Common Bean Gene Pools Research Articles

Characterization of Uromyces appendiculatus First Races in Sri Lanka and Identification of Genes for the Development of Rust-Resistant Snap Beans.

Bean rust is a devastating disease of snap beans in Sri Lanka. Our study endeavored to develop snap beans with resistance to Uromyces appendiculatus, the bean rust pathogen reported to have numerous virulent races. Accordingly, we needed a detailed understanding of the virulence of U. appendiculatus and to identify genes conferring effective rust resistance. To investigate the virulence, we collected leaves of snap bean with rust symptoms from four snap bean producing districts of Sri Lanka. From these samples we established 57 single pustule isolates. Each isolate was inoculated on a set of 12 differential cultivars, six from the Andean and six from the Middle American gene pools of common bean. The virulence of the isolates segregated into four distinct groups that comprised the first four reported races of U. appendiculatus in Sri Lanka, 23-5, 31-1, 31-11, and 63-21. All races were significantly more virulent on the Andean than on the Middle American differential cultivars. PI 1819966, a Middle American differential cultivar containing the Ur-11 gene, conferred resistance to all four races. Three other Middle American cultivars were resistant to three races. Conversely, five Andean differential cultivars were susceptible to all four races. PI 160418 was the only Andean differential cultivar with resistance to three races. The results suggested that rust resistance genes from the Middle American differential cultivars could be combined in different ways with the resistance of Andean PI 260418 to develop snap bean varieties with broad resistance to all races of U. appendiculatus in Sri Lanka.

Last-Generation Genome-Environment Associations Reveal the Genetic Basis of Heat Tolerance in Common Bean (Phaseolus vulgaris L.).

Genome–environment associations (GEAs) are a powerful strategy for the study of adaptive traits in wild plant populations, yet they still lack behind in the use of modern statistical methods as the ones suggested for genome-wide association studies (GWASs). In order to bridge this gap, we couple GEA with last-generation GWAS algorithms in common bean to identify novel sources of heat tolerance across naturally heterogeneous ecosystems. Common bean (Phaseolus vulgaris L.) is the most important legume for human consumption, and breeding it for resistance to heat stress is key because annual increases in atmospheric temperature are causing decreases in yield of up to 9% for every 1°C. A total of 78 geo-referenced wild accessions, spanning the two gene pools of common bean, were genotyped by sequencing (GBS), leading to the discovery of 23,373 single-nucleotide polymorphism (SNP) markers. Three indices of heat stress were developed for each accession and inputted in last-generation algorithms (i.e. SUPER, FarmCPU, and BLINK) to identify putative associated loci with the environmental heterogeneity in heat stress. Best-fit models revealed 120 significantly associated alleles distributed in all 11 common bean chromosomes. Flanking candidate genes were identified using 1-kb genomic windows centered in each associated SNP marker. Some of these genes were directly linked to heat-responsive pathways, such as the activation of heat shock proteins (MED23, MED25, HSFB1, HSP40, and HSP20). We also found protein domains related to thermostability in plants such as S1 and Zinc finger A20 and AN1. Other genes were related to biological processes that may correlate with plant tolerance to high temperature, such as time to flowering (MED25, MBD9, and PAP), germination and seedling development (Pkinase_Tyr, Ankyrin-B, and Family Glicosil-hydrolase), cell wall stability (GAE6), and signaling pathway of abiotic stress via abscisic acid (histone-like transcription factors NFYB and phospholipase C) and auxin (Auxin response factor and AUX_IAA). This work offers putative associated loci for marker-assisted and genomic selection for heat tolerance in common bean. It also demonstrates that it is feasible to identify genome-wide environmental associations with modest sample sizes by using a combination of various carefully chosen environmental indices and last-generation GWAS algorithms.

Combining Ability for Agromorphological and Physiological Traits in Different Gene Pools of Common Bean Subjected to Water Deficit

Water stress is one of the main limiting factors for common bean crops, negatively affecting grain yield and seed quality. Thus, the objective of this study was to evaluate the inheritance of agromorphological and physiological traits related to drought tolerance in order to identify promising combinations. The experiment was carried out in a greenhouse with a partial diallel scheme between three drought-tolerant genotypes (IAPAR 81, BAT 477. and SEA 5), and nine cultivars widely grown in Brazil (BRS Estilo, IAC Alvorada, IPR Campos Gerais, IPR Uirapuru, IPR Nhambu, BRS Esteio, IPR Garça, BRS Radiante, and DRK 18), in a randomized block design with four replicates. The plants were grown in pots with substrate under 80% of pot capacity until they reached the stage R5, when water supply was restricted to 30% for 20 days in the pots under stress treatment. A wide variability for the agromorphological and physiological traits was observed. Water deficit reduced plant performance for most agromorphological traits and altered their physiological metabolism. Additive and non-additive effects are involved in the genetic control of the majority of agromorphological and physiological traits both under water stress and control (well-watered) conditions. The parental genotypes BAT 477 (group I) and IAC Alvorada, IPR Uirapuru, and BRS Esteio (group II) may be included in breeding programs aiming at improving drought tolerance in common bean since they present high positive general combining abilities for agromorphological traits. The crosses IAPAR 81 × IPR Campos Gerais, and SEA 5 × BRS Radiante resulted in the best combinations considering grain yield per plant and total dry biomass, when cultivated under water deficit.

Parallel origins of photoperiod adaptation following dual domestications of common bean.

Common bean (Phaseolus vulgaris L.) is an important grain legume domesticated independently in Mexico and Andean South America approximately 8000 years ago. Wild forms are obligate short-day plants, and relaxation of photoperiod sensitivity was important for expansion to higher latitudes and subsequent global spread. To better understand the nature and origin of this key adaptation, we examined its genetic control in progeny of a wide cross between a wild accession and a photoperiod-insensitive cultivar. We found that photoperiod sensitivity is under oligogenic control, and confirm a major effect of the Ppd locus on chromosome 1. The red/far-red photoreceptor gene PHYTOCHROME A3 (PHYA3) was identified as a strong positional candidate for Ppd, and sequencing revealed distinct deleterious PHYA3 mutations in photoperiod-insensitive Andean and Mesoamerican accessions. These results reveal the independent origins of photoperiod insensitivity within the two major common bean gene pools and demonstrate the conserved importance of PHYA genes in photoperiod adaptation of short-day legume species.

Characterization of genetic diversity in Turkish common bean gene pool using phenotypic and whole-genome DArTseq-generated silicoDArT marker information.

Turkey presents a great diversity of common bean landraces in farmers’ fields. We collected 183 common bean accessions from 19 different Turkish geographic regions and 5 scarlet runner bean accessions to investigate their genetic diversity and population structure using phenotypic information (growth habit, and seed weight, flower color, bracteole shape and size, pod shape and leaf shape and color), geographic provenance and 12,557 silicoDArT markers. A total of 24.14% markers were found novel. For the entire population (188 accessions), the expected heterozygosity was 0.078 and overall gene diversity, Fst and Fis were 0.14, 0.55 and 1, respectively. Using marker information, model-based structure, principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA) algorithms clustered the 188 accessions into two main populations A (predominant) and B, and 5 unclassified genotypes, representing 3 meaningful heterotic groups for breeding purposes. Phenotypic information clearly distinguished these populations; population A and B, respectively, were bigger (>40g/100 seeds) and smaller (<40g/100 seeds) seed-sized. The unclassified population was pure and only contained climbing genotypes with 100 seed weight 2–3 times greater than populations A and B. Clustering was mainly based on A: seed weight, B: growth habit, C: geographical provinces and D: flower color. Mean kinship was generally low, but population B was more diverse than population A. Overall, a useful level of gene and genotypic diversity was observed in this work and can be used by the scientific community in breeding efforts to develop superior common bean strains.

Seriously Outbreak of Rice Bacterial Brown Stripe in 2018 in China

Angular leaf spot (ALS) caused by the fungus Pseudocercospora griseola is one of the most economically important disease affecting common bean production in Ethiopia. Until now, no information has been generated regarding the pathotype and pathogenic variability and its distribution in Ethiopia. A study was undertaken to characterize the pathotype and virulence variability among 39 P. griseola isolates, ALS pathogen, occurring in Ethiopia. A total of 21 pathotypes (63:63, 63:59, 63:23, 61:51, 56:36, 55:39, 49:7, 48:60, 42:59, 41:10, 34:53, 23:61, 19:33, 17:45, 8:18, 8:0, 4:16, 1:24, 1:10, 16:18. and 4:37) were determined using 12 sets of ALS common bean differentials cultivars. These results revealed the presence of high and diverse pathogenic variability of the pathogen. Among the determined pathotypes 63:59 and 19:33 were the most frequently appeared. And the occurrence of three pathotypes (63:63, 63:59 and 63:23) were confirmed as well as the previous reports in central America and Argentina. This will be the first comprehensive report of P. griseola pathotypes existing in the common bean growing areas of Ethiopia. Except pathotype 8:0 that were compatible with Andean common bean groups, most of the isolates were pathogenic to both Andean and Mesoamerican common bean gene pools. Based on that, the isolates were classified as Mesoamerican origin pathotypes. This specific study provided major information about the pathogenic diversity and determined the pathotype of P. griseola from common bean in Ethiopia.

In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping

BackgroundCommon bean is a legume of social and nutritional importance as a food crop, cultivated worldwide especially in developing countries, accounting for an important source of income for small farmers. The availability of the complete sequences of the two common bean genomes has dramatically accelerated and has enabled new experimental strategies to be applied for genetic research. DArTseq has been widely used as a method of SNP genotyping allowing comprehensive genome coverage with genetic applications in common bean breeding programs.ResultsUsing this technology, 6286 SNPs (1 SNP/86.5 Kbp) were genotyped in genic (43.3%) and non-genic regions (56.7%). Genetic subdivision associated to the common bean gene pools (K = 2) and related to grain types (K = 3 and K = 5) were reported. A total of 83% and 91% of all SNPs were polymorphic within the Andean and Mesoamerican gene pools, respectively, and 26% were able to differentiate the gene pools. Genetic diversity analysis revealed an average HE of 0.442 for the whole collection, 0.102 for Andean and 0.168 for Mesoamerican gene pools (FST = 0.747 between gene pools), 0.440 for the group of cultivars and lines, and 0.448 for the group of landrace accessions (FST = 0.002 between cultivar/line and landrace groups). The SNP effects were predicted with predominance of impact on non-coding regions (77.8%). SNPs under selection were identified within gene pools comparing landrace and cultivar/line germplasm groups (Andean: 18; Mesoamerican: 69) and between the gene pools (59 SNPs), predominantly on chromosomes 1 and 9. The LD extension estimate corrected for population structure and relatedness (r2SV) was ~ 88 kbp, while for the Andean gene pool was ~ 395 kbp, and for the Mesoamerican was ~ 130 kbp.ConclusionsFor common bean, DArTseq provides an efficient and cost-effective strategy of generating SNPs for large-scale genome-wide studies. The DArTseq resulted in an operational panel of 560 polymorphic SNPs in linkage equilibrium, providing high genome coverage. This SNP set could be used in genotyping platforms with many applications, such as population genetics, phylogeny relation between common bean varieties and support to molecular breeding approaches.

Trait Associations in Diversity Panels of the Two Common Bean (Phaseolus vulgaris L.) Gene Pools Grown under Well-watered and Water-Stress Conditions.

Common beans are a warm-season, food legume cultivated in areas prone to water limitation throughout their growing season. This study assessed the magnitude and pattern of trait associations for a total of 202 common bean genotypes divided into panels of 81 Andean and 121 Mesoamerican gene pool accessions grown under contrasting treatments of well-watered, non-stress, and water-limited, terminal drought-stress conditions. Linear correlation, complex path coefficient, and genetic divergence analyses were used to dissect the relationship dynamics between traits and the relative contribution of adaptive traits to differentiation among gene pools and genotypes based on drought stress. Drought severity level for the trial was high and created the ideal condition to reveal genotypic differences, as seen by the differential response of the genotypes for the various traits measured. The value for phenotypic coefficients of variation for all traits was higher than the corresponding genotypic values. Seed yield had positive and strong genotypic and phenotypic correlation with pods per plant across gene pools and stress levels. The overall amount of genetic correlation was greater than the corresponding phenotypic correlation matrix for all the traits within the gene pool and across stress levels. Moreover, the results depicted the phenotypic correlation as equal or better than its genotypic counterpart in estimating drought tolerance in common bean plants. Clustering analysis with Mahanalobis's coefficient of generalized distance grouped genotypes with a differential level of drought adaptation into different classes within each panel. This indicates drought tolerance involves different mechanisms of plant response and is present separately in each gene pool panel. Pods per plant, seed weight, pod partitioning index, and harvest index are useful selection objectives to improve drought adaptation in common bean, but must be differentially weighted in each gene pool. The analysis of genetic variation and association between adaptive traits on the two panels provided useful insights on which traits could be used to improve common bean adaptation to low water availability during the growth season.

Variability of nodulation traits in Andean and Mesoamerican common bean gene pools

Abstract: The objective of this work was to evaluate the genotypic diversity for nodulation in common bean (Phaseolus vulgaris) genotypes of Andean and Mesoamerican gene pools present in the core collections of Embrapa, in Brazil. Evaluations were carried out in two stages: the first one with 879 genotypes, taking the cultivar 'Ouro Negro' as reference; and the second one with 116 genotypes with greater nodulation, to identify those showing stability in nodulation in the two stages. Rhizobium strains were inoculated in pre-germinated common bean seed. Plants received weekly a nutrient solution without N, and nodulation was evaluated 35 days after planting. The percentage of genotypes that exceeded the reference cultivar was 22% for number of nodules, 46% for nodule dry weight, and 33% for one nodule dry weight. The combined analysis of data from the two evaluation phases showed wide differences among genotypes, and significant interactions between genotypes and stages. By the orthogonal contrasts analysis, the Mesoamerican genotypes showed a greater nodulation than the Andean ones. In both stages, twenty-six more stable genotypes were identified, most of them belonging to the Mesoamerican gene pool. There is a large variability in nodulation traits among the common bean genotypes present in the core germplasm collections of Embrapa, which suggests that there are genotypes with improved nodulation.

Comparison among recognized and non-recognized Phaseolus vulgaris L. landraces as traditional agro-food products of the Campania region (Italy)

Efforts to safeguard and promote the on-farm maintenance of common bean (Phaseolus vulgaris L.) landraces should take seed quality into high consideration. Seed quality, in addition to suitable agronomic performances, is a good criterion to identify the most interesting materials among those traditionally cultivated. Ten landraces, still cultivated in the Campania region (southern Italy), were investigated. Five of these landraces, recognized as regional traditional agro-food products, are included in the list of the Italian typical products. Landraces belonging to both Mesoamerican and Andean common bean gene pools were present in the ten studied materials. The harvests of two subsequent growing seasons were analysed in order to compare the physico-chemical, culinary and nutritional seed quality of, recognised or not, landraces. Eighteen agronomic and nutritional traits were scored. When individually considered, none of the scored traits was able to discriminate the two groups of landraces. Conversely, submitting all traits to cluster analysis, two sub-clusters corresponding to recognised or not traditional products were obtained. Two landraces, one for each group, remained isolated. On the bases of these results, it can be inferred that the landraces recognized as traditional agro-food products have different culinary and nutritional characteristics in respect to the non-recognized ones.

Pyramiding white mould resistance between and within common bean gene pools

Singh, S. P., Schwartz, H. F., Terán, H., Viteri, D. and Otto, K. 2014. Pyramiding white mould resistance between and within common bean gene pools. Can. J. Plant Sci. 94: 947–954. White mould caused by Sclerotinia sclerotiorum (Lib.) de Bary is a severe disease of common bean (Phaseolus vulgaris L.) in North America and similar production regions. Low to high levels of white mould resistance exist in cultivated and wild common bean and the secondary gene pool. But, cultivars with high levels of resistance are not yet available. The objectives of this study were: (1) to combine or pyramid high levels of resistance from multiple-parent populations between and within gene pools, and (2) to compare the response of pyramided breeding lines (PBL) to four isolates of the white mould pathogen with that of known sources of resistance. Two Andean PBL each derived from an Andean intra-gene pool and inter-gene pool, four Middle American pinto bean PBL from one inter-gene pool multiple-parent population, their seven resistant parents, and susceptible pinto, Othello, were inoculated in the greenhouse with pathogen isolates ARS12D and ND710 at University of Idaho, Kimberly in 2012, and isolates CO467 and NY133 at Colorado State University, Fort Collins in 2013. The percentage of resistant plants for the PBL ranged from 62.5 to 81.9, and mean white mould score from 4.0 to 4.6. The respective values for the white mould resistant parents ranged from 3.1 to 57.0 for the percentage of resistant plants and from 4.8 to 7.5 for the mean white mould score. Furthermore, PBL SE154-1 inoculated with isolate ARS12D, and SE152-6 with isolates ARS12D and ND710 had 100% resistant plants. But, only SE153-1 and SE155-9 inoculated with isolates CO467 and NY133 had significantly (P ≤0.05) higher levels of resistance than the most resistant parents A 195 and VA 19. The pinto bean PBL SE153-1, SE153-6, and SE153-7, and Andean types SE152-6 and SE155-9 were the most resistant among all genotypes inoculated with the four isolates of the white mould pathogen in both greenhouses.

Identification of resistance to rust (Uromyces appendiculatus) and powdery mildew (Erysiphe diffusa) in Portuguese common bean germplasm

AbstractPortugal has a diverse common bean germplasm, which is still grown in farmers' fields. In this work, we searched for resistance to rust (Uromyces appendiculatus) and powdery mildew (Erysiphe diffusa) in a representative collection of the Portuguese common bean germplasm. Despite many accessions depicting intermediate levels of resistance when compared to the susceptible check, 24 and 13 accessions showed low levels of infection, in spite of a compatible interaction (disease severity (DS) values lower than 5% and infection type (IT) of 4), to rust and powdery mildew, respectively, indicative of partial resistance. Moreover, a resistant reaction was observed in 11 accessions when inoculated with powdery mildew (IT = 0–1) and in additional 11 accessions (one in common) when inoculated with rust (IT = 0–2). The levels of resistance found in this report anticipate great potential of the Portuguese national germplasm, recently reported as genetically closer to the Andean common bean gene pool, for disease resistance breeding of this important crop.

Demographic factors shaped diversity in the two gene pools of wild common bean Phaseolus vulgaris L.

Wild common bean (Phaseolus vulgaris L.) is distributed throughout the Americas from Mexico to northern Argentina. Within this range, the species is divided into two gene pools (Andean and Middle American) along a latitudinal gradient. The diversity of 24 wild common bean genotypes from throughout the geographic range of the species was described by using sequence data from 13 loci. An isolation-migration model was evaluated using a coalescent analysis to estimate multiple demographic parameters. Using a Bayesian approach, Andean and Middle American subpopulations with high percentage of parentages were observed. Over all loci, the Middle American gene pool was more diverse than the Andean gene pool (π(sil)=0.0089 vs 0.0068). The two subpopulations were strongly genetically differentiated over all loci (F(st)=0.29). It is estimated that the two current wild gene pools diverged from a common ancestor ∼111 000 years ago. Subsequently, each gene pool underwent a bottleneck immediately after divergence and lasted ∼40 000 years. The Middle American bottleneck population size was ∼46% of the ancestral population size, whereas the Andean was 26%. Continuous asymmetric gene flow was detected between the two gene pools with a larger number of migrants entering Middle American gene pool from the Andean gene pool. These results suggest that because of the complex population structure associated with the ancestral divergence, subsequent bottlenecks in each gene pool, gene pool-specific domestication and intense selection within each gene pool by breeders; association mapping would best be practised within each common bean gene pool.

Direct and Marker‐Assisted Selection for Resistance to Common Bacterial Blight in Common Bean

ABSTRACTCommon bacterial blight (CBB) caused by Xanthomonas campestris pv. phaseoli and X. campestris pv. phaseoli var. fuscans is a seed‐borne disease that can significantly reduce yield and seed quality of common bean (Phaseolus vulgaris L.). Disease resistance is the most effective management strategy, but most common bean cultivars have no CBB resistance. Marker‐assisted selection (MAS) shows promise as a method to facilitate pyramiding CBB resistance between common bean gene pools. This study compared the efficiency of direct disease resistance selection (DDS) and MAS for the pyramiding and transfer of CBB resistance into dark red kidney bean. Direct disease resistance selection and MAS were applied independently, from the F1 through the F5, in an inter‐gene pool double‐cross population, Wilkinson 2/dark red kidney (DRK) 2//DRK 1/VAX 3. Replicated trials were performed in the greenhouse and field in 2006 and 2007 to assess levels of CBB resistance in 15 breeding lines independently developed with each method. Under high disease pressure, in two greenhouse environments, 12 resistant breeding lines were obtained with DDS compared with six using MAS, and the overall CBB mean disease severity index was 3.3 for DDS and 4.2 for MAS. Under moderate disease pressure in the field, there was no significant difference (p &gt; 0.05) between the responses of breeding lines developed by the two selection methods. The cost of DDS was US$1.55 per plant compared to $2.03 for MAS.

Genetic Relationships of Common Bean (Phaseolus vulgaris L.) Race Chile with Wild Andean and Mesoamerican Germplasm

The Chilean common bean (Phaseolus vulgaris L.) belongs to the cultivated race Chile and its origin is presumably Andean. The objective of this study was to identify the origin of a group of Chilean accessions based on their genetic relationship with wild material from the Mesoamerican and Andean common bean gene pool. To achieve this objective, universal primers of chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA) were used to detect polymorphism using Polymerase Chain Reaction - Restriction Fragment Length Polymorphism (PCR-RFLP). Thirtytwo genotypes were analyzed, including wild material from Mexico, Ecuador, Peru, Bolivia, and Argentina, as well as Chilean cultivated genotypes belonging to endemic Chilean accession types (Tortola, Coscorron, and Cuyano) and naturalized commercial lines (Frutilla, Bayo, Manteca, and Blanco grande). Results showed a low level of polymorphism for cpDNA (23%) and mtDNA (24%) in wild and cultivated Chilean common bean accessions. Some universal primers and restriction enzyme combinations were more efficient than others in detecting polymorphism. The Chilean materials were closely related to wild accessions collected in Argentina, Bolivia, and Peru indicating their Andean origin. The wild accessions from Ecuador were located in a intermediate position between the Mesoamerican and Andean accessions.

Evaluation of diversity among common beans (Phaseolus vulgaris L.) from two centers of domestication using 'omics' technologies

BackgroundGenetic diversity among wild accessions and cultivars of common bean (Phaseolus vulgaris L.) has been characterized using plant morphology, seed protein allozymes, random amplified polymorphic DNA, restriction fragment length polymorphisms, DNA sequence analysis, chloroplast DNA, and microsatellite markers. Yet, little is known about whether these traits, which distinguish among genetically distinct types of common bean, can be evaluated using omics technologies.ResultsThree 'omics' approaches: transcriptomics, proteomics, and metabolomics were used to qualitatively evaluate the diversity of common bean from two Centers of Domestication (COD). All three approaches were able to classify common bean according to their COD using unsupervised analyses; these findings are consistent with the hypothesis that differences exist in gene transcription, protein expression, and synthesis and metabolism of small molecules among common bean cultivars representative of different COD. Metabolomic analyses of multiple cultivars within two common bean gene pools revealed cultivar differences in small molecules that were of sufficient magnitude to allow identification of unique cultivar fingerprints.ConclusionsGiven the high-throughput and low cost of each of these 'omics' platforms, significant opportunities exist for their use in the rapid identification of traits of agronomic and nutritional importance as well as to characterize genetic diversity.

Phytogeographical origin of Madeiran common beans based on phaseolin patterns

The objective of this work was to determine the geographic origin of the Madeiran common bean (Phaseolus vulgaris) gene pool. Phaseolin patterns of 50 accessions representing the diversity of common bean collected in Madeira, Portugal, and conserved in the ISOPlexis Germplasm Bank, were analysed using the Experion automated electrophoresis system, based on lab-on-a-chip technology. Five common bean standard varieties with typical phaseolin patterns were used to determine the phytogeographical origin of the Madeiran common bean accessions. Ninety two percent of the accessions exhibited a phaseolin pattern consistent with the one of common bean types belonging to the Andean gene pool, while the origin of the remaining 8% of the accessions was indistinguishable. The application of a similarity coefficient of 85%, based on Pearson correlations, increases the number of accessions with uncertain pattern. The analytical approach used permitted the determination of the origin of the common bean gene pool, which is Andean in 98% of the cases, and clustering of the observed variability among the Madeiran common beans.

Molecular Analysis of a Large Subtelomeric Nucleotide-Binding-Site–Leucine-Rich-Repeat Family in Two Representative Genotypes of the Major Gene Pools of Phaseolus vulgaris

In common bean, the B4 disease resistance gene cluster is a complex cluster localized at the end of linkage group (LG) B4, containing at least three R specificities to the fungus Colletotrichum lindemuthianum. To investigate the evolution of this R cluster since the divergence of Andean and Mesoamerican gene pools, DNA sequences were characterized from two representative genotypes of the two major gene pools of common bean (BAT93: Mesoamerican; JaloEEP558: Andean). Sequences encoding 29 B4-CC nucleotide-binding-site-leucine-rich-repeat (B4-CNL) genes were determined-12 from JaloEEP558 and 17 from BAT93. Although sequence exchange events were identified, phylogenetic analyses revealed that they were not frequent enough to lead to homogenization of B4-CNL sequences within a haplotype. Genetic mapping based on pulsed-field gel electrophoresis separation confirmed that the B4-CNL family is a large family specific to one end of LG B4 and is present at two distinct blocks separated by 26 cM. Fluorescent in situ hybridization on meiotic pachytene chromosomes revealed that two B4-CNL blocks are located in the subtelomeric region of the short arm of chromosome 4 on both sides of a heterochromatic block (knob), suggesting that this peculiar genomic environment may favor the proliferation of a large R gene cluster.

Structure of genetic diversity in the two major gene pools of common bean (Phaseolus vulgaris L., Fabaceae)

Domesticated materials with well-known wild relatives provide an experimental system to reveal how human selection during cultivation affects genetic composition and adaptation to novel environments. In this paper, our goal was to elucidate how two geographically distinct domestication events modified the structure and level of genetic diversity in common bean. Specifically, we analyzed the genome-wide genetic composition at 26, mostly unlinked microsatellite loci in 349 accessions of wild and domesticated common bean from the Andean and Mesoamerican gene pools. Using a model-based approach, implemented in the software STRUCTURE, we identified nine wild or domesticated populations in common bean, including four of Andean and four of Mesoamerican origins. The ninth population was the putative wild ancestor of the species, which was classified as a Mesoamerican population. A neighbor-joining analysis and a principal coordinate analysis confirmed genetic relationships among accessions and populations observed with the STRUCTURE analysis. Geographic and genetic distances in wild populations were congruent with the exception of a few putative hybrids identified in this study, suggesting a predominant effect of isolation by distance. Domesticated common bean populations possessed lower genetic diversity, higher F(ST), and generally higher linkage disequilibrium (LD) than wild populations in both gene pools; their geographic distributions were less correlated with genetic distance, probably reflecting seed-based gene flow after domestication. The LD was reduced when analyzed in separate Andean and Mesoamerican germplasm samples. The Andean domesticated race Nueva Granada had the highest F(ST) value and widest geographic distribution compared to other domesticated races, suggesting a very recent origin or a selection event, presumably associated with a determinate growth habit, which predominates in this race.

The N-terminus of the Begomovirus Nuclear Shuttle Protein (BV1) Determines Virulence or Avirulence in Phaseolus vulgaris

The BV1 gene of the bipartite Begomovirus genome encodes a nuclear shuttle protein (NSP) that is also an avirulence determinant in common bean. The function of the NSP of two common bean-infecting bipartite begomoviruses, Bean dwarf mosaic virus (BDMV) and Bean golden yellow mosaic virus (BGYMV), was investigated using a series of hybrid DNA-B components expressing chimeric BDMV and BGYMV NSP, and genotypes of the two major common bean gene pools: Andean (cv. Topcrop) and Middle American (cvs. Alpine and UI 114). BDMV DNA-A coinoculated with HBDBG4 (BDMV DNA-B expressing the BGYMV NSP) and HBDBG9 (BDMV DNA-B expressing a chimeric NSP with the N-terminal 1 to 42 amino acids from BGYMV) overcame the BDMV resistance of UI 114. This established that the BDMV NSP is an avirulence determinant in UI 114, and mapped the domain involved in this response to the N-terminus, which is a variable surface-exposed region. BDMV DNA-A coinoculated with HBDBG10, expressing a chimeric NSP with amino acids 43 to 92 from BGYMV, was not infectious, revealing an essential virus-specific domain. In the BGYMV background, the BDMV NSP was a virulence factor in the Andean cv. Topcrop, whereas it was an avirulence factor in the Middle American cultivars, particularly in the absence of the BGYMV NSP. The capsid protein (CP) also played a gene pool-specific role in viral infectivity; it was dispensable for infectivity in the Andean cv. Topcrop, but was required for infectivity of BDMV, BGYMV, and certain hybrid viruses in the Middle American cultivars. Redundancy of the CP and NSP, which are nuclear proteins involved directly or indirectly in viral movement, provides a masking effect that may allow the virus to avoid host defense responses.