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

Abstract

Nucleotide-binding site and leucine-rich repeat (NBS-LRR) genes represent the largest and most important disease resistance genes in plants. The genome sequence of the common bean (Phaseolus vulgaris L.) provides valuable data for determining the genomic organization of NBS-LRR genes. However, data on the NBS-LRR genes in the common bean are limited. In total, 178 NBS-LRR-type genes and 145 partial genes (with or without a NBS) located on 11 common bean chromosomes were identified from genome sequences database. Furthermore, 30 NBS-LRR genes were classified into Toll/interleukin-1 receptor (TIR)-NBS-LRR (TNL) types, and 148 NBS-LRR genes were classified into coiled-coil (CC)-NBS-LRR (CNL) types. Moreover, the phylogenetic tree supported the division of these PvNBS genes into two obvious groups, TNL types and CNL types. We also built expression profiles of NBS genes in response to anthracnose and common bacterial blight using qRT-PCR. Finally, we detected nine disease resistance loci for anthracnose (ANT) and seven for common bacterial blight (CBB) using the developed NBS-SSR markers. Among these loci, NSSR24, NSSR73, and NSSR265 may be located at new regions for ANT resistance, while NSSR65 and NSSR260 may be located at new regions for CBB resistance. Furthermore, we validated NSSR24, NSSR65, NSSR73, NSSR260, and NSSR265 using a new natural population. Our results provide useful information regarding the function of the NBS-LRR proteins and will accelerate the functional genomics and evolutionary studies of NBS-LRR genes in food legumes. NBS-SSR markers represent a wide-reaching resource for molecular breeding in the common bean and other food legumes. Collectively, our results should be of broad interest to bean scientists and breeders.

North-Western Himalayan Common Beans: Population Structure and Mapping of Quantitative Anthracnose Resistance Through Genome Wide Association Study

“…Hence, in recent years, use of GWAS for mapping economically important QTLs in agricultural crops has increased and P. vulgaris is not behind. Many QTLs having economic importance in common bean have been mapped using a GWAS approach ( Moghaddam et al, 2016 ; Wu et al, 2017 ; Kelly and Bornowski, 2018 ; Kamfwa et al, 2019 ; Bisneta and Gonçalves-Vidigal, 2020 ; Bornowski et al, 2020 ; Gonçalves-Vidigal et al, 2020 ; Mungalu et al, 2020 ). In the present study, significant differences observed in NW Indian bean genotypes led to the identification of SNPs associated with the anthracnose resistance.…”

“…Most of the plant disease resistance genes belong to the NBS-LRR class and play a significant roles in plant disease resistance ( Jones and Dangl, 2006 ; Padder, 2014 ). The common bean genome also contains NBS-LRR regions that are distributed across all chromosomes ( Ferrier-Cana et al, 2003 ; Richard et al, 2017 ; Wu et al, 2017 ) and a recent GWAS study showed associations between these NBS-LRR regions with anthracnose resistance ( Wu et al, 2017 ). Anthracnose resistance genes Co-3 and its alleles, Co-16 are mapped to common bean Pv04 and this study also found association of SNPs on Pv04 with anthracnose resistance to races 3, 87, and 503 ( Geffroy et al, 1999 ; David et al, 2008 ; Coimbra-Gonçalves et al, 2016 ; Murube et al, 2019 ).…”

“…Recently, a major QTL for anthracnose resistance against race 1545 was mapped to Pv05 with candidate gene Phvul.005G117900 that encodes a NBS-LRR protein ( Gonzalez et al, 2015 ). Genome wide association studies (GWAS) showed association of a SNP and SSR marker located at Pv10 with anthracnose resistance ( Zuiderveen et al, 2016 ; Wu et al, 2017 ). Access to P. vulgaris whole genome ( Schmutz et al, 2014 ; Vlasova et al, 2016 ) and SNP Bean Chips ( Hyten et al, 2010 ; Song et al, 2015 ) has resulted in the fine mapping of many economically important traits in beans including anthracnose resistance ( Richard et al, 2014 ; Burt et al, 2015 ; Gonzalez et al, 2015 ; Oblessuc et al, 2015 ; Padder et al, 2016 ; Zuiderveen et al, 2016 ; Chen et al, 2017 ; de Lima Castro et al, 2017 ; Mungalu et al, 2020 ).…”

Genetic Variation of Landraces of Common Bean Varying for Seed Coat Glossiness and Disease Resistance: Valuable Resources for Conservation and Breeding

“…SAB carries the dominant allele Asp, which confers the intense glossy aspect of the seed coat, while SAF has a dull seed coat [12] (Figure 1A). This gene is known to be located in chromosome 7 [15], where genes associated with anthracnose and angular leaf spot resistance [16,17], common bacterial blight [17] and nodulation [18] are also located.…”

Common bean resistance to Xanthomonas is associated with upregulation of the salicylic acid pathway and downregulation of photosynthesis

“…However, to our knowledge, transcriptomic studies during X. phaseoli pv. phaseoli infection are limited to a cDNA-AFLP analysis [46] and qRT-PCR assays focused on R genes [47,48]. Previous work using X. phaseoli pv.…”