Users¢â‚¬â„¢ Manual of QTL IciMapping v3 chr 1 chr 2 chr 3 chr 4 chr 5 chr 6 Testing position LOD score

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    Users’ Manual of QTL IciMapping v3.1

    Jiankang Wang, Huihui Li, Luyan Zhang, Chunhui Li and Lei Meng

    Quantitative Genetics Group

    Institute of Crop Science

    Chinese Academy of Agricultural Sciences (CAAS) Beijing 100081, China

    and Crop Research Informatics Lab

    International Maize and Wheat Improvement Center (CIMMYT) Apdo. Postal 6-641, 06600 Mexico, D.F., Mexico

    January 2011

    Webpage: http://www.isbreeding.net

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  • Users’ Manual of QTL IciMapping

    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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    3.7.6 BIP file: The input file for QTL mapping in QTL IciMapping .............................................. 46

    3.8 Draw linkage maps ................................................................................................ 46

    Chapter 4. QTL Mapping in Biparental Populations (BIP) .................................. 49

    4.1 Input file for QTL mapping in biparental populations (*.bip) ............................... 49

    4.1.1 General information of the mapping population .................................................................... 49

    4.1.2 Linkage group or chromosome information ........................................................................... 51

    4.1.3 Marker type information ........................................................................................................ 53

    4.1.4 Phenotype information ........................................................................................................... 54

    4.2 Input file for QTL mapping in the EXCEL format ................................................ 54

    4.3 Setting mapping parameters ................................................................................... 54

    4.3.1 Handling missing phenotype .................................................................................................. 55

    4.3.2 Parmeters for SMA (Single Marker Analysis, Figure 4.2) ..................................................... 56

    4.3.3 Parameters for SIM (Simple Interval Mapping, Figure 4.3) ..............