Coding Mutations in Vacuolar Protein-Sorting 4 AAA+ ATPase Endosomal Sorting Complexes Required for Transport Protein Homologs Underlie bc-2 and New bc-4 Gene Conferring Resistance to Bean Common Mosaic Virus in Common Bean

The alleles bc-ud and bc-ur (previously bc-4 gene), representing coding mutations within Vps4 AAA+ ATPase ESCRT protein, interact with other genes to condition resistance to BCMV and BCMNV in common bean

Bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV) have a damaging impact on global common bean (Phaseolus vulgaris L.) cultivation, causing potential yield losses of over 80%. The primary strategy for controlling these viruses is through host plant resistance. This research aimed to identify and validate structural variations for the bc-ud gene as revealed by long-read sequencing, develop an efficient DNA marker to assist selection of bc-ud in snap and dry beans, and examine the interactions between the bc-ud allele and other BCMV resistance genes. A gene (Phvul.005G125100) model on chromosome Pv05, encoding a vacuolar protein-sorting 4 (Vps4) AAA+ ATPase endosomal sorting complexes required for transport (ESCRT) protein, was identified as the best candidate gene for bc-ud. An 84-bp repetitive insertion variant within the gene, exhibited 100% co-segregation with the bc-ud resistance allele across 264 common bean accessions. The 84-bp repetitive insertion was labeled with an indel marker IND_05_36225873 which was useful for tracking the bc-ud allele across diverse germplasm. A different single nucleotide polymorphism variant within the same candidate gene was associated with the bc-4 gene. Segregation in F2 populations confirmed bc-ud and bc-4 were alleles, so bc-4 was renamed bc-ur to fit gene nomenclature guidelines. The interactions of bc-ud and bc-ur with other resistance genes, such as bc-1 (receptor-like kinase on Pv03) and bc-2 (Vps4 AAA+ ATPase ESCRT protein on Pv11), validated gene combinations in the differential "host groups" effective against specific BCMV/BCMNV "pathogroups." These findings increase our understanding of the Bc-u locus, and enhance our ability to develop more resilient bean varieties through marker-assisted selection, reducing the impact of BCMV and BCMNV.

A natural substitution of a conserved amino acid in eIF4E confers resistance against multiple potyviruses

Eukaryotic translation initiation factor 4E (eIF4E), which plays a pivotal role in initiating translation in eukaryotic organisms, is often hijacked by the viral genome-linked protein to facilitate the infection of potyviruses. In this study, we found that the naturally occurring amino acid substitution D71G in eIF4E is widely present in potyvirus-resistant watermelon accessions and disrupts the interaction between watermelon eIF4E and viral genome-linked protein of papaya ringspot virus-watermelon strain, zucchini yellow mosaic virus or watermelon mosaic virus. Multiple sequence alignment and protein modelling showed that the amino acid residue D71 located in the cap-binding pocket of eIF4E is strictly conserved in many plant species. The mutation D71G in watermelon eIF4E conferred resistance against papaya ringspot virus-watermelon strain and zucchini yellow mosaic virus, and the equivalent mutation D55G in tobacco eIF4E conferred resistance to potato virus Y. Therefore, our finding provides a potential precise target for breeding plants resistant to multiple potyviruses.

Genetic variation in a tepary bean (Phaseolus acutifolius A. Gray) diversity panel reveals loci associated with biotic stress resistance

Tepary bean (Phaseolus acutifolius A. Gray), indigenous to the arid climates of northern Mexico and the Southwest United States, diverged from common bean (Phaseolus vulgaris L.), approximately 2 million years ago and exhibits a wide range of resistance to biotic stressors. The tepary genome is highly syntenic to the common bean genome providing a foundation for discovery and breeding of agronomic traits between these two crop species. Although a limited number of adaptive traits from tepary bean have been introgressed into common bean, hybridization barriers between these two species required the development of bridging lines to alleviate this barrier. Thus, to fully utilize the extant tepary bean germplasm as both a crop and as a donor of adaptive traits, we developed a diversity panel of 422 cultivated, weedy, and wild tepary bean accessions which were then genotyped and phenotyped to enable population genetic analyses and genome-wide association studies for their response to a range of biotic stressors. Population structure analyses of the panel revealed eight subpopulations and the differentiation of botanical varieties within P. acutifolius. Genome-wide association studies revealed loci and candidate genes underlying biotic stress resistance including quantitative trait loci for resistance to weevils, common bacterial blight, Fusarium wilt, and bean common mosaic necrosis virus that can be harnessed not only for tepary bean but also common bean improvement.

Plant eIF4E isoforms as factors of susceptibility and resistance to potyviruses

Potyviruses are the largest group of plant-infecting RNA viruses that affect a wide range of crop plants. Plant resistance genes against potyviruses are often recessive and encode translation initiation factors eIF4E. The inability of potyviruses to use plant eIF4E factors leads to the development of resistance through a loss-of-susceptibility mechanism. Plants have a small family of eIF4E genes that encode several isoforms with distinct but overlapping functions in cell metabolism. Potyviruses use distinct eIF4E isoforms as susceptibility factors in different plants. The role of different members of the plant eIF4E family in the interaction with a given potyvirus could differ drastically. An interplay exists between different members of the eIF4E family in the context of plant-potyvirus interactions, allowing different eIF4E isoforms to modulate each other's availability as susceptibility factors for the virus. In this review, possible molecular mechanisms underlying this interaction are discussed, and approaches to identify the eIF4E isoform that plays a major role in the plant-potyvirus interaction are suggested. The final section of the review discusses how knowledge about the interaction between different eIF4E isoforms can be used to develop plants with durable resistance to potyviruses.

A novel study on bean common mosaic virus accumulation shows disease resistance at the initial stage of infection in Phaseolus vulgaris

Accurate and early diagnosis of bean common mosaic virus (BCMV) in Phaseolus vulgaris tissues is critical since the pathogen can spread easily and have long-term detrimental effects on bean production. The use of resistant varieties is a key factor in the management activities of BCMV. The study reported here describes the development and application of a novel SYBR Green-based quantitative real-time PCR (qRT-PCR) assay targeting the coat protein gene to determine the host sensitivity to the specific NL-4 strain of BCMV. The technique showed high specificity, validated by melting curve analysis, without cross-reaction. Further, the symptoms development of twenty advanced common bean genotypes after mechanical BCMV-NL-4 infection was evaluated and compared. The results showed that common bean genotypes exhibit varying levels of host susceptibility to this BCMV strain. The YLV-14 and BRS-22 genotypes were determined as the most resistant and susceptible genotypes, respectively, in terms of aggressiveness of symptoms. The accumulation of BCMV was analyzed in the resistant and susceptible genotypes 3, 6, and 9 days following the inoculation by the newly developed qRT-PCR. The mean cycle threshold (Ct) values showed that the viral titer was significantly lower in YLV-14, which was evident in both root and leaf 3 days after the inoculation. The qRT-PCR thus facilitated an accurate, specific, and feasible assessment of BCMV accumulation in bean tissues even in low virus titers, allowing novel clues in selecting resistant genotypes in the early stages of infection, which is critical for disease management. To the best of our knowledge, this is the first study of a successfully performed qRT-PCR to estimate BCMV quantification.

A single substitution in Vacuolar protein sorting 4 is responsible for resistance to Watermelon mosaic virus in melon

In plants, introgression of genetic resistance is a proven strategy for developing new resistant lines. While host proteins involved in genome replication and cell to cell movement are widely studied, other cell mechanisms responsible for virus infection remain under investigated. Endosomal sorting complexes required for transport (ESCRT) play a key role in membrane trafficking in plants and are involved in the replication of several plant RNA viruses. In this work, we describe the role of the ESCRT protein CmVPS4 as a new susceptibility factor to the Potyvirus Watermelon mosaic virus (WMV) in melon. Using a worldwide collection of melons, we identified three different alleles carrying non-synonymous substitutions in CmVps4. Two of these alleles were shown to be associated with WMV resistance. Using a complementation approach, we demonstrated that resistance is due to a single non-synonymous substitution in the allele CmVps4P30R. This work opens up new avenues of research on a new family of host factors required for virus infection and new targets for resistance.

Exploring New Routes for Genetic Resistances to Potyviruses: The Case of the Arabidopsis thaliana Phosphoglycerates Kinases (PGK) Metabolic Enzymes

The development of recessive resistance by loss of susceptibility is a consistent strategy to combat and limit damages caused by plant viruses. Susceptibility genes can be turned into resistances, a feat that can either be selected among the plant’s natural diversity or engineered by biotechnology. Here, we summarize the current knowledge on the phosphoglycerate kinases (PGK), which have emerged as a new class of susceptibility factors to single-stranded positive RNA viruses, including potyviruses. PGKs are metabolic enzymes involved in glycolysis and the carbon reduction cycle, encoded by small multigene families in plants. To fulfil their role in the chloroplast and in the cytosol, PGKs genes encode differentially addressed proteins. Here, we assess the diversity and homology of chloroplastic and cytosolic PGKs sequences in several crops and review the current knowledge on their redundancies during plant development, taking Arabidopsis as a model. We also show how PGKs have been shown to be involved in susceptibility—and resistance—to viruses. Based on this knowledge, and drawing from the experience with the well-characterized translation initiation factors eIF4E, we discuss how PGKs genes, in light of their subcellular localization, function in metabolism, and susceptibility to viruses, could be turned into efficient genetic resistances using genome editing techniques.