Can Phaseolin Patterns Help Resolve the Phaseolus–Vigna Complex?

Although common bean (Phaseolus vulgaris L.) is cultivated throughout India, the Himalayas hold largest diversity of bean germplasm. No studies on characterization of phaseolin types on this germplasm have been conducted earlier. In order to determine whether the common bean cultivars collected from various areas in the Northern Himalayas represent introductions from the Central American and Andean domestication centers or are local domesticates, we have analyzed the electrophoretic variation (SDS-PAGE) of phaseolin types in several bean accessions. A few species of Vigna were also included in this study to determine whether phaseolin (vignin in Vigna) patterns can be used to resolve the Phaseolus–Vigna complex. The present investigation on phaseolin (globulin) patterns of Phaseolus vulgaris and Vigna spp. clearly shows much variability in globulin patterns. Three new types of phaseolin patterns were recorded. An attempt to resolve phylogenetic problems in this complex was made using the phaseolin data.     

Tracing the origin of Spanish common bean cultivars using biochemical and molecular markers

Fifty-four accessions of Phaseolus vulgaris cultivated in Spain and representing a broad variability for this country, were studied together with 30 samples of wild forms of American origin. Two reference cultivars (from the Andes and Mesoamerica) plus two outgroups (P. coccineus and Vigna unguiculata) were also included. RAPD analysis of DNA leaf extracts were carried out with four selected primers. We also studied morphological characters of the seeds and the phaseolin electrophoretic patterns. Multivariate analysis with the UPGMA method using RAPD data clustered the samples in four groups and, comparing with morphological data and phaseolin types, showed that the Spanish cultivars were mainly of Andean origin. Nevertheless, occurrence of introgression in Spain and the consideration of the country as a second center of variability for beans can also explain the obtained results.     

Analysis of the contribution of Mesoamerican and Andean gene pools to European common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.) germplasm and strategies to establish a core collection

Common bean (Phaseolus vulgaris L.) was introduced in Europe from both Mesoamerican and Andean centres of origin. In this study, a collection including 544 accessions from all European regions showed that the Andean phaseolin types ‘T’ (45.6%) and ‘C’ (30.7%) prevailed over the Mesoamerican ones ‘S’ (23.7%), and accessions with cuboid seed shape (34.9%), maroon coat darker colour seed (44.3%), uniform seed colour (69.6%) were the most frequent. European accessions with phaseolin ‘S’ showed a significantly larger average seed size compared to those from America in the same phaseolin class while those presenting ‘T’ and ‘C’ phaseolin did not. This suggests that, during crop expansion in Europe, sampling or selection favoured the large-seeded races within the Mesoamerican ‘S’ gene pool or, possibly, introgression from Andean germplasm did occur. A core collection was developed using sampling approaches based on the information available in the genebank databases and on phaseolin patterns. Four sampling strategies were used: simple random sampling, and three random-stratified samplings, by logarithm of frequency of accessions by country, by European region, and by phaseolin pattern, respectively. Two sampling strategies resulted in core collections significantly different for phaseolin electrophoretic patterns from the whole collection. Stratification by phaseolin patterns increased the frequency of ‘S’ types (‘C’ type = 33%, ‘T’ type = 5.7% and ‘S’ type = 31.3%). The core collections were validated using seven seed characters, and no significant difference was observed in all strategies. This first developed European bean core collection will help to assess the contribution of the two American gene pools to the European germplasm and their relative importance for breeding purposes.     

Seed compositional and disease resistance differences among gene pools in cultivated common bean

It is widely accepted that two major gene pools exist in cultivatedcommon bean, one Middle American and one Andean. Recently another gene pool,designated as North Andean and a fourth group (not considered to be adistinct gene pool) have been reported by the senior author and hiscolleagues. Many of the agronomic and seed compositional attributes of the twomajor gene pools are well known, but the seed compositional value and diseaseresistance of the North Andean gene pool has not yet been characterized. Torectify this situation, the seed compositional characters, percentage of proteinconcentrations (phaseolin, lectin and -amylaseinhibitor), the nutrient elements (calcium, phosphorus, iron andzinc) and the disease and pest attributes (angular leaf spot,anthracnose, common bacterial blight and empoasca damage) were considered.The Middle American gene pool gave higher lectin, calcium, phosphorus, sulfurand zinc than the Andean gene pool but lower phaseolin and iron. The NorthAndean gene pool is more like the Andean gene pool for phaseolin, resistance toangular leaf spot and anthracnose from Andean pathogen isolates, but more likethe Middle American gene pool for lectin, zinc, sulfur and resistance toanthracnose from Middle American pathogen isolates. On the other hand, it hadthe highest iron concentration and was more resistant to common bacterialblight. These results indicate the potential value of this gene pool in a commonbean breeding program.     

Morphotype relationships in Lima bean (Phaseolus lunatus L.) deduced from variation of the evolutionary marker phaseolin

Summary Variation of the seed storage protein phaseolin was analysed in a collection of 100 accessions of Phaseolus lunatus L. using one-dimensional SDS/PAGE. Cultivated small-seeded genotypes belonging to Sieva and Potato morphotypes and intermediate Sieva-Potato and Sieva-Big Lima morphotypes showed the M (Mesoamerican) pattern, confirming their origin in the same gene pool. Cultivated Big Lima morphotypes showed the A (Andean) pattern, confirming that they belong to a distinct gene pool.     

The common bean populations from Basilicata (Southern Italy). An evaluation of their variation

The variation within a collection constituted by 36 populations of common bean (Phaseolus vulgarisL.) recently collected in Basilicata region (Southern Italy) was studied. These populations are cultivated in marginal areas of the region mainly for farms' self-consumption. An appreciable variation of seed shape, colour and type of pattern was observed; 34 populations are of climbing growth habit. The frequency of the phaseolin types within the collection was investigated. C, T and S phaseolin types were observed, the type C being predominant (18 of 36 landraces); intra-population variation was detected only for two landraces. Local populations were compared with 28 commercial cultivars widely grown in the Basilicata region and accounting for 80–90% of common bean production. Significant divergences in growth habit and frequency of phaseolin types were observed: 22 cultivars had bush growth habit and 20 showed T phaseolin type. These results stress the urgency of actions devoted to the safeguard of this local germplasm. In fact, the diffusion of alloctonous and not typical germplasm is the first step towards the erosion of useful or valuable genes present in those established local populations.     

Genetic variability in cultivated common bean beyond the two major gene pools

It is generally accepted that two major gene pools exist in cultivatedcommon bean (Phaseolus vulgaris L.), a MiddleAmerican and an Andean one. Some evidence, based on unique phaseolin morphotypesand AFLP analysis, suggests that at least one more gene pool exists incultivated common bean. To investigate this hypothesis, 1072 accessions from acommon bean core collection from the primary centres of origin, held at CIAT,were investigated. Various agronomic and morphological attributes (14categorical and 11 quantitative) were measured. Multivariate analyses,consisting of homogeneity analysis and clustering for categorical data,clustering and ordination techniques for quantitative data and nonlinearprincipal component analysis for mixed data, were undertaken. The results ofmost analyses supported the existence of the two major gene pools. However, theanalysis of categorical data of protein types showed an additional minor genepool. The minor gene pool is designated North Andean and includes phaseolintypes CH, S and T; lectin types 312, Pr, B and K; and mostly A5, A6 and A4 types-amylase inhibitor. Analysis of the combined categorical data ofprotein types and some plant categorical data also suggested that some othergermplasm with C type phaseolin are distinguished from the major gene pools.     

Phaseolin diversity in wild Lima bean (Phaseolus lunatus L.) in American centres of origin

Summary Phaseolin variability was analyzed in 86 wild Phaseolus lunatus accessions, representing a wide geographical distribution from Mexico to Argentina, to determine geographical patterns of variability. The collection can be divided into two major groups. One group consists of accessions from Mexico, Central America, Cuba, Columbia, Argentina showing two Mesoamerican (M) phaseolin pattern types, already described in cultivated materials, as well as a variety of additional banding patterns. This suggests that at least two genotypes in the Mesoamerican gene pool were involved in a domestication process and spread throughout the world. The other group, consisting of wild Andean (A) forms from Northern Peru and belonging to the Andean gene pool, showed, among others, two A pattern types comparable to those found in cultivated large-seeded accessions.     

Extensive introgression of Middle American germplasm into Chilean common bean cultivars

Summary The genetic diversity of 95. representative Chilean common bean (Phaseolus vulgaris L.) landraces was analyzed using phaseolin seed protein and eight isozyme systems as genetic markers. Four types of phaseolin were found, “C”, “T”, “S” and “H”, in decreasing order of frequency. Each type had a different distribution between the Northern and Southern regions of the country. Nei’s genetic distance based on isozyme diversity indicated that a high percentage of the total variation found in this sample occurred between landraces and only a small percentage of the variation was detected within populations. Cluster analysis based on Nei’s genetic distance and a principal component analysis of isozyme frequencies did not detect a clear association between the geographic distribution of the landraces and their isozyme constitution. However, Nei’s genetic distance analysis clustered the bean landraces into two major groups which had a specific isozyme pattern, seed color, and seed size. The genetic analysis also detected a rare polymorphism for theMdh-2 locus, a null allele at theDiap-2 locus, and polymorphism for theAco-2 locus. The principal component analysis of isozyme frequencies showed that only 30% of the genotypes analyzed were similar to the Andean check and 5% of the samples were similar to Middle American check. This finding suggests a high frequency of hybridization between the Middle America and Andean gene pools in cultivated common bean from Chile.     

Diversity of common bean (Phaseolus vulgaris L.) germplasm from Portugal

Common bean (Phaseolus vulgarisL.) is a traditional crop in Portugal, where farmers growvarieties selected and maintained by themselves. A collection of 88landraces of common bean was evaluated for 17 quantitative andqualitative traits and the biochemical marker phaseolin to displaythe degree of variation of this germplasm. Agronomic data weresubjected to cluster analysis and several groups were identified,with three groups clustering most of the landraces. Regardingphaseolin variation the C and T banding patterns are the mostfrequent ones, so the origin of the Portuguese beans is thus probablythe Andean region of South America. These results give informationabout the origin, diversity and breeding value of the Portuguesegermplasm, that could be useful to widen the genetic base ofcurrently cultivated bean varieties in Europe.     

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. Contribution n. 40 from Institute of Plant Genetics-CNR, Bari, Italy.     

Insight into the origin of common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.) grown in the state of Jammu and Kashmir of north-western Himalayas

Common bean (Phaseolus vulgaris L.) is considered as one of the principal grain legume crops grown in north-western Himalayan state of Jammu and Kashmir (J&K), India. Huge diversity has been observed for this crop in state Jammu and Kashmir. The hilly regions of the state J&K are famous for producing high quality, tasty and highly flavoured beans. In order to characterise this huge diversity and trace the origin of common bean, systematic efforts have been made for the first time in collection, evaluation and characterization of bean collection from Jammu & Kashmir. A set of 428 common bean lines were initially collected/procured and based on cluster analysis using few qualitative traits/site of collection, a diverse set of 96 lines was selected. The PCR assay for phaseolin locus led to the characterization of 96 lines into Meso-american and Andean types. Out of 96 lines tested, 45 possessed “S” type phaseolin and 51 possess “T” type phaseolin. The ITS region of selected local and exotic lines was Sanger sequenced and the sequence analysis of ~ 800 bp long region revealed the presence of 12 SNPs including one promising SNPs showing significant association with phaseolin patterns. The clustering based on ITS sequence data led to the clear cut separation of common bean lines into two distinct clusters based on their phaseolin types. The results of the present study helped to gain insights into the origin of common bean landraces grown in state of J&K, India.     

Characterization of Some Italian Common Bean (<Emphasis Type="Italic">Phaseolus Vulgaris</Emphasis> L.) Landraces by RAPD,Semi-random and ISSR Molecular Markers

Randomly amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR) and a semi-random PCR system were used to analyze the genetic diversity of 16 Italian common bean landraces and their relationship to four commercial cultivars. Of the primers tested, 8 ISSR, 6 RAPD and 7 semi-random primers produced polymorphic and reproducible DNA fragments. A higher proportion of polymorphic bands were observed using ISSR (85%) and semi-random (90%) primers than RAPD (69%) method. The combination of any two semi-random markers allowed the identification of all 20 bean genotypes. In contrast ISSR (except for primer (CAC)₃GC) and RAPD markers appeared to be less informative as more than two markers were necessary to achieve the same diagnostic level. Moreover, 7 ISSR, 2 RAPD and 8 semi-random exclusive bands were identified as putative population-specific markers. Semi-random and ISSR derived dendrograms showed similar tendencies in terms of genetic relatedness, whereas clustering of genotypes within groups was not similar when compared with the RAPD technique. Despite the different ability to resolve genetic variation among the investigated landraces, two major clusters with less than 60% (ISSR) and 40% (RAPD and semi-random) genetic similarity were formed with all three marker systems. The two groups were correlated with the phaseolin patterns and seed size of the landraces. The analysis showed that the cultivar ȁ8Lingua di Fuocoȁ9 and most of the landraces (13 out of 16) collected in Italy belong to the Andean gene pool, whereas only the three populations from Pratomagno belong to the Middle American gene pool.     

Genetic relationships and diversity among Brazilian cultivars and landraces of common beans (Phaseolus vulgaris L.) revealed by AFLP markers

The genetic variation and relationships among 31 accessions of Phaseolus vulgaris L., and two representatives of Vigna unguiculata L., were evaluated by AFLP analysis. A total of 263 DNA fragments across all materials were scored using nine primer combinations, averaging 32 per primer. More than 95% of the amplification products showed polymorphism, indicating high variation at the DNA level among these accessions. Pair-wise genetic similarity (Jaccard's coefficient) ranged from 0.553 to 0.840, with a mean of 0.765. Twenty-three accessions (70%) clustered into three groups. A majority of the commercial cultivars (91%) clustered within a single group, whereas the landraces were distributed along all the variation. An apparent correlation with phaseolin types was detected. Results of this study suggest that Brazilian landraces truly represent the overall genetic variability of Phaseolus vulgaris, confirming the multiple origins of these materials, and their potential as a source of variation for breeding programs.     

Molecular characterisation of common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.) accessions from Southwestern Uganda reveal high levels of genetic diversity

Common bean (Phaseolus vulgaris L.) was introduced to East Africa over 400 years ago and is today a fundamental part of food and income security of many smallholder farmers in the region. East Africa is among the top three bean producing and consuming regions of Africa with Uganda, Rwanda and Kenya being leaders in production. The leading common bean producing region in Uganda is the Southwestern (SW) highlands. Production is subsistent and farmers grow mixed varieties (accessions) to minimize losses. The aim of this study was to investigate the impact of farmer selection and production practices on genetic diversity of common bean in SW Uganda. 100 accessions were assembled from SW Uganda and assayed with 6 DNA simple sequence repeat (SSR) markers. A total of 41 alleles were detected giving an overall average gene diversity of 0.299 (30%) in both districts. The accessions clustered into two major gene pools i.e., Mesoamerican and Andean. Within each gene pool there was evidence of clonal populations suggesting wide distribution of certain accessions. Kabale district had a higher average gene diversity (38%) compared to Kisoro district (22%). Detection of Andean phaseolin in a clone set of Mesoamerican gene pool suggests introgession between the two groups.     

Antioxidant profiling of native Andean potato tubers (Solanum tuberosum L.) reveals cultivars with high levels of beta-carotene, alpha-tocopherol, chlorogenic acid, and petanin

The antioxidant profile of 23 native Andean potato cultivars has been investigated from a human nutrition perspective. The main carotenoid and tocopherol compounds were studied using high-performance liquid chromatography coupled with a diode array detector (HPLC-DAD) and a fluorescence detector, respectively, whereas polyphenols (including anthocyanins in colored tubers) were identified by means of both HPLC-mass spectrometry and HPLC-DAD. Antioxidant profiling revealed significant genotypic variations as well as cultivars of particular interest from a nutritional point of view. Concentrations of the health-promoting carotenoids, lutein and zeaxanthin, ranged from 1.12 to 17.69 microg g(-1) of dry weight (DW) and from 0 to 17.7 microg g(-1) of DW, with cultivars 704353 and 702472 showing the highest levels in lutein and zeaxanthin, respectively. Whereas beta-carotene is rarely reported in potato tubers, remarkable levels of this dietary provitamin A carotenoid were detected in 16 native varieties, ranging from 0.42 to 2.19 microg g(-1) of DW. The amounts of alpha-tocopherol found in Andean potato tubers, extending from 2.73 to 20.80 microg g(-1) of DW, were clearly above the quantities generally reported for commercial varieties. Chlorogenic acid and its isomers dominated the polyphenolic profile of each cultivar. Dark purple-fleshed tubers from the cultivar 704429 contained exceptionally high levels of total anthocyanins (16.33 mg g(-1) of DW). The main anthocyanin was identified as petanin (petunidin-3-p-coumaroyl-rutinoside-5-glucoside). The results suggest that Andean potato cultivars should be exploited in screening and breeding programs for the development of potato varieties with enhanced health and nutritional benefits.     

Phaseolin in vitro pepsin digestibility: role of acids and phenolic compounds

Great Northern bean (Phaseolus vulgaris L.) phaseolin proteolysis at 37 degrees C, varying HCl concentrations (10 mM to 1 M), phaseolin:pepsin ratios ranging from 5:1 to 100:1 (w/w), and incubation times up to 24 h was investigated. The results suggest that phaseolin is not resistant to in vitro pepsin hydrolysis. At a phaseolin-to-pepsin ratio of 100:1 (w/w), native phaseolin was completely digested in 24 h when incubated in 50 mM HCl, while heat-denatured phaseolin (30 min at 100 degrees C, boiling water bath) was digested in 1 h under similar conditions. When incubated at 37 degrees C for 24 h, acid alone, even at as low a concentration as 10 mM, caused a partial breakdown of native phaseolin. The degree of phaseolin hydrolysis by HCl was dependent on the acid concentration used. The rate of native phaseolin hydrolysis increased with increasing HCl concentration rather than pepsin concentration. Common food acids were able to partially hydrolyze phaseolin. Among the food acids tested, oxalic acid was the most effective in hydrolyzing phaseolin. Spectroscopic studies revealed a significant change in secondary and tertiary structures when native phaseolin was incubated in dilute HCl. None of the tested phenolic compounds adversely affected phaseolin hydrolysis by pepsin.     

Increase of potato genetic resources in their center of diversity: the role of natural outcrossing and selection by the Andean farmer

Summary The Andean farmer conserves and maintains the existing genetic diversity of potato cultivars by means of clonal propagation of tubers. However, surveys of traditional farms showed that botanical seed propagation was used for disease elimination, stock rejuvenation and the creation of new cultivars. Electrophoretic surveys based on 542 tubers collected from 18 markets sampled in the Cusco area disclosed a total of 229 different cultivars from diploid, triploid and tetraploid forms of Solanum tuberosum L. These could be classified by isozyme cluster analysis into four major groups and six minor groups. However, they did not agree with groups based on flesh or skin color. It is therefore concluded that all genotypes belong to a single, large gene pool with considerable gene flow between cultivars of different groups. When the samples were grouped by the three most common tuber skin colors, namely red/pink (Q'ompis type), purple (Yana Imilla type), and yellowish/brown (Yuraq Kusi type), similar allozymes were observed in all three classes. The structure of the isozymic phenotypes within each group indicate that they may have been derived as segregants after outcrossing of diverse parental types. In order to provide further evidence for the origin of new types by hybridization, two segregating diploid progenies were generated by crossing purple by yellow skin types. In the resulting F₁, most of the tuber phenotypes observed in the Andean varieties were reproduced in these crosses. It can be concluded that the Andean potatoes form a large and plastic gene pool amplified and renovated by outcrossing followed in some cases by human selection of desirable phenotypes.     

Breadmaking Use of Andean Crops Quinoa,Kañiwa,Kiwicha, and Tarwi

The effect of addition of flours from the highly nutritious Andean crops quinoa (Chenopodium quinoa), kañiwa (Chenopodium pallidicaule), kiwicha (Amaranthus caudatus), and tarwi (Lupinus mutabilis) has been investigated in wheat doughs and fresh bread quality. The thermomechanical profile of wheat doughs and bread quality has been explored by increasing substitution of wheat flour at 0–100% by Andean crop flours. Dough blends were evaluated using the Chopin Mixolab device, whereas bread quality assessment comprised sensory (overall acceptability) and physicochemical (moisture, specific volume, texture, color) determinations in composite breads. In general, no breads with aerated crumb structure could be obtained from 100% Andean crop flours, with the exception of quinoa breads that had overall sensory values about half a completely perfect score, and which were not significantly different from the breads made from a 50:50 blend of wheat and quinoa. Replacement of wheat flour by ≤12.5% (tarwi), 25% (kañiwa), and 50% (kiwicha), respectively, still produced breads with good sensory acceptability but variable color and doughs with acceptable thermomechanical patterns. Partial substitution of wheat flour by Andean crop flours constitutes a viable option to improve the nutritional value of the breads, with acceptable technological performance of dough blends and composite breads.     

Investigation of the genetic structure of some common bean (Phaseolus vulgaris L.) commercial varieties and genotypes used as a genitor with SSR and SNP markers

Common bean is a species belonging to the Phaseolus genus of the Leguminosae family. It has economic importance due to being rich in protein, vitamin A and C, and minerals. Being one of the most cultivated species of legumes, the determination of genetic diversity in bean genotypes or populations has an important role in terms of our genetic resources. The objective of this study was to evaluate the genetic structure of 94 genotypes which were cultivated in different parts of the world and our country with SSR and SNP markers. 10 SSR loci and 73 SNP primers were used for the determination of genetic structure in commercial cultivars and breeding lines. All of the SSR and SNP loci used in the study were found to be polymorphic. A total of 89 alleles were identified for 10 SSR loci. Mean number of alleles per locus (Na?=?8.9), effective allele number (Ne?=?3.731), Shannon information index (I?=?1.468), observed heterozygosity (Ho?=?0.023), and expected heterozygosity (He?=?0.654) were calculated based on SSR analysis. According to the results of Bayesian-based STRUCTURE analysis using SSR and SNP data, 94 bean genotypes were genetically divided into three main clusters. According to genetic distance based UPGMA dendrogram obtained from SNP analysis, 94 bean genotypes were divided into 2 main clusters corresponding Mesoamerican and Andean gene pools. The obtained results provide important information about the genetic structures of the studied bean cultivars and breeding lines. With the obtained results, it will be possible to develop breeding programs to develop new cultivars by using our gene resources.