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1 QTL mapping of pomological traits in peach and related species breeding germplasm Jonathan Fresnedo-Ramírez1§*, Marco C.A.M. Bink2, Eric Van de Weg3, Thomas R. Famula4, Carlos H. Crisosto1, Terrence J. Frett5**, Ksenija Gasic5, Cameron P. Peace6, Thomas M. Gradziel1§ Molecular Breeding 1 Department of Plant Sciences, University of California, Davis, CA 95616, USA 2 Biometris, Wageningen University and Research Centre, P.O. Box 100, 6700 AC Wageningen, The Netherlands 3 Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ Wageningen, The Netherlands 4 Department of Animal Science, University of California, Davis, CA 95616, USA 5 School of Agricultural, Forest, and Environmental Sciences, Clemson University, Clemson, SC 29634, USA 6 Department of Horticulture, Washington State University, Pullman, WA 99164, USA § Author for correspondence * Current address: Institute of biotechnology, Bioinformatics Facility, Cornell University, Ithaca, NY 14853, USA ** Current address: Horticulture Department, University of Arkansas, Fayetteville, AR 72701 USA Email addresses: JFR: jfresnedo@cornell.edu MCAMB: marco.bink@wur.nl EVW: eric.vandeweg@wur.nl TRF: trfamula@ucdavis.edu CHC: chcrisosto@ucdavis.edu TJF: tjfrett@email.uark.edu KG: kgasic@clemson.edu CPP: cpeace@wsu.edu TMG: tmgradziel@ucdavis.edu 2 Fig. S1: The SNP linkage map used for QTL mapping. 3 Fig. S2. Visualization of the pedigree analyzed. A: Horizontal visualization of a representative pedigree of the Processing Peach Breeding Program at UC Davis. B: Horizontal visualization of the progenies with Almond (P. dulcis) ancestry. C: Vertical visualization of progenies with P. argentea ancestry. D: Vertical representation of progenies with P. mira ancestry. E: Vertical visualization of a full-sib family highlighting a male parent introgression line (persXdavidiana = P. persica × P. davidiana). 4 Table S1. Corrected parentages. Dummy# specifies that the parent was not available in the analyzed pedigree set. The parentages were corrected based on results from FRANz having a minimum LOD score of 20 and posterior probability > 0.99. Italicized individuals depict the corrected pedigrees for four cultivars. Individual Parent 1 Parent 2 2005_10_065 2005_10_073 2005_10_126 2005_10_160 2005_10_236 2005_10_259 2005_10_263 2005_16_150 2005_17_023 2005_17_027 2005_17_031 2005_17_034 2005_17_036 2005_17_039 2005_17_046 2005_17_053 2005_17_054 2005_17_054 2005_17_057 2005_17_061 2005_17_061 2005_17_065 2005_17_069 2005_17_089 2005_17_089 2005_17_094 2005_17_096 2005_17_116 2005_17_129 2005_17_130 2005_17_136 2005_17_140 2005_17_148 2005_18_036 2005_18_070 2005_18_096 2005_18_096 2005_18_104 2005_18_111 2005_18_118 2005_18_142 2005_18_148 2005_18_151 2005_18_156 2005_18_158 2005_18_162 2005_18_168 2005_18_185 2005_19_139 2005_20_11 2005_20_117 2005_20_141 2005_20_192 2007_10_212 2007_13_248 2009_18_187 2009_19_150 2009_19_18 90_10_91 96_9_292 Halford Hesse Rizzi Woltemade DrDavis DrDavis DrDavis DrDavis DrDavis DrDavis DrDavis OHenry Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Loadel 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 19_2_72 Carson Carson 2000_3_205 91_16_154 2000_2_9 2000_3_205 Andross Andross Andross Hesse E22_59 Riegels Everts Kakamas D62_193 D62_193 D62_193 D62_193 D62_193 D62_193 D62_193 F8_1_42 Vilmos Vilmos Vilmos Vilmos Vilmos Vilmos Vilmos Vilmos Vilmos Vilmos Vilmos Vilmos Vilmos Vilmos Vilmos Vilmos Vilmos Vilmos Vilmos Vilmos Vilmos Vilmos Vilmos Vilmos persXdavidiana 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2000_3_205 2000_3_205 2000_3_205 2000_3_205 Ogawa 2000_2_9 2000_3_205 96_9_292 96_9_292 96_9_292 Vilmos E22_59 Riegels F_Rizzi F_Wolvamade Corrected Parent1 DrDavis DrDavis DrDavis DrDavis DrDavis DrDavis DrDavis OHenry Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Goodwin Loadel 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2001_7_180 2000_2_8 Rizzi Carson Carson 2000_3_205 91_16_154 2000_2_9 2000_3_205 Andross Andross Andross Hesse E22_59 StJohn Riegels Everts Kakamas Corrected Parent2 Carson Carson Rizzi Rizzi Rizzi Carson Rizzi RioOsoGem 91_9_161 91_9_161 DrDavis DrDavis F8_5_147 DrDavis dummy030 Halford DrDavis DrDavis Ogawa DrDavis DrDavis Goodwin Ogawa dummy031 dummy031 dummy032 Goodwin Goodwin Goodwin 91_12_54 Goodwin Goodwin Loadel dummy035 dummy036 91_12_54 dummy037 dummy038 dummy039 dummy040 dummy041 dummy042 dummy012 dummy043 dummy044 dummy045 dummy046 dummy048 Rizzi Nemaguard DrDavis 91_12_54 F10C_20_51 dummy050 2000_16_133 2000_8_157 2000_8_157 2000_8_157 P_90_10_91 dummy028 Lovell_CA 18_8_23 19_2_72 Kakamas 5 Fig. S3. Determination of the genetic structure for 258 individual members of a pedigree, including peach and almond cultivars and interspecific hybrids, as well as introgression breeding lines. 6 Fig S4. Correlation between genome-wide estimated breeding values (GEBVs) of each trait between years 2011 and 2012
