Additional file 3: Table S2. of Transcriptional and physiological analyses of Fe deficiency response in maize reveal the presence of Strategy I components and Fe/P interactions

Differentially expressed transcripts resulted by the comparison of root transcriptional profiles of Fe-deficient plants with root transcriptional profile of Fe-sufficient ones (−Fe vs + Fe). (XLSX 160 kb

Historical Introgression of the Downy Mildew Resistance Gene <i>Rpv12</i> from the Asian Species <i>Vitis amurensis</i> into Grapevine Varieties

<div><p>The Amur grape (<i>Vitis amurensis</i> Rupr.) thrives naturally in cool climates of Northeast Asia. Resistance against the introduced pathogen <i>Plasmopara viticola</i> is common among wild ecotypes that were propagated from Manchuria into Chinese vineyards or collected by Soviet botanists in Siberia, and used for the introgression of resistance into wine grapes (<i>Vitis vinifera</i> L.). A QTL analysis revealed a dominant gene <i>Rpv12</i> that explained 79% of the phenotypic variance for downy mildew resistance and was inherited independently of other resistance genes. A Mendelian component of resistance–a hypersensitive response in leaves challenged with <i>P. viticola</i>–was mapped in an interval of 0.2 cM containing an array of coiled-coil NB-LRR genes on chromosome 14. We sequenced 10-kb genic regions in the <i>Rpv12⁺</i> haplotype and identified polymorphisms in 12 varieties of <i>V. vinifera</i> using next-generation sequencing. The combination of two SNPs in single-copy genes flanking the NB-LRR cluster distinguished the resistant haplotype from all others found in 200 accessions of <i>V. vinifera</i>, <i>V. amurensis</i>, and <i>V. amurensis</i> x <i>V. vinifera</i> crosses. The <i>Rpv12⁺</i> haplotype is shared by 15 varieties, the most ancestral of which are the century-old ‘Zarja severa’ and ‘Michurinets’. Before this knowledge, the chromosome segment around <i>Rpv12⁺</i> became introgressed, shortened, and pyramided with another downy mildew resistance gene from North American grapevines (<i>Rpv3</i>) only by phenotypic selection. <i>Rpv12⁺</i> has an additive effect with <i>Rpv3⁺</i> to protect vines against natural infections, and confers foliar resistance to strains that are virulent on <i>Rpv3⁺</i> plants.</p> </div

Phenotypic distribution of downy mildew resistance.

<p>Two families segregating for <i>Rpv12⁺</i> (panel <b>A</b>) and for the combination of <i>Rpv12⁺</i> and <i>Rpv3⁺</i> (panel <b>B</b>) were analysed. Resistance scores in panel <b>A</b> are based on the OIV452 parameter (1 = most sensitive, 9 = most resistant) scored on field-grown seedlings under natural infection. Resistance scores in panel <b>B</b> are based on the cumulative OIV452 parameter (∑OIV452 = sum of daily OIV452 scores from 3 to 8 dpi) in artificially inoculated leaf discs. The average phenotypic value in the upper left corner of the panels <b>A</b>–<b>B</b> refers to individuals grouped by their allelic status at the <i>Rpv12</i> and <i>Rpv3</i> genes, which was estimated based on the flanking markers UDV014/UDV370 for <i>Rpv12</i>, and on UDV305/UDV737 for <i>Rpv3 </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061228#pone.0061228-DiGaspero1" target="_blank">[8]</a>. Recombinants in those intervals were excluded from this estimate. QTL plots that explain the phenotypic variance shown in panel <b>B</b> are given in panel <b>C</b>.</p

Host–pathogen interaction observed between host and pathogen genotypes.

<p>Leaf discs of four host genotypes including (panels <b>A</b>, <b>E</b>) a double homozygous recessive grapevine (<i>Rpv12⁻</i> and <i>Rpv3⁻</i>), (panels <b>B</b>, <b>F</b>) a grapevine carrying <i>Rpv3⁺</i> in the absence of <i>Rpv12⁺</i>, (panels <b>C</b>, <b>G</b>) a grapevine carrying <i>Rpv12⁺</i> in the absence of <i>Rpv3⁺</i>, and (panels <b>D</b>, <b>H</b>) a double heterozygous grapevine for both <i>Rpv12⁺</i> and <i>Rpv3⁺</i> were inoculated with two isolates of <i>P. viticola</i>, (panels <b>A</b>–<b>D</b>) <i>Rude</i> (<i>avrRpv3⁺</i>/<i>avrRpv12⁺</i>) and (panels <b>E</b>–<b>H</b>) <i>Pv127</i> (<i>avrRpv3⁻</i>/<i>avrRpv12⁺</i>). Pictures were taken at 6 dpi.</p