Common Bean Gene Pools Research Articles

Structure of genetic diversity among common bean (Phaseolus vulgaris L.) varieties of Mesoamerican and Andean origins using new developed microsatellite markers

A common bean genomic library was constructed using the ‘IAC-UNA’ variety enriched for (CT) and (GT) for microsatellite motifs. From 1,209 sequenced clones, 714 showed microsatellites distributed over 471 simple and 243 compound motifs. GA/CT and GT/CA were the most frequent motifs found among these sequences. A total of 123 microsatellites has been characterized. Out of these, 87 were polymorphic (73.7%), 33 monomorphic (26.8%), and 3 (2.4%) did not amplify at all. In a sample of 20 common bean materials selected from the Agronomic Institute Germplasm Bank, the number of alleles per locus varied 2–9, with an average of 2.82. The polymorphic information content (PIC) of each marker varied from 0.05 to 0.83, with a 0.45 average value. Cluster and principal coordinate analysis of the microsatellite data were consistent with the original assignment of the germplasm accessions into the Andean and Mesoamerican gene pools of common bean. Low polymorphism levels detected could be associated with the domestication process. These microsatellites could be a valuable resource for the bean community because of their use as new markers for genetic studies.

Phenotypic and Genetic Diversity in Strains of Common Blight Bacteria (Xanthomonas campestrispv.phaseoliandX. campestrispv.phaseolivar.fuscans) in a Secondary Center of Diversity of the Common Bean Host Suggests Multiple Introduction Events

ABSTRACT Common bacterial blight (CBB) disease of the common bean (Phaseolus vulgaris) is caused by Xanthomonas campestris pv. phaseoli and the brown-pigmented variant X. campestris pv. phaseoli var. fuscans. CBB first was described in Castilla y León County, Spain, in 1940, and is now a major constraint on common bean production. In this secondary center of diversity of the common bean, large-seeded Andean cultivars predominate, although medium-seeded Middle American cultivars also are grown. Xanthomonad-like bacteria associated with CBB in Castilla y León were characterized on the basis of carbohydrate metabolism, brown pigment production, genetic analyses (repetitive-element polymerase chain reaction [rep-PCR] and random amplified polymorphic DNA [RAPD]) and pathogenicity on cultivars representing the two common bean gene pools (Andean and Middle American). X. campestris pv. phaseoli was more prevalent (80%) than X. campestris pv. phaseoli var. fuscans (20%). Patterns of carbohydrate metabolism of Spanish CBB bacteria were similar to those of known strains; and only X. campestris pv. phaseoli var. fuscans strains utilized mannitol as a sole carbon source. rep-PCR and RAPD analyses revealed relatively little genetic diversity among Spanish X. campestris pv. phaseoli strains, and these strains were placed together with New World strains into a large cluster. Similar to other New World strains, representative Spanish X. campestris pv. phaseoli strains were highly pathogenic on bean cultivars of both gene pools, showing no gene pool specialization such as that found in certain East African strains. Genetic analyses and pathogenicity tests confirmed and extended previous results, indicating that these East African strains represent distinct xanthomonads that independently evolved to be pathogenic on common bean. X. campestris pv. phaseoli var. fuscans strains were more closely related and genetically distinct from X. campestris pv. phaseoli strains. However, two distinct clusters of X. campestris pv. phaseoli var. fuscans strains were identified, one having the most New World strains and the other having the most African strains. Spanish strains were placed in both clusters, but all strains tested were highly pathogenic on bean cultivars of both gene pools. Together, our results are consistent with multiple introductions of CBB bacteria into Spain. These findings are discussed in terms of breeding for CBB resistance and the overall understanding of the genetic diversity and evolution of CBB bacteria.

Common Bean (Phaseolus vulgaris L.) Landraces from Abruzzo and Lazio Regions (Central Italy)

Marginal areas of Central Italy, i.e., areas where socio-economic conditions are weak and agriculture is carried on with traditional farming methods, are known to retain highly interesting local legume populations. The variation within a collection constituted by 44 populations belonging to 19 common bean (Phaseolus vulgaris L.) landraces, recently collected in Central Italy, was studied. Most landraces from the Lazio region were collected in the inner valleys of Aniene river basin, those from the Abruzzo region were collected in the Valley Peligna and the basin of the Aterno–Pescara river. Some morphological traits of plant and seeds and the phaseolin pattern were analysed to evaluate the degree of genetic variation among and within the landraces. Both common bean gene pools were represented in the investigated collection, the populations belonging to Andean gene pool were predominant. The landraces ‘Cioncone’, from Lazio and ‘Fagiolo pane aquilano’, from Abruzzo showed the rare A phaseolin type. All the collected data were submitted to cluster analysis. Two main subgroups were identified, the former included mainly populations from Abruzzo region and the latter including all the others. Despite this, a considerable resemblance exists between the common bean landraces from Abruzzo and Lazio, as proved by the low rankings on the tree among the populations. The observed similarity is discussed also on the basis of historical relationships between the two sides of the Apennine ridge.

Morphological and Molecular Characterization of Common Bean Landraces and Cultivars from the Caribbean

Little information is available regarding the relationship of Caribbean bean landraces with the Andean and Mesoamerican gene pools of common bean (Phaseolus vulgaris L.) While small‐seeded Mesoamerican black beans are prevalent in parts of the Caribbean, many of the regionally preferred red mottled and medium‐to‐large‐seeded bean landraces found there are postulated to belong to the Andean gene pool. To test this hypothesis, we analyzed the morphological characteristics, phenological traits, phaseolin status, and random amplified polymorphic DNA (RAPD) banding patterns of 54 red mottled or large‐seeded bean landraces and cultivars from the Caribbean (16 from the Dominican Republic, 14 from Haiti, 1 from Jamaica and 23 from Puerto Rico) compared with 11 Andean bean lines from other regions. To estimate phylogenetic relationships among the lines, distances were calculated and dendrograms constructed for morphological and/or phenological and molecular characteristics by the complete clustering method. The landraces were grouped into two clusters morphologically: one with Mesoamerican characteristics, which included all the red mottled lines from Haiti and three landraces from the Dominican Republic collected near the Haitian border and the other with Andean characteristics, which included all the lines from Puerto Rico and the remaining lines from the Dominican Republic. RAPD and phaseolin polymorphisms identified three groups, one corresponding to the genotypes with Mesoamerican morphologies, one to those with Andean morphologies, and another that had Andean phenotypes but proximity to the Mesoamerican group, suggesting possible introgression between the gene pools. Phaseolin variability agreed with other molecular and morphological data allowing the assignment of genotypes to a Mesoamerican or Andean gene pool. Knowledge of this variability may provide useful information concerning the potential value of Caribbean landraces to Andean bean breeding programs.

Genetic Diversity and Pathogenic Variation of Common Blight Bacteria (Xanthomonas campestrispv.phaseoliandX. campestrispv.phaseolivar.fuscans) Suggests Pathogen Coevolution with the Common Bean

ABSTRACT Common bacterial blight (CBB), caused by Xanthomonas campestris pv. phaseoli and X. campestris pv. phaseoli var. fuscans, is one of the most important diseases of common bean (Phaseolus vulgaris) in East Africa and other bean-growing regions. Xanthomonad-like bacteria associated with CBB in Malawi and Tanzania, East Africa, and in Wisconsin, U.S., were characterized based on brown pigment production, pathogenicity on common bean, detection with an X. campestris pv. phaseoli- or X. campestris pv. phaseoli var. fuscans-specific PCR primer pair, and repetitive element polymerase chain reaction (rep-PCR) and restriction fragment length polymorphism (RFLP) analyses. The common bean gene pool (Andean or Middle American) from which each strain was isolated also was determined. In Malawi, X. campestris pv. phaseoli and X. campestris pv. phaseoli var. fuscans were isolated predominantly from Andean or Middle American beans, respectively. In Tanzania, X. campestris pv. phaseoli var. fuscans was most commonly isolated, irrespective of gene pool; whereas, in Wisconsin, only X. campestris pv. phaseoli was isolated from Andean red kidney beans. Three rep-PCR fingerprints were obtained for X. campestris pv. phaseoli strains; two were unique to East African strains, whereas the other was associated with strains collected from all other (mostly New World) locations. RFLP analyses with repetitive DNA probes revealed the same genetic diversity among X. campestris pv. phaseoli strains as did rep-PCR. These probes hybridized with only one or two fragments in the East African strains, but with multiple fragments in the other X. campestris pv. phaseoli strains. East African X. campestris pv. phaseoli strains were highly pathogenic on Andean beans, but were significantly less pathogenic on Middle American beans. In contrast, X. campestris pv. phaseoli strains from New World locations were highly pathogenic on beans of both gene pools. Together, these results indicate the existence of genetically and geographically distinct X. campestris pv. phaseoli genotypes. The rep-PCR fingerprints of X. campestris pv. phaseoli var. fuscans strains from East African and New World locations were indistinguishable, and were readily distinguished from those of X. campestris pv. phaseoli strains. Genetic diversity among X. campestris pv. phaseoli var. fuscans strains was revealed by RFLP analyses. East African and New World X. campestris pv. phaseoli var. fuscans strains were highly pathogenic on Andean and Middle American beans. Breeding for CBB resistance in East African beans should utilize X. campestris pv. phaseoli var. fuscans and New World X. campestris pv. phaseoli strains in order to identify germ plasm with the highest levels of resistance.

Virulence and Molecular Diversity within Colletotrichum lindemuthianum Isolates from Andean and Mesoamerican bean Varieties and Regions

Virulence on a standard set of 12 common bean differential varieties, DNA sequence of repetitive-elements (Rep-PCR) and random amplified microsatellites (RAMS) were used to assess the genetic variability of 200 Colletotrichum lindemuthianum isolates collected from Andean and Mesoamerican bean varieties and regions. High levels of pathotypic (90 pathotypes) and genetic diversity (0.97) were identified among 200 isolates, revealing that C. lindemuthianum is a highly diverse pathogen. Although a significant number of pathotypes were common to Andean and Mesoamerican regions, many more were only found in the Mesoamerican region. Cluster analysis of virulence and molecular data did not separate isolates into groups that were structured with common bean gene pools. No genetic differentiation (GST=0.03) was apparent between Andean and Mesoamerican isolates of C. lindemuthianum. The diversity exhibited by C. lindemuthianum does not appear to cluster according to common bean gene pools, and the high diversity found in the Mesoamerican region seems to indicate that C. lindemuthianum originated and was disseminated from this region. Due to the high genetic variation exhibited by C. lindemuthianum, stacking major resistance genes appears to be the best option for developing cultivars with durable anthracnose resistance.

Using molecular markers to assess the effect of introgression on quantitative attributes of common bean in the Andean gene pool.

Progress in bean breeding programs requires the exploitation of genetic variation that is present among races or through introgression across gene pools of Phaseolus vulgaris L. Of the two major common bean gene pools, the Andean gene pool seems to have a narrow genetic base, with about 10% of the accessions in the CIAT core collection presenting evidence of introgression. The objective of this study was to quantify the degree of spontaneous introgression in a sample of common bean landraces from the Andean gene pool. The effects of introgression on morphological, economic and nutritional attributes were also investigated. Homogeneity analysis was performed on molecular marker data from 426 Andean-type accessions from the primary centres of origin of the CIAT common bean core collection and two check varieties. Quantitative attribute diversity for 15 traits was studied based on the groups found from the cluster analysis of marker prevalence indices computed for each accession. The two-group summary consisted of one group of 58 accessions (14%) with low prevalence indices and another group of 370 accessions (86%) with high prevalence indices. The smaller group occupied the outlying area of points displayed from homogeneity analysis, yet their geographic origin was widely distributed over the Andean region. This group was regarded as introgressed, since its accessions displayed traits that are associated with the Middle American gene pool: high resistance to Andean disease isolates but low resistance to Middle American disease isolates, low seed weight and high scores for all nutrient elements. Genotypes generated by spontaneous introgression can be helpful for breeders to overcome the difficulties in transferring traits between gene pools.

Inter simple sequence repeat (ISSR) markers as a tool for the assessment of both genetic diversity and gene pool origin in common bean (Phaseolus vulgaris L.)

In this study, we report the use of ISSR to assess genetic diversity and to determine the relationships among ten cultivars of common bean developed in Argentina and three materials from France. ISSR markers resolved two major groups corresponding to the Andean and Mesoamerican gene pools of common bean. We compared the results of previous analysis, performed with RAPD markers (Galvan et al., 2001), with the results generated by means of ISSR. It appears that ISSR are better tools than RAPDs to identify beans by gene pool of origin though they did not revealed as many differences between individuals as RAPDs.

Sources of resistance to angular leaf spot (Phaeoisariopsis griseola) in common bean core collection, wild Phaseolus vulgaris and secondary gene pool

Angular leaf spot (ALS) is one of the most devastating diseases of common bean (Phaseolus vulgaris L.) in tropical and subtropical countries. The causal fungus, Phaeoisariopsis griseola(Sacc.) Ferr. is highly variable and a diverse source of resistance genes is required to manage this disease. We evaluated a common bean core collection,primary and secondary gene pools and lines derived from inter-specific crosses of P. vulgaris and P. coccineus or P. polyanthus (secondary gene pool) for resistance to angular leaf spot. Of the 1441 accessiones in the core collection, only 2.2% were resistant to both Andean and Mesoamerican races of P. griseola, 28% were resistant only to Andean and 9% to Mesoamerican races. Of the 32 resistant accessions, 68%originated from Bolivia, Colombia,Guatemala and Mexico. More accessions from these countries should be examined for P. griseola reaction. Very few wild P. vulgaris accessions (4%), were resistant to ALS. In contrast, high levels of resistance (62%) were found in the secondary gene pool. Among the 1010 lines from inter-specific crosses, 109 lines were highly resistant. These genotypes from the primary and secondary common bean gene pools resistant to Andean and Mesoamerican races of P. griseola offer a potential for developing broad and durable ALS resistance.

Characterization of expressed NBS-LRR resistance gene candidates from common bean

A complex ancestral resistance (R) gene cluster, localized at the end of linkage group B4, and referred to as the B4 R gene cluster, has been previously genetically characterized. The B4 R gene cluster existed prior to the separation of the two major gene pools of cultivated common bean and contains several resistance specificities effective against the fungus Colletotrichum lindemuthianum. In this paper we report the molecular analysis of four expressed resistance gene candidates (RGCs) that map at the B4 R-cluster and co-localize with R-specificities or R-QTLs effective against C. lindemuthianum. These RGCs have been isolated from two genotypes that are representative of the two major gene pools of common bean: the BA8 and BA11 RGCs originating from the Mesoamerican BAT93 genotype, and the JA71 and JA78 RGCs originating from the Andean JaloEEP558 genotype. These RGCs encode NBS-LRR resistance-like proteins that are closely similar to the tomato I2 R-protein. Based upon sequence comparisons and genetic localization, we established that these four bean RGCs belong to two different subfamilies of R-sequences independently of their gene pool of origin. No feature discriminating the four RGCs according to their gene pool of origin has been observed yet. Comparative sequence analyses of the full-length RGCs and their flanking genomic sequences confirmed the ancestral origin of the B4 R-cluster.

Broadening the Genetic Base of Common Bean Cultivars

Knowledge, access, and use of diversity available in cultivated and wild relatives are essential for broadening the genetic base of cultivars to sustain improvement. My objectives are to review briefly the origin, domestication, and organization of genetic diversity in Phaseolus beans, highlight production problems and traits deficient in the common bean (P. vulgaris L.) cultivars, cite sources of useful gemplasm, and review progress achieved in broadening the genetic base of cultivars. Phaseolus beans originated in the Americas. Only five species, P. acutifolius A. Gray, P. coccineus L., P. lunatus L., P. polyanthus Greenman, and P. vulgaris L. were domesticated. The interspecies diversity in relation to common bean is organized in primary, secondary, tertiary, and quaternary gene pools. Intraspecies diversity in common bean is separated into two major gene pools (Andean and Middle American). Cultivars are further divided into races, each with their distinguishing characteristics. Also, cultivars of dry seed and snap bean exist. Abiotic and biotic stresses limit common bean production. The genetic base of cultivars within market classes is narrow and inadequate level of resistance to common bacterial blight [caused by Xanthomonas campestris pv. phaseoli (Smith) Dye] and white mold [caused by Sclerotinia sclerotiorum (Lib) de Bary] exist in cultivars. High levels of resistance to these and other desirable traits exist in the relatives and gene pools of P. vulgaris Early maturity, adaptation to higher latitude, upright plant type, high pod quality and seed yield, and resistance to Bean common mosaic virus (a potyvirus) and/or rust [caused by Uromyces appendiculatus (Pers.:Pers.) Unger] have been bred into cultivars. However, most of the genetic variability available in the common bean races, gene pools, and wild relatives remains to be utilized. To maximize and sustain bean production, high yielding, high quality cultivars that are less dependent on water, fertilizer, pesticides, and manual labor should be developed. This need warrants sustained, comprehensive, and integrated genetic improvement, in which favorable alleles from cultivated and wild relatives are accumulated in superior cultivars. A three‐tiered breeding approach involving: (i) gene introgression from alien germplasm, (ii) pyramiding favorable alleles from different sources, and (iii) simultaneous improvement of multiple traits for common bean cultivars would be the most appropriate strategies to meet theses needs.

Genetic Control of the Domestication Syndrome in Common Bean

The marked pbenotypic differences for morphological and physiological traits that distinguish wild progenitors and cultivated descendants (“the domestication syndrome”) and the lack of information about their genetic control have limited the utilization of wild germplasm for crop involvement. This study was conducted to assess the genetic control of the domestication syndrome in common bean (Phaseolus vulgaris L.). A recombinant inbred population resulting from a cross between a wild and a cultivated common bean was subjected to molecular linkage mapping and evaluation in short‐day and long‐day environments. We show that the genetic control of this syndrome in common bean involves genes that can have a large effect (>25–30%) and account for a substantial part of the phenotypic variation observed (>40–50%). The distribution of domestication syndrome genes appears to be concentrations in three genomic regions with a major effect on the syndrome, one of which greatly affects growth habit and phenology, the other seed dispersal and dormancy, and a third, the size of fruit and seed, all of which are important traits in determining adaptation to a cultivated environment. Whereas the influence of genetic background and environment on the expression of some traits will have to be further analyzed, our results suggest, however, that domestication of common bean could have proceeded rapidly (provided that genetic diversity and selection intensity were high) and that evolution can proceed through changes involving a few genes with large effect rather than through a gradual accumulation of changes coded by changes with small effects. They also suggest that adaptation to rapidly changing environmental conditions may involve genes with large phenotypic effects. The information presented here should lead to marker‐assisted selection experiments of introgression of additional genetic diversity into the cultivated common bean gene pool.

Random Amplified Polymorphic DNA (RAPD) Marker Variability between and within Gene Pools of Common Bean

The objective of this study was to evaluate the degree of RAPD marker variability between and within commercially productive market classes representative of the Andean and Middle American gene pools of common bean (Phaseolus vulgaris L.). Six sets of near-isogenic lines were screened with oligonucleotide primers in the polymerase chain reaction-based RAPD assay. Simultaneous analyses with at least three sets of lines enabled us to score RAPD markers between the two major gene pools, races within the same gene pool, and different genotypes of the same race (within race). A “three-tiered” pattern of polymorphism was observed: between gene pools> between races> within races. The overall level of polymorphism between the Andean and Middle American gene pools was 83.4%. The overall level of polymorphism between races within the same gene pool was similar for Andean races (60.4%) and Middle American races (61.7%). The level of polymorphism between related commercial navy bean lines was 39.2% and between related commercial snap bean lines was 53.6 %. The inherent simplicity and efficiency of RAPD analyses, coupled with the number of polymorphisms detectable between related commercial genotypes, should facilitate the construction of RAPD-based genetic linkage maps in the context of populations representative of most bean breeding programs.

Diversidad genetica y distribución ecológica dePhaseolus vulgaris (Fabaceae) en el noroeste de Suramerica

Our goal was to investigate in more detail wild and cultivated common bean (Phaseolus vulgaris) accessions from northwestern South America (Colombia, Ecuador, and northern Peru) because prior research had shown this region to be the meeting place of the two major gene pools (Middle American and Andean) of common bean. Explorations were conducted in these countries to collect additional materials not represented in germplasm collections. It was possible to identify wild common bean populations in Ecuador and northern Peru, where they had never been described before. In addition, we were able to extend the distribution of wild common bean in Colombia beyond what was known prior to this study. In all areas, the wild common bean habitat had suffered severely from destruction of natural vegetation. In Colombia, wild common beans were found on the Eastern slope of the Andes (in continuation of its distribution in Venezuela), whereas in Ecuador and northern Peru they were found on the western slope of this mountain range. This geographic distribution was correlated with an ecological distribution in relatively dry environments with intermediate temperatures (known as “dry mountain forest”). Isozyme andphaseolin seed protein analyses of the northern Peruvian and Ecuadoran wild populations showed that they were intermediate between the Middle American and Andean gene pools of the species. Phaseolin analyses conducted on landraces of the Upper Magdalena Valley in Colombia showed that Andean domesticates were grown at a higher altitude than Middle American domesticates suggesting that the former are adapted to cooler temperatures. Our observations and results have the following consequences for the understanding and conservation of genetic diversity in common bean and other crops: 1) Our understanding of the distribution of the wild relative of common bean (and other crops) is imperfect and further explorations are needed to more precisely identify and rescue wild ancestral populations; 2) For crops for which the wild ancestor has not yet been identified, it may be worthwhile to conduct additional explorations in conjunction with genetic diversity studies at the molecular level to guide the explorations; 3) Our study shows the benefit for more efficient germplasm conservation which can be derived from the dynamic interplay between field explorations (and other conservation operations) and molecular analyses to determine genetic distances and diversities; 4) The intermediate materials identified in northern Peru and Ecuador may have basic importance to understand the origin of the common bean and an applied role as a bridge between the Middle American and Andean gene pools; and 5) The differential adaptation to temperature of the two major cultivated gene pools may help breeders select genotypes based at least partially on their evolutionary origin.