linkage groups assignments


In order to facilitate integration of information between genetic linkage maps constructed from different mapping populations and using different sets of molecular markers, it is important to be able to anchor to a commonly agreed set of chromosomes and ultimately to genome sequence. The MBGP Steering Committee has agreed to adopt the nomenclature originally described in (1,2) and considerable ongoing effort is currently focused in assigning additional existing linkage maps within this nomenclature system. The Brassica rapa sequencing project is also actively engaged in ensuring that the BAC seed contigs are anchored to genetic maps within this system (6, 12). This information has been compiled amongst others by G. King, G. Teakle, J. Kim and K. Suwabe.

Summary

B. nigra B. juncea B. oleracea B. napus B. rapa NIAB Korea original LG NIAB Korea chromosome [*] Suwabe et al. (NVITS) LG
  A1 (J1)   A1 (N1) A1 (R1) LG10 Chr3 6
  A2 (J2)   A2 (N2) A2 (R2) LG3 Chr6 8
  A3 (J3)   A3 (N3) A3 (R3) LG1 Chr2 1
  A4 (J4)   A4 (N4) A4 (R4) LG4 Chr8 10
  A5 (J5)   A5 (N5) A5 (R5) LG7 Chr5 3
  A6 (J6)   A6 (N6) A6 (R6) LG5 Chr4 2
  A7 (J7)   A7 (N7) A7 (R7) LG6 Chr7 4
  A8 (J8)   A8 (N8) A8 (R8) LG9 Chr9 7
  A9 (J9)   A9 (N9) A9 (R9) LG2 Chr1 5
  A10 (J10)   A10 (N10) A10 (R10) LG8 Chr10 9
    C1 (O1) C1 (N11)        
    C2 (O2) C2 (N12)        
    C3 (O3) C3 (N13)        
    C4 (O4) C4 (N14)        
    C5 (O5) C5 (N15)        
    C6 (O6) C6 (N16)        
    C7 (O7) C7 (N17)        
    C8 (O8) C8 (N18)        
    C9 (O9) C9 (N19)        
B1 B1 (J11)            
B2 B2 (J12)            
B3 B3 (J13)            
B4 B4 (J14)            
B5 B5 (J15)            
B6 B6 (J16)            
B7 B7 (J17)            
B8 B8 (J18)            

Formalised convention

At the Jan 2007 MBGP Steering Committee meeting, it was agreed that it was timely to assign consistent chromosome/linkage group nomenclature to the canonical diploid Brassica genomes in the 'triangle of U' as: 'A', 'B' and 'C'. To ensure that this is universally agreed and adopted, it was agreed that it would then be necessary to a) publish a short paper describing the definitive nomenclature system in a recognised journal; b) notify key Journal editors; and c) also to publicise this more generally on websites/mailing lists etc.
  As a result Derek Lydiate (AAFC, Sasaktoon) agreed to follow-up with Graham King and other concerned participants by drafting a paper on nomenclature for publication. This is now underway, and further details will be posted here. The paper will propose the universal reference nomenclature convention that aims to simplify subsequent comparative genetic and genomic studies. It will describe the freely available resources required to characterise new populations, and describe a methodology to increase the likelihood of correctly identifying (assigning) chromosomes within new linkage maps.
  In addition, the paper will describe the historic accumulation of evidence and series of deductions that have enabled identification of each diploid chromosome with freely available genetic markers, the alignments and relationships between sets of maps and populations that have been developed in different laboratories over the past two decades In the meantime, authors are encouraged to adopt the consensus nomenclature of A1-A10, C1-C9 and B1-B8 in new publications. This has already been adopted by a number of research groups for reference maps (e.g. the TNDH B. napus map at JIC link) and in submitted manuscripts. References to these will be posted here as they become published.
  In Jan 2010, the MBGP Steering Committee agreed that for the B genome, the linkage group assignments described by Lagercrantz & Lydiate (1996) should would remain the reference point for subsequent publications.

References


Note relating to chromosomes (karyotype)

To minimise ambiguity, and maximise the ability to navigate between cytogenetic, linkage, physical and sequence maps the recommendation is to standardise reference to chromosomes in terms of standardised nomenclature: eg. "Chromsome C6" sensu ref 11; eg "Chromosome A9" is the first chromosome currently being sequenced in the Korean B. rapa sequencing project as a major contribution to the multinational effort. [*] N.B. Chromosome assignments from NIAB Korea updated 25 Sep 2006 .





This Page Was Last Edited: 11-Feb-2010