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Laboratoire Commun de |
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IRILmap : Linkage map distance conversion software for Intermated
Recombinant Inbred Lines |
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Intermated
recombinant inbred lines (IRILs) are obtained by including generations of intermating
among F2 individuals before selfing or sib-mating. Compared to usual
recombinant inbred lines (RILs), such IRILs offer an increase of map
resolution, due to additional recombination events occurring during
intermating generations (Liu et al., 1996, Genetics 142:247-258). |
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However,
as far as we know today, mapping software available to date cannot take into
account this populations structure to compute "actual" centiMorgan
distances. For instance, if one uses MapMaker software (Lander et al., 1987,
Genomics 2: 174-181) with "RIself" or "RIsib" options to
compute map distances from IRIL populations, distance units are no
"actual" centiMorgans, and thus may not be directly compared to
distances obtained from backcross, F2 or RIL populations. |
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Based
on the reference work of Haldane and Waddington (1931, Genetics 16: 357-374)
on RILs, theoretical developments were carried out more recently by Winkler
et al. (2003, Genetics 164: 741-745) to establish the relationship between
the recombination Rn observed in an IRIL population obtained with n
generations of random intermating, and the recombination fraction r per
meiosis. |
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IRILmap
was developed to compute "actual" centiMorgan distances from
MapMaker output files (result of "Map" command obtained with the
"photo" command) obtained from IRIL data with "RI self"
or "RI sib" options (see "Distance calculation" section
for details). It is also possible to use IRILmap to convert Haldane distances
into Kosambi's, or reciprocally. Mapping data produced with other software
than MapMaker can be used, provided that file formats are respected (see
"Format specifications" section for details) and that distances
were computed as for RILs by using Haldane & Waddington's formula. For
this purpose, tabulated files are also accepted in addition to MapMaker
output files. |
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“IRILmap.exe”
was compiled to run on Windows-based platforms. The
perl script “RIL2IRIL” is also included in the package, to perform similar distance
conversions from UNIX or LINUX shell. This script reads no file, but accepts
one input distance value as argument and returns the converted distance. It
is then easy to embed in any shell, perl, or other type application. Upon
request, we may consider producing executables for other platforms. To estimate which level of maintenance should be dedicated to this
software, I will appreciate to be informed if you download it. So please click here to let me know, and put “IRILmap” and your name in the subject
field. You can either let the message blank,
or add your comments. Sending me your name is not required for downloading, but it is
helpful to me and ensures that I can inform you of possible improvements that
I would bring to the software. So please do. I will keep your e-mail address
strictly confidential.
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