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数量遗传分析软件:SPLITLOC  

2010-11-14 09:01:41|  分类: 数量遗传学 |  标签: |举报 |字号 订阅

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      The aim of this computer program is to split a basic dataset for JoinMap version 2.0 into separate files for the construction of linkage maps of individual chromosomes. The second and more important aim of this computer program is to RECODE the data (written according to the input file format for the option CP (=cross pollinators)) into separate datasets for the construction of maternal, paternal and integrated linkage groups of individual chromosomes.

In 1993 the computer program JoinMap 1.4 (Stam, 1993) was released. Since that moment we have used this software to construct genetic linkage maps of obligatory allogamous species (such as potato or animal species) which lack homozygous inbred lines (see Jacobs et al., 1995; Van Eck, 1995). The segregation of marker loci in the F1 or BC1 derived from non-inbred parents was interpreted as if it were a "double-pseudo-testcross" (Grattapaglia and Sederoff, 1994; Van Eck, 1995) for details on usage of JoinMap 1.4.

More recently JoinMap 2.0 was released. In this version the special option called 'CP' allows the construction of chromosome maps by integrated analysis of maternal and paternal segregation data. Nevertheless we felt that the construction of such integrated (female & male) maps do not reveal the same information as the separate linkage maps based on the maternal or paternal meiosis alone. The separate maps reflect a biological reality: the meiosis in a parental genotype, whereas the integrated map reflects a statistical compromise between the maternal and paternal recombination (including artefacts when male and female recombination values are different.
As JoinMap 1.4 is no longer maintained and updated, it is recommended to use JoinMap 2.0. However, there is no method implemented in JoinMap 2.0 to generate separate paternal maps. Our method to generate separate paternal maps involves a time-consuming modification of the original data: removal of information on segregating alleles from the alternate parent. This is now easily done according to the rules described in the help file of the SplitLoc software.


References:
Grattapaglia D., R. Sederoff (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: Mapping strategy and RAPD markers. Genetics 137:1121-1137.

Jacobs JME, Van Eck HJ, Arens P, Verkerk-Bakker B, te Lintel Hekkert B, Bastiaanssen HJM, El-Kharbotly A, Pereira A, Jacobsen E, Stiekema WJ (1995) A genetic map of potato (Solanum tuberosum) integrating molecular markers, including transposons, and classical markers. Theor Appl Genet 91:289-300.


Stam P. (1993) Construction of integrated genetic linkage maps by means of a new computer package: Joinmap. Plant J. 3:739-744.


Van Eck HJ (1995) Localisation of morphological traits on the genetic map of potato using RFLP and isozyme markers. PhD Thesis, Wageningen Agricultural University, Department of Plant Breeding, The Netherlands. ISBN 90-5485-342-5.

转自:http://www.plantbreeding.wur.nl/UK/software_splitloc.html

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