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
) 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
- 1 Parkin et al. (1995) Genome 38:1122-1133
- 2 Sharpe et al. (1995) Genome 38:1112-112
- 3 Parkin et al. (2005) Genetics, 171: 765-781
- 4 Bohuon et al. (1996) Theor. Appl. Genet., 93, 883-839, 1996
- 5 Sebastian et al. (2000) Theor. Appl. Genet. 100:75-8
- 6 Kim et al. (2006) Genetics. 174: 29-39
- 7 Kim et al., (2004) Joint Meeting of the 14th Crucifer Genetics Workshop and the 4th ISHS Symposium on Brassica, October 24~28, pp146, Poster
- 8 Lim et al. (2005) Mol. Cells, 19:436-444
- 9 Suwabe, K. et al., (2007) Genetics, 173, 309-319
- 10 http://www.intl-pag.org/12/abstracts/P5e_PAG12_522.html
- 11 Howell et al. Genome. 48(6): 1093-1103
- 12 Choi et al., (2007)Theor. Appl. Genet. 115:777-7922
- 13 Lagercrantz U & Lyidate DJ (1996) Comparative Genome Mapping in Brassica. Genetics 144:1903-1910