A High-Resolution Map of Wheat QYr.ucw-1BL, an Adult Plant Stripe Rust Resistance Locus in the Same Chromosomal Region as Yr29.

The appearance of highly virulent and more aggressive races of f. sp. () during the last two decades has led to stripe rust epidemics worldwide and to the rapid erosion of effective resistance genes. In this study, we mapped an adult-plant resistance locus from the Argentinean wheat ( L.) cultivar Klein Chajá, which is effective against these new races. By using wheat exome capture data and a large population of 2480 segregating plants (4960 gametes), we mapped within a 0.24-cM region [332 kb in International Wheat Genome Sequencing Consortium (IWGSC) RefSeq version 1.0] on chromosome arm 1BL. This region overlaps with current maps of the adult-plant resistance gene , which has remained effective for more than 60 yr. An allelism test failed to find recombination between and and yielded similar resistance phenotypes for the two loci. These results, together with similar haplotypes in the candidate region, suggested that and might represent the same gene. However, we cannot rule out the possibility of tightly linked but different genes because most of the 13 genes in the candidate region are annotated with functions associated with disease resistance. To evaluate their potential as candidate genes, we characterized their polymorphisms between resistant and susceptible haplotypes. Finally, we used these polymorphisms to develop high-throughput markers to accelerate the deployment of these resistance loci in wheat breeding programs

A High-Resolution Map of Wheat QYr.ucw-1BL, an Adult Plant Stripe Rust Resistance Locus in the Same Chromosomal Region as Yr29

The appearance of highly virulent and more aggressive races of f. sp. () during the last two decades has led to stripe rust epidemics worldwide and to the rapid erosion of effective resistance genes. In this study, we mapped an adult-plant resistance locus from the Argentinean wheat ( L.) cultivar Klein Chajá, which is effective against these new races. By using wheat exome capture data and a large population of 2480 segregating plants (4960 gametes), we mapped within a 0.24-cM region [332 kb in International Wheat Genome Sequencing Consortium (IWGSC) RefSeq version 1.0] on chromosome arm 1BL. This region overlaps with current maps of the adult-plant resistance gene , which has remained effective for more than 60 yr. An allelism test failed to find recombination between and and yielded similar resistance phenotypes for the two loci. These results, together with similar haplotypes in the candidate region, suggested that and might represent the same gene. However, we cannot rule out the possibility of tightly linked but different genes because most of the 13 genes in the candidate region are annotated with functions associated with disease resistance. To evaluate their potential as candidate genes, we characterized their polymorphisms between resistant and susceptible haplotypes. Finally, we used these polymorphisms to develop high-throughput markers to accelerate the deployment of these resistance loci in wheat breeding programs

Insular Organization of Gene Space in Grass Genomes

Wheat and maize genes were hypothesized to be clustered into islands but the hypothesis was not statistically tested. The hypothesis is statistically tested here in four grass species differing in genome size, Brachypodium distachyon, Oryza sativa, Sorghum bicolor, and Aegilops tauschii. Density functions obtained under a model where gene locations follow a homogeneous Poisson process and thus are not clustered are compared with a model-free situation quantified through a non-parametric density estimate. A simple homogeneous Poisson model for gene locations is not rejected for the small O. sativa and B. distachyon genomes, indicating that genes are distributed largely uniformly in those species, but is rejected for the larger S. bicolor and Ae. tauschii genomes, providing evidence for clustering of genes into islands. It is proposed to call the gene islands ‘‘gene insulae’ ’ to distinguish them from other types of gene clustering that have been proposed. An average S. bicolor and Ae. tauschii insula is estimated to contain 3.7 and 3.9 genes with an average intergenic distance within an insula of 2.1 and 16.5 kb, respectively. Inter-insular distances are greater than 8 and 81 kb and average 15.1 and 205 kb, in S. bicolor and Ae. tauschii, respectively. A greater gene density observed in the distal regions of the Ae. tauschi

Fitting the regression model (7) to the <i>Ae. tauschii</i> data.

<p>Fitting the regression model (7) to the <i>Ae. tauschii</i> data.</p

Insular structure in sorghum and <i>Ae. tauschii.</i>

<p>Insular structure in sorghum and <i>Ae. tauschii.</i></p

Density functions for intergenic distances in <i>B. distachyon</i> (A), rice (B), sorghum (C), and <i>Ae. tauschii</i> (D).

<p>Shown is the exponential density fitted by Maximum Likelihood (2) (solid) and the non-parametric density estimate (4) (dashed), with bandwidth <i>h</i> = 1.25 (<b>A</b>), <i>h</i> = 1.75 (<b>B</b>), <i>h</i> = 1.50 (<b>C</b>), and <i>h</i> = 15.00 (<b>D</b>).</p

Summary of test results for the null hypothesis that gene locations are uniformly distributed in the four species.

*<p>The estimated exponential rate parameter is the maximum likelihood estimator of as given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054101#pone.0054101.e002" target="_blank">Equation (1</a>).</p>**<p>Based on a χ²- goodness of fit test.</p

Relationships between inter-insular distances (A), intra-insular distances (B) and the number of genes per insula (C) and gene location along the centromere-telomere axes of <i>Ae. tauschii</i> chromosome arms.

<p>(<b>A</b>) shows a fitted regression line from Model (7) of the inter-insular distances and gene location on centromere-telomere axes of <i>Ae. tauschii</i> chromosome arms.</p

Fitting the full regression model specified in equation (5) to the <i>Ae. tauschii</i> data.

<p>Fitting the full regression model specified in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054101#pone.0054101.e031" target="_blank">equation (5</a>) to the <i>Ae. tauschii</i> data.</p