of A9 shared the block arrangement N-I-H-A with C8. No LG from the B genome seemed to possess any major block homoeologous with A9. Members of group 10 (A10/B8/C9) shared the blocks R-W which constituted a major portion of the linkage group in all 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