Zea mays MAGIC RIL population - field trial phenotyping data

MIAPPE compliant ISA-tab files of the Zea mays MAGIC RIL population derived from eight genetically diverse founder lines.</p

Additional file 7: of QTL mapping and candidate genes for resistance to Fusarium ear rot and fumonisin contamination in maize

Table S5. List of candidate genes for Fusarium verticillioides resistance in the 1-LOD and 2-LOD confidence interval in the genomic regions containing QTLs for FER and FB1 contamination. (XLSX 100 kb

Variant discovery in <i>PpeMYB25</i> (annotation refinement of <i>ppa023143m</i>).

<p>Five nectarine genotypes (‘Madonna di Agosto’, MdA; ‘Quetta’, Q; ‘Stark Red Gold’, SRG; ‘Goldmine’, G; ‘Ambra’, A) were analyzed to confirm the presence of the insertion within exon 3 of <i>PpeMYB25</i>. (A) Long-range amplification products reveal for all the accessions a fragment of about 7 kb (compared to 960 bp expected from the reference genome). (B) Double digestion results of the long-range PCR products show the same pattern for all the genotypes. (C) Position and structure of the Ty-<i>copia</i> retrotransposon deduced by the by the NGS analysis of ‘Quetta’ long-range amplicon. The insertion results in a truncated version of the R2R3-MYB protein.</p

Alignment of Quetta reads against a 635 kb interval of Peach v1.0 pseudomolecule 5.

<p>Alignment results of reads, obtained by the resequencing of ‘Quetta’, against the peach genome region identified by the mapping interval in LG5 (from 15,853,006 bp to 16,488,104 bp). Top panel: intron-exon structure of <i>ppa023143m</i>. Central panel: plot of ‘Quetta’ paired-end distance (blue) and frequencies of single reads (yellow) at the <i>ppa023143m</i> locus. Bottom panel: blue lines are paired reads, green and red lines correspond to single reads with missing mate on the right and left side, respectively. The orange arrow points to the putative insertion inside exon 3 of <i>ppa023143m</i>.</p

Functional Marker indelG.

<p>A marker assay was developed based on sequence information on the <i>PpeMYB25</i> gene and the Ty1<i>-copia</i> insertion. Three primers were designed to discriminate peach and nectarine genotypes (A, B). A panel of nectarines including the putative donors of the trait, show a unique fragment of about 200 bp (C). A set of peaches, of diverse pedigree and origins (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090574#pone-0090574-t001" target="_blank">Table 1</a>) (D), shows homozygous or heterozygous patterns.</p

SNP markers.

a<p>SNP detection was performed by Sequenom MassArray technology, except for the SNPs in italics that were genotyped by Sanger sequence.</p>b<p>the genetic distances estimated by the analysis of informative recombinant plants are reported in italics.</p>c<p>the first nucleotide correspond to the reference allele in the peach genome (Peach v1.0).</p>d<p>lower case bases correspond to the tails added to the SNP extension primer for Sequenom MassArray analysis.</p><p>For each marker the following information is reported: marker name, position in cM with respect to the map in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090574#pone-0090574-g001" target="_blank">Figure 1</a>, position in bp with respect to the peach genome sequence (Peach v1.0), SNP allele and the primer sequences used.</p

LG 5 CxA map around the <i>G</i> locus.

<p>Linkage map obtained from analysis of the CxA F₂ progeny. On the left side distances are indicated in cM; on the right the marker name, the physical position on Peach v1.0 and marker skewedness are reported. The peach/nectarine locus and the indelG marker are shown in bold.</p

Expression analysis of <i>PpeMYB25</i> in peach and nectarine flower buds.

<p>(A) The expression patterns of the R2R3-MYB gene were evaluated in ‘Contender’ [C] and ‘Ambra’ [A] buds at seven, five, four and one week before anthesis (WBA). Genomic DNA of the two cultivars was also tested as a control. The same samples were analyzed for expression of <i>RPII</i> as standard (B) and checked for DNA contamination (C).</p

List of Primers.

<p>Name, sequence, position on Peach v1.0 and length of primers used to perform long-range PCR, RT-PCR and indelG assay.</p

Aminoacid alignment of the R2 and R3 MYB repeat sequences.

<p>MYB domains (pfam00249) of peach PpeMYB25, cotton GhMYB25 (ACJ07153.1, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090574#pone.0090574-Li1" target="_blank">[39]</a>) and <i>Antirrhinum</i> AmMYBML1 (CAB433991.1, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090574#pone.0090574-Finn1" target="_blank">[54]</a>) were aligned using the Muscle on line tool at EBI (<a href="http://www.ebi.ac.uk/Tools/msa/muscle/" target="_blank">http://www.ebi.ac.uk/Tools/msa/muscle/</a>). Graphic display of the alignment was obtained using BoxShade (<a href="http://www.ch.embnet.org/software/BOX_form.html" target="_blank">http://www.ch.embnet.org/software/BOX_form.html</a>). Black shaded residues are identical, grey shaded residues are similar. Coordinates in the protein sequences are indicated.</p