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The European Arabidopsis Stock Centre

Lister and Dean Recombinant inbred mapping lines

Donated by

  • Caroline Dean Department of Cell and Developmental Biology, John Innes Centre
  • Clare Lister Department of Cell and Developmental Biology, John Innes Centre
  • Clare Lister Department of Cell and Developmental Biology, John Innes Centre

Click here to view all 302 of these lines.

Description

Sets in this collection

Nasc code Description Set contents
N1899 Complete Dean RI lines Set 1 (100 lines) View set contents
N4858 Complete Dean RI lines Set 2 (200 lines) View set contents
N4859 Complete Dean RI lines Set 1 and Set 2 (300 lines) View set contents
N4857 Dean RI arms kit

Mapping using the Lister & Dean RI lines

The Recombinant Inbred (RI) lines were generated from a cross between the Arabidopsis ecotypes Columbia (N933) and Landsberg erecta (NW20) (Lister , C. & Dean, C. 1993) with Columbia as the male parent.

300 lines were generated to be used for mapping but a large number of markers have been mapped using 100 of these lines (N1899). Mapping a new marker using these 100 will give an accurate map position relative to >1000 other markers however a rough map position can be determined with a much smaller number of these lines (20 - 30, see below).

For very fine mapping the additional 200 lines can be used but markers in the area of interest would then need to be scored on the 200 lines.

One can only directly map something on these lines if it is polymorphic between Columbia and Landsberg erecta and its segregation is therefore scorable in the RI lines. QuantitativeTrait Loci (QTL), ie. loci affecting quantitative traits, can also be mapped as they are segregating in the RI population, although these may not be obviously polymorphic in the parental ecotypes.

Steps to Mapping a Locus.


1. Identify a difference

Identify an RFLP or other polymorphic feature in the parental ecotypes (see above) or a quantitative trait which can be scored in the RI lines.

2. Sow out the RI lines

Plants to be used for DNA preps can be grown either in the glasshouse and tissue culture (for leaves) or in liquid media in flasks (for mainly root material).
Plants that are grown for phenotypic or biochemical examination may require special growing conditions or treatments to reveal/accentuate the differences between Columbia and Landsberg erecta (ie inoculation with fungus, different light regimes, etc.).

If only using 20-30 RI lines for mapping the following lines have been selected as having the highest frequency of recombination over the five chromosomes and therefore should be the most informative for mapping purposes:-

20 lines +10 lines (= 30 total)
CS/N1911 (33)
CS/N1929 (115)
CS/N1945 (190)
CS/N1946 (191)
CS/N1948 (194)
CS/N1951 (217)
CS/N1953 (231)
CS/N1954 (232)
CS/N1957 (238)
CS/N1960 (245)
CS/N1963 (263)
CS/N1966 (267)
CS/N1968 (283)
CS/N1969 (284)
CS/N1970 (288)
CS/N1971 (295)
CS/N1974 (302)
CS/N1978 (332)
CS/N1984 (356)
CS/N1989 (370)
CS/N1900 (4)
CS/N1901 (5)
CS/N1903 (13)
CS/N1913 (35)
CS/N1915 (37)
CS/N1959 (242)
CS/N1975 (303)
CS/N1985 (358)
CS/N1988 (367)
CS/N1990 (377)

3. Score the lines for your locus

  1. RFLP markers. Harvest plant material (leaves or roots), make DNA. Do restriction digests, Southern blots, and hybridization experiments or do PCR reactions and run gels. Score.
  2. Phenotypic difference. Score differential phenotype in the lines.
  3. Biochemical difference. Carry out the biochemical assay and score.
  4. QTL Count or measure the trait under examination (usually recorded as a mean from 5-10 individuals/RI line.)

In all the above experiments do not forget to include the Columbia and Landsberg erecta parents at the same time, as controls.

Mapping using Mapmaker

RI mapping can be conducted using Mapmaker (Lander et al 1987) and in this case the data has to conform to the Mapmaker format. Note: concerning plant order:

The 101 plants in the Dean/Lister population are presented in the following order. Each symbol corresponds to one an RI line (for example, "4" corresponds to CL4, which is Nottingham strain N1900).

PLEASE look at the RI data pages (EXCEL FILE LINKED BELOW) to correlate these with stock numbers, - they are NOT simply consecutive. Some are given above e.g. 4 = CS/N1900.

4 5 13 14 17 19A 19B 25 29 30
32 33 34 35 36 37 46 52 53 54
59 62 67 68 71 79 84 90 107 113
115 123 125 131 160 161 166 167 173 175
177 179 180 181 182 188 190 191 193 194
199 209 214 217 231 232 235 237 238 240
242 245 253 257 259 263 264 266 267 279
283 284 288 295 296 297 302 303 311 321
332 342 345 349 350 351 356 358 359 363
367 370 377 378 386 390 394 395 397 398
400

Enter your scores for the RI lines data into a Text file as follows:-
A = like Columbia parent
B = like Landsberg parent
H = heterozygote (if possible to score)
- = unscorable or no score

Marker names should start with a * followed by a letter (small or capital) ie. *w23 and should have a single space or tab between each entry. Names MUST BE LESS than EIGHT characters. Mapmaker is not case sensitive and so reads "a" and "A" as the same thing.

Your file should look like this: 

RI line Number		4	5	13	14	17	25	29

*A1			A	A	B	-	A	B	B

*b2			B	B	B	A	H	-	B

*C4			B	A	-	A	B	B	A

Save as TEXT ONLY.

Enter data into Mapmaker.

Mapmaker for different machines can be somewhat different to run (Lander et al 1987). If the database of 67 markers is being used with these programs we strongly suggest that you READ THE INSTRUCTION MANUALS and DO THE TUTORIALS before attempting to run the program.

Use of the Kosambi mapping function (as opposed to Haldane) appears to give the best fit for recombination data generated in Arabidopsis (Koorneef and Stam, 1992). Kosambi mapping function takes into account the effects of interference; which means that after one recombination event has occurred it is less likely that a second one will occur in adjacent regions, in the same generation.

Before entering data into Mapmaker one needs to add two lines of information above the markers scores. The top line indicates what type of mapping population the data is from, the options depend on the version of Mapmaker being used (see below). The second line indicates the numbers of individuals, the number of markers scored and defines the genotype symbols.

If Mapmaker V1.0 is being used the data is considered as coming from an F2 segregating population. This requires using a LOD value of 6.0 (default is 3.0) for the group and three-point commands, to take account of the multiple rounds of recombination. The top line of the data file should read:-

data type f2 intercross

If Mapmaker V2.0 is being used on UNIX one can run the data as coming from an RI population ( and therefore use the default LOD of 3.0). The default genotypes for this version are A=Columbia and B=Landsberg. The top line of the file should read:-

data type ri self

The second line indicates the number of individuals in the population (ie. 100), the number of markers being scored (ie. 46) and defines the genotype symbols used in the mapping data (ie. CLXYHU or AB-). The respective second lines will look something like:-

(V1.0) 100 46 0 0 CLXYHU (V2.0) 100 46 0 AB-

(PLEASE CHECK the manual of the version of Mapmaker being used that these lines are correct for that version, they do vary).

At the end the program will produce a list of the markers with the centimorgan distances and recombination fractions between them. This can be converted into a map. If Mapmaker V1.0 has been used the centimorgan distances will have to be recalculated, they are approximately two-fold too big as they were calculated for an F2 population. The formula is:-

r = R/2(1-R)
where R is the recombination fraction.
eg. the distance between two markers is 16.5cM (R=15.9%)
r = 0.159/2(1-0.159)
= 0.094
= 9.4cM

Related links

References

  • Chang C., et al. 1988. Restriction fragment length polymorphism linkage map for Arabidopsis thaliana. PNAS 85(18): 6856-6860. PMID. 2901107.
  • Koornneef, M. & Stam, P. 1992. Genetic analysis. In Methods in Arabidopsis Research (Koncz C.,Chua N-H and Schell J., eds.) World Scientific Publishing Co. Pte. Ltd., Singapore. pp83-99.
  • Lander, E.S. et al. 1987. Mapmaker: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1(2): 174-181. PMID. 3692487.
  • Lister C. & Dean C. 1993. Recombinant inbred lines for mapping RFLP and phenotypic markers in Arabidopsis thaliana. The Plant Journal 4(2): 745-750. Link to Article
  • Nam, H.G. et al. 1989. Restriction fragment length polymorphism linkage map of Arabidopsis thaliana. The Plant Cell 1(7): 699-705. PMID. 12359906.
  • Parker, J.E. et al. 1993. Phenotypic characterization and molecular mapping of the Arabidopsis thaliana locus RPP5 determining resistance to Peronospora parasitica. The Plant Journal 4(5): 821-831. Link to Article.