High-resolution analysis of a QTL for resistance to Stagonospora nodorum glume blotch in wheat reveals presence of two distinct resistance loci in the target interval

Stagonospora nodorum glume blotch (SNG), caused by the necrotrophic fungus Stagonospora nodorum, is one of the economically important diseases of bread wheat (Triticum aestivum L.). Resistance to SNG is known to be quantitative and previous studies of a recombinant inbred line (RIL) population identified a major quantitative trait locus (QTL) for resistance to SNG on the short arm of chromosome 3B. To localize this QTL (QSng.sfr-3BS) with high resolution, we constructed a genetic map for the QTL target region using information from sequenced flow-sorted chromosomes 3B of the two parental cultivars ‘Arina' and ‘Forno', the physical map of chromosome 3B of cultivar ‘Chinese Spring' and BAC-clone sequences. The mapping population of near-isogenic lines (NIL) was evaluated for SNG resistance in field infection tests. NILs segregated for disease resistance as well as for plant height; additionally, we observed a high environmental influence on the trait. Our analysis detected a strong negative correlation of SNG resistance and plant height. Further analysis of the target region identified two linked loci associated with SNG resistance. One of them was also associated with plant height, revealing an effect of QSng.sfr-3BS on plant height that was hidden in the RIL population. This result demonstrates an unexpectedly high genetic complexity of resistance controlled by QSng.sfr-3BS and shows the importance of the study of QTL in mendelized form in NILs

High-resolution analysis of a QTL for resistance to Stagonospora nodorum glume blotch in wheat reveals presence of two distinct resistance loci in the target interval

Stagonospora nodorum glume blotch (SNG), caused by the necrotrophic fungus Stagonospora nodorum, is one of the economically important diseases of bread wheat (Triticum aestivum L.). Resistance to SNG is known to be quantitative and previous studies of a recombinant inbred line (RIL) population identified a major quantitative trait locus (QTL) for resistance to SNG on the short arm of chromosome 3B. To localize this QTL (QSng.sfr-3BS) with high resolution, we constructed a genetic map for the QTL target region using information from sequenced flow-sorted chromosomes 3B of the two parental cultivars ‘Arina’ and ‘Forno’, the physical map of chromosome 3B of cultivar ‘Chinese Spring’ and BAC-clone sequences. The mapping population of near-isogenic lines (NIL) was evaluated for SNG resistance in field infection tests. NILs segregated for disease resistance as well as for plant height; additionally, we observed a high environmental influence on the trait. Our analysis detected a strong negative correlation of SNG resistance and plant height. Further analysis of the target region identified two linked loci associated with SNG resistance. One of them was also associated with plant height, revealing an effect of QSng.sfr-3BS on plant height that was hidden in the RIL population. This result demonstrates an unexpectedly high genetic complexity of resistance controlled by QSng.sfr-3BS and shows the importance of the study of QTL in mendelized form in NILs

A physical map of the short arm of wheat chromosome 1A

Bread wheat (Triticum aestivum) has a large and highly repetitive genome which poses major technical challenges for its study. To aid map-based cloning and future genome sequencing projects, we constructed a BAC-based physical map of the short arm of wheat chromosome 1A (1AS). From the assembly of 25,918 high information content (HICF) fingerprints from a 1AS-specific BAC library, 715 physical contigs were produced that cover almost 99% of the estimated size of the chromosome arm. The 3,414 BAC clones constituting the minimum tiling path were end-sequenced. Using a gene microarray containing ∼40 K NCBI UniGene EST clusters, PCR marker screening and BAC end sequences, we arranged 160 physical contigs (97 Mb or 35.3% of the chromosome arm) in a virtual order based on synteny with Brachypodium, rice and sorghum. BAC end sequences and information from microarray hybridisation was used to anchor 3.8 Mbp of Illumina sequences from flow-sorted chromosome 1AS to BAC contigs. Comparison of genetic and synteny-based physical maps indicated that ∼50% of all genetic recombination is confined to 14% of the physical length of the chromosome arm in the distal region. The 1AS physical map provides a framework for future genetic mapping projects as well as the basis for complete sequencing of chromosome arm 1AS

Genetic markers linked to the chromosome 1AS physical map.

1<p>Position of the closest gene in the reference zipper.</p>2<p>TmGxG: T. monococcum G1777×G2528 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080272#pone.0080272-Dubcovsky1" target="_blank">[67]</a>.</p>3<p>TaBxT: Banks×Banks+tin (Spielmeyer et al., unpublished).</p>4<p>TaAxF: Arina×Forno <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080272#pone.0080272-Paillard1" target="_blank">[68]</a>.</p>5<p>TaNxW: Nanda2419×Wangshuibai <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080272#pone.0080272-Xue1" target="_blank">[69]</a>.</p>6<p>TaSxO : Syntethic×Opata <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080272#pone.0080272-Nelson3" target="_blank">[70]</a>.</p>7<p>TaCxCS: Courtot×Chinese Spring (Sourdille, unpublished).</p>8<p>ConSSR: Consensus SSR <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080272#pone.0080272-Somers1" target="_blank">[53]</a>.</p>9<p>Com2004: Wheat-Composite 2004 (Appels et al., unpublished).</p>10<p>ConsPos: Consensus position (approximate average of all cM positions for each marker).</p><p>Genetic positions (telomere to centromere) from different maps were taken from published genetic maps in GrainGenes (wheat.pw.usda.gov). The numbers in the individual marker fields indicate the cM position of the respective marker. Note that markers mapping to the same position in the reference zipper can have multiple different cM positions, depending on the map/population.</p

Physical map of wheat chromosome 1AS.

<p>The figure integrates multiple sequence resources. <b>a.</b> Chromosome 1AS deletion bin map with the three bins shown in (yellow, green and gray). ESTs from the three deletion bins which were mapped to <i>Brachypodium</i> reference zipper genes are indicated with boxes with colour of the corresponding bin. If more than one EST mapped to the same Brachypodium gene, the boxes were stacked on top of each other. This information was used to estimate the boundaries of each deletion bin in the <i>Brachypodium</i> reference zipper (dashed lines). <b>b. </b><i>Brachypodium</i> reference zipper. <b>c.</b> Physical map of the 1AS chromosme arm. BAC contigs are symbolised with blue lines (see enlarged legend at the right). The length of the line reflects the number of putative syntenic genes found on the contig, not its physical size. Syntenic genes are also symbolised by black boxes. The number of non-syntenic genes for each contig is indicated with a stack of red boxes. Grey boxes indicate place holders for contigs that contained no syntenic genes but were anchored by means other than synteny (e.g. genetic markers of centromere-specific repeats. <b>d.</b> Published genetic markers from chromosome 1AS that were used to deduce an estimated genetic map (marker and map names and genetic distances are detailed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080272#pone-0080272-t001" target="_blank">Table 1</a>).</p

Information contained in the definition lines of Illumina sequences that were used for the integrated 1AS sequence model in the order it is given in the definition line.

<p>Information contained in the definition lines of Illumina sequences that were used for the integrated 1AS sequence model in the order it is given in the definition line.</p

Numbers of genes which were assigned to 1AS BAC contigs during level 1 anchoring.

a<p>Genes that have homologs in the 1AS reference zipper and which could be used for level 2 anchoring.</p

Small scale validation of the chromosome 1AS physical map using information from the previously published <i>Pm3</i> powdery mildew resistance locus.

<p>Two assembled physical contigs (ltc132 and ltc5245) were linked together using a previously published 178 kb sequence from chromosome 1AS (cv. Chinese Spring) covering the the <i>Pm3</i> locus (Wicker et al. 2007). Approximate locations of NimbleGen transcriptome hybridisation probes are shown in blue. The <i>Pm3</i> and the low molecular weight (LMW) glutenin loci are known to be closely linked (Wicker et al. 2003; Wang et al. 2010). The inset shows a phylogenetic analysis that compares glutenin UniGene sequences with previously published glutenin genes from 1AS (TmGluA3, green), 1BS (TaGluB) and 1DS (TaGluD).</p