Journal of Heredity 2003:94(4)
© 2003 The American Genetic Association 94:358-359
Computer Note |
TetraploidMap: Construction of a Linkage Map in Autotetraploid Species
From Biomathematics and Statistics Scotland, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DE, UK (Hackett) and School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK (Luo).
Address correspondence to Christine Anne Hackett at the address above or James McNicol, Biomathematics and Statistics Scotland, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DE, UK, or e-mail: christine{at}bioss.ac.uk or jim{at}bioss.sari.ac.uk.
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Abstract |
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TetraploidMap is a suite of Fortran 90 routines run from Microsoft Windows with a text-based input and output. TetraploidMap enables the user to assemble a linkage map from dominant and codominant (multiallelic) marker loci scored for the parents and full-sib progeny of a cross in an autotetraploid species. It includes routines for the inference of the parental genotypes, identification of linkage groups, two-point analysis to estimate the recombination frequency and LOD score between all pairs of marker in a linkage group, and locus ordering by simulated annealing.
Linkage analysis in polyploid plant species is less advanced than in diploid species due to the complexities of polysomic inheritance (De Winton and Haldane 1931; Fisher 1947). The development of molecular markers led to an interest in mapping in polyploid species, and Wu et al. (1992) showed that single-dose markers present in one parent of a polyploid cross (i.e., parental genotypes AOOO x OOOO) segregate in a 1:1 ratio in the offspring and recombination can be analyzed as for a diploid species if two such markers are in a coupling phase. The power of single-dose markers in a repulsion phase to identify homologous chromosomes is low, and Hackett et al. (1998) developed a theory for using double-dose dominant markers (i.e., AAOO x OOOO) to identify homologues in autotetraploids. Their approach was used to construct an amplified fragment length polymorphism (AFLP) map in potato by Meyer et al. (1998). Software for calculating two-point linkages for dominant markers in polyploids, Polylink, has been described by He et al. (2001).
Much more information is available if multiallelic markers such as microsatellites can be scored, as these facilitate identification of homologous chromosomes in both parents. Estimates of recombination frequencies based on multiallelic markers are up to four times as informative as the best estimates from dominant markers (Luo et al. 2001). However, the possibility of different allele dosages means that the parental genotypes cannot always be deduced directly from their phenotypes, as shown by gel band patterns, but need to be inferred from both parent and offspring phenotypes (Luo et al. 2000).
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The Program |
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TopAbstractThe ProgramReferences |
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TetraploidMap is a suite of routines, written in Fortran 90, for constructing a linkage map in an autotetraploid species, based on dominant and codominant (multiallelic) markers scored for two parents and their full-sib progeny. The main features of the routines are described here and more information is available in a user's guide.
FINDGENO
This infers the most likely parental genotype(s) at each locus from the parental and offspring phenotypes for each allele, using Bayes's theorem. The methodology is described in Luo et al. (2000). Null alleles (Callen et al. 1993) can be inferred, and a test for the presence of a significant degree of double reduction (Mather 1936) is included. The routine displays the probability of each parental genotype that is compatible with the phenotypic data and a test of goodness-of-fit of the observed offspring phenotype frequencies to that expected, in the presence and absence of double reduction. A typing error in a multiallelic locus may result in an offspring configuration that cannot be derived from any compatible parental genotype, and expected offspring phenotype frequencies can be displayed to assist in data checking.
CLUSTER
This routine searches for linkage groups. A chi-square test of independence is performed for each pair of markers. The markers are then clustered using the significance of this test as a measure of distance between pairs. The routine displays both single-linkage and average distance (between clusters) dendrograms (Anderson 1973). The locus data are printed in a form that the user can divide into linkage groups.
TWOPOINT
This routine is run for each linkage group and calculates the recombination frequency, the likelihood, and the LOD score for each pair of markers and for all possible phases using the most likely parental genotype. (If more than one parental genotype has a probability greater than 0.1, then the analysis is repeated for each such genotype.) The routine assumes random chromosomal pairing (De Winton and Haldane 1931) and does not allow double reduction. The method for calculating recombination frequencies for any configuration of dominant and/or multiallelic markers is based on the EM algorithm and is described in detail by Luo et al. (2001). The phases for each marker pair are sorted according to their likelihood, and the recombination frequency and LOD score for the phase with the highest likelihood and recombination frequency less than 0.5 are written to a pairwise data file.
SIMANNEAL
This routine orders the marker loci in each linkage group using simulated annealing to optimize the weighted least squares criterion (Stam 1993). It requires the pairwise data file from TWOPOINT, and an initial order, which can be chosen randomly. Alternatively the JMMAP module of JoinMap (Stan and Van Ooijen 1995) carries out a stepwise search to order pairwise data, and the output from this can be used as an initial order. Details of the simulated annealing method and a simulation study of its use in ordering markers in autotetraploid species are given in Hackett et al. (in press). Unless the proportion of multiallelic markers is quite high, the map should be constructed for the two parents separately, as dominant bridging markers (i.e., AOOO x AOOO) have large standard errors associated with their recombination frequencies (Meyer et al. 1998) and are particularly difficult to order precisely.
The SIMANNEAL routine gives a single order for the markers in a linkage group, which can lie on up to four homologous chromosomes for each parent. The marker can be located on the homologous chromosomes by the user, using phase information from the TWOPOINT routine. The resulting map can easily be displayed in a program such as MapChart (Voorrips 2002).
Availability
TetraploidMap is available free at ftp://ftp.bioss.sari.ac.uk/pub/cah as a zipped file containing the programs, user's guide, and example data.
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Acknowledgments |
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This work was financially supported by grants from the UK Biotechnology and Biological Research Council, and by the Scottish Executive Environment and Rural Affairs Department. We thank J. E. Bradshaw and B. Pande for testing early versions of the software.
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Footnotes |
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Corresponding Editor: Prem Jauhar
Received August 12, 2002
Accepted March 23, 2003
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References |
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TopAbstractThe ProgramReferences |
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Anderson MR, 1973. Cluster analysis for applications. New York: Academic Press.
Callen DF, Thompson AD, Shen Y, Phillips HA, Richards RI, Mulley JC, Sutherland GR, 1993. Incidence and origin of null alleles in the (AC)n microsatellite markers. Am J Hum Genet. 52:922-927.[Web of Science][Medline]
De Winton D, Haldane JBS, 1931. Linkage in the tetraploid Primula sinensis. J Genet. 24:121-144.
Fisher RA, 1947. The theory of linkage in polysomic inheritance. Philos Trans R Soc B. 233:55-87.
Hackett CA, Bradshaw JE, Meyer RC, McNicol JW, Milbourne D, Waugh R, 1998. Linkage analysis in tetraploid potato: a simulation study. Genet Res. 71:143-154.[CrossRef]
Hackett CA, Pande B, Bryan G, in press. Linkage mapping in autotetraploid species using simulated annealing. Theor Appl Genet.
He Y, Xu X, Tobutt KR, Ridout MS, 2001. Polylink: to support two-point linkage analysis in autotetraploids. Bioinformatics. 17:740-741.
Luo ZW, Hackett CA, Bradshaw JE, McNicol JW, Milbourne D, 2000. Predicting parental genotypes and gene segregation for tetrasomic inheritance. Theor Appl Genet. 100:1067-1073.[CrossRef]
Luo ZW, Hackett CA, Bradshaw JE, McNicol JW, Milbourne D, 2001. Construction of a genetic linkage map in tetraploid species using molecular markers. Genetics. 157:1369-1385.
Mather K, 1936. Segregation and linkage in autotetraploids. J Genet. 32:287-314.
Meyer RC, Milbourne D, Hackett CA, Bradshaw JE, McNicol JW, Waugh R, 1998. Linkage analysis in tetraploid potato and association of markers with quantitative resistance to late blight (Phytophthora infestans). Mol Gen Genet. 259:150-160.[CrossRef][Web of Science][Medline]
Stam P, 1993. Construction of integrated genetic linkage maps by means of a new computer package: JOINMAP. Plant J. 3:739-744.
Stam P, Van Ooijen JW, 1995. JoinMapTM version 2.0: software for the calculation of genetic linkage maps. CPRO-DLO Wageningen.
Voorrips RE, 2002. MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered. 93:77-78.
Wu KK, Burnquist W, Sorrells ME, Tew TL, Moore PH, Tanksley SD, 1992. The detection and estimation of linkage in polyploids using single-dose restriction fragments. Theor Appl Genet. 83:294-300.
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