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Comparative mapping of Brassica juncea and Arabidopsis thaliana using intron polymorphism (IP) markers: homeologous relationships, diversification and evolution of the A, B and C Brassica genomes

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Title Comparative mapping of Brassica juncea and Arabidopsis thaliana using intron polymorphism (IP) markers: homeologous relationships, diversification and evolution of the A, B and C Brassica genomes
 
Creator Panjabi, Priya
Jagannath, Arun
Bisht, Naveen C.
Padmaja, K Lakshmi
Sharma, Sarita
Gupta, Vibha
Pradhan, Akshay K
Pental, Deepak
 
Subject Brassica genomes
Brassica juncea
Arabidopsis thaliana
Intron Polymorphism
mapping
markers
 
Description 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.
The work was financially supported by Dhara Vegetable Oil and Food Company Ltd (DOFCO), a subsidiary of the National Dairy Development Board
(NDDB), India. Partial support came from the UGC-SAP programme. SS
was funded by a fellowship from the Department of Science and Technology (DST) under the SERC Fast Track Scheme for Young Scientists. LP was
supported by a research fellowship from the Council of Scientific and Industrial Research (CSIR).
 
Date 2013-11-11T07:07:25Z
2013-11-11T07:07:25Z
2008
3 March 2008
 
Type Article
 
Identifier BMC Genomics, 9: 113
http://hdl.handle.net/123456789/97
 
Language en
 
Publisher BioMed Central