Fall 2016 - HORT6033 Molecular Plant Breeding Instructor: Ainong Shi

Fall 2016 - HORT6033 Molecular Plant Breeding Lecture Week 10 (10/24/2016) QTL Mapping Data Format Examples

QTL Mapping Data Format Procedure SNP Data Phenotypic Data Allele Ratio Quality Check JMP F2 true/false WinQTLCart Data Format MapChart QGene QTL Analysis QTLNetwork SNP LOD R^2 R298331 8.753 0.378 R347577 6.972 0.315 R296495 6.766 0.307 QTL Map SNP Marker

QTL Mapping Data Format Procedure 1. SNP data format (1) Using IUPAC nucleotide code (http://www.bioinformatics.org/sms/iupac.html): A, C, G, T, R, Y, S, W, K,W, N, and ‘-’ (left Table) (2) Using two characters: AA, AC, AG, AT, CC, CG, CT GG, GT TT NN or ‘-’

QTL Mapping Data Format Procedure 1. SNP data format How to transfer SNP from IUPAC nucleotide code to diploid type ? SNP two_allels SNP_type chrom pos L235347 L437586C L567733 L587674B L253665B L594398B L567696B M715579299 CT C/T 1 3926083 T C M715580310 51919349 H M715580481 AG A/G 53867625 G A M715579666 47130768 U M715580502 53993540 M715580868 9483101 M715580083 GT G/T 50169512 M715580388 52700834 M715579496 44304195 M715580876 9658162 M715579359 40793702 M715579184 36798122 * A, C, G, and T are homozygous allele, H = heterozygous; and U=missing

How to transfer SNP from IUPAC nucleotide code to diploid type ? * A, C, G, and T are homozygous allele, H = heterozygous; and U=missing Sub mono_SNP_trans_di_SNP() ' define some parameters Dim cln_marker_data_start As Integer Dim row_marker_data_start As Integer 'find the last column of the active sheet clnLast = Cells(1, ActiveSheet.Columns.Count).End(xlToLeft).Column 'assign the last row for marker data row_last = Cells(50000, 1).End(xlUp).Row cln_marker_data_start = 6 row_marker_data_start = 2 For i = row_marker_data_start To row_last For k = 1 To cln_marker_data_start - 1 Cells(row_last + 2, k) = Cells(1, k) Cells(i + row_last + 1, k) = Cells(i, k) Next k For j = cln_marker_data_start To clnLast Cells(row_last + 2, j) = Cells(1, j) If Cells(i, j) = "A" Then Cells(i + row_last + 1, j) = "AA" ElseIf Cells(i, j) = "C" Then Cells(i + row_last + 1, j) = "CC" ElseIf Cells(i, j) = "G" Then Cells(i + row_last + 1, j) = "GG" ElseIf Cells(i, j) = "T" Then Cells(i + row_last + 1, j) = "TT" ElseIf Cells(i, j) = "U" Then Cells(i + row_last + 1, j) = "NN" ElseIf Cells(i, j) = "H" Then Cells(i + row_last + 1, j) = Cells(i, 2) Else Cells(i + row_last + 1, j) = "error" End If Next j Next i End Sub Excel file with the SNP data of Single letter and the VB code to transfer To diploid type. Please run it! Text (.txt) file with the VB code

QTL Mapping Data Format Procedure 2. F1 true/false and selfing testing (1) One [A/C] SNP for example P1 x P2 F1 AA CC AC Female male F1 True (T) False (F) Selfing (S) C T   S F Y IUPAC nucleotide code Base A Adenine C Cytosine G Guanine T (or U) Thymine (or Uracil) R A or G Y C or T S G or C W A or T K G or T M A or C B C or G or T D A or G or T H A or C or T V A or C or G N any base . or - gap Y = A/C

Progeny Testing I. F1 true/false and selfing: One [A/C] SNP for example Female male F1 True (T) False (F) Selfing (S) Unknown C T   S F Y - U Y=A/C; ‘-’ = missing data

Progeny Testing Female male F1 True (T) False (F) Selfing A T S B F H I. F1 true/false and selfing: 2. One SNP with ABH format Female male F1 True (T) False (F) Selfing A T   S B F H H=A/B

Progeny Testing I. F1 true/false and selfing: 2. One SNP with ABHM format Female male F1 True (T) False (F) Unknown Selfing A T   S B F H M U H=A/B; M=‘missing’

Progeny Testing Female male F2 or above True (T) False (F) Selfing (S) II. F2 or above true/false and selfing: 1. One SNP [C/T] format Female male F2 or above True (T) False (F) Selfing (S) Maybe (P) C T   S F Y P

Progeny Testing Female male F2 True (T) False (F) Selfing Maybe (P) A II. F2 or above true/false and selfing: 2. One SNP with ABH format Female male F2 True (T) False (F) Selfing Maybe (P) A T   S B F H P H=A/B; M=‘missing’

F2 True/false or selfing VB code F2_plantID M042843 M018895 M029431 …… M038631 7 AG TT GG 8 AA 10 12 ……… ……. 626 CG Female_N095 Male_P5678 CC F2 ABH and ratio testing With VB codes F2 Ratio Testing P1 x P2 F1 F2 AA AC CC AA CC AC 1 2 1 F2_plantID Female_N095 Male_P5678 7 8 10 12 …… 626 M042843 GG AA AG ……… M018895 TT ……. M029431 M050787 CC AC M054083 CG

WinQTLCart, QGene, and QTLNetwork Download the Windows QTL Cartographer 2.5 User Manual  or view manual or view online help how to use the WinQTLCart HERE! Download QGene Manual at http://www.qgene.org/qgene/Download_QGene_all.php, view QGene 4.3 user manual online! Download QTLNetwork User Manual and the article or view them online! Article examples: 1| Online web sites are: WinQtlCart user manual at http://statgen.ncsu.edu/qtlcart/HTML/index.html?whentousewinqtlcart.htm or download it from http://statgen.ncsu.edu/qtlcart/WQTLCart-3.htm Qgene user manual at http://www.qgene.org/qgene/current/docs/manual/Main_window.html or Download QGene Manual at http://www.qgene.org/qgene/Download_QGene_all.php QTLNetwork uaer manual at http://ibi.zju.edu.cn/software/qtlnetwork/QTLNetworkUserManual.pdf or http://bioinformatics.oxfordjournals.org/content/24/5/721.full.pdf+html or http://ibi.zju.edu.cn/BCL/softwareNetwork.html

WinQTLCart, QGene, and QTLNetwork Below attached the excel file (QTL_example_formatQgene_QTLCart_Network.xlsb) shows how to make .mcd, .qdf, .txt + .map files to run tools, which are also attached below: PMR16_for_WinQtlCart.mcd for WINQTLCart; PMR16_forQGene.qdf for Qgene; and PMR16_forQtlNetwork.txt + PMR16_for_QTLNetwork_Map.map for QTLNetwork. Two files: .txt and .map For running QTLNetwork Excel file for data format To run WinQTLCart, Qgene, and QtlNetwork MCD file format for running WinQTLCart QDF file format for running QGene

QTL Mapping Procedure Draw QTL mapping figures by Mapchart