Genome-wide identification and characterization of NB-ARC resistant genes in wheat (Triticum aestivum L.) and their expression during leaf rust infection

Abstract

NB-ARC domain-containing resistance genes from the wheat genome were identified, characterized and localized on chromosome arms that displayed differential yet positive response during incompatible and compatible leaf rust interactions. Wheat (Triticum aestivum L.) is an important cereal crop; however, its production is affected severely by numerous diseases including rusts. An efficient, cost-effective and ecologically viable approach to control pathogens is through host resistance. In wheat, high numbers of resistance loci are present but only few have been identified and cloned. A comprehensive analysis of the NB-ARC-containing genes in complete wheat genome was accomplished in this study. Complete NB-ARC encoding genes were mined from the Ensembl Plants database to predict 604 NB-ARC containing sequences using the HMM approach. Genome-wide analysis of orthologous clusters in the NB-ARC-containing sequences of wheat and other members of the Poaceae family revealed maximum homology with Oryza sativa indica and Brachypodium distachyon. The identification of overlap between orthologous clusters enabled the elucidation of the function and evolution of resistance proteins. The distributions of the NB-ARC domain-containing sequences were found to be balanced among the three wheat sub-genomes. Wheat chromosome arms 4AL and 7BL had the most NB-ARC domain-containing contigs. The spatio-temporal expression profiling studies exemplified the positive role of these genes in resistant and susceptible wheat plants during incompatible and compatible interaction in response to the leaf rust pathogen Puccinia triticina. Two NB-ARC domain-containing sequences were modelled in silico, cloned and sequenced to analyze their fine structures. The data obtained in this study will augment isolation, characterization and application NB-ARC resistance genes in marker-assisted selection based breeding programs for improving rust resistance in wheat.

QTL Mapping of Web Blotch Resistance in Peanut by High-throughput Genome-wide Sequencing

“…The 41 candidate genes covered by the intervals of qWBRA04 and qWBRA14 included 21 TIR-NBS-LRR and 3 CC-NBS-LRR, which are the two well-known R gene types [25]. Also, there were two candidate genes encoded LRR and NB-ARC (nucleotide-binding domain shared with APAF-1, various R-proteins and CED-4) domain, which also encoded resistance genes [26]. The rest genes located in the target region encoding proteins contain disease resistance response related domains but could not assigned to the well-known R-gene types for eight of them, and the other seven with indirect functions for resistances or downstream of resistant signaling pathways (Table 3).…”

Exploring sources of resistance to brown rot in an interspecific almond × peach population

“…Finally, using The Genome Database for Rosaceae (GDR) it was possible to identify genes of interest in silico . Within the position of markers for the QTLs for non‐wounded incidence trait located on G4 (9 947 470–16 076 720 bp), the NB‐ARC domain‐containing disease resistance protein involved in regulation of programmed cell death was retrieved . In the same chromosome: there are candidate genes encoding endopolygalacturonases (endo‐PGs).…”

“…Within the position of markers for the QTLs for non-wounded incidence trait located on G4 (9 947 470-16 076 720 bp), the NB-ARC domain-containing disease resistance protein involved in regulation of programmed cell death was retrieved. 50,51 In the same chromosome: there are candidate genes encoding endopolygalacturonases (endo-PGs). The plant cell wall has three main components: cellulose, hemicellulose, and pectin, that necrotrophic pathogens break down and utilize as nutrients.…”

QTL Mapping of Web Blotch Resistance in Peanut by High-throughput Genome-wide Sequencing

“…The 40 candidate genes covered by the intervals of qWBRA04 and qWBRA14 included 21 TIR-NBS-LRR and 3 CC-NBS-LRR, which are the two well-known R gene types [32]. Also, there were two candidate genes encoded LRR and NB-ARC (nucleotide-binding domain shared with APAF-1, various R-proteins and CED-4) domain, which also encoded resistance genes [33]. Among the remained 15 genes, seven of them function in the downstream pathways of resistant signaling, the other eight encoded proteins contain disease resistance response related domains but could not assigned to the well-known R-gene types ( Table 3).…”