Supplemental material for Ben Hassen et al., 2018

<p> Two Supplementary figures and seven Supplementary tables. Detailed description of each figure and table is presented in the first page of the file.<br></p

Expression analysis of Resistance Genes Analogs (RGAs) candidates for Gigante Vercelli (GV) resistance functions.

<p><b>A</b>: Chromosome localization of candidate resistance (<i>R</i>) genes. Red bars: GV-specific induced RGAs called as DEGs; blue bars: RGAs expressed in GV only (i.e. expressed in GV, not expressed in Vialone Nano -VN-, regardless to infection responsiveness); black bars: RGAs with at least twofold expression ratio among infected GV and infected VN. Nipponbare loci corresponding to known blast <i>R</i> genes are indicated with green, thick bars; physical distances for each rice chromosome are also indicated (mapping position values in millions bp). <b>B</b>: Read mapping patterns in mock and blast inoculation conditions of selected RGAs from the three groups listed above for Gigante Vercelli (GV) and Vialone Nano (VN). Each group is color-coded as in legend of panel A. Red and blue bars in the upper panel represent gene, mRNA and coding sequence structure respectively from the upper to the lower bar. Red and blue segments above and below the midlines represent reads mapping to forward and reverse strands, respectively.</p

Local genetic maps of the target region of <i>P</i>. <i>deltoides</i> and <i>P</i>. <i>nigra</i> and their alignment onto the scaffold 5 of <i>P</i>. <i>trichocarpa</i> v2.0.

<p>Alignment of SNPs with physical position on scaffold 5 of the <i>P</i>. <i>trichocarpa</i> genome with their position in the P. <i>deltoides</i> and <i>P</i>. <i>nigra</i> maps. Map distances in cM (Kosambi distances) are indicated on the left of the linkage groups (LGs). On the right of the LG are reported the SNP names, composed by a first number representing the number of scaffold conferred by RAPiD-seq genotyping and a second number identifying the physical position in bp of each SNP on the scaffold.</p

Hierarchical clustering of OsWAK gene expression.

<p>Gigante Vercelli (GV) and Vialone Nano (VN) <i>OsWAK</i> gene expression as affected by blast infection in the different treatments (blast or mock inoculated) and biological replicates (R1, R2, R3). Genes called as DEGs are indicated on the right border of the heatmap. Colored bars on the left of the heatmap mark distinct major branches in the clustering tree grouping genes with similar expression pattern. The colour scale indicates the expression value (light blue indicate higher expression value, darker blue indicates lower gene expression values). The heat map was generated with custom scripts based on heatmap.2 function as available in the ‘gplots’ Bioconductor package.</p

Differentially Expressed Genes in the common enriched GO term “defence response to fungus, incompatible interaction” (GO:0009817) in Gigante Vercelli and Vialone Nano.

a<p>Expression values are reported as DESeq-normalized read counts.</p

Chromosomal regions carrying the wpa resistance QTLs.

<p>The map position, the peak markers of each QTL and the LOD score are plotted. The horizontal line at 4.59 LOD value represents the LOD threshold determining the statistically significance of QTLs in the <i>P</i>. <i>deltoides</i> map.</p

QTLs for Woolly Poplar Aphid (<i>Phloeomyzus passerinii</i> L.) Resistance Detected in an Inter-Specific <i>Populus deltoides</i> x <i>P</i>. <i>nigra</i> Mapping Population

<div><p>The genus <i>Populus</i> represents one of the most economically important groups of forest trees. It is composed by approximately 30 species used for wood and non-wood products, phytoremediation and biomass. Poplar is subjected to several biological and environmental threats although, compared to annual crops, we know far less about the genetic bases of biotic stress resistance. Woolly poplar aphid (<i>Phloeomyzus passerinii</i>) is considered a main pest of cultivated poplars in European and American countries. In this work we present two high density linkage maps in poplar obtained by a genotyping by sequencing (GBS) approach and the identification of QTLs involved in <i>Ph</i>. <i>passerinii</i> resistance. A total of 5,667 polymorphic markers (5,606 SNPs and 61 SSRs) identified on expressed sequences have been used to genotype 131 plants of an F1 population <i>P ×canadensis</i> obtained by an interspecific mate between <i>Populus deltoides</i> (resistant to woolly poplar aphid) and <i>Populus nigra</i> (susceptible to woolly poplar aphid). The two linkage maps, obtained following the two-way pseudo-testcross mapping strategy, have been used to investigate the genetic bases of woolly poplar aphid resistance. One major QTL and two QTLs with minor effects (mapped on LGV, LGXVI and LG XIX) explaining the 65.8% of the genetic variance observed in the progeny in response to <i>Ph</i>. <i>passerinii</i> attack were found. The high density coverage of functional markers allowed the identification of three genes belonging to disease resistance pathway as putative candidates for <i>P</i>. <i>deltoides</i> resistance to woolly poplar aphid. This work is the first report on genetic of woolly poplar aphid genetic resistance and the resistant loci associated markers identified represent a valuable tool in resistance poplar breeding programs.</p></div

Comparative Transcriptome Profiling of the Early Response to <em>Magnaporthe oryzae</em> in Durable Resistant <em>vs</em> Susceptible Rice (<em>Oryza sativa</em> L.) Genotypes

<div><p>Durable resistance to blast, the most significant fungal disease of rice, represents an agronomically relevant character. Gigante Vercelli (GV) and Vialone Nano (VN) are two old temperate <em>japonica</em> Italian rice cultivars with contrasting response to blast infection: GV displays durable and broad resistance while VN is highly susceptible. RNA-seq was used to dissect the early molecular processes deployed during the resistance response of GV at 24 h after blast inoculation. Differential gene expression analysis identified 1,070 and 1,484 modulated genes, of which 726 and 699 were up regulated in response to infection in GV and VN, respectively. Gene ontology (GO) enrichment analyses revealed a set of GO terms enriched in both varieties but, despite this commonality, the gene sets contributing to common GO enriched terms were dissimilar. The expression patterns of genes grouped in GV-specific enriched GO terms were examined in detail including at the transcript isoform level. GV exhibited a dramatic up-regulation of genes encoding diterpene phytoalexin biosynthetic enzymes, flavin-containing monooxygenase, class I chitinase and glycosyl hydrolase 17. The sensitivity and high dynamic range of RNA-seq allowed the identification of genes critically involved in conferring GV resistance during the early steps of defence perception-signalling. These included chitin oligosaccharides sensing factors, wall associated kinases, MAPK cascades and WRKY transcription factors. Candidate genes with expression patterns consistent with a potential role as GV-specific functional resistance (<em>R</em>) gene(s) were also identified. This first application of RNA-seq to dissect durable blast resistance supports a crucial role of the prompt induction of a battery of responses including defence-related genes as well as members of gene families involved in signalling and pathogen-related gene expression regulation.</p> </div

Numbers of aligned and mapped reads.

a<p>GV =  Gigante Vercelli; VN =  Vialone Nano.</p

<i>WAK</i> (Wall Associated Kinase) genes modulated in Gigante Vercelli and Vialone Nano.

a<p>Expression values are reported as DESeq-normalized read counts.</p