QTL IciMapping Version 3.1 Released May 2011

Development and application environments

In QTL IciMapping, kernel modules for building linkage maps were written by C#, those for QTL mapping was written by Fortran 90/95, and the interface was written by C#. QTL IciMapping runs on Windows XP/Vista/7, with .NET Framework 2.0(x86)/3.0/3.5.

Fully implemented functionalities

1. MAP: Construction of Genetic Linkage Maps in Biparental Populations

Grouping can be based on (i) anchored marker information, (ii) a threshold of LOD score, and (iii) a threshold of marker distance.

Three ordering algorithms are (i) SER: SERiation (K. H. Buetow and A. Charavarti. 1987. Am. J. Hum. Genet. 41: 180-188), (ii) RECORD: REcombination Counting and ORDering (H. Van Os. 2005. Theor. Appl. Genet. 112: 30-40), and (iii) MF: Multi-Fragment heuristic algorithm.

Five rippling criteria are (i) SARF (Sum of Adjacent Recombination Frequencies), (ii) SAD (Sum of Adjacent Distances), (iii) SALOD (Sum of Adjacent LOD scores), (iv) COUNT (number of recombination events), and (v) LogL (Logarithm Likelihood of the marker sequence).

2. BIP: Mapping of Additive and Digenic Epistasis Genes in Biparental Populations

SMA: Single Marker Analysis (K. Sax. 1923. Genetics 8: 552-560; M. Soller and T. Brody. 1976. Theor. Appl. Genet. 47: 35-39)

SIM: the conventional Simple Interval Mapping (E. S. Lander and D. Botstein. 1989. Genetics 121: 185-199)

ICIM-ADD: Inclusive Composite Interval Mapping of ADDitive (and dominant) QTL (H. Li et al. 2007. Genetics 175: 361-374; L. Zhang et al. 2008. Genetics 180: 1177-1190)

ICIM-EPI: Inclusive Composite Interval Mapping of digenic EPIstatic QTL (H. Li et al. 2008. 116: 243-260)

SGM: Selective Genotyping Mapping (R. L. Lebowitz et al. 1987 Theor. Appl. Genet. 73: 556-562; E. S. Lander and D. Botstein. 1989. Genetics 121: 185-199; Y. Sun et al. 2010. Mol. Breed.)

3. CSL: Mapping of Additive and Digenic Epistasis Genes with Chromosome Segment Substitution Lines

SMA: Single Marker Analysis (K. Sax. 1923. Genetics 8: 552-560)

RSTEP-LRT-ADD: Stepwise regression based likelihood ratio tests of additive QTL (J. Wang et al. 2006. Genet. Res. 88: 93-104; J. Wang et al. 2007.Theor. Appl. Genet. 115: 87-100)

RSTEP-LRT-EPI: Stepwise regression based likelihood ratio tests of digenic epistasis QTL (J. Wang et al. 2006. Genet. Res. 88: 93-104; J. Wang et al. 2007.Theor. Appl. Genet. 115: 87-100)

4. MET: QTL by Environment Interaction in Biparental Populations

ICIM-ADD: ICIM of additive QTL by environment interaction

ICIM-EPI: ICIM of digenic epistatic QTL by environment interaction

5. NAM: QTL Mapping in NAM Populations

JICIM: Joint Inclusive Composite Interval Mapping of additive QTL

6. SDL: Mapping of Segregation Distortion Loci in Biparental Populations

SMA: Segregation Distortion Loci Mapping through single marker analysis

SIM: Segregation Distortion Loci Mapping through simple interval mapping

Disclaimer

QTL IciMapping is freely-avaiable public software. We have attempted to provide, to the best of our knowledge, accurate data and information within the Veriosn 3.1 of QTL IciMapping. All data and information within the software are supplied with no guarantee, implicit or explicit, as to their accuracy. Though all data and information within this software may be freely used and modified for non-commercial purposes, we are not responsible for decisions taken on account of these data or information.

Acknowledgements

Research and development of QTL IciMapping was supported by the Generation Challenge Program (http://www.generationcp.org), the National 863 Program, 973 Program, and Natural Science Foundation of China.

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