Image1_Genome-wide characterization and identification of cyclophilin genes associated with leaf rust resistance in bread wheat (Triticum aestivum L.).TIF

Cyclophilins (CYPs) are a group of highly conserved proteins involved in host-pathogen interactions in diverse plant species. However, the role of CYPs during disease resistance in wheat remains largely elusive. In the present study, the systematic genome-wide survey revealed a set of 81 TaCYP genes from three subfamilies (GI, GII, and GIII) distributed on all 21 wheat chromosomes. The gene structures of TaCYP members were found to be highly variable, with 1–14 exons/introns and 15 conserved motifs. A network of miRNA targets with TaCYPs demonstrated that TaCYPs were targeted by multiple miRNAs and vice versa. Expression profiling was done in leaf rust susceptible Chinese spring (CS) and the CS-Ae. Umbellulata derived resistant IL “Transfer (TR). Three homoeologous TaCYP genes (TaCYP24, TaCYP31, and TaCYP36) showed high expression and three homoeologous TaCYP genes (TaCYP44, TaCYP49, and TaCYP54) showed low expression in TR relative to Chinese Spring. Most of the other TaCYPs showed comparable expression changes (down- or upregulation) in both contrasting TR and CS. Expression of 16 TaCYPs showed significant association (p < 0.05) with superoxide radical and hydrogen peroxide abundance, suggesting the role of TaCYPs in downstream signaling processes during wheat-leaf rust interaction. The differentially expressing TaCYPs may be potential targets for future validation using transgenic (overexpression, RNAi or CRISPR-CAS) approaches and for the development of leaf rust-resistant wheat genotypes.</p

Image4_Genome-wide characterization and identification of cyclophilin genes associated with leaf rust resistance in bread wheat (Triticum aestivum L.).TIF

Cyclophilins (CYPs) are a group of highly conserved proteins involved in host-pathogen interactions in diverse plant species. However, the role of CYPs during disease resistance in wheat remains largely elusive. In the present study, the systematic genome-wide survey revealed a set of 81 TaCYP genes from three subfamilies (GI, GII, and GIII) distributed on all 21 wheat chromosomes. The gene structures of TaCYP members were found to be highly variable, with 1–14 exons/introns and 15 conserved motifs. A network of miRNA targets with TaCYPs demonstrated that TaCYPs were targeted by multiple miRNAs and vice versa. Expression profiling was done in leaf rust susceptible Chinese spring (CS) and the CS-Ae. Umbellulata derived resistant IL “Transfer (TR). Three homoeologous TaCYP genes (TaCYP24, TaCYP31, and TaCYP36) showed high expression and three homoeologous TaCYP genes (TaCYP44, TaCYP49, and TaCYP54) showed low expression in TR relative to Chinese Spring. Most of the other TaCYPs showed comparable expression changes (down- or upregulation) in both contrasting TR and CS. Expression of 16 TaCYPs showed significant association (p < 0.05) with superoxide radical and hydrogen peroxide abundance, suggesting the role of TaCYPs in downstream signaling processes during wheat-leaf rust interaction. The differentially expressing TaCYPs may be potential targets for future validation using transgenic (overexpression, RNAi or CRISPR-CAS) approaches and for the development of leaf rust-resistant wheat genotypes.</p

Evaluation of 19,460 Wheat Accessions Conserved in the Indian National Genebank to Identify New Sources of Resistance to Rust and Spot Blotch Diseases

<div><p>A comprehensive germplasm evaluation study of wheat accessions conserved in the Indian National Genebank was conducted to identify sources of rust and spot blotch resistance. Genebank accessions comprising three species of wheat–<i>Triticum aestivum</i>, <i>T</i>. <i>durum</i> and <i>T</i>. <i>dicoccum</i> were screened sequentially at multiple disease hotspots, during the 2011–14 crop seasons, carrying only resistant accessions to the next step of evaluation. Wheat accessions which were found to be resistant in the field were then assayed for seedling resistance and profiled using molecular markers. In the primary evaluation, 19,460 accessions were screened at Wellington (Tamil Nadu), a hotspot for wheat rusts. We identified 4925 accessions to be resistant and these were further evaluated at Gurdaspur (Punjab), a hotspot for stripe rust and at Cooch Behar (West Bengal), a hotspot for spot blotch. The second round evaluation identified 498 accessions potentially resistant to multiple rusts and 868 accessions potentially resistant to spot blotch. Evaluation of rust resistant accessions for seedling resistance against seven virulent pathotypes of three rusts under artificial epiphytotic conditions identified 137 accessions potentially resistant to multiple rusts. Molecular analysis to identify different combinations of genetic loci imparting resistance to leaf rust, stem rust, stripe rust and spot blotch using linked molecular markers, identified 45 wheat accessions containing known resistance genes against all three rusts as well as a QTL for spot blotch resistance. The resistant germplasm accessions, particularly against stripe rust, identified in this study can be excellent potential candidates to be employed for breeding resistance into the background of high yielding wheat cultivars through conventional or molecular breeding approaches, and are expected to contribute toward food security at national and global levels.</p></div

Seedling resistance in wheat accessions.

<p>These genebank accessions were identified as resistant in the primary field evaluation at the hotspots. The seedling resistance was recorded as resistant either to only one rust disease (leaf, stem or stripe) or a combination of two or all the three rust diseases. Seedling resistance screening was carried out under controlled condition at the Regional Station of Indian Institute of Wheat and Barley Research (IIWBR), Flowerdale, Shimla. Accession-wise details are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167702#pone.0167702.s003" target="_blank">S3 Table</a>.</p

Amplicon profile of 137 wheat accessions for SSR marker G<i>wm427</i> linked to <i>Sr13</i>. M = 100bp ladder.

<p>Amplicon profile of 137 wheat accessions for SSR marker G<i>wm427</i> linked to <i>Sr13</i>. M = 100bp ladder.</p

Diversity among rust resistant genotypes based on profiles of linked molecular markers.

<p>Diversity among rust resistant genotypes based on profiles of linked molecular markers.</p

Locations of evaluation experiments of wheat germplasm against rusts and spot blotch.

<p>Primary screening against the three rusts was carried out at Wellington. Subsequent screening for stripe rust resistance was done at Gurdaspur and for spot blotch resistance at Cooch Behar. The seedling resistance assay was carried out at Flowerdale and molecular profiling was done at New Delhi. Base map was generated using DIVA-GIS data (<a href="http://www.diva-gis.org/gdata" target="_blank">www.diva-gis.org/gdata</a>).</p

Results of primary screening of wheat germplasm against three rusts.

<p>Stem: Stem rust; Leaf: Leaf rust; Stripe: Stripe rust S: Susceptible; MS: Moderately susceptible; MR: Moderately resistant; R: Resistant.</p

Experimental layout, flow of germplasm and salient results of the study.

<p>Blue filled boxes denote germplasm at various stages of the experiment. Trapezoids denote screening (green for field evaluation and red for lab assay). Figures and tables containing details corresponding to each stage of the flow are mentioned in italics below boxes.</p

Gene combinations present in 137 wheat accessions.

<p>These wheat accessions were screened for the amplification of markers linked to five <i>Lr</i> genes, three <i>Sr</i> genes, four <i>Yr</i> genes and one spot blotch resistance QTL. Disease reaction recorded at Gurdaspur for yellow rust and at Cooch Behar for spot blotch are also given. R- resistant; MR- Moderately resistant; MS- moderately susceptible, S- susceptible and #N/A—no data.</p