Isolation and Characterization of Nucleotide-Binding Site Resistance Gene Homologues in Common Bean (Phaseolus vulgaris)

Abstract

Common bean production is constrained by many fungal, viral, and bacterial pathogens. Thus, the identification of resistance (R) genes is an important focal point of common bean research. The main goal of our study was to identify resistance gene homologues (RGH) in the crop, using degenerate primers designed from conserved sequences in the nucleotide-binding site (NBS) domains of R-genes from the model legume Medicago truncatula. Total DNA of the Andean common bean genotype G19833 was used for amplification of over 500 primer combinations. Sequencing of amplicons showed that 403 cloned fragments had uninterrupted open reading frames and were considered representative of functional RGH genes. The sequences were grouped at two levels of nucleotide identity (90 and 80%) and representative sequences of each group were used for phylogenetic analyses. The RGH sequence diversity of common bean was divided into TIR and non-TIR families, each with different clusters. The TIR sequences grouped into 14 clades while non-TIR sequences grouped into seven clades. Pairwise comparisons showed purifying selection, although some sequences may have been the result of diversifying selection. Knowledge about RGH genes in common bean can allow the design of molecular markers for pyramiding of resistance genes against various pathogens.

Differentially Expressed Genes in Resistant and Susceptible Common Bean (Phaseolus vulgaris L.) Genotypes in Response to Fusarium oxysporum f. sp. phaseoli

“…Most plant disease resistance ( R ) genes known today encode proteins with a central nucleotide binding site (NBS) and a C-terminal Leu-rich repeat (LRR) domain and this is also the case in common beans[ 48 , 49 , 50 ]. Interestingly, only one R gene-like gene was discovered in this study with those domains although one PK-LRR gene was discovered as described above.…”

Genome-Wide Association Study Identifies NBS-LRR-Encoding Genes Related with Anthracnose and Common Bacterial Blight in the Common Bean

“…In addition, the bean common mosaic virus resistance I gene is located on Pv02 containing a cluster of NBS-LRR-type genes (Vallejos et al, 2006 ). Many TIR and non-TIR sequences in the common bean were obtained from conserved sequences in the NBS domains of Medicago truncatula (Garzon et al, 2013 ). In conclusion, information on NBS genes in the common bean is limited.…”

Common bean reaction to angular leaf spot comprises transcriptional modulation of genes in the ALS10.1 QTL

“…Common bean R genes can be divided into TIR and non-TIR classes (Liu et al, 2012; Garzón et al, 2013), where members of the non-TIR class are found mostly in the chromosomes Pv04 and Pv11, and members of the TIR class are found mainly in Pv10 (Schmutz et al, 2014). Although TIR-NB-ARC proteins are found in all bean chromosomes, they are overrepresented on Pv10 and most of them (51.1%) are coded from genes in the ALS10.1 locus, highlighting the importance of this subfamily of R genes in the common bean response to P. griseola .…”