title: Characterization of novel wheat NBS domain-containing sequences and their utilization, in silico, for genome-scale R-gene mining.
abstract: In crop improvement, the isolation, cloning and transfer of disease resistance genes (R-genes) is an ultimate goal usually starting from tentative R-gene analogs (RGAs) that are identified on the basis of their structure. For bread wheat, recent advances in genome sequencing are supporting the efforts of wheat geneticists worldwide. Among wheat R-genes, nucleotide-binding site (NBS)-encoding ones represent a major class. In this study, we have used a polymerase chain reaction-based approach to amplify and clone NBS-type RGAs from a bread wheat cultivar, 'Salambo 80.' Four novel complete ORF sequences showing similarities to previously reported R-genes/RGAs were used for in silico analyses. In a first step, where analyses were focused on the NBS domain, these sequences were phylogenetically assigned to two distinct groups: a first group close to leaf rust Lr21 resistance proteins; and a second one similar to cyst nematode resistance proteins. In a second step, sequences were used as initial seeds to walk up and downstream the NBS domain. This procedure enabled identifying 8 loci ranging in size between 2,115 and 7,653 bp. Ab initio gene prediction identified 8 gene models, among which two had complete ORFs. While GenBank survey confirmed the belonging of sequences to two groups, subsequent characterization using IWGSC genomic and proteomic data showed that the 8 gene models, reported in this study, were unique and their loci matched scaffolds on chromosome arms 1AS, 1BS, 4BS and 1DS. The gene model located on 1DS is a pseudo-Lr21 that was shown to have an NBS-LRR domain structure, while the potential association of the RGAs, here reported, is discussed. This study has produced novel R-gene-like loci and models in the wheat genome and provides the first steps toward further elucidation of their role in wheat disease resistance.
authors.affiliation: Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), Faculté des Sciences de Tunis, Université de Tunis El-Manar, El-Manar, 2092, Tunis, Tunisia, dhia_bouktila2000@yahoo.fr.
authors.forename: Dhia
authors.initials: D
authors.lastname: Bouktila
authors.forename: Yosra
authors.initials: Y
authors.lastname: Habachi-Houimli
authors.forename: Yosra
authors.initials: Y
authors.lastname: Khalfallah
authors.forename: Maha
authors.initials: M
authors.lastname: Mezghani-Khemakhem
authors.forename: Mohamed
authors.initials: M
authors.lastname: Makni
authors.forename: Hanem
authors.initials: H
authors.lastname: Makni
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics*; D003001:Cloning, Molecular; D017931:DNA Primers / Q000235:genetics; D015723:Gene Library; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D008969:Molecular Sequence Data; D010802:Phylogeny; D010935:Plant Diseases / Q000276:immunology*; D057865:Plant Immunity; D010940:Plant Proteins / Q000235:genetics*; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D014908:Triticum / Q000235:genetics* / Q000276:immunology
chemical_list: D017931:DNA Primers; D010940:Plant Proteins