The presence of seed color in common bean (Phaseolus vulgaris) requires the dominantacting P (pigment) gene, and white seed is a recessive phenotype in all domesticated races of the species. P was ...classically associated with seed size, thus describing it as the first genetic marker for a quantitative trait. The molecular structure of P was characterized to understand the selection of white seeds during bean diversification and the relationship of P to seed weight.
P was identified by homology searches, a genome-wide association study (GWAS) and gene remodeling, and confirmed by gene silencing. Allelic variation was assessed by a combination of resequencing and marker development, and the relationship between P and seed weight was assessed by a GWAS study.
P is a member of clade B of subclass IIIf of plant basic helix–loop–helix (bHLH) proteins. Ten race-specific P alleles conditioned the white seed phenotype, and each causative mutation affected at least one bHLH domain required for color expression. GWAS analysis confirmed the classic association of P with seed weight.
In common bean, white seeds are the result of convergent evolution and, among plant species, orthologous convergence on a single transcription factor gene was observed.
Understanding and anticipating the impacts of climate change on plant-pathogen interactions are a major challenge for the agriculture of the 21st century. Prediction models forecast an increase in ...atmospheric carbon dioxide (CO2) levels by 2100 that could reach 1045 ppm. Plant physiology is directly affected by an increase of atmospheric CO2 as plants are living organisms that consume CO2 through photosynthesis to produce organic matter. Since the early days of agriculture, plant diseases can alter not only quality of plant productions but can also be responsible for important yield losses. Plant viruses are obligate, acellular pathogens that cause serious epidemics in major agricultural crops with annual yield losses of more than $ 30 billion. As elevated concentration of atmospheric CO2 (eCO2) modulates plant primary and secondary metabolisms and as viruses are obligate pathogens, it is likely that eCO2 can modulate plant molecular defenses to viruses. In that context, the present review focuses on the effect of eCO2 on plant physiological and molecular responses to virus infections. First, we will compare the different experimental methodologies used to study the impact of eCO2 enrichment on plant-virus interactions and discuss the different designs applied for experiments. We will also present the impact of eCO2 on virus-infection parameters in infected plants and describe the impact of combined abiotic stresses, including eCO2 and temperature, on plant-virus interactions.
•We present the different experimental methodologies used to study the impact of eCO2 enrichment on plant-virus interactions.•We emphasize the impact of eCO2 on plant physiological and molecular responses to virus infections.•Data from the literature show that the impact of eCO2 appears to be dependent on the studied plant/virus pathosystem.•We also present the impact of combined abiotic stresses, including eCO2 and temperature, on plant-virus interactions.•Limited research work is available on the impact of eCO2 / combined abiotic stresses on plant molecular responses to virus.
Plants are under strong evolutionary pressure to maintain surveillance against pathogens. One major disease resistance mechanism is based on NB-LRR (NLR) proteins that specifically recognize pathogen ...effectors. The cluster organization of the NLR gene family could favor sequence exchange between NLR genes via recombination, favoring their evolutionary dynamics. Increasing data, based on progeny analysis, suggest the existence of a link between the perception of biotic stress and the production of genetic diversity in the offspring. This could be driven by an increased rate of meiotic recombination in infected plants, but this has never been strictly demonstrated. In order to test if pathogen infection can increase DNA recombination in pollen meiotic cells, we infected
Fluorescent Tagged Lines (FTL) with the virulent bacteria
. We measured the meiotic recombination rate in two regions of chromosome 5, containing or not an NLR gene cluster. In all tested intervals, no significant difference in genetic recombination frequency between infected and control plants was observed. Although it has been reported that pathogen exposure can sometimes increase the frequency of recombinant progeny in plants, our findings suggest that meiotic recombination rate in
may be resilient to at least some pathogen attack. Alternative mechanisms are discussed.
Anthracnose, white mold, powdery mildew, and root rot caused by Colletotrichum lindemuthianum , Scletorinia sclerotiorum , Erysiphe spp., and Pythium ultimum , respectively, are among the most ...frequent diseases that cause significant production losses worldwide in common bean ( Phaseolus vulgaris L.). Reactions against these four fungal diseases were investigated under controlled conditions using a diversity panel of 311 bean lines for snap consumption (Snap bean Panel). The genomic regions involved in these resistance responses were identified based on a genome-wide association study conducted with 16,242 SNP markers. The highest number of resistant lines was observed against the three C. lindemuthianum isolates evaluated: 156 lines were resistant to CL124 isolate, 146 lines resistant to CL18, and 109 lines were resistant to C531 isolate. Two well-known anthracnose resistance clusters were identified, the Co-2 on chromosome Pv11 for isolates CL124 and CL18, and the Co-3 on chromosome Pv04 for isolates CL124 and C531. In addition, other lesser-known regions of anthracnose resistance were identified on chromosomes Pv02, Pv06, Pv08, and Pv10. For the white mold isolate tested, 24 resistant lines were identified and the resistance was localized to three different positions on chromosome Pv08. For the powdery mildew local isolate, only 12 resistant lines were identified, and along with the two previous resistance genes on chromosomes Pv04 and Pv11, a new region on chromosome Pv06 was also identified. For root rot caused by Pythium , 31 resistant lines were identified and two main regions were located on chromosomes Pv04 and Pv05. Relevant information for snap bean breeding programs was provided in this work. A total of 20 lines showed resistant or intermediate responses against four or five isolates, which can be suitable for sustainable farm production and could be used as resistance donors. Potential genes and genomic regions to be considered for targeted improvement were provided, including new or less characterized regions that should be validated in future works. Powdery mildew disease was identified as a potential risk for snap bean production and should be considered a main goal in breeding programs.
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•Common bean is an agronomically relevant crop that is infected by many viruses.•Many dominant or recessive resistance genes that confer resistance to viruses have been identified in ...common bean.•Resistance phenotypes to viruses in common bean vary from extreme resistance to local or systemic necrosis.•Temperature variation is an important factor that may influence resistance phenotypes.•Common bean is good plant model to study plant-virus interactions at a molecular level.
Viruses are obligate parasites that replicate intracellularly in many living organisms, including plants. Consequently, no chemicals are available that target only the virus without impacting host cells or vector organisms. The use of natural resistant varieties appears as the most reliable control strategy and remains the best and cheapest option in managing virus diseases, especially in the current ecological context of preserving biodiversity and environment in which the use of phytosanitary products becomes limited. Common bean is a grain legume cultivated mainly in Africa and Central-South America. Virus diseases of common bean have been extensively studied both by breeders to identify natural resistance genes in existing germplasms and by pathologists to understand the molecular bases of plant-virus interactions. Here we present a critical review in which we synthesize previous and recent information concerning 1) main viruses causing diseases in common bean, 2) genetic resistance to viruses in common bean, 3) the different resistance phenotypes observed and more particularly the effect of temperature, 4) the molecular bases of resistance genes to viruses in common bean, and 5) future prospects using transgenic-engineered resistant lines.
Powdery mildew is one of the most important diseases of flax and is particularly prejudicial to its yield and oil or fiber quality. This disease, caused by the obligate biotrophic ascomycete
Oïdium ...lini
, is progressing in France. Genetic resistance of varieties is critical for the control of this disease, but very few resistance genes have been identified so far. It is therefore necessary to identify new resistance genes to powdery mildew suitable to the local context of pathogenicity. For this purpose, we studied a worldwide diversity panel composed of 311 flax genotypes both phenotyped for resistance to powdery mildew resistance over 2 years of field trials in France and resequenced. Sequence reads were mapped on the CDC Bethune reference genome revealing 1,693,910 high-quality SNPs, further used for both population structure analysis and genome-wide association studies (GWASs). A number of four major genetic groups were identified, separating oil flax accessions from America or Europe and those from Asia or Middle-East and fiber flax accessions originating from Eastern Europe and those from Western Europe. A number of eight QTLs were detected at the false discovery rate threshold of 5%, located on chromosomes 1, 2, 4, 13, and 14. Taking advantage of the moderate linkage disequilibrium present in the flax panel, and using the available genome annotation, we identified potential candidate genes. Our study shows the existence of new resistance alleles against powdery mildew in our diversity panel, of high interest for flax breeding program.
The B4 resistance (R) gene cluster is one of the largest clusters known in common bean (Phaseolus vulgaris Pv). It is located in a peculiar genomic environment in the subtelomeric region of the short ...arm of chromosome 4, adjacent to two heterochromatic blocks (knobs). We sequenced 650 kb spanning this locus and annotated 97 genes, 26 of which correspond to Coiled-Coil-Nucleotide-Binding-Site-Leucine-Rich-Repeat (CNL). Conserved microsynteny was observed between the Pv B4 locus and corresponding regions of Medicago truncatula and Lotus japonicus in chromosomes Mt6 and Lj2, respectively. The notable exception was the CNL sequences, which were completely absent in these regions. The origin of the Pv B4-CNL sequences was investigated through phylogenetic analysis, which reveals that, in the Pv genome, paralogous CNL genes are shared among nonhomologous chromosomes (4 and 11). Together, our results suggest that Pv B4-CNL was derived from CNL sequences from another cluster, the Co-2 cluster, through an ectopic recombination event. Integration of the soybean (Glycine max) genome data enables us to date more precisely this event and also to infer that a single CNL moved from the Co-2 to the B4 cluster. Moreover, we identified a new 528-bp satellite repeat, referred to as khipu, specific to the Phaseolus genus, present both between B4-CNL sequences and in the two knobs identified at the B4 R gene cluster. The khipu repeat is present on most chromosomal termini, indicating the existence of frequent ectopic recombination events in Pv subtelomeric regions. Our results highlight the importance of ectopic recombination in R gene evolution.
Subtelomeres of most eukaryotes contain fast-evolving genes usually involved in adaptive processes. In common bean (
), the
anthracnose resistance (
) locus corresponds to a cluster of ...nucleotide-binding-site leucine-rich-repeat (NL) encoding sequences, the prevalent class of plant
genes. To study the recent evolution of this
gene cluster, we used a combination of sequence, genetic and cytogenetic comparative analyses between common bean genotypes from two distinct gene pools (Andean and Mesoamerican) that diverged 0.165 million years ago.
is a large subtelomeric cluster on chromosome 11 comprising from 32 (Mesoamerican) to 52 (Andean) NL sequences embedded within
satellite repeats. Since the recent split between Andean and Mesoamerican gene pools, the
cluster has experienced numerous gene-pool specific NL losses, leading to distinct NL repertoires. The high proportion of solo-LTR retrotransposons indicates that the
cluster is located in a hot spot of unequal intra-strand homologous recombination. Furthermore, we observe large segmental duplications involving both Non-Homologous End Joining and Homologous Recombination double-strand break repair pathways. Finally, the identification of a Mesoamerican-specific subtelomeric sequence reveals frequent interchromosomal recombinations between common bean subtelomeres. Altogether, our results highlight that common bean subtelomeres are hot spots of recombination and favor the rapid evolution of
genes. We propose that chromosome ends could act as
gene incubators in many plant genomes.
•Genomic distribution of R genes and NB-LRR sequences in common bean.•Whole genome sequence as a powerful tool for R gene identification and marker-assisted selection.•Origin and evolution of huge ...subtelomeric NB-LRR clusters in common bean.
Common bean (Phaseolus vulgaris) is the most important grain legume for direct human consumption in the world, particularly in developing countries where it constitutes the main source of protein. Unfortunately, common bean yield stability is constrained by a number of pests and diseases. As use of resistant genotypes is the most economic and ecologically safe means for controlling plant diseases, efforts have been made to genetically characterize resistance genes (R genes) in common bean. Despite its agronomic importance, genomic resources available in common bean were limited until the recent sequencing of common bean genome (Andean genotype G19833). Besides allowing the annotation of Nucleotide Binding-Leucine Rich Repeat (NB-LRR) encoding gene family, which is the prevalent class of disease R genes in plants, access to the whole genome sequence of common bean can be of great help for intense selection to increase the overall efficiency of crop improvement programs using marker-assisted selection (MAS). This review presents the state of the art of common bean NB-LRR gene clusters, their peculiar location in subtelomeres and correlation with genetically characterized monogenic R genes, as well as how the availability of the whole genome sequence can boost the development of molecular markers for MAS.
Key message
R-BPMV
is located within a recently expanded TNL cluster in the
Phaseolus
genus with suppressed recombination and known for resistance to multiple pathogens including potyviruses ...controlled by the
I
gene.
Bean pod mottle virus
(BPMV) is a comovirus that infects common bean and legumes in general. BPMV is distributed throughout the world and is a major threat on soybean, a closely related species of common bean. In common bean, BAT93 was reported to carry the
R-BPMV
resistance gene conferring resistance to BPMV and linked with the
I
resistance gene. To fine map
R-BPMV
, 182 recombinant inbred lines (RILs) derived from the cross BAT93 × JaloEEP558 were genotyped with polymerase chain reaction (PCR)-based markers developed using genome assemblies from G19833 and BAT93, as well as BAT93 BAC clone sequences. Analysis of RILs carrying key recombination events positioned
R-BPMV
to a target region containing at least 16 TIR-NB-LRR (TNL) sequences in BAT93. Because the
I
cluster presents a suppression of recombination and a large number of repeated sequences, none of the 16 TNLs could be excluded as
R-BPMV
candidate gene. The evolutionary history of the TNLs for the
I
cluster were reconstructed using microsynteny and phylogenetic analyses within the legume family
.
A single
I
TNL was present in
Medicago truncatula
and lost in soybean, mirroring the absence of complete BPMV resistance in soybean. Amplification of TNLs in the
I
cluster predates the divergence of the
Phaseolus
species, in agreement with the emergence of
R-BPMV
before the separation of the common bean wild centers of diversity. This analysis provides PCR-based markers useful in marker-assisted selection (MAS) and laid the foundation for cloning of
R-BPMV
resistance gene in order to transfer the resistance into soybean.
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