Abstract
Pathogens are among the most limiting factors for crop success and expansion. Thus, finding the underlying genetic cause of pathogen resistance is the main goal for plant geneticists. The activation of a plant’s immune system is mediated by the presence of specific receptors known as disease-resistance genes (R genes). Typical R genes encode functional immune receptors with nucleotide-binding sites (NBS) and leucine-rich repeat (LRR) domains, making the NBS-LRRs the largest family of plant resistance genes. Establishing host resistance is crucial for plant growth and crop yield but also for reducing pesticide use. In this regard, pyramiding R genes is thought to be the most ecologically friendly way to enhance the durability of resistance. To accomplish this, researchers must first identify the related genes, or linked markers, within the genomes. However, the duplicated nature, with the presence of frequent paralogues, and clustered characteristic of NLRs make them difficult to predict with the classic automatic gene annotation pipelines. In the last several years, efforts have been made to develop new methods leading to a proliferation of reports on cloned genes. Herein, we review the bioinformatic tools to assist the discovery of R genes in plants, focusing on well-established pipelines with an important computer-based component.
Highlights
Crops have long been experiencing an increase in the frequency and range of pests and diseases they are exposed to [1]
This mainly applies to the nucleotide-binding sites (NBS) domains, and not so much to the leucine-rich repeat (LRR) domains involved in pathogen recognition
The recovered genomic fragments were paired-end sequenced with Illumina technology, de novo assembled in contigs, and searched in for specific sequence motifs putatively characteristic of NB-LRR proteins [41], using a Motif Alignment and Search Tool (MAST) sequence homology search algorithm [39]
Summary
Crops have long been experiencing an increase in the frequency and range of pests and diseases they are exposed to [1]. Race-specific resistance relies on molecules with antimicrobial properties, such as secondary metabolites, and molecules that trigger a hypersensitive response, leading to rapid cell death in response to infection with an avirulent pathogen [4] This R-gene mediated response prevents the spread of the infection. A comprehensive collection of experimentally validated plant NLRs has been recently gathered and contains 442 NLRs from 31 different genera [6] Within the genomes, they typically appear in clusters, which contain several copies of high-homologous duplicated genes. On one hand, the NLR gene sequences tend to be highly conserved among plant species This mainly applies to the NBS domains, and not so much to the LRR domains involved in pathogen recognition. We briefly outline traditional map-based approaches to clone resistance genes, followed by a more extensive review on novel methods with an important high-throughput data analysis component
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
