ManualIciMapping_v3.1.pdf

【实例截图】

【核心代码】

Contents
Chapter 1. Introduction ............................................................................................10
1.1 Genetic populations in linkage analysis and QTL mapping ..................................10
1.2 Estimation of recombination frequency.................................................................11
1.3 Construction of linkage map..................................................................................13
1.4 Statistical methods of QTL mapping .....................................................................14
1.5 Principle of Inclusive Composite Interval Mapping (ICIM) .................................16
1.6 QTL mapping with non-idealized chromosome segment substitution lines..........17
1.7 Joint Inclusive Compossite Interval Mapping (JICIM) .........................................17
Chapter 2. Structure of the QTL IciMapping Software ........................................19
2.1 Development and application environments..........................................................19
2.2 User interface .........................................................................................................19
2.3 Functionalities........................................................................................................20
2.3.1 MAP, construction of genetic linkage maps in biparental populations..................................21
2.3.2 BIP, mapping of additive and digenic epistasis genes in biparental populations...................21
2.3.3 CSL, mapping of additive and digenic epistasis genes with chromosome segment substitution
(CSS) lines......................................................................................................................................21
2.3.4 MET, mapping of additive and digenic epistasis genes from multi-environmental trials......21
2.3.5 NAM, joint inclusive composite interval mapping for NAM populations.............................22
2.3.6 SDL, segregation distortion locus mapping ...........................................................................22
2.4 Menu bar................................................................................................................22
2.5 Tool bar..................................................................................................................23
2.6 The project concept in QTL IciMapping ...............................................................24
2.6.1 Start from a new project......................................................................................25
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2.6.2 Open an existing project .....................................................................................25
2.6.3 Manage the Project Window...............................................................................26
2.6.4 Manage the Display Window..............................................................................28
2.7 Major folders and files included in the software ...................................................29
2.8 Miscellaneous ........................................................................................................30
2.8.1 See the task list....................................................................................................30
2.8.2 See the running message.....................................................................................31
Chapter 3. Construction of Genetic Linkage Maps (MAP)...................................32
3.1. Linkage map input file (*.map or EXCEL) ..........................................................32
3.1.1 General information of the mapping population....................................................................32
3.1.2 Marker type information ........................................................................................................33
3.1.3 Marker anchoring information ...............................................................................................35
3.1.4 Linkage map input file in EXCEL (*.xls or *.xlsx)...............................................................35
3.2 Summary of marker data........................................................................................36
3.3 Anchoring ..............................................................................................................37
3.4 Grouping ................................................................................................................38
3.5 Ordering .................................................................................................................40
3.6 Rippling..................................................................................................................42
3.7 Outputting ..............................................................................................................42
3.7.1 TXT file: Linkage map information.......................................................................................42
3.7.2 LOD file: LOD scores matrix between markers ....................................................................43
3.7.3 REC file: recombination frequency matrix between markers................................................44
3.7.4 STD file: standard deviation matrix between markers...........................................................44
3.7.5 MTP file: marker summary and marker types .......................................................................45

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4.5.1 Figures from ICIM additive mapping (ICIM-ADD)..............................................................68
4.5.2 Figures from ICIM epistatic mapping (ICIM-EPI)................................................................69
4.5.3 Figures from simple interval mapping (SIM) ........................................................................70
4.5.4 Figures from single marker analysis (SMA)..........................................................................70
4.5.5 Figures from selective genotyping mapping (SGM)..............................................................70
Chapter 5. Power analysis in biparental populations (BIP) ..................................73
5.1 Input file for power analysis in biparental populations (*.bip)..............................73
5.1.1 General population information of the mapping population..................................................73
5.1.2 Linkage group information or chromosome information.......................................................75
5.1.3 QTL information ....................................................................................................................76
5.2 Input file for power analysis in biparental populations (*.xls or *.xlsx)...............77
5.3 Setting mapping parameters...................................................................................78
5.3.1 General information ...............................................................................................................79
5.3.2 Parmeters for SMA (Single Marker Analysis, Figure 5.2).....................................................79
5.3.3 Parameters for SIM (Simple Interval Mapping, Figure 5.3)..................................................79
5.3.4 Parameters for ICIM of QTL with additive (and dominance) effects or one dimensional ICIM
(Abbreviated as ICIM-ADD, Figure 5.4)........................................................................................80
5.3.5 Parameters for ICIM of digenic QTL networks or two dimensional ICIM (Abbreviated as
ICIM-EPI, Figure 5.5).....................................................................................................................80
5.3.6 Parameters for SGM (Selective Genotyping Mapping, Figure 5.6).......................................81
5.4 Outputs...................................................................................................................81
5.4.1 General files...........................................................................................................................81
5.4.2 Results files from power analysis ..........................................................................................83
5.4.3 Results files from significant QTL.........................................................................................88
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5.4.4 Results files from power analysis ..........................................................................................90
5.5 Figures....................................................................................................................94
5.5.1 Figures from ICIM additive mapping (ICIM-ADD)..............................................................94
5.5.2 Figures from ICIM epistatic mapping (ICIM-EPI)................................................................96
5.5.3 Figures from simple interval mapping (SIM) ........................................................................96
5.5.4 Figures from single marker analysis (SMA)..........................................................................97
5.5.5 Figures from selective genotyping mapping (SGM)..............................................................97
Chapter 6. QTL Mapping with CSS Lines (CSL).................................................100
6.1 Input file for QTL mapping with CSS Lines (*.csl)............................................100
6.1.1 General population information ...........................................................................................100
6.1.2 Marker type information ......................................................................................................101
6.1.3 Phenotype information.........................................................................................................102
6.2 Input file for QTL mapping with CSS Lines (*.xls or *.xlsx).............................103
6.3 Setting mapping parameters.................................................................................103
6.3.1 Handling multi-collinearity..................................................................................................104
6.3.2 Parameters for single marker analysis (Figure 6.2)..............................................................104
6.3.3 Parameters for RSTEP-LRT for additive (Figure 6.3).........................................................105
6.3.4 Parameters for RSTEP-LRT for epistasis (Figure 6.4) ........................................................105
6.4 Outputs.................................................................................................................106
6.4.1 General information output files..........................................................................................106
6.4.2 Results from all markers after handling multi-collinearity ..................................................108
6.4.3 Results files from significant QTL.......................................................................................109
6.4.4 Results files from permutation tests.....................................................................................110
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6.5 Figures..................................................................................................................110
6.5.1 RSTEP –LRT-ADD (Figure 6.6).......................................................................................... 111
6.5.2 Figures of single marker analysis (Figure 6.7)..................................................................... 111
Chapter 7. Power analysis with CSS lines (CSL)..................................................113
7.1 Input file for power analysis with CSS Lines (*.csl)...........................................113
7.1.1 General population information ...........................................................................................113
7.1.2 Marker type information ......................................................................................................113
7.1.3 Predefined QTL information................................................................................................114
7.2 Input file for power analysis with CSS Lines (*.xls or *.xlsx)............................115
7.3 Setting mapping parameters.................................................................................115
7.3.1 Handling multi-collinearity..................................................................................................116
7.3.2 Parameters for single marker analysis (Figure 7.2)..............................................................116
7.3.3 Parameters for RSTEP-LRT for additive (Figure 6.3).........................................................116
7.4 Outputs.................................................................................................................117
7.4.1 General files.........................................................................................................................117
7.4.2 Result files from power analysis..........................................................................................117
Chapter 8. QTL by Environment Interactions for Multi-Environment Trials
(MET)........................................................................................................................119
8.1 Input file for QTL by environment interactions (*.met)......................................119
8.1.1 General information of the mapping population..................................................................119
8.1.2 Linkage group or chromosome information.........................................................................121
8.1.3 Marker type information ......................................................................................................122
8.1.4 Phenotyp information...........................................................................................................123
8.2 Input file for QTL by environment analysis in the EXCEL format.....................125
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8.3 Setting mapping parameters.................................................................................125
8.3.1 Handling missing phenotype................................................................................................125
8.3.2 Parameters for JICIM of QTL with additive effects ............................................................126
8.4 Outputs.................................................................................................................126
8.4.1 General information output files..........................................................................................126
8.4.2 Results from all scanning markers or chromsomal positions...............................................129
8.4.3 Results files for significant QTL..........................................................................................129
Chapter 9. QTL Mapping for the NAM Design (NAM).......................................131
9.1 Input file for the NAM design (*.nam)................................................................131
9.1.1 General information of the mapping population..................................................................131
9.1.2 Family information ..............................................................................................................132
9.1.3 Linkage group or chromosome information.........................................................................132
9.1.4 Marker type information ......................................................................................................133
9.1.5 Phenotype information.........................................................................................................134
9.2 Input file for the NAM design in the EXCEL format..........................................134
9.3 Setting mapping parameters.................................................................................134
9.3.1 Handling missing phenotype................................................................................................135
9.3.2 Parameters for JICIM of QTL with additive effects ............................................................135
9.4 Outputs.................................................................................................................135
9.4.1 General information output files..........................................................................................135
9.4.2 Results from chromosomal positions...................................................................................136
9.4.3 Results files for significant QTL..........................................................................................137
Chapter 10. Mapping of Segregation Distortion Locus........................................138
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10.1 Input file for mapping segregation distortion locus (*.sdl)................................138
10.1.1 General information of the mapping population................................................................138
10.1.2 Linkage group or chromosome information.......................................................................140
10.1.3 Marker type information ....................................................................................................141
10.2 Input file for SDL mapping in the EXCEL format............................................141
10.3 Setting mapping parameters...............................................................................141
10.3.1 Parmeters for SMA (Single Marker Analysis)...................................................................142
10.3.2 Parameters for SIM (Simple Interval Mapping) ................................................................142
10.4 Outputs...............................................................................................................142
10.4.1 Results from all scanning markers or chromsomal positions.............................................142
10.4.2 Results files for significant SDL........................................................................................143
References.................................................................................................................145
Acknowledgements ..................................................................................................146