Bioinformatics Advance Access originally published online on June 16, 2005
Bioinformatics 2005 21(16):3441-3442; doi:10.1093/bioinformatics/bti543
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IRILmap: linkage map distance correction for intermated recombinant inbred lines/advanced recombinant inbred strains
INRA-UPS-CNRS-INA.PG, U.M.R. de Génétique Végétale 91190, Gif-sur-Yvette, France
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Summary: Intermated Recombinant Inbred Lines (IRILs) in plants, or Advanced Recombinant Inbred Strains in animals, are constructed by carrying out generations of intermating between F2 individuals before starting recurrent inbreeding generations by selfing or sib-mating. IRILs are powerful for high-resolution genetic mapping because they have undergone more recombination than usual Recombinant Inbred Lines (RILs). However, there is no mapping software able to generate actual centiMorgan distances from the segregation data obtained with IRILs. IRILmap software converts genetic distances computed with any linkage mapping program designed for RILs, so that IRIL-derived data can be used to get actual centiMorgan distances, directly comparable to F2, backcross or RIL-derived maps.
Availability: IRILmap is available with a user-friendly interface on Microsoft Windows operating systems, and as a perl v5.6.1 script with a minimal interface, for command-line use on any platform, or embedding in other applications. Both versions are freely available at http://moulon.inra.fr/~bioinfo/mapping/irilmap1.html
Contact: falque{at}moulon.inra.fr
Intermated Recombinant Iinbred Lines (IRILs) in plants (Liu et al., 1996; Lee et al., 2002), or Advanced Recombinant Inbred (ARI) strains in animals (Peirce et al., 2004), are high-resolution linkage mapping panels obtained by including generations of random intermating among F2 individuals before inbreeding generations conducted by selfing or sib-mating. Compared with usual Recombinant Inbred Lines (RILs) in plants, or Recombinant Inbred Strains (RISs) in animals, such IRILs offer an increase of map resolution, owing to additional recombination events occurring during intermating generations (Liu et al., 1996).
However, to our knowledge, linkage mapping software available to date cannot use IRIL-derived data to compute actual centiMorgan distances, which should be related to the expected frequency of crossover events per meiosis. Such a frequency is not directly observed in segregation data from mapping populations where several meioses have contributed to the final recombination rate. In the case of F2, F3 and RIL populations, theoretical developments were available for a long time to infer actual centiMorgan distances from the observed segregation data (see for instance Haldane and Waddington, 1931), and usual linkage mapping software such as MapMaker (Lander et al., 1987) or JoinMap (Stam, 1993) implement them. But if one uses these software to compute map distances from IRIL populations, distance values are not actual centiMorgans any more, and thus may not be directly comparable to distances obtained from backcross, F2 or RIL populations.
Theoretical developments were carried out by Winkler et al. (2003) based on the reference work of Haldane and Waddington (1931) on RILs, and these authors established the relationship between the recombination rate Rn observed in an IRIL population obtained with n generations of random intermating and the recombination fraction r per meiosis, thus opening the door to proper calculations of actual centiMorgan distances from IRIL-derived data. This is true only for autosomal loci, since similar theory for the X chromosome is, to our knowledge, not available yet. Winkler's calculation is based on a model of panmictic intermating in an infinite-sized population. This situation can be approached as much as possible in mice in spite of the small population sizes, by avoiding sibling pairing as compared with true random mating (Iraqi et al., 2000). Winkler's theory is also based on completely inbreeded lines or strains. Teuscher et al. (2005) developed a theory for finite numbers of inbreeding generations, but these authors used approximations that require small distances between adjacent loci, which is not the case with Winkler's method.
IRILmap was developed to compute corrected centiMorgan distances based on Winkler's calculation (Winkler et al., 2003) from distances improperly generated with IRIL-derived segregation data by using calculation methods designed for non-intermated RILs. As input data, IRILmap uses distances computed by any linkage mapping software, provided (1) the distances are computed as for RILs, inbreeded either by selfing (plant RILs) or by sib-mating (animal RISs) and (2) the distance function is either Haldane's (1919) or Kosambi's (1944). This may be useful since both mapping functions are frequently used in mapping projects on different species. The number of random intermating generations of the IRILs can be set from 0 to 10 in the IRILmap Windows interface or as argument in the RIL2IRIL perl script. Zero intermating generations corresponds to RILs. The use of IRILmap with this setting is only useful to perform distance conversions from selfed to sib-mated panels or back, and/or from Haldane's to Kosambi's distance function or back.
IRILmap follows the scheme presented in Figure 1, the formalism that will be used hereafter. According to Winkler et al. (2003) one needs to know R in order to compute actual IRIL-based distances. However, we don't have access to R in the output of most linkage mapping software that produce genetic distances (D). So IRILmap calculates R from D by using, first, the reversed distance functions given below (step 1 of Fig. 1),
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Input file format for the Windows version of IRILmap can be either the commonly-used MapMaker-like output format or tabulated files. IRILmap then produces a tabulated output file and a MapMaker-like output file with one additional column for corrected distances if input format was MapMaker-like. Sample data files are provided with the package. The perl script RIL2IRIL directly returns corrected distance values from initial distance entered as argument, so that it can be easily embedded in other applications.
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The author would like to thank Marie-Cécile Leclerc-Falque and Johann Joets for the assistance and advice during the development of the software, and two anonymous reviewers for their comments on the manuscript.
Conflict of Interest: none declared.
Received on April 18, 2005; revised on June 13, 2005; accepted on June 14, 2005
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Haldane, J.B.S. (1919) The combination of linkage values and the calculation of distance between loci of linked factors. J Genet., 8, 299–309[Web of Science].
Haldane, J.B.S. and Waddington, C. (1931) Inbreeding and linkage. Genetics, 16, 357–374
Iraqi, F., et al. (2000) Fine mapping of trypanosomiasis resistance loci in murine advanced intercross lines. Mammalian Genome, 11, 645–648.
Kosambi, D. (1944) The estimation of map distances from recombination values. Ann. Eugen., 12, 172–175.
Lander, E.S., et al. (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics, 2, 174–181.
Lee, M., et al. (2002) Expanding the genetic map of Maize with the intermated B73 x Mo17 (IBM) population. Plant Mol. Biol., 48, 453–461[CrossRef][Web of Science][Medline].
Liu, S.C., et al. (1996) Genome-wide high-resolution mapping by recurrent intermating using Arabidopsis thaliana as a model. Genetics, 142, 247–258[Abstract].
Peirce, J.L., et al. (2004) A new set of BXD recombinant inbred lines from advanced intercross populations in mice. BMC Genetics, 5, 7.
Stam, P. (1993) Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J, 3, 739–744.
Genetics Teuscher, F., et al. (2005) The map expansion obtained with recombinant inbred strains and intermated recombinant inbred populations for finite generation designs. 2005 Jun 3; [Epub ahead of print].
Winkler, C.R., et al. (2003) On the determination of recombination rates in intermated recombinant inbred populations. Genetics, 164, 741–745
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