Andean Gene Pool Research Articles

Testing Domestication Scenarios of Lima Bean (Phaseolus lunatus L.) in Mesoamerica: Insights from Genome-Wide Genetic Markers.

Plant domestication can be seen as a long-term process that involves a complex interplay among demographic processes and evolutionary forces. Previous studies have suggested two domestication scenarios for Lima bean in Mesoamerica: two separate domestication events, one from gene pool MI in central-western Mexico and another one from gene pool MII in the area Guatemala-Costa Rica, or a single domestication from gene pool MI in central-western Mexico followed by post-domestication gene flow with wild populations. In this study we evaluated the genetic structure of the wild gene pool and tested these two competing domestication scenarios of Lima bean in Mesoamerica by applying an ABC approach to a set of genome-wide SNP markers. The results confirm the existence of three gene pools in wild Lima bean, two Mesoamerican gene pools (MI and MII) and the Andean gene pool (AI), and suggest the existence of another gene pool in central Colombia. The results indicate that although both domestication scenarios may be supported by genetic data, higher statistical support was given to the single domestication scenario in central-western Mexico followed by admixture with wild populations. Domestication would have involved strong founder effects reflected in loss of genetic diversity and increased LD levels in landraces. Genomic regions affected by selection were detected and these may harbor candidate genes related to domestication.

Establishing the Bases for Introducing the Unexplored Portuguese Common Bean Germplasm into the Breeding World.

Common bean (Phaseolus vulgaris L.) is among the most important grain legumes for human consumption worldwide. Portugal has a potentially promising common bean germplasm, resulting from more than five centuries of natural adaptation and farmers' selection. Nevertheless, limited characterization of this resource hampers its exploitation by breeding programs. To support a more efficient conservation of the national bean germplasm and promote its use in crop improvement, we performed, for the first time, a simultaneous molecular marker (21 microsatellites and a DNA marker for phaseolin-type diversity analysis) and seed and plant morphological characterization (14 traits) of 175 accessions from Portuguese mainland and islands traditional bean-growing regions. A total of 188 different alleles were identified and an average pairwise Cavalli-Sforza and Edwards' chord genetic distance of 0.193 was estimated among accessions. To relate the Portuguese germplasm with the global common bean diversity, 17 wild relatives and representative accessions from the Andean and Mesoamerican gene pools were evaluated at the molecular level. No correlation was detected between the variability found and the geographic origin of accessions. Structure analysis divided the collection into three main clusters. Most of the Portuguese accessions grouped with the race representatives and wild relatives from the Andean region. One third of the national germplasm had admixed genetic origin and might represent putative hybrids among gene pools from the two original centers of domestication in the Andes and Mesoamerica. The molecular marker-based classification was largely congruent with the three most frequent phaseolin haplotype patterns observed in the accessions analyzed. Seed and plant morphological characterization of 150 Portuguese common bean accessions revealed a clear separation among genetic structure and phaseolin haplotype groups of accessions, with seed size and shape and the number of locules per pod the most discriminant traits. Additionally, we used molecular and morphological data to develop a series of smaller core collections that, by maximizing the genetic and morphological diversity of the original collection, represents the Portuguese common bean germplasm with minimum repetitiveness. A core collection with 37 accessions contained 100% of the genetic variation found in the entire collection. This core collection is appropriate for a more detailed characterization and should be explored, as a priority, in national and international common bean breeding efforts. Furthermore, the identified intermediate accessions (with admixed genetic origin) may have novel genetic combinations useful in future bean breeding.

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.

Beans (Phaseolus ssp.) as a Model for Understanding Crop Evolution.

Here, we aim to provide a comprehensive and up-to-date overview of the most significant outcomes in the literature regarding the origin of Phaseolus genus, the geographical distribution of the wild species, the domestication process, and the wide spread out of the centers of origin. Phaseolus can be considered as a unique model for the study of crop evolution, and in particular, for an understanding of the convergent phenotypic evolution that occurred under domestication. The almost unique situation that characterizes the Phaseolus genus is that five of its ∼70 species have been domesticated (i.e., Phaseolus vulgaris, P. coccineus, P. dumosus, P. acutifolius, and P. lunatus), and in addition, for P. vulgaris and P. lunatus, the wild forms are distributed in both Mesoamerica and South America, where at least two independent and isolated episodes of domestication occurred. Thus, at least seven independent domestication events occurred, which provides the possibility to unravel the genetic basis of the domestication process not only among species of the same genus, but also between gene pools within the same species. Along with this, other interesting features makes Phaseolus crops very useful in the study of evolution, including: (i) their recent divergence, and the high level of collinearity and synteny among their genomes; (ii) their different breeding systems and life history traits, from annual and autogamous, to perennial and allogamous; and (iii) their adaptation to different environments, not only in their centers of origin, but also out of the Americas, following their introduction and wide spread through different countries. In particular for P. vulgaris this resulted in the breaking of the spatial isolation of the Mesoamerican and Andean gene pools, which allowed spontaneous hybridization, thus increasing of the possibility of novel genotypes and phenotypes. This knowledge that is associated to the genetic resources that have been conserved ex situ and in situ represents a crucial tool in the hands of researchers, to preserve and evaluate this diversity, and at the same time, to identify the genetic basis of adaptation and to develop new improved varieties to tackle the challenges of climate change, and food security and sustainability.

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.

English

The Ethiopian genetic center is considered to be one of the secondary centers of diversity for the common bean. This study was conducted to characterize the distribution of genetic diversity between and within ecological/geographical regions of Ethiopia. A germplasm sample of 116 landrace accessions was developed, which represented different common bean production ecologies and seed types common in the country. This sample was then analyzed with 24 simple sequence repeat (SSR) markers to assess the genetic diversity within and between common bean landraces, classifying them based on SSR clustering, and determining relationships between genetic and agroecological diversity. Representatives of both Andean and Mesoamerican gene pools were identified by STRUCTURE software analysis, as well as a high proportion of hybrid accessions as evidenced by a STRUCTURE K = 2 preset. At the optimum K = 5 preset value, mixed membership of Andean and Mesoamerican genotypes in some of the clusters was also seen, which supported previous findings. Cluster analyses, principal coordinate analysis, and analysis of molecular variance all indicated clustering of accessions from different collection sites, accompanied by high gene flow levels, highlighting the significant exchange of planting materials among farmers in different growing regions in the country. Values of allelic diversity were comparable to those reported in previous similar studies, showcasing the high genetic diversity in the landrace germplasm studied. Moreover, the distribution of genetic diversity across various bean-growing population groups in contrasting geographical/ecological population groups suggests elevated but underutilized potential of Ethiopian germplasm in common bean breeding. In summary, this study demonstrated the geographical, as well as gene pool diversity in common bean germplasm of Ethiopia. This substantial diversity, in turn, should be utilized in future common bean breeding and conservation endeavors in the nation. Key words: Hybridity, simple sequence repeat, microsatellite, structure, seed exchange, gene flow.

Physiological traits associated with drought resistance in Andean and Mesoamerican genotypes of common bean (Phaseolus vulgaris L.)

Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption, and drought stress affects over 60 % of dry bean production worldwide. Field and rainout shelter studies were conducted at the International Center for Tropical Agriculture (CIAT), Palmira, Colombia to (i) evaluate phenotypic differences in drought resistance in Andean and Mesoamerican gene pools, (ii) identify genotypes of both Andean and Mesoamerican with superior drought resistance, and (iii) identify phenotypic traits that may be useful for breeding to improve drought resistance in common bean. A total of 24 bean genotypes, twelve genotypes belonging to Mesoamerican gene pool and twelve to Andean gene pool were evaluated under field with two levels of water supply (irrigated and rainfed) and managed drought under rainout shelter conditions. Results showed that five Mesoamerican lines SEA 5, SEA 15, SER 22, SER 16, SER 8 and one Andean line SEQ 1003 have superior resistance to drought. The superior performance of these lines under drought stress was associated with better canopy biomass at mid-pod filling that could be related to deeper root system and effective use of water, combined with efficient remobilization of photosynthates from vegetative structures to pod development (pod partitioning index, PPI) and grain filling (pod harvest index, PHI). Pod harvest index could be a useful selection criteria for drought resistance, to improve the efficiency of breeding programs for selecting superior genotypes of common bean.

CUBAN BEAN DIVERSITY: Study could lead to new germplam sources, markets

CUBAN BEAN DIVERSITY: Study could lead to new germplam sources, markets

SNP discovery in common bean by restriction-associated DNA (RAD) sequencing for genetic diversity and population structure analysis.

Researchers have made great advances into the development and application of genomic approaches for common beans, creating opportunities to driving more real and applicable strategies for sustainable management of the genetic resource towards plant breeding. This work provides useful polymorphic single-nucleotide polymorphisms (SNPs) for high-throughput common bean genotyping developed by RAD (restriction site-associated DNA) sequencing. The RAD tags were generated from DNA pooled from 12 common bean genotypes, including breeding lines of different gene pools and market classes. The aligned sequences identified 23,748 putative RAD-SNPs, of which 3357 were adequate for genotyping; 1032 RAD-SNPs with the highest ADT (assay design tool) score are presented in this article. The RAD-SNPs were structurally annotated in different coding (47.00%) and non-coding (53.00%) sequence components of genes. A subset of 384 RAD-SNPs with broad genome distribution was used to genotype a diverse panel of 95 common bean germplasms and revealed a successful amplification rate of 96.6%, showing 73% of polymorphic SNPs within the Andean group and 83% in the Mesoamerican group. A slightly increased He (0.161, n=21) value was estimated for the Andean gene pool, compared to the Mesoamerican group (0.156, n=74). For the linkage disequilibrium (LD) analysis, from a group of 580 SNPs (289 RAD-SNPs and 291 BARC-SNPs) genotyped for the same set of genotypes, 70.2% were in LD, decreasing to 0.10%in the Andean group and 0.77% in the Mesoamerican group. Haplotype patterns spanning 310Mb of the genome (60%) were characterized in samples from different origins. However, the haplotype frameworks were under-represented for the Andean (7.85%) and Mesoamerican (5.55%) gene pools separately. In conclusion, RAD sequencing allowed the discovery of hundreds of useful SNPs for broad genetic analysis of common bean germplasm. From now, this approach provides an excellent panel of molecular tools for whole genome analysis, allowing integrating and better exploring the common bean breeding practices.

Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes.

BackgroundLegumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million year old whole genome duplication shared by most crop legumes.ResultsWe report the genome and the transcription atlas of coding and non-coding genes of a Mesoamerican genotype of common bean (Phaseolus vulgaris L., BAT93). Using a comprehensive phylogenomics analysis, we assessed the past and recent evolution of common bean, and traced the diversification of patterns of gene expression following duplication. We find that successive rounds of gene duplications in legumes have shaped tissue and developmental expression, leading to increased levels of specialization in larger gene families. We also find that many long non-coding RNAs are preferentially expressed in germ-line-related tissues (pods and seeds), suggesting that they play a significant role in fruit development. Our results also suggest that most bean-specific gene family expansions, including resistance gene clusters, predate the split of the Mesoamerican and Andean gene pools.ConclusionsThe genome and transcriptome data herein generated for a Mesoamerican genotype represent a counterpart to the genomic resources already available for the Andean gene pool. Altogether, this information will allow the genetic dissection of the characters involved in the domestication and adaptation of the crop, and their further implementation in breeding strategies for this important crop.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-0883-6) contains supplementary material, which is available to authorized users.

<b>AFLP analysis of genetic diversity in determinate and indeterminate snap bean accessions

The present study aimed to estimate and characterize the genetic divergence between determinate and indeterminate snap bean accessions from the Universidade Estadual de Londrina (UEL) germplasm bank based on amplified fragment length polymorphism (AFLP) markers. A total of 40 and 32 accessions with determinate and indeterminate growth habits, respectively, were characterized for this purpose. Seven combinations of primers corresponding to EcoR1 and Mse1 were tested for the AFLP analysis, and the combinations E-AAG/M-CTC, E-ACT/M-CTT and E-ACC/M-CTT were selected. These selective AFLP combinations revealed 485 informative loci in total, and the combination E-ACC/M-CTT detected the greatest number of informative loci (49%). The analysis of dissimilarity frequency distribution showed that the distribution was uniform, ranging from 0.1285 to 0.7310 with a mean of 0.4801, and the accessions with indeterminate growth habits exhibited greater variability than the accessions with determinate growth habits. The clustering UPGMA, PCoA and Bayesian analyses showed the formation of two large clusters, wherein there is a possible association between snap bean growth habit and gene pool. The determinate accessions may be more closely associated with the Andean gene pool, while the indeterminate ones may be associated with the Mesoamerican gene pool. The Bayesian analysis showed accessions intermediate to both groups, suggesting introgression between the Andean and Mesoamerican gene pools.

Epistasis in intra- and inter-gene pool crosses of the common bean.

Epistasis has been shown to have an important role in the genetic control of several quantitative traits in the common bean. This study aimed to investigate the occurrence of epistasis in intra- and inter-pool gene crosses of the common bean. Four elite lines adapted to Brazilian conditions were used as parents, two from the Andean gene pool (ESAL 686; BRS Radiante) and two from the Mesoamerican gene pool (BRSMG Majestoso; BRS Valente). Four F2 populations were obtained: "A" (ESAL 686 x BRS Radiante), "B" (BRSMG Majestoso x BRS Valente), "C" (BRS Radiante x BRSMG Majestoso), and "D" (BRS Valente x ESAL 686). A random sample of F2 plants from each population was backcrossed to parents and F1 individuals, according to the triple test cross. Three types of progenies from each population were evaluated in contiguous trials. Seed yield and 100-seed weight were evaluated. Dominance genetic variance was predominant in most cases. However, the estimates of genetic variance may be biased by the occurrence of linkage disequilibrium and epistasis. Epistasis was detected for both traits; however, the occurrence differed among the populations and between the two traits. The results of this study reinforce the hypothesis that epistasis is present in the genetic control of traits in the common bean and suggest that the phenomenon is more frequent in inter-gene pool crosses than in intra-gene pool crosses.

Morphoagronomic characterization and genetic diversity of a common bean RIL mapping population derived from the cross Rudá x AND 277.

Recombinant inbred lines (RILs) are a valuable resource for building genetic linkage maps. The presence of genetic variability in the RILs is essential for detecting associations between molecular markers and loci controlling agronomic traits of interest. The main goal of this study was to quantify the genetic diversity of a common bean RIL population derived from a cross between Rudá (Mesoamerican gene pool) and AND 277 (Andean gene pool). This population was developed by the single seed descent method from 500 F2 plants until the F10 generation. Seven quantitative traits were evaluated in the field in 393 RILs, the parental lines, and five control cultivars. The plants were grown using a randomized block design with additional controls and three replicates. Significant differences were observed among the RILs for all evaluated traits (P < 0.01). A comparison of the RILs and parental lines showed significant differences (P < 0.01) for the number of days to flowering (DFL) and to harvest (DH), productivity (PROD) and mass of 100 beans (M100); however, there were no significant differences for plant architecture, degree of seed flatness, or seed shape. These results indicate the occurrence of additive x additive epistatic interactions for DFL, DH, PROD, and M100. The 393 RILs were shown to fall into 10 clusters using Tocher's method. This RIL population clearly contained genetic variability for the evaluated traits, and this variability will be crucial for future studies involving genetic mapping and quantitative trait locus identification and analysis.

Genetic diversity of common bean accessions from former Yugoslav Republic of Macedonia as revealed by molecular and morphological markers

Cultivation of common bean has a long tradition in the Former Yugoslav Republic of Macedonia (FYROM) and is still nowadays important part of the human diet. In a study reported here 71 accessions from the FYROM were assessed for genetic diversity with the aim to provide information on genetic structure of Macedonian common bean germplasm and to depict its peculiarities. A total of 71 accessions were assessed using 13 microsatellite and 16 morphological markers. The average number of alleles per microsatellite was 5.8, and ranged from three to 16 alleles. High capacity of selected markers for distinguishing genotypes was identified by the calculation of a very low value of probability of identity. The relationship among 71 studied accessions was assessed by hierarchical cluster analysis. A very clear separation of accessions into two groups was observed in the UPGMA dendrogram. The larger represented Andean gene pool and contained 40 accessions (56% of total), while the other 31 accessions (44% of total) composed Mesoamerican gene pool. The two groups were successfully discriminated by eight morphological traits. Within the larger Andean cluster in the UPGMA dendrogram a sub-group of 16 climbing accessions was separated from 24 bush accessions. The absence of the string in the pods of the climbers suggests that this sub-group comprises snap beans grown primarily for their fresh pods. There were eight morphological traits in total that distinguished the two Andean sub-groups. Assessment of genetic relationship among accessions, their classification into respective gene pool and identification of morphological peculiarities provided valuable information for the management of plant gene bank and Macedonian bean breeding program.

A Phaseolus vulgaris Diversity Panel for Andean Bean Improvement

ABSTRACTDry beans (Phaseolus vulgaris L.) of the Andean gene pool, including red mottled, kidney, cranberry, and yellow seed types are important in Africa and the Americas. Andean dry bean breeding gains have lagged behind those of Mesoamerican beans. This difference may result from a narrower genetic base in the Andean gene pool and reduced breeding efforts. The objective of this research was to establish, genotype, and phenotype a panel of bean germplasm to be used for Andean dry bean breeding. An Andean diversity panel (ADP) was assembled, consisting of 396 accessions and including important cultivars, breeding lines, and landraces that originate mostly from Africa, the Caribbean, and North and South America. The panel was genotyped using the Illumina BARCBean6K_3 SNP BeadChip. The population contained two subgroups: Andean and Mesoamerican bean germplasm. The ADP was comprised of 349 Andean, 21 Mesoamerican, and 26 Andean–Mesoamerican admixed accessions. Most admixed lines came from Africa (12 accessions) and the Caribbean (five accessions). Association mapping was conducted for determinacy. Significant single‐nucleotide polymorphism (SNP) trait associations were found on chromosome Pv01, with the most significant SNP marker being 3.1 kb from the Terminal Flower 1 PvTFL1y gene. The ADP was evaluated for numerous traits in field trials in the United States and Africa. Variability was found for resistance to rust, angular leaf spot and common bacterial blight diseases; tolerance to low soil fertility; cooking time; and other traits that can be used to improve Andean bean germplasm for Africa and the Americas.

Examination of Genetic Diversity of Common Bean from the Western Balkans

In this study, genetic diversity of 119 accessions of common bean (Phaseolus vulgaris) from five former Yugoslav republics constituting the western Balkans was assessed by 13 microsatellite markers. This set of markers has proven before to efficiently distinguish between bean genotypes and assign them to either the Andean or the Mesoamerican gene pool of origin. In this study, 118 alleles were detected or 9.1 per locus on average. Four groups (i.e., Slovene, Croatian, Bosnian, and Serbian) showed similarly high levels of genetic diversity as estimated by the number of different alleles, number of effective alleles, Shannon’s information index, and expected heterozygosity. Mildly narrower genetic diversity was identified within a group of Macedonian accessions; however, this germplasm yielded the highest number of private alleles. All five germplasms share a great portion of genetic diversity as indicated by the analysis of molecular variance (AMOVA). On the basis of the scored number of migrants, we concluded that the most intensive gene flow in the region exists in Bosnia and Herzegovina. Cluster analysis based on collected molecular data classified the accessions into two large clusters that corresponded to two gene pools of origin (i.e., Andean and Mesoamerican). We found that Andean genotypes are more prevalent than Mesoamerican in all studied countries, except Macedonia, where the two gene pools are represented evenly. This could indicate that common bean was introduced into the western Balkans mainly from the Mediterranean Basin. Bayesian cluster analysis revealed that in the area studied an additional variation exists which is related to the Andean gene pool. Different scenarios of the origin of this variation are discussed in the article.

Molecular and Biological Characterization of Distinct Strains of Jatropha mosaic virus from the Dominican Republic Reveal a Potential to Infect Crop Plants.

In the Dominican Republic (DO), jatropha plants with yellow mosaic symptoms are commonly observed in and around fields of various crop plants. Complete nucleotide sequences of DNA-A and DNA-B components of four bipartite begomovirus isolates associated with symptomatic jatropha plants collected from three geographical locations in the DO were determined. Sequence comparisons revealed highest identities (91 to 92%) with the DNA-A component of an isolate of Jatropha mosaic virus (JMV) from Jamaica, indicating that the bipartite begomovirus isolates from the DO are strains of JMV. When introduced into jatropha seedlings by particle bombardment, the cloned components of the JMV strains from the DO induced stunting and yellow mosaic, indistinguishable from symptoms observed in the field, thereby fulfilling Koch's postulates for the disease. The JMV strains also induced disease symptoms in Nicotiana benthamiana, tobacco, and several cultivars of common bean from the Andean gene pool, including one locally grown in the DO. Asymmetry in the infectivity and symptomatology of pseudorecombinants provided further support for the strain designation of the JMV isolates from the DO. Thus, JMV in the DO is a complex of genetically distinct strains that have undergone local evolution and have the potential to cause disease in crop plants.

Genetic divergence in landraces of common bean (Phaseolus vulgarisL.) from the Nilgiris

Genetic diversity of common bean (Phaseolus vulgaris L.) was assessed based on morphological traits and RAPD markers. The principal component analysis identified eight components with eigenvalue above 1.0 and together explained 84.35% of the total variation. RAPD based dendrogram showed two major groups corresponding to the Andean and Mesoamerican gene pools. These bean landraces retain a considerable level of heterogeneity. Our results suggest that a deep knowledge of germplasm is the best strategy for preserving the diversity of common bean available with tribal farmers in remote villages of Nilgiri hills.

BAC-end microsatellites from intra and inter-genic regions of the common bean genome and their correlation with cytogenetic features.

Highly polymorphic markers such as simple sequence repeats (SSRs) or microsatellites are very useful for genetic mapping. In this study novel SSRs were identified in BAC-end sequences (BES) from non-contigged, non-overlapping bacterial artificial clones (BACs) in common bean (Phaseolus vulgaris L.). These so called “singleton” BACs were from the G19833 Andean gene pool physical map and the new BES-SSR markers were used for the saturation of the inter-gene pool, DOR364×G19833 genetic map. A total of 899 SSR loci were found among the singleton BES, but only 346 loci corresponded to the single di- or tri-nucleotide motifs that were likely to be polymorphic (ATT or AG motifs, principally) and useful for primer design and individual marker mapping. When these novel SSR markers were evaluated in the DOR364×G19833 population parents, 136 markers revealed polymorphism and 106 were mapped. Genetic mapping resulted in a map length of 2291 cM with an average distance between markers of 5.2 cM. The new genetic map was compared to the most recent cytogenetic analysis of common bean chromosomes. We found that the new singleton BES-SSR were helpful in filling peri-centromeric spaces on the cytogenetic map. Short genetic distances between some new singleton-derived BES-SSR markers was common showing suppressed recombination in these regions compared to other parts of the genome. The correlation of singleton-derived SSR marker distribution with other cytogenetic features of the bean genome is discussed.

Evaluating two-dimensional electrophoresis profiles of the protein phaseolin as markers of genetic differentiation and seed protein quality in common bean (Phaseolus vulgaris L.).

High-resolution two-dimensional electrophoresis (2-DE) profiles of the protein phaseolin, the major seed storage protein of common bean, display great number of spots with differentially glycosylated and phosphorylated α- and β-type polypeptides. This work aims to test whether these complex profiles can be useful markers of genetic differentiation and seed protein quality in bean populations. The 2-DE phaseolin profile and the amino acid composition were examined in bean seeds from 18 domesticated and wild accessions belonging to the Mesoamerican and Andean gene pools. We found that proteomic distances based on 2-DE profiles were successful in identifying the accessions belonging to each gene pool and outliers distantly related. In addition, accessions identified as outliers from proteomic distances showed the highest levels of methionine content, an essential amino acid deficient in bean seeds. These findings suggest that 2-DE phaseolin profiles provide valuable information with potential of being used in common bean genetic improvement.