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Selective Mapping Tutorial

The selective mapping tutorial introduces selective QTL mapping based on analysis using subsets of a population selected based on genotype or phenotype. MapPop v. 1.0 software is used to select individuals based on genotype. The tutorial also includes comparison of QTL detection for Maize virus resistance based on selective mapping and the whole population

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Selective Mapping Tutorial

  1. 1. Selective Mapping Jose Luis Zambrano Mendoza 1
  2. 2. Selective Mapping Content• What is selective mapping, and why we would want to use it.• Explanation of how to do it using MAPPOP• Provide a case study based on maize virus resistance. 2
  3. 3. Selective Mapping What is selective mapping ?An approach that has been used mainly forAssociation and QTL mapping to reduce the numberof individuals to be genotyped and phenotypedfrom a large population. The lines in a mapping population can be defined as random samples from an infinitely large population. 3
  4. 4. Selective Mapping Why, When ?Credit: JL Zambrano, INIAP Can we save resources without losing experimental or selection power by concentrating on the most informative individuals in a population? 4
  5. 5. Selective Mapping Choose • We needindividuals Quantitative data based on (trait of interest)phenotype • Excel Credit: JL Zambrano, OSU Choose • We needindividuals Qualitative data based on (genetic markers) genotype • MapPop v. 1.0 Credit: JL Zambrano, OSU 5
  6. 6. Frequency Selection Based on Phenotype σ Credit: JL Zambrano, OSU Credit: JL Zambrano, OSU Disease symptoms Highly Resistant Highly Susceptible 6
  7. 7. Selection Based on PhenotypeHow to make selections? Excel, Sort your data Line Disease % 45 0 84 0 Selection = 201 1 X – 1 Stand. Dev. … …•Be sure that your data is X = Meannormally distributed•Apply a measure of strength Line Disease %of selection, for instance: 1 63 78Standard Deviation 12 80 Selection = 7 85 X + 1 Stand. Dev. … … 7
  8. 8. Selection Based on Phenotype Individuals in extreme high and low range of distribution tend to have accumulated more positive and negative alleles Credit: JL Zambrano, OSU Credit: JL Zambrano, OSU AABBCCDD… aabbccdd… More information: Lander and Bostein, 1989; Gallais et al., 2007; Sun et al., 2010) 8
  9. 9. Selection Based on Genotype (Selective Mapping) This method concentrates on: 1. Individuals with maximum information (recombinant individuals) 2. Different combinations of individuals with more desirable combinations of breakpoints MapPop provides a tool to select the most informative individuals This program quickly and consistently finds much-reduced samples with map resolution approaching that of the larger populations from which they are derived (Vision et al., 2000) 9
  10. 10. Selection Based on Genotype (Selective Mapping)Before we use MapPop, we need some genotypicinformation for the entire population to feed intothe program. Usually genetic information from a couple of markers from each chromosome arm is enough to build framework data. Markers and their genetic positions can be found in databases or consensus genetic maps. (http://www.maizegdb.org/map.php#) 10
  11. 11. Selection Based on Genotype Steps (Selective Mapping)1. Build the file of the marker framework data as shown First, be sure that marker segregation fits your expectation according to population type Columns = Line number Rows = Markers Parent 1 = A Parent 2 = B Hetero = H Missing = ? Save the file as Tab delimited (txt format) 11
  12. 12. Based on Genotype Steps (Selective Mapping)2. Where do we find and how do we install MapPop ? 12
  13. 13. Based on Genotype Steps (Selective Mapping) 2. Where to find and how to install MapPop http://www.bio.unc.edu/faculty/vision/lab/mappop/MapPop is a Free Program! 13
  14. 14. Based on Genotype Steps (Selective Mapping)2. Where to find and how to install MapPop Then, extract all the files from the zip folder. 14
  15. 15. Based on Genotype Steps (Selective Mapping)2. Where to find and how to install MapPop 15
  16. 16. Based on Genotype Steps (Selective Mapping)2. Where to find and how to install MapPop 16
  17. 17. Based on Genotype Steps (Selective mapping)3-1. MapPop “Welcome” windows You can create a shortcut to MapPop on your desktop 17
  18. 18. Based on Genotype Steps (Selective Mapping)3-2. To run MapPop: insert code and then Enter:loadframe “name of the file.txt” “genotyping code” Genotype Code Parent 1 A Parent 2 B Missing ? Dominant P1 X Dominant P2 X Heterozygous H Make sure that the txt file is in the same directory as MapPop (C:/MapPop/oh1xva35.txt) 18
  19. 19. Based on Genotype Steps (Selective Mapping)3-3. To run MapPop using the default options, inserteither code: samplemax or sampleexp, then type thedesired population size as shown (More details in themanual)samplemax 113 113 ≈ 1/3 of my population size 19
  20. 20. Based on Genotype Steps (Selective Mapping) These default options can be modified (details in the manual)This screen appears while the computer is performing the analysis 20
  21. 21. Based on Genotype Steps (Selective Mapping)MapPop Results: (may take a couple of minutes to display results) 21
  22. 22. Selective Mapping Case StudyA Post-Hoc analysis was conducted using the same data thatwas analyzed and published in Theoretical and AppliedGenetics (2004) 110: 48-57Identification of quantitative trait loci controllingresistance to maize chlorotic dwarf virusMark W. Jones, Margaret G. Redinbaugh, Robert J. Anderson, R. Louie 22
  23. 23. Selective Mapping Published Results Figure modified from Jones et al., 2004Linkage map for 314 Va35 × Oh1VI F2 progeny. The positions for the two majorQTL associated with MCDV resistance, mcd1 and mcd2, are noted to the right ofchromosomes 3 and 10, respectively. Two minor QTL on chromosomes 4 and 6are also indicated. 23
  24. 24. Selective Mapping Case Study - ObjectiveTo compare the results using the whole population (314lines) versus selective mapping based on phenotype andgenotype Questions How does selective mapping affect the genetic map? How does selective mapping affect QTL detection? 24
  25. 25. Selective Mapping Questions ? – Case StudyBased on Genotype Based on Phenotype Vs. Compared with the published study 25
  26. 26. Selective MappingResults : Based on Genotype Vs. Based on Phenotype 113 Lines 114 Lines The two sets of selected lines share 40 lines (35% of the selected population) Notes: Selection represents ± 1σ Quantitative data has normal distribution Markers segregate as expected for an F2 Population (1:2:1) Linkage mapping and QTL analysis were conducted using the same procedures for the 2 sets of lines. 26
  27. 27. Selective MappingResults based on genotypic selection (Genetic map of individual lines) Selected line Unselected line More recombination or breakpoints are observed in a selected line compared with an Graphs made using Graphical Genotypes 2.0 unselected line 27
  28. 28. Results in Linkage Map, Group 3 1 2 3 4 1 2 3 1 4 2 5 3 6 74 5 6 7 0 3_1 0 3_1 0 1_26 0 3_1 0 10_3 0 2_2 0 0 1_1 3_2 0 1_2 2 1_2 0 6_1 13 0 10_19 0 3_2 9_1 400 7_1 10_1 10 00 1_25 3_24_1 4_1 0 5 7_110_4 0 9_1 0 5_ 4 6_2 21 3_3 2 1_1 6 10_218 3_3 11 3 7_2 1_24 4 10 7_210_2 6 1_3 33 3_4 4 1_3 11 10_4 9 10_2 19 3_3 10 5_ 32 3_4 15 10_4 32 16 3_4 17 10_115 1_4 15 6_3 34 3_512 1_4 15 10_3 20 38 3_623 34 3_5 18 19 10_3 3417 7_3 3_54_2 4_224 1_5 24 6_4 1_5 37 23 3_6 9_2 27 1_23 38 28 3_64_3 22 7_3 27 2_3 27 43 3_7 36 10_5 27 9_2 27 5_ 41 29 3_7 3_8 35 10_5 41 3430 1_6 44 3_829 1_6 37 10_5 9_3 3631 7_4 1_22 3_7n_n2 34 38 7_410_6 31 38 9_32_4 30 405_ 35 6_5 3_942 1_7 44 3_9 41 34 10_6 4233 7_5 4_3 3_84_443 1_7 47 51 42 n_n1 10_651 41 3_10 9_4 46 10_7 4439 44 992 3_94_7 37 43 7_510_7 38 445_54 991 43 6_6 53 3_16 47 10_7 4841 7_6 1_21 56 42 44 7_610_9 46 9_4 60 3_11 3_12 1_8 48 10_852 46 3_12 3_11 9_5 5247 10_8 53 57 1_20 3_16 4_6 46 10_1050 58 5265 1_10 54 10_9 5454 4_4 9_52_5 5169 1_8 62 3_13 1_9 49 10_9 53 3_13 9_6 48 59 3_14 4_5 48 10_8 52 62 9_92_9 5_ 56 6_7 56 65 3_14 3_15 1_10 51 54 10_10 3_16 3_14 50 59 10_10 5567 7_7 63 4_5 3_15 4_8 59 59 7_710_115871 1_9 55 3_15 60 10_11 5669 4_6 65 9_62_877 1_11 59 71 3_10 1_11 61 10_11 7065 1_19 7_8 69 3_13 3_11 4_9 63 60 7_810_12 71 61 10_12 5770 4_7 68 2_7 2_682 1_12 64 77 3_17 1_12 63 10_12 69 3_17 9_7 62 71 3_12 4_10 65 10_1371 9_7 67 78 3_18 66 64 1_13 1_14 10_13 75 3_18 9_8 65 8975 10_13 6074 1_18 7_9 76 4_8 3_10 4_11 75 69 7_910_1477 7985 1_13 77 6_8 74 3_19 10_14 6680 4_9 9_8 78 5_86 1_14 76 81 3_19 1_15 70 10_14 9269 1_17 77 3_17 4_12 75 10_15 89 2_10 83 82 3_20 1_16 77 10_15 86 9_9 9977 10_15 7183 1_16 4_10 3_18 79 10_16 9288 1_15 79 10_16 7887 4_1190 1_16 85 87 3_21 1_17 81 10_16 10093 1_15 3_19 90 89 7_10 10_17 7_10 8690 4_1295 1_17 96 6_9 88 1_18 88 10_17 10385 10_17 1_14 3_20 99 10_18 98 10_18 101 3_22 9_1010494 10_18 88 1_13 3_21 104 n_n3100 9_10 10798 1_18 103 104 4_13 109 3_22 103 993 10798 n_n3 1_12 110 3_22 109 10_19 112 6_10 111 1_19 108 10_19 105 109 10_19 112 1_11 4_14116 1_19 115 1_9 117 126 4_13 3_23 123 10_20 117 1_8 125 4_14 128 3_23 129 1_20 121 1_10133 1_20 131 n_n1138 1_21 136 1_21 141 1_7148 1_22 145 1_22 155 1_6 150 3_24 161 1_5155 1_23 156 1_23 171 1_4168 1_24 180 1_3 172 1_24 184 1_2175 1_25 178 1_25181 1_26 186 1_1 180 1_26 There were no major differences for groups 1, 2, 5, 7, and 9 28
  29. 29. Results in Linkage Map, Group 44 1 5 1 2 6 2 3 7 3 4 4 5 5 6 6 7 7 8 0 3_1 10_1 0 0 1_26 9_1 1_2 0 3_1 7_1 0 0 9 00 3_2 10_3 0 4_1 0 10_1 2_2 0 0 4_1 9_1 0 0 7_1 7_1 0 0 9_1 4_2 0 0 5_1 6_1 10_2 4 2 1_25 1_1 3 7_2 5 10_4 4 4 7_2 7_2 4 6_2 10 3_2 18 3_3 10_411 4 1_24 1_3 19 3_3 32 10 3_4 10_2 9 10_2 10 5_2 10_3 12 1_4 15 10_4 16 4_2 14 6_3 32 19 3_4 7_3 34 17 173_5 10_1 4_2 18 10_3 18 7_3 20 9_2 22 20 4_3 27 23 23 1_23 9_234 1_5 3_5 37 3_6 27 2_3 28 27 4_3 9_3 26 7_3 7_4 27 9_2 n_n227 24 5_3 6_4 10_5 29 29 9_338 31 3_6 7_4 1_6 41 36 3_8 10_5 35 3_7 10_5 34 n_n2 34 31 7_4 7_5 31 29 30 5_4 41 34 3_7 7_5 44 333_9 4_3 41 10_6 9_3 10_636 1_22 42 1_7 38 10_6 36 7_5 7_6 37 41 51 9_442 41 3_8 7_6 n_n1 51 393_10 43 992 46 10_7 38 2_4 44 40 4_4 9_4 10_7 37 38 5_5 6_5 10_7 56 44 4_7 9_5 42 7_6 46 47 9_4 4_4 10_848 46 1_21 9_544 60 1_8 3_9 3_12 3_11 44 10_9 47 10_8 57 4_6 47 6_6 53 3_16 52 543_13 4_4 48 10_9 59 52 4_5 9_6 50 9_5 10_952 53 1_20 9_654 62 1_9 3_14 54 46 67 10_10 4_5 50 58 2_5 56 7_7 52 58 9_9 4_5 51 5_7 5_6 65 1_10 3_16 3_14 48 10_8 62 10_10 2_9 63 4_8 59 10_10 55 59 3_157_7 55 693_15 59 4_6 60 10_11 10_11 61 7_7 7_8 58 62 9_6 4_6 10_11 71 1_11 65 2_8 69 4_9 63 7_8 63 4_7 70 56 65 3_137_8 69 1_19 9_7 1_12 77 3_11 61 703_17 60 4_7 62 10_12 10_12 2_671 71 4_10 9_7 67 6_7 10_12 57 3_12 64 74 4_8 65 68 2_7 73 7_9 71 69 9_7 4_8 75 78 1_13 1_14 9_860 75 3_107_9 3_18 65 10_13 10_13 76 79 4_11 9_8 10_13 89 1_18 81 1_15 74 803_19 69 4_9 69 10_14 10_14 75 7_9 77 76 9_8 4_9 78 5_8 10_14 83 4_10 77 77 4_12 78 4_10 92 66 3_17 10_15 10_15 86 1_17 9_971 82 1_16 3_18 75 87 10_15 4_11 79 89 2_10 83 4_11 99 10_16 1_16 87 1_17 79 10_16 10_16 92 9_9 90 92 7_10 7_10 91 4_12 100 1_15 88 78 93 3_197_10 1_18 90 89 4_12 85 10_17 10_17 10_17 86 3_20 103 10_18 101 1_14 9_10 99 10_1894 10_18 100 9_10 88 3_21103 3_22 n_n3 98 n_n3 104 107 4_13 9_10 993104 1_13 104 107 10_19 1_12 110 111 1_19 3_22 109 105 10_19 10_19 112 4_14 109 1_11 117 4_13 115 10_20 1_9 126 3_23 125 4_14 117 1_8 129 1_20 121 1_10 131 136 n_n1 1_21 141 1_7 145 1_22 155 1_6 161 1_5 156 1_23 171 1_4 180 172 1_3 1_24 184 178 1_2 1_25 180 1_26 186 1_1 There were no major differences for groups 1, 2, 5, 7, and 9 29
  30. 30. Results in Linkage Map, Group 61 2 3 1 4 2 3 5 9 6 4 10 7 5 8 8 6 7 0 3_1 1_26 0 3_1 0 0 1_1 10_3 0 0 6_1 2_2 13 0 3_29_10 0 6_1 7_110_1 0 8_5 0 0 0 0 2_2 0 6_1 7_1 4_2 9_10 0 4_1 1_25 2 5 1_2 10_4 4 6_2 21 3_3 3 4 6_2 7_210_2 6 4 3 6_2 7_2 10 3_2 6 1_3 1_24 19 3_3 10 10_2 33 3_4 11 1010_4 8_4 15 1_4 15 6_3 34 3_5 13 6_3 14 6_3 32 3_4 17 10_1 20 18 15 7_310_320 8_3 6_4 19 19 7_3 17 4_2 34 3_5 38 3_69_2 20 23 4_3 23 9_2 2_3 24 6_4 1_23 24 1_5 24 27 6_4 2_3 43 27 3_79_3 26 7_4 38 3_6 36 10_5 6_5 7_510_529 29 n_n2 9_3 31 7_4 41 3_7 30 1_6 44 3_8 30 31 37 34 2_4 33 4_3 1_22 38 10_6 35 38 6_5 2_4 47 36 3_99_4 36 42 6_6 7_610_6 37 34 6_5 7_5 42 3_8 43 43 1_7 10_7 40 39 992 54 991 43 6_6 53 3_16 47 10_7 41 9_4 41 7_6 44 3_9 44 9_5 1_21 53 3_16 44 65 10_9 1_10 54 52 3_11 3_12 48 9_6 48 6_7 10_847 46 4_4 9_547 6_6 54 4_4 1_20 46 10_10 58 2_5 54 3_14 69 48 1_8 10_8 56 6_7 3_13 56 49 7_710_958 53 4_5 9_6 2_5 58 67 4_5 55 3_15 71 1_9 62 2_9 56 3_14 3_15 61 51 62 7_810_10 4_6 62 2_6 59 2_7 7_7 69 4_6 59 10_11 65 2_8 59 3_10 61 63 10_11 4_7 56 3_13 3_11 77 60 1_11 10_12 68 63 2_8 67 65 6_7 7_8 70 4_7 1_19 2_7 2_6 64 71 3_17 68 9_7 6_8 7_910_12 69 69 4_8 9_7 2_9 57 3_12 82 65 1_12 10_13 73 63 66 74 4_8 85 1_13 67 79 3_18 9_8 66 76 75 10_13 4_9 9_8 75 7_9 1_18 60 3_10 69 86 10_14 77 1_14 6_8 76 3_19 70 78 10_14 4_10 80 4_9 1_17 66 3_17 75 10_15 89 83 4_10 71 3_18 88 1_15 2_10 83 3_20 77 83 86 10_15 4_11 9_9 87 4_11 1_16 78 3_19 79 90 10_16 1_16 85 92 9_9 3_21 92 81 7_10 91 10_16 4_12 93 7_10 90 4_12 1_15 89 10_17 96 6_9 88 10_17 94 2_10 86 3_20 95 1_17 1_14 99 98 10_18 1_18 98 10_18 101 9_10 1_13 88 3_21 104 n_n3 107 9_10 109 3_22 103 993 1_12 110 3_22 109 10_19 112 6_10 108 10_19 1_11 116 1_19 117 4_13 1_9 126 3_23 123 10_20 125 4_14 1_8 128 3_23 1_10 133 1_20 n_n1 138 1_21 1_7 148 1_22 150 3_24 1_6 1_5 155 1_23 1_4 168 1_24 1_3 175 1_25 1_2 181 1_26 1_1 There were no major differences for groups 1, 2, 5, 7, and 9 30
  31. 31. Results in Linkage Map, Group 8 8 9 10 9 10 8 9 100 2_1 0 5_1 0 8_2 0 6_1 0 8_5 0 2_20 5_1 0 8_3 3 6_2 11 5_2 10 8_4 11 5_2 9 8_413 2_2 13 6_3 20 6_4 19 8_3 18 8_5 23 2_3 31 5_3 30 6_5 30 5_334 2_3 34 5_4 36 6_6 34 34 2_4 5_4 37 8_3 40 5_5 41 5_548 2_4 46 8_4 48 6_7 54 5_7 5_6 56 8_5 58 2_5 58 5_766 2_5 62 2_6 2_7 59 5_670 2_6 63 2_8 68 6_8 66 2_972 2_773 2_876 2_9 82 5_8 83 5_897 2_10 94 97 2_10 5_9 There were no major differences for groups 1, 2, 5, 7, and 9 31
  32. 32. Results in Linkage Map, Group 10 2 3 1 4 2 5 3 6 1 4 27 5 3 6 4 7 5 6 0 3_1 0 3_11_1 0 6_1 13 0 3_2 1_2 0 10_1 0 9_1 00 0 7_1 1_26 10_1 00 4_1 3_1 4_1 0 0 7_1 10_3 0 0 9_1 0 2_2 5_1 0 9_1 01_2 2 1_1 6 9 3_2 4 6_2 21 3_3 10_2 18 3_3 43 7_2 1_25 10 3_2 4 5 7_2 10_4 41_3 33 4 3_4 1_3 11 10_4 9 11 10_2 1_24 10 10_2 10 5_2 12 1_4 15 32 3_4 15 10_4 19 3_31_4 15 6_3 34 3_5 10_3 16 3217 4_2 3_4 4_2 17 10_1 18 34 3_5 18 19 10_3 7_3 20 9_2 38 3_6 23 1_5 37 23 3_6 9_2 34 3_5 22 7_31_5 24 6_4 43 3_7 27 1_23 28 4_3 27 27 9_2 27 2_3 5_3 27 9_3 261_6 29 1_6 37 41 29 3_8 9_3 3_7 35 31 10_5 7_4 38 34 3_6 n_n2 34 36 10_5 31 44 3_8 10_5 31 9_3 30 5_4 35 6_5 47 42 3_9 1_7 42 44 10_6 3_9 41 34 36 10_6 1_22 7_5 4133 44 4_3 3_7 4_4 38 7_4 10_6 38 2_4 361_7 51 n_n1 51 3_10 46 41 10_7 4239 992 37 3_8 43 7_5 10_7 38 40 5_5 9_4991 43 6_6 53 3_16 47 10_7 41 9_4 7_6 56 4_7 46 3_11 3_12 47 48 10_8 1_21 44 3_9 42 44 7_6 46 10_9 9_4 44 9_51_10 3_11 3_12 1_8 48 60 10_8 52 9_5 57 5354 4_6 3_16 4_4 50 9_5 52 9_6 54 62 3_13 1_9 49 3_13 53 9_6 48 52 10_9 1_20 59 4_5 46 10_10 58 9_9 51 2_5 5_7 5_61_8 56 6_7 10_9 5467 3_14 4_5 52 56 3_14 3_15 1_10 65 54 3_16 3_14 50 59 10_10 63 4_8 48 7_7 10_81_9 56 71 1_11 51 10_10 55 3_15 60 7_7 10_11 5569 69 4_6 59 3_15 4_9 59 7_8 58 10_11 62 9_6 2_9 611_11 59 3_10 77 1_12 61 10_11 61 3_17 69 9_7 62 65 70 7_8 10_12 1_19 5670 71 4_7 63 3_13 3_11 4_10 60 10_12 65 2_8 71 9_71_12 64 3_17 63 10_12 5774 4_8 3_12 71 68 9_7 2_7 2_6 73 67 78 3_18 1_13 1_14 66 64 10_13 3_18 75 9_8 65 75 10_13 7_9 76 4_11 75 65 7_9 10_131_13 77 6_8 74 3_19 69 10_14 6080 4_9 3_10 77 9_8 78 79 5_8 9_81_14 76 81 3_19 1_1570 10_14 89 1_18 77 4_12 69 10_14 82 1_16 77 92 10_15 1_17 6683 4_10 3_17 75 10_151_15 83 3_20 77 10_15 86 9_9 7187 4_11 90 3_18 89 2_10 85 87 3_21 1_1781 10_16 79 99 10_16 1_16 79 7_10 10_16 92 9_9 921_161_17 96 6_9 88 1_1888 10_17 10093 85 7_10 10_17 1_15 7890 4_12 3_19 89 10_17 101 94 9_10103 10_18 1_14 86 3_20 99 100 10_18 9_101_18 98 10_18 103 3_22 104 88 4_13 3_21 107 9_10 103 993 98 104 n_n3 1_13 104 n_n3 109 3_22 111 1_19 105 10_19 110 3_22 112 6_10 108 10_19 107 1_12 112 4_14 109 10_191_19 109 1_11 117 4_13 123 10_20 115 1_9 126 125 3_23 4_14 128 3_23 129 1_20 117 1_81_20 121 1_101_21 136 1_21 131 n_n1 145 1_22 141 1_71_22 150 3_24 155 1_61_23 156 1_23 161 1_51_24 171 1_4 172 1_24 180 1_31_25 178 1_25 184 1_21_26 There were no major differences for groups 1, 2, 5, 7, and 9 180 1_26 186 1_1 32
  33. 33. Selective MappingResults – QTLs Detected:Published study (Jones et al., 2004) Post-Hoc analysis 33
  34. 34. Selective MappingResults – QTLs: SUMMARY Whole Population Selective Selective 314 F2 Phenotyping Genotyping 114 F2 113F2 Number of QTLs 4 4 2 detected Number of Major 2 2 2 QTLs detected Variance explained 48 % 64 % 45 % by QTLs Variance explained 42 % 50 % 45 % only by major QTLs Variance explained 21 % 26 % 32 % by the largest QTL 34
  35. 35. Conclusions Selective mapping may affect the length of the linkage map Power of QTL detection based on selective mapping was not affected for major QTL. Power to detect minor QTL (<10%) was possibly reduced Mapping based on phenotypic selection explained a higher proportion of variance; mapping based on selective genotyping explained the same variance relative to the whole population 35
  36. 36. Conclusions Selective mapping based on phenotype is marginally more powerful for detecting QTL than selective mapping based on genotype Selective mapping based on genotype can have similar QTL detection power relative to mapping using the whole population Selective mapping is a valid strategy when resources are limited 36
  37. 37. References Cited and External LinksReferences Cited• Gallais, A., L. Moreau, and L. Charcosset. 2007. Detection of marker-QTL association by studying changing in marker frequencies with selection. Theoretical and Applied Genetics 114: 669-681. (Available online at: http://dx.doi.org/10.1007/s00122-006-0467-z) (verified 29 Nov 2011).• Jones, M. W., M. G. Redinbaugh, R. J. Anderson, and R. Louie. 2004. Identification of quantitative trait loci controlling resistance to maize chlorotic dwarf virus. Theoretical and Applied Genetics 110: 48-57. (Available online at: http://dx.doi.org/10.1007/s00122-004-1757-y) (verified 29 Nov 2011).• Lander, E. S., and D. Bostein. 1989. Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199.• Sun, Y. P., J. K. Wang, J. H. Crouch, and Y. B. Xu. 2010. Efficiency of selective genotyping for genetic analysis of complex traits and potential applications in crop improvements. Molecular Breeding 26: 493-511. (Available online at: http://dx.doi.org/10.1007/s11032-010-9390-8) (verified 29 Nov 2011).• Vision, T. J., D. G. Brown, D. B. Shmoys, R. T. Durrett, and S. D. Tanksley. 2000. Selective mapping: A strategy for optimizing the construction of high-density linkage maps. Genetics 155: 407-420.External Links• Brown, D., and T. Vision. MapPop 1.0: Software for selective mapping and bin mapping [Online]. Department of Biology, The University of North Carolina at Chapel Hill. Available at: http://www.bio.unc.edu/faculty/vision/lab/mappop/manual.pdf (verified 29 Nov 2011).• MaizeGDB: Maize genetics and genomics database [Online]. Available at: www.maizegdb.org (verified 29 Nov 2011). 37
  38. 38. Acknowledgments • Mark Jones • David Francis • Margaret Redinbaugh • Sung-Woo Lee • Heather Merk, Carlos Hernandez, and Zhifen Zhang (tutorial reviewers)Photo: J.L. Zambrano. San Jose de Minas, Ecuador 38
  • Basavaraj1046

    Feb. 6, 2021
  • ZhenhuiWang

    Nov. 30, 2016

The selective mapping tutorial introduces selective QTL mapping based on analysis using subsets of a population selected based on genotype or phenotype. MapPop v. 1.0 software is used to select individuals based on genotype. The tutorial also includes comparison of QTL detection for Maize virus resistance based on selective mapping and the whole population

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