Application of Whole Genome Sequencing and High Resolution Mapping to Characterize Brown Rot (Monilinia spp.) Resistance in Peach [Prunus persica (L.) Batsch]

Wednesday, July 24, 2013
Desert Ballroom: Salons 7-8 (Desert Springs J.W Marriott Resort )
Pedro J. Martinez-Garcia , University of California, Davis, Davis
Jonathan Fresnedo , University of California, Davis, Davis
Dan Parfitt, Dr. , University of California, Davis, Davis, CA
Thomas Gradziel , University of California, Davis, Davis, CA
Richard M. Bostock , University of California, Davis, Davis
Joseph Fass , University of California, Davis, Davis
Dawei Lin , University of California, Davis, Davis
Ebenezer A. Ogundiwin , Nunheims, Davis
Helen M. Chan , Plant Sciences, MS2, University of California, Davis, Davis
Riaz Ahmad , NA, NA
Carlos H. Crisosto , Plant Sciences, University of California, Davis, Davis, CA
Sequencing, map development, and QTL discovery referenced to genome annotation are summarized for three peach genomes and their progeny, generated as part of the California peach/almond breeding programs. Three parents, ‘Dr. Davis', ‘F8, 1-42’, and ‘Georgia Belle’ were sequenced to identify SNPs for genotyping two breeding populations, Pop-DF (‘Dr. Davis’ × ‘F8, 1-42’) and Pop-DG (‘Dr. Davis’ × ‘Georgia Belle’). A combination of Roche 454 and Ilumina/Solexa sequencing were used to generate a consensus genome sequence for each parent. Burrows Wheeler alignment (BWA) with SAMtools were used to align raw data. Velvet/Columbus software was used to assemble the contigs, referenced to the draft Peach 1.0 genome from the International Peach Initiative. Comparison of aligned and overlapping sequences from both Roche 454 and Illumina-Solexa were compared to select 6654 high quality SNPs for ‘Dr. Davis’ vs. ‘F8, 1-42’ and ‘Georgia Belle’, distributed on the eight major peach genome scaffolds from the physical Peach 1.0 assembly. The eight scaffolds from our populations contained about 215–225 Mb of peach genomic sequences with one selected SNP/ ~40,000 bases. Populations DF and DG were scored for 1536 SNPs, evenly distributed across the eight major peach scaffolds, with the Illumina GoldenGate® Genotyping assay. There were 1,400 high quality SNPs used in Pop-DF and 962 were used in Pop-DG to construct two linkage maps with JoinMap®4.0. The Pop-DF map covered 422 cM (1,037 SNPs), Pop-DG map covered 369 cM (738 SNPs), and a consensus map  with 588 SNPs in eight linkage groups covered 454 cM with ave. 0.81 cM between SNPs. Placements of SNPs on the ‘peach v1.0’ physical map were compared to placement on the linkage maps and several differences were observed. The Pop-DF map was used to identify QTLs for brown rot on linkage groups 1 and 4. SnpEff ver. 3.0c. software was used to identify 2,163 SNP effects, 282 effects were located in exonic regions (13.04%) and 294 placed in intronic regions (13.59%). SNP effects in brown rot QTL regions were evaluated for putative function.
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