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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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Genetic map of B. juncea showing three linkage groups of the B genome (B6, B7 and B8). The corresponding nomenclature followed earlier for the B genome of B. juncea (with a prefix J) [11] and B. nigra (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 (A. thaliana) 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 B. juncea 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.
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Figure 5: Genetic map of B. juncea showing three linkage groups of the B genome (B6, B7 and B8). The corresponding nomenclature followed earlier for the B genome of B. juncea (with a prefix J) [11] and B. nigra (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 (A. thaliana) 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 B. juncea 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.

Mentions: Of the 1180 primer pairs thus designed, 383 (32%) showed polymorphism between the B. juncea lines, Heera and Varuna, parents of the DH mapping population used in this study and in the earlier mapping studies on B. juncea [11,30]. Genotyping using the 383 polymorphic primer pairs (for primer sequences see Additional file 1) generated 486 loci in B. juncea of which 67% were scored as co-dominant markers and the remaining 33% were scored as dominant markers. These 486 loci were incorporated into the framework map developed by Pradhan et al. [30]. Additionally 34 RFLP markers placed earlier on the B. juncea map [11] were assigned corresponding At loci by subjecting the available sequence data to NCBI BLASTN search and identifying the most significant BLASTN hit as the source At gene. A linkage map of B. juncea consisting of 533 At loci (486 IP, 34 RFLP and 13 gene markers) and covering a total genetic length of 1992.2 cM is shown in Figure 1, 2, 3, 4, 5. The ten A genome linkage groups (LGs) of the B. juncea map were designated A1–A10 and correspond to the N1–N10 linkage groups of B. napus [16]. The remaining eight B genome LGs were designated B1–B8 based on homoeology between the A, B and C genomes as determined in the present study. The corresponding linkage group nomenclature proposed earlier for the B. nigra genome (G1–G8) [18] and the B genome of B. juncea (J11–J18) [11] is also given in parentheses in Figure 4, 5 and Table 1.


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)

Genetic map of B. juncea showing three linkage groups of the B genome (B6, B7 and B8). The corresponding nomenclature followed earlier for the B genome of B. juncea (with a prefix J) [11] and B. nigra (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 (A. thaliana) 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 B. juncea 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.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Genetic map of B. juncea showing three linkage groups of the B genome (B6, B7 and B8). The corresponding nomenclature followed earlier for the B genome of B. juncea (with a prefix J) [11] and B. nigra (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 (A. thaliana) 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 B. juncea 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.
Mentions: Of the 1180 primer pairs thus designed, 383 (32%) showed polymorphism between the B. juncea lines, Heera and Varuna, parents of the DH mapping population used in this study and in the earlier mapping studies on B. juncea [11,30]. Genotyping using the 383 polymorphic primer pairs (for primer sequences see Additional file 1) generated 486 loci in B. juncea of which 67% were scored as co-dominant markers and the remaining 33% were scored as dominant markers. These 486 loci were incorporated into the framework map developed by Pradhan et al. [30]. Additionally 34 RFLP markers placed earlier on the B. juncea map [11] were assigned corresponding At loci by subjecting the available sequence data to NCBI BLASTN search and identifying the most significant BLASTN hit as the source At gene. A linkage map of B. juncea consisting of 533 At loci (486 IP, 34 RFLP and 13 gene markers) and covering a total genetic length of 1992.2 cM is shown in Figure 1, 2, 3, 4, 5. The ten A genome linkage groups (LGs) of the B. juncea map were designated A1–A10 and correspond to the N1–N10 linkage groups of B. napus [16]. The remaining eight B genome LGs were designated B1–B8 based on homoeology between the A, B and C genomes as determined in the present study. The corresponding linkage group nomenclature proposed earlier for the B. nigra genome (G1–G8) [18] and the B genome of B. juncea (J11–J18) [11] is also given in parentheses in Figure 4, 5 and Table 1.

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
Related in: MedlinePlus