PAG-IV Plant Genome IV Conference

Town & Country Conference Center, San Diego, CA, January, 1995.

P316
MapQTL Version 3.0: Software for the Calculation of QTL Positions on Genetic Maps

JOHAN W. VAN OOIJEN and Chris Maliepaard
DLO Centre for Plant Breeding and Reproduction Research (CPRO-DLO), P.O.Box 16, 6700 AA Wageningen, The Netherlands

MapQTL is a computer program for the mapping of quantitative trait loci (QTLs). It can handle three different methods: interval mapping, MQM mapping and nonparametric mapping. It can deal with a wide variety of mapping populations: BC1, F2, RILs, (doubled) haploids, and a full-sib family of a cross pollinating species (CP). MapQTL is easy to use, is extremely fast, and produces clearly arranged output of results. For all population types except CP, straightforward interval mapping is applied [1]. To calculate the likelihood of a segregating QTL in a CP population interval mapping has been enhanced to 'all-markers' mapping, which employs the segregation information of all linked markers, each of which may follow a different segregation type, with two up to four alleles [2]. With MQM mapping (not yet available for CP) markers can be used as cofactors to absorb the effects of nearby QTLs, thereby increasing the power for mapping other segregating QTLs [3],[4]. It may even enable the separation and mapping of linked QTLs. In the nonparametric mapping the Kruskal-Wallis rank sum test is used to assess the segregation of QTLs for non-normally distributed data.

[1] Lander & Botstein, 1989. Genetics 121: 185-199.
[2] Maliepaard & Van Ooijen, 1994. In: [5]: 140-146.
[3] Jansen, 1993. Genetics 135: 205-211.
[4] Van Ooijen, 1994. In: [5]: 205-212.
[5] Van Ooijen & Jansen (eds), 1994. Biometrics in Plant Breeding: Applications of Molecular Markers. Proc. 9th Meeting Eucarpia Section Biometrics. CPRO-DLO, Wageningen, 272 pp.

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