中国农业科学院 作物科学研究所
Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China

 

专业软件 Professional Software

 

  • Windows QTL IciMapping

    IciMappng provides the Windows version for ICIM (Inclusive Composite Interval Mapping) for QTL detection in standard mapping populations such as backcross, doubled haploids, and recombination inbred lines (Genetics, 2007, 175: 361-374). This software also implements the RSTEP-LRT (likelihood ratio test based on stepwise regression) for QTL detection using chromosome segment substitute lines (Genetical Research, 2006, 88: 93-104). Windows QTL IciMapping can not only complete a conventional QTL mapping study, but can also conduct a QTL detection power analysis for a set of predefined QTL. The mapping populations generated from a power simulation study can be re-analyzed in QTL IciMapping and Windows QTL Cartographer.

    This software will be updated regularly. If you have any problem or find any bugs, please report to shuliang318@yahoo.com.cn .

     

     

    QTL Icimapping v1.4                                    QTL Icimapping v2.2

     

     

  • ICIM: A Modified Algorithm for the Improvement of Composite Interval Mapping

    Composite interval mapping (CIM) is the most commonly used method for mapping quantitative trait locus (QTL) with populations derived from biparental crosses. However the algorithm implemented in the popular QTL Cartographer software may not completely ensure all its advantageous properties. In addition, different background marker selection methods may give very different mapping results, and the nature of the preferred method is not clear. We proposed a modified algorithm called inclusive composite interval mapping (abbreviated as ICIM). In ICIM, marker selection is conducted only once through stepwise regression by considering all marker information simultaneously, and the phenotypic values are then adjusted by all markers retained in the regression equation except the two markers flanking the current mapping interval. The adjusted phenotypic values are finally used in interval mapping. The proposed algorithm has a simpler form than that used in CIM, but a faster convergence speed. ICIM retains all advantages of CIM over interval mapping (IM), and avoids the possible increase of sampling variance and the complicated background marker selection process in CIM. Extensive simulations using two genomes and various genetic models indicated that ICIM has increased detection power, reduced false detection rate and less biased estimates of QTL effects. (Genetics (in press))

 

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  • RSTEP-LRT: A Likelihood Ratio Test Based on Stepwise Regression for QTL Mapping with Non-idealized Chromosome Segment Substitution Lines

Chromosome segment substitution (CSS) lines have the potential for use in QTL fine mapping and map-based cloning. The standard t-test used in the idealized case that each CSS line has a single segment from the donor parent is not suitable for non-idealized CSS lines carrying a few segments from the donor parent. We presented a likelihood ratio test based on stepwise regression (RSTEP-LRT) that can be used for QTL mapping in a population consisting of non-idealized CSS lines.

Three steps are needed in the analysis. (1) Detecting multicolinearity and deleting redundant markers; (2) Performing marker selection using stepwise regression; and (3) Conducting likelihood ratio test to declare statistical significance for each marker. The stepwise regression was used to select the most important segments for the trait of interest, and the likelihood ratio test was used to calculate the LOD score of each chromosome segment. This method is equivalent to the standard t-test with idealized CSS lines. (Genetical Research, 2006, 88: 93-104; TAG, 2007,115:87-100)

 

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  • QuLine (previously called QuCim): A Simulation Tool Helping Breeders Make Hard Decisions

    QuLine is a computer tool capable of defining a range from simple to complex genetic models and simulating breeding processes for developing final advanced lines. Based on the results from simulation experiments, breeders can optimize their breeding methodology and greatly improve the breeding efficiency. QuLine in the current status can simulate almost all breeding activities in CIMMYT wheat breeding program, including male master selection, female master selection, parental selection, single cross, backcross, top cross, double cross, doubled haploid, marker-assisted selection etc. QuLine can simulate not only CIMMYT’s wheat breeding program but also in principle any other breeding programs for selecting inbred lines, which means all major food cereals in the world, plus basically all leguminous crops. It can also be used when inbred lines are developed that later are to be used in hybrids, such as in the case of maize. Hence its potential to increase breeding effectiveness encompasses all CGIAR mandated crops.

 

Available From http://www.uq.edu.au/lcafs/qugene/

 

 

 

  • GRSimulator:

    A computer program called GRSimulator (Germplasm Regeneration Simulator) was developed to determine the probability of retaining alleles of interest and calculate the average number of alleles lost after several regeneration cycles. The parameters included in a regeneration strategy are sample size (number of plants to be regenerated) at stage 1, mating method, and the number of seeds taken from each plant at stage 2. The mating methods available with GRSimulator are panmixia, random pollen pollination (bulk of pollen from all n regenerated plants applied to stigmas of the same plants), chain cross (plant 1 crossed to plant 2, plant 2 crossed to plant 3, plant 3 crossed to plant 4, etc.), paired without reciprocal cross (plant 1 crossed to plant 2, plant 3 crossed to plant 4, etc.), paired with reciprocal cross (plant 1 crossed to plant 2, plant 2 crossed to plant 1, plant 3 crossed to plant 4, plant 4 crossed to plant 3, etc.), and self-pollination (plant 1 crossed to plant 1, plant 2 crossed to plant 2, etc.). The parameters of a regeneration strategy may have different values in different cycles. The computer simulation program was written in Fortran 90/95 and can run under Microsoft Windows.

 

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  • Power simulation of two QTL mapping methods: CIM and ICIM

Genome 1                                     Genome 2

 

 

 

 

 

 

DISCLAIMER:To the best of our knowledge all data contained within the softwares above may be freely used and modified for NON-COMMERCIAL purposes. All data and information are supplied with no guarantee, implicit or explicit, as to their accuracy. We have attempted to provide, to the best of our knowledge, accurate data and information and all sources of data and information are described fully. However, the authors cannot be responsible for decisions taken on account of these data or information.