NAC Candidate Gene Marker for bgm-1 and Interaction With QTL for Resistance to Bean Golden Yellow Mosaic Virus in Common Bean

Abstract

Genetic resistance is the primary means for control of Bean golden yellow mosaic virus (BGYMV) in common bean (Phaseolus vulgaris L.). Breeding for resistance is difficult because of sporadic and uneven infection across field nurseries. We sought to facilitate breeding for BGYMV resistance by improving marker-assisted selection (MAS) for the recessive bgm-1 gene and identifying and developing MAS for quantitative trait loci (QTL) conditioning resistance. Genetic linkage mapping in two recombinant inbred line populations and genome-wide association study (GWAS) in a large breeding population and two diversity panels revealed a candidate gene for bgm-1 and three QTL BGY4.1, BGY7.1, and BGY8.1 on independent chromosomes. A mutation (5 bp deletion) in a NAC (No Apical Meristem) domain transcriptional regulator superfamily protein gene Phvul.003G027100 on chromosome Pv03 corresponded with the recessive bgm-1 resistance allele. The five bp deletion in exon 2 starting at 20 bp (Pv03: 2,601,582) is expected to cause a stop codon at codon 23 (Pv03: 2,601,625), disrupting further translation of the gene. A Tm-shift assay marker named PvNAC1 was developed to track bgm-1. PvNAC1 corresponded with bgm-1 across ∼1,000 lines which trace bgm-1 back to a single landrace “Garrapato” from Mexico. BGY8.1 has no effect on its own but exhibited a major effect when combined with bgm-1. BGY4.1 and BGY7.1 acted additively, and they enhanced the level of resistance when combined with bgm-1. Tm-shift assay markers were generated for MAS of the QTL, but their effectiveness requires further validation.

Genome-Wide Association Mapping of bc-1 and bc-u Reveals Candidate Genes and New Adjustments to the Host-Pathogen Interaction for Resistance to Bean Common Mosaic Necrosis Virus in Common Bean

“…Candidate gene analysis of targeted traits is facilitated by new molecular tools for common bean, including millions of SNPs identified by resequencing genotypes and diversity panels ( Cichy et al, 2015 ; Moghaddam et al, 2016 ; Lobaton et al, 2018 ; Wallace et al, 2018 ; Oladzad et al, 2019 ; Diaz et al, 2020 ; Wu et al, 2020 ), 6 and 12 K SNP BeadChip assays ( Song et al, 2015 ; Miklas et al, 2020 ), and assembled bean genomes representing different gene pools, such as the Andean G19833 landrace (Chaucha Chuga; Schmutz et al, 2014 ) and “UI-111” cultivar for race Durango (DDP). These genomic tools contributed to candidate gene discovery for several traits in common bean, including the NAC candidate gene for bgm-1 resistance to Bean golden yellow mosaic virus (BGYMV; Soler-Garzón et al, 2021 ), a bHLH transcription factor for the seed pigment P gene ( McClean et al, 2018 ), and truncated CRINKLY4 kinase acting as a decoy to condition Co-x anthracnose resistance ( Richard et al, 2021 ).…”

Resistant Sources and Genetic Control of Resistance to ToLCNDV in Cucumber

“…Thus, the candidate region identified here may be in a different region, associated with different resistance genes. Among the list of annotated genes in the candidate region of cucumber chromosome 2 ( Table S3 ), there are three LRR receptor-like serine/threonine-protein kinases (CsGy2G012160, CsGy2G015920, and CsGy2G016150) implicated in resistance to ToLCNDV and other geminiviruses [ 56 , 57 , 58 , 59 ], four NAC domain transcription factors (CsGy2G015830, CsGy2G016100, CsGy2G016110, and CsGy2G016220), gene family associated with an increase in tomato plant susceptibility during ToLCNDV infection and resistance to a begomovirus in common bean ( Phaseolus vulgaris L.) [ 60 , 61 ], and an RNA-directed DNA methylation protein (CsGy2G016290.1), one of the components of the RNA silencing pathway used against plant viruses in the defense response [ 62 ]. More interestingly, a 26S proteasome non-ATPase regulatory subunit 12 (CsGy2G015260) is included in this region.…”

Rendimiento y resistencia al mosaico amarillo dorado de genotipos de frijol negro tropical

“…El hecho de que líneas carentes del MM SR2 hayan sobresalido por su mayor rendimiento en condiciones de presión de mosaico amarillo dorado, en comparación con las líneas que poseen este marcador, destaca la importancia de confirmar la resistencia mediante la confrontación con el patógeno, ya que si bien, bgm-1 es el gen más ampliamente usado, el MM SR2, según los estándares actuales, no está estrechamente ligado a este gen (~3-7 cM), lo que resulta en la selección de unas pocas líneas que poseen el marcador, pero que no obstante, son susceptibles al virus, además de que existen otros genes y QTLs cuya acumulación condiciona altos niveles de resistencia a BGYMV (Soler-Garzón et al, 2021), así como otros mecanismos de resistencia al vector, como la antibiosis o antixenosis (Santos et al, 2020), cuya presencia en los materiales evaluados requiere ser estudiada.…”

“…Esta enfermedad se presenta desde 1977 en Veracruz, Chiapas, Yucatán, Tamaulipas y en las Huastecas (Cuéllar y Morales, 2006), tanto en las siembras de temporal, como de humedad residual, y puede provocar hasta 100% de pérdidas en el rendimiento cuando se presenta desde la fase vegetativa del cultivo (Villar et al, 2003). El control de BGYMV se ha enfocado al desarrollo de variedades resistentes (Morales y Anderson, 2001;Soler-Garzón et al, 2021).…”