Abstract
Efficient use of DNA markers for genomic research and crop improvement will depend as much on computational tools as on laboratory technology. The large size and multidimensional character of marker datasets invite novel approaches to data visualization. Described here is a software application embodying two design principles: conventional reduction of raw genetic marker data to numerical summary statistics, and fast, interactive graphical display of both data and statistics. The program performs various analyses for mapping quantitative-trait loci in real or simulated datasets and other analyses in aid of phenotypic and marker-assisted breeding. Functionality is described and some output is illustrated.
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References
Bailey NTJ: Mathematical Theory of Genetic Linkage. Clarendon Press, Oxford (1961).
Darvasi A, Soller M: Advanced intercross lines, an experimental population for fine genetic mapping. Genetics 141: 1199–1207 (1995).
Doerge RW: The relationship between the LOD score and the analysis of variance F-statistic when detecting QTLs using single markers. Theor Appl Genet 90: 980–981 (1995).
Haley CS, Knott SA: A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69: 315–324 (1992).
Haley CS, Knott SA, Elsen JM: Mapping quantitative trait loci in crosses between outbred lines using least squares. Genetics 136: 1197–1207 (1994).
Hyne V, Kearsey MJ, Pike DJ, Snape JW: QTL analysis: unreliability and bias in estimation procedures. Mol Breed 1: 273–282 (1995).
Jansen RC, Stam P: High resolution of quantitative traits into multiple loci via interval mapping. Genetics 136: 1447–1455 (1994).
Kendall M, Gibbons JD: Rank Correlation Methods. Oxford University Press, London; E. Arnold, New York (1990).
Knott SA, Haley CS: Maximum likelihood mapping of quantitative trait loci using full-sib families. Genetics 132: 1211–1222 (1992).
Kruglyak L, Lander ES: A nonparametric approach for mapping quantitative trait loci. Genetics 139: 1421–1428 (1995).
Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L: MAPMAKER: an interactive computer package for constructing primary genetic maps of experimental and natural populations. Genomics 1: 174–181 (1987).
Mart'nez O, Curnow RN: Missing markers when estimating quantitative trait loci using regression mapping. Heredity 73: 198–206 (1994).
Matthews DM: GrainGenes: the Triticeae Genome Database. Electronic address: greengenes.cit.cornell.edu port 70 (1996).
Murigneux A, Barloy D, Leroy P, Beckert M: Molecular and morphological evaluation of doubled haploid lines in maize. 1. Homogeneity within DH lines. Theor Appl Genet 86: 837–842 (1993).
Press WH, Teukolsky SA, Vetterling WT, Flannery BP: Numerical Recipes in C: the Art of Scientific Computing. Cambridge University Press, New York (1992).
Tanksley SD, Nelson JC: Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92: 191–203 (1996).
Tinker NA, Mather DE: Methods for QTL analysis with progeny replicated in multiple environments. JQTL 1(2) (1995).
Young ND, Tanksley SD: Restriction fragment length polymorphism maps and the concept of graphical genotypes. Theor Appl Genet 77: 95–101 (1989).
Zeng ZB: Precision mapping of quantitative trait loci. Genetics 136: 1457–1468 (1994).
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Nelson, J.C. QGENE: software for marker-based genomic analysis and breeding. Molecular Breeding 3, 239–245 (1997). https://doi.org/10.1023/A:1009604312050
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DOI: https://doi.org/10.1023/A:1009604312050