2-point mapping data examples
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You need only give the names of the mapped genes if more than two
genes are mentioned in the genotype.
The calculation line is designed to help us combine data correctly.
It replicates some information from the Results line together with an
initial keyword describing how the map distance calculation should be
performed. After the keyword should follow the numbers to be used in
the calculation, by themselves without phenotypes. Three commonly
used types are given below, and a more extensive listing is also
available. In some cases the same calculation keyword may be
appropriate even when a cross is done slightly differently, e.g. when
using a dominant gene in cis to a recessive one. Almost all 2 point
data reported for C. elegans thus far can be classified into a total
of 10 categories or 19 different types:
(1) A. Recessive markers x and y, segregation from xy/++ hermaphrodites:
Types 1-5
(2) A' Recessive markers x and y, segregation from xy+/++z, where z is
tightly linked and z/z is lethal or otherwise not scored:
Type 6
(3) B Recessive markers, segregation from x+/+y hermaphrodites:
Types 7-8
(4) C Recessive markers, scored by backcross: xy/++ males crossed with
xy/xy hermaphrodites. Usually only males scored:
Types 9-10
(5) D Recessive sex-linked markers, x+/+y hermaphrodites crossed with wild
males, male progeny scored:
Types 11-12
(6) D' Recessive sex-linked markers, xy/++ hermaphrodites crossed with wild
males, male progeny scored:
Type 13
(7) E One marker (d) is dominant or semidominant. Segregation from x+/+d
hermaphrodites. For Type 16 (Dom_semi), D = d/+, not d/d (as in sqt):
Types 14-16
(8) E' One marker (d) is dominant, and either d or x is recessive lethal:
Type 17
(9) F Direct: single progeny picked and tested for genotype
on both chromosomes:
Type 18
(10) G Complex:
Type 19
Click to see the description of these 19 types.
If desired, specific examples from the existing database, will be supplied by e-mail.
1.Full |
2.One recombinant |
3.Selected |
4.One all |
5.Recs all |
6.One let |
7.Tested |
8.Selected trans |
9.Backcross |
10.Back one |
11.Sex all |
12.Sex one |
13.Sex cis |
14.Dom one |
15.Dom selected |
16.Dom semi |
17.Dom let |
18.Direct |
19.Complex mixed |
Calculation Data used How calc is done
----------- --------- ----------------
Full WT X Y XY (2p-p^2)/2 = (X+Y)/(WT+X+Y+XY)
One_recombinant WT X (2p-p^2)/3 = X/(X+WT)
Selected X XY (2p-p^2) = X/(X+XY)
Note that this is a guide for us on how to do the calculation; you do
not need to submit a calculated distance.
--2 point data
Mapper: Brenner S ! surname initials
Date: 01/72 ! just month and year
Temp: 20
Genotype: sma-4(e729) unc-32(e189)/+ +
Mapped_genes: sma-4, unc-32
Results: 928 WT, 9 Dpy, 8 Unc, 326 DpyUnc
Calculation: Full 928 9 8 326
--2 point data
Mapper: Brenner S
Date: 4/70
Temp: 20
Genotype: sma-2(e297) unc-36(e251) / + +
Mapped_genes: sma-2, unc-36
Results: 482 WT, 2 Unc, 1 Sma, 117 SmaUnc ! numbers with phenotypes
Calculation: One_recombinant 482 2 ! see explanation above
Comment: used One_recombinant not Full because
of deviation from Mendelian ratios ! any text you want
--2 point data
Mapper: Hodgkin JA
Date: 01/98
Temp: 20
Mapped_genes: unc-42, let-560
Genotype: unc-42(e270) let-560(e2658) / + +
Calculation: One_recombinant 700 10
Results: 700 WT, 10 Unc
Comment:
EMAIL : jah@mrc-lmb.cam.ac.uk
Notes for 2-point data
Most measurements of linkage between pairs of
loci in C. elegans have been made by scoring segregation in the
progeny of a hermaphrodite which is a cis-heterozygote for two
recessive mutations: for example, sma-4 unc-32 / + +, as in the case
given below (Type 1). This will produce four kinds of phenotypically
distinguishable progeny: WT (Wild type), SmaUnc, Sma and Unc.
If all four progeny types are scored, linkage can be measured
by the ratio of recombinant phenotypes (Sma and Unc) to total progeny,
which is given by (2p - p^2)/2.
This is Type 1 (Full) , in the classification below.
If two of the phenotypic classes are hard to distinguish,
or subviable, then linkage is determined by scoring just WT and one
recombinant phenotype. For example, if Unc and SmaUnc were hard to
distinguish, only WT and Sma would be counted. The ratio of Sma to
(WT + Sma) is given by (2p - p^2)/3.
This is Type 2 (One_recombinant), in the classification below.
Initial measurements of linkage are often made by picking
individual animals in the progeny of a trans-heterozygous hermaphrodite,
and determining their full genotype by progeny testing. For example,
Sma animals could be picked from the progeny of a hermaphrodite of
genotype sma-4 + / + unc-32. Those that produced only Sma progeny
are sma-4 + / sma-4 + , whereas those that produce Sma and SmaUnc
progeny are sma-4 unc-32 / sma-4 +. The proportion of Sma animals
that segregate SmaUnc is given by 2p/(1 + p).
This is Type 7 (Tested), in the classification below.
These three Types account for most of the 2_point_data listed
in ACeDB. In addition, a variety of alternative crosses and
calculations have been used, to deal with special cases. A total of
19 different calculations have been used so far. These are listed
below, together with a specific example for each type.
Complete classification of two-factor data
Phenotypic abbreviations used:
WT = wild type
nonWT = viable non-wild-type,
ALL = total viable progeny
X = x/x and xy/x+ (for recessive marker x)
Y = y/y and xy/+y (for recessive marker y)
XY = xy/xy
D = d/+ and d/d, dx/+ etc (for dominant marker d)
H = xy/x+
--------------------------------------------------------------------
Type Phenotypes Calculation
A. Recessive markers x and y, segregation from xy/++ hermaphrodites
1. Full WT X Y XY (2p-p^2)/2 = (X+Y)/(WT+X+Y+XY)
Example (Full):
--2 point data
Mapper: Brenner S
Date: 01/72
Temp: 20
Genotype: sma-4(e729) unc-32(e189)/+ +
Results: 928 WT, 9 Sma, 8 Unc, 326 SmaUnc
Calculation: Full 928 9 8 326
Comment:
2. One_recombinant WT X (2p-p^2)/3 = X/(WT+X)
Example (One_recombinant):
--2 point data
Mapper: Brenner S
Date: 11/68
Temp: 20
Genotype: dpy-10(e128) rol-1(e91)/+ +
Results: 1121 WT, 53 Rol, 377 Dpy & RolDpy
Calculation: One_recombinant 1121 53
Comment: Dpy and RolDpy not distinguishable
3. Selected X XY (2p-p^2) = X/(X+XY)
Example (Selected):
--2 point data
Mapper: Hartman PS
Date: 02/81
Temp: 20
Genotype: dpy-5(e61) rad-1(mn155)/+ +
Results: 1 Dpy, 11 DpyRad
Calculation: Selected 1 11
Comment: non-Dpy were not scored
4. One_all X ALL (2p-p^2)/4 = X/ALL>
Example (One_all):
--2 point data
Mapper: Meneely PM
Date: 05/83
Temp: 20
Genotype: dpy-7(e88) unc-3(151)/+ +
Results: 209 Dpy, 1954 total
Calculation: One_all 209 1954
Comment:
5. Recs_all X Y ALL (2p-p^2)/2 = (X+Y)/ALL
Example (Recs_all):
--2 point data
Mapper: Kusch M
Date: 12/79
Temp: 20
Genotype: dpy-13(e184) unc-24(e138)/+ +
Results: 44 Dpy, 40 Unc, 2085 WT & DpyUnc
Calculation: Recs_all 44 40 2169
Comment: WT and DpyUnc scored together, therefore appropriate
calculation is Recs_all.
A' Recessive markers x and y, segregation from xy+/++z, where z is
tightly linked and z/z is lethal or otherwise not scored.
6. One_let X ALL (2p-p^2)/2 = X/ALL
Example (One_let):
--2 point data
Mapper: Rosenbluth RE
Date: 05/89
Temp: 20
Genotype: let-344(s376) unc-46(e177)/unv-42(e270) ama-2(m323)
Results: 1293 WT, 49 Unc-46, 26 Unc-42
Calculation: One_let 49 1368
Comment: ama-2(m323) is recessive lethal, linked in trans,
therefore One_let is appropriate calculation.
B Recessive markers, segregation from x+/+y hermaphrodites
7. Tested H X 2p/(1+p) = H/X
Example (Tested):
--2 point data
Mapper: Rand JB
Date: 11/88
Temp: 20
Genotype: unc-10(e102) +/+ dpy-6(e14)
Results: 15 of 276 Unc-10 carried dpy-6
Calculation: Tested 15 276
Comment:
8. Selected_trans X XY p^2 = XY/(X+XY)
Example (Selected_trans):
--2 point data
Mapper: Sulston JE
Date: 02/74
Temp: 20
Genotype: cat-2(e1112)/dpy-10(e128)
Results: 327 Dpy, 19 CatDpy
Calculation: Selected_trans 327 19
Comment:
C Recessive markers, scored by backcross: xy/++ males crossed with
xy/xy hermaphrodites. Usually only males scored.
9. Backcross WT X Y XY p = (X+Y)/(WT+X+Y+XY)
Example (Backcross):
--2 point data
Mapper: Hodgkin JA
Date: 05/87
Temp: 20
Genotype: smg-2(e2008) unc-13(e51) x smg-2 unc-13/+ + males
Results: (Males scored) 67 WT, 19 Smg, 14 Unc, 65 SmgUnc
Calculation: Backcross 67 19 14 65
Comment: The Smg phenotype is scored easily only in males
10. Back_one WT X p = X/(WT+X)
Example (Back_one):
--2 point data
Mapper: Hodgkin JA
Date: 05/88
Temp: 20
Genotype: mab-12(e2166) unc-17(e113)/+ + males x mab-12 unc-17
Results: 42 WT males, 8 Mab males, 6 Unc males, 21 MabUnc males
Calculation: Back_one 42 8
Comment: MabUnc and possibly Unc males underscored, therefore
these are omitted from calculation.
D Recessive sex-linked markers, x+/+y hermaphrodites crossed with wild
males, male progeny scored.
11. Sex_all WT X Y XY p = (WT+XY)/(WT+X+Y+XY)
Example (Sex_all ):
--2 point data
Mapper: Baird SE
Date: 11/89
Temp: ?
Genotype: him-5/+; ram-5(bx30) +/+ unc-3 x him-5(e1490) males
Results: 149 Ram males, 207 Unc males, 1 WT male, 1 RamUnc male
Calculation: Sex_all 1 149 207 1
Comment:
12. Sex_one WT X p = WT/(WT+X)
Example (Sex_one):
--2 point data
Mapper: Thierry-Mieg D
Date: 05/88
Temp: 20
Genotype: unc-27(e155)/dpy-7(e155) unc-115 x wildtype males
Results: 446 Unc-27 males, 256 Dpy-7Unc-115 males, 4 WT males,
2 Unc-27Unc-115 males
Calculation: Sex_one 4 446
Comment: Unc-115 class is under-represented, therefore
calculation is based on Unc-27 and WT males only
D' Recessive sex-linked markers, xy/++ hermaphrodites crossed with wild
males, male progeny scored.
13. Sex_cis X ALL p/2 = X/ALL
Example (Sex_cis):
--2 point data
Mapper: Meneely PM
Date: 03/78
Temp: 20
Genotype: lon-2(e678) dpy-6/+ + x wildtype males
Results: 163 Lon males, 6316 total males
Calculation: Sex_cis 163 6316
Comment:
E One marker (d) is dominant or semidominant. Segregation from x+/+d
hermaphrodites. For Type 16 (Dom_semi), D = d/+, not d/d (as in sqt)
14. Dom_one WT nonWT (2p-p^2)/4 = WT/(WT+nonWT)
Example (Dom_one):
--2 point data
Mapper: Kusch M
Date: 12/79
Temp: 20
Genotype: bli-6(mn4)/unc-24(e138)
Results: 19 WT, 2467 Bli & Unc & BliUnc
Calculation: Dom_one 19 2467
Comment: mn4 is dominant
15. Dom_selected WT X (2p-p^2) = WT/(WT+X)
Example (Dom_selected):
--2 point data
Mapper: Golden JW
Date: 08/82
Temp: 20
Genotype: sqt-1(e1350)/daf-22(m130)
Results: 161 Daf, 31 daf-22/+
Calculation: Dom_selected 31 161
Comment:
16. Dom_semi XD ALL (p-p^2)/2 = XD/ALL
Example (Dom_semi):
--2 point data
Mapper: Laufer JS
Date: 03/79
Temp:
Genotype: sqt-2(sc3)/unc-4(e120)
Results: 45 RolUnc, 472 total
Calculation: Dom_semi 45 472
Comment: Only animals of genotype sc3 e120/+ e120 are scored as
RolUnc. Double homozygotes (sc3 e120/sc3 e120) will be SqtUnc, which
cannot be distinguished from Unc.
E' One marker (d) is dominant, and either d or x is recessive lethal
17. Dom_let WT ALL (2p-p^2)/3 = WT/ALL
Example (Dom_let):
--2 point data
Mapper: Hodgkin JA
Date: 12/92
Temp: 20
Genotype: dpy-25(e817)/let-552(e2542)
Results: 3 WT, 615 Dpy
Calculation: Dom_let 3 618
Comment:
F Direct: single progeny picked and tested for genotype
on both chromosomes
18. Direct
R = # recombinant chromosomes p = R/T
T = # total chromosomes
Example (Direct):
--2 point data
Mapper: Jacobson LA
Date: 05/83
Temp: 16
Genotype: dpy-10(e128)/cad-1(j1)
Results: Of Dpy F2, scored for cad, 23 +/+, 15 +/-, 2 -/-
Calculation: Direct 19 80
Comment:
G Complex:
19. Complex_mixed X ALL (2p-p^2)/5 = X/ALL
Example (Complex_mixed):
--2 point data
Mapper: Meneely PM
Date: 04/77
Temp: 20
Genotype: mnDp1/+; let-3(mn104) unc-3(e151)/ + +
Results: 92 Unc, 6057 total
Calculation: Complex_mixed 92 6057
Comment: For explanation of this calculation, see
Meneely & Herman (1979)
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