New gene-derived simple sequence repeat markers for common bean (Phaseolus vulgaris L.)

Common bean is an important and diverse crop legume with several wild relatives that are all part of the Phaseoleae tribe of tropical crop legumes. Sequence databases have been a good source of sequences to mine for simple sequence repeats (SSRs). The objective of this research was to evaluate 14 sequence collections from common bean for SSRs and to evaluate the diversity of the polymorphic microsatellites derived from these collections. SSRs were found in 10 of the GenBank sequence collections with an average of 11.3% of sequences containing microsatellite motifs. The most common motifs were based on tri- and dinucleotides. In a marker development programme, primers were designed for 125 microsatellites which were tested on a panel of 18 common bean genotypes. The markers were named as part of the bean microsatellite-database (BMd) series, and the average polymorphism information content was 0.404 for polymorphic markers and predicted well the genepool structure of common beans and the status of the wild and cultivated accessions that were included in the study. Therefore, the BMd series of microsatellites is useful for multiple studies of genetic relatedness and as anchor markers in future mapping of wide crosses in the species.     

Development of mapped simple sequence repeat markers from common bean (Phaseolus vulgaris L.) based on genome sequences of a Chinese landrace and diversity evaluation

Microsatellite or single sequence repeat (SSR) markers have been commonly used in genetic research in many crop species, including common bean (Phaseolus vulgaris L.). A limited number of existing SSR markers have been designed from high-throughput sequencing of the genome, warranting the exploitation of new SSR markers from genomic regions. In this paper, we sequenced total DNA from the genotype Hong Yundou with a 454-FLX pyrosequencer and found numerous SSR loci. Based on these, a large number of SSR markers were developed and 90 genomic-SSR markers with clear bands were tested for mapping and diversity detection. The new SSR markers proved to be highly polymorphic for molecular polymorphism, with an average polymorphism information content value of 0.44 in 131 Chinese genotypes and breeding lines, effective for distinguishing Andean and Mesoamerican genotypes. In addition, we integrated 85 primers of the 90 polymorphism markers into the bean map using an F2 segregating population derived from Hong Yundou crossed with Jingdou. The distribution of SSR markers among 11 chromosomes was not random and tended to cluster on the linkage map, with 14 new markers mapped on chromosome Pv01, whereas only four loci were located on chromosome Pv04. Overall, these new markers have potential for genetic mapping, genetic diversity studies and map-based cloning in common bean.     

Integration of simple sequence repeat (SSR) markers into a molecular linkage map of common bean (Phaseolus vulgaris L.)

Microsatellite or simple sequence repeat (SSR) markers have been successfully used for genomic mapping, DNA fingerprinting, and marker-assisted selection in many plant species. Here we report the first successful assignment of 15 SSR markers to the Phaseolus vulgaris molecular linkage map. A total of 37 SSR primer pairs were developed and tested for amplification and product-length polymorphism with BAT93 and Jalo EEP558, the parental lines of an F7 recombinant inbred (RI) population previously used for the construction of a common bean molecular linkage map. Sixteen of the SSRs polymorphic to the parental lines were analyzed for segregation and 15 of them were assigned to seven different linkage groups, indicating a widespread distribution throughout the bean genome. Map positions for genes coding for DNAJ-like protein, pathogenesis-related protein 3, plastid-located glutamine synthetase, endochitinase, sn-glycerol-3 phosphate acyltransferase, NADP-dependent malic enzyme, and protein kinase were determined for the first time. Addition of three SSR loci to linkage group B4 brought two separated smaller linkage groups together to form a larger linkage group. Analysis of allele segregation in the F7 RI population revealed that all 16 SSRs segregated in the expected 1:1 ratio. These SSR markers were stable and easy to assay by polymerase chain reaction (PCR). They should be useful markers for genetic mapping, genotype identification, and marker-assisted selection of common beans.     

Genetic diversity of common bean (Phaseolus vulgaris L.) nodulating rhizobia in Nepal

Background and Aims

This study was conducted to reveal the genetic diversity of common bean (Phaseolus vulgaris L.) nodulating rhizobia in various agroecological regions in Nepal.

Method

A total of 63 strains were isolated from common bean grown in the soils collected from seven bean fields in Nepal and characterized based on the partial sequences of 16S–23S internal transcribed spacer (ITS) regions, 16S rDNA, nodC, and nifH. Symbiotic properties of some representative strains with host plants were examined to elucidate their characteristics in relation to genotype and their origin.

Results

The isolated strains belonged to Rhizobium leguminosarum, Rhizobium etli, Rhizobium phaseoli, and one unknown Rhizobium lineage, all belonging to a common symbiovar (sv.) phaseoli. Nine ITS genotypes were detected mainly corresponding to a single site, including a dominant group at three sites harboring highly diverse multiple ITS sequences. Three symbiotic genotypes corresponded to a geographical region, not to the ribosomal DNA group, suggesting horizontal transfer of symbiotic genes separately in each region. Great differences in nitrogenase activity and nodule forming ability among the strains irrespective of their species and origin were observed.

Conclusions

Nepalese Himalaya harbor phylogenetically highly diverse and site-specific strains of common bean rhizobia, some of which could have high potential of symbiotic nitrogen fixation.     

Microsatellite marker diversity in common bean (Phaseolus vulgaris L.)

A diversity survey was used to estimate allelic diversity and heterozygosity of 129 microsatellite markers in a panel of 44 common bean (Phaseolus vulgaris L.) genotypes that have been used as parents of mapping populations. Two types of microsatellites were evaluated, based respectively on gene coding and genomic sequences. Genetic diversity was evaluated by estimating the polymorphism information content (PIC), as well as the distribution and range of alleles sizes. Gene-based microsatellites proved to be less polymorphic than genomic microsatellites in terms of both number of alleles (6.0 vs. 9.2) and PIC values (0.446 vs. 0.594) while greater size differences between the largest and the smallest allele were observed for the genomic microsatellites than for the gene-based microsatellites (31.4 vs. 19.1 bp). Markers that showed a high number of alleles were identified with a maximum of 28 alleles for the marker BMd1. The microsatellites were useful for distinguishing Andean and Mesoamerican genotypes, for uncovering the races within each genepool and for separating wild accessions from cultivars. Greater polymorphism and race structure was found within the Andean gene pool than within the Mesoamerican gene pool and polymorphism rate between genotypes was consistent with genepool and race identity. Comparisons between Andean genotypes had higher polymorphism (53.0%) on average than comparisons among Mesoamerican genotypes (33.4%). Within the Mesoamerican parental combinations, the intra-racial combinations between Mesoamerica and Durango or Jalisco race genotypes showed higher average rates of polymorphism (37.5%) than the within-race combinations between Mesoamerica race genotypes (31.7%). In multiple correspondance analysis we found two principal clusters of genotypes corresponding to the Mesoamerican and Andean gene pools and subgroups representing specific races especially for the Nueva Granada and Peru races of the Andean gene pool. Intra population diversity was higher within the Andean genepool than within the Mesoamerican genepool and this pattern was observed for both gene-based and genomic microsatellites. Furthermore, intra-population diversity within the Andean races (0.356 on average) was higher than within the Mesoamerican races (0.302). Within the Andean gene pool, race Peru had higher diversity compared to race Nueva Granada, while within the Mesoamerican gene pool, the races Durango, Guatemala and Jalisco had comparable levels of diversity which were below that of race Mesoamerica.     

Microsatellite diversity and genetic structure among common bean (Phaseolus vulgaris L.) landraces in Brazil, a secondary center of diversity

Brazil is the largest producer and consumer of common bean (Phaseolus vulgaris L.), which is the most important source of human dietary protein in that country. This study assessed the genetic diversity and the structure of a sample of 279 geo-referenced common bean landraces from Brazil, using molecular markers. Sixty-seven microsatellite markers spread over the 11 linkage groups of the common bean genome, as well as Phaseolin, PvTFL1y, APA and four SCAR markers were used. As expected, the sample showed lower genetic diversity compared to the diversity in the primary center of diversification. Andean and Mesoamerican gene pools were both present but the latter gene pool was four times more frequent than the former. The two gene pools could be clearly distinguished; limited admixture was observed between these groups. The Mesoamerican group consisted of two sub-populations, with a high level of admixture between them leading to a large proportion of stabilized hybrids not observed in the centers of domestication. Thus, Brazil can be considered a secondary center of diversification of common bean. A high degree of genome-wide multilocus associations even among unlinked loci was observed, confirming the high level of structure in the sample and suggesting that association mapping should be conducted in separate Andean and Mesoamerican Brazilian samples.     

Genetic diversity of rhizobia nodulating common bean (Phaseolus vulgaris L.) in the Central Black Sea Region of Turkey

We have analyzed 30 rhizobial isolates obtained from common bean (Phaseolus vulgaris L.) root nodules grown in the Middle Blacksea Region of Turkey, using ARDRA and nucleotide sequence data. ARDRA analysis with enzymes CfoI, HinfI, NdeII, MspI and PstI revealed three patterns. Based on sequence data from 16S rDNA, the patterns were identified as, Rhizobium leguminosarum bv. phaseoli (n = 16), R. etli bv. phaseoli (n = 8) and R. phaseoli (n = 6). On the other hand, nucleotide sequence phylogenies of housekeeping genes (recA, atpD and glnII) selected to confirm the 16S rDNA phylogeny revealed different evolutionary relationships. These results suggested the possibility of lateral transfers of these genes amongst different rhizobial species (including R. leguminosarum, R. etli and R. phaseoli) sharing the same ecological niche (nodulating P. vulgaris) which also indicates that there may be no true genetic barier among these species. Phylogenetic analysis based on DNA sequence data from the nodA and nifH genes showed that all rhizobial species obtained in this study were carrying nodA and nifH haplotypes which were the same or similar to those of CFN42 (R. etli type strain), suggesting a further support for the lateral transfer of CFN42 Sym plasmid, p42, amongst Turkish common bean nodulating rhizobial isolates.     

Phylogeny and genetic diversity of native rhizobia nodulating common bean (Phaseolus vulgaris L.) in Ethiopia

The diversity and phylogeny of 32 rhizobial strains isolated from nodules of common bean plants grown on 30 sites in Ethiopia were examined using AFLP fingerprinting and MLSA. Based on cluster analysis of AFLP fingerprints, test strains were grouped into six genomic clusters and six single positions. In a tree built from concatenated sequences of recA, glnII, rpoB and partial 16S rRNA genes, the strains were distributed into seven monophyletic groups. The strains in the groups B, D, E, G1 and G2 could be classified as Rhizobium phaseoli, R. etli, R. giardinii, Agrobacterium tumefaciens complex and A. radiobacter, respectively, whereas the strains in group C appeared to represent a novel species. R. phaseoli, R. etli, and the novel group were the major bean nodulating rhizobia in Ethiopia. The strains in group A were linked to R. leguminosarum species lineages but not resolved. Based on recA, rpoB and 16S rRNA genes sequences analysis, a single test strain was assigned as R. leucaenae. In the nodC tree the strains belonging to the major nodulating groups were clustered into two closely linked clades. They also had almost identical nifH gene sequences. The phylogenies of nodC and nifH genes of the strains belonging to R. leguminosarum, R. phaseoli, R. etli and the putative new species (collectively called R. leguminosarum species complex) were not consistent with the housekeeping genes, suggesting symbiotic genes have a common origin which is different from the core genome of the species and indicative of horizontal gene transfer among these rhizobia.     

Genetic diversity of rhizobia in a Brazilian oxisol nodulating Mesoamerican and Andean genotypes of common bean (Phaseolus vulgaris L.)

Brazil is the largest producer and consumer of common bean worldwide, and the crop can benefit from its symbiosis with a variety of rhizobia by means of biological nitrogen fixation in root nodules. In this study, the role of Mesoamerican and Andean genotypes of common bean in trapping rhizobia directly from a Brazilian oxisol in the field or in pots in greenhouse conditions with unaltered or diluted soil solutions was investigated. Genetic diversity was evaluated by the profiles of BOX-PCR obtained, and by estimates of Shannon and Abundance-based Coverage Estimator (ACE) indices. Rhizobia trapped by Mesomaerican genotypes had greater diversity, reinforcing the hypothesis of an important and long-time contribution of this genetic center to the establishment of common bean in Brazil. Greater diversity was also seen in rhizobia trapped straight from the soil than from plants inoculated with diluted soil solutions, emphasizing a highly diverse and competitive rhizobial indigenous population. Studies on genetic diversity of common bean rhizobia are important not only for helping to understand the evolution of the legume-rhizobia symbiosis, but also to devise strategies to increase the contribution of the biological nitrogen-fixation process.     

2-DE-based proteomic analysis of common bean (Phaseolus vulgaris L.) seeds

Common bean (Phaseolus vulgaris L.) is the most important grain legume for direct human consumption. Proteomic studies in legumes have increased significantly in the last years but few studies have been performed to date in P. vulgaris. We report here a proteomic analysis of bean seeds by two-dimensional electrophoresis (2-DE). Three different protein extraction methods (TCA-acetone, phenol and the commercial clean-up kit) were used taking into account that the extractome can have a determinant impact on the level of quality of downstream protein separation and identification. To demonstrate the quality of the 2-DE analysis, a selection of 50 gel spots was used in protein identification by mass spectrometry (MALDI-TOF MS and MALDI-TOF/TOF). The results showed that a considerable proportion of spots (70%) were identified in spite of incomplete genome/protein databases for bean and other legume species. Most identified proteins corresponded to storage protein, carbohydrate metabolism, defense and stress response, including proteins highly abundant in the seed of P. vulgaris such as the phaseolin, the phytohemagglutinin and the lectin-related α-amylase inhibitor.     

Variability in nitrogen fixation of common bean (Phaseolus vulgaris L.) intercropped with maize

Thirty one selected bean lines were evaluated in the field for ability to support N₂ fixation when intercropped with maize which received 0, 30 and 60 kg N ha^–1 as ammonium sulphate. The amount of fixed N₂ was estimated using the natural variation of ¹⁵N and wheat as the standard non-fixing crop. Nitrogen as low as 15 kg N ha^–1 at sowing suppressed nodule weight and activity (acetylene reduction activity) but not nodule number, suggesting that the main effect of mineral N was on nodule development and function. ¹⁵N data revealed a high potential of the bean genotypes to fix N₂, with the most promising ones averaging between 50–60% of seed N coming from fixation. Bean lines CNF-480, Puebla-152, Mexico-309, Negro Argel, CNF-178, Venezuela-350 and WBR22-3, WBR22-50 and WBR22-55 were ranked as good fixers.     

Inheritance of partial resistance to bean rust in the common bean (Phaseolus vulgaris L.)

The inheritance of partial resistance within eight bean cultivars to a single-pustule isolate of bean rust was studied by means of a F₁ diallel test. General combining ability (GCA) and specific combining ability (SCA) were very highly significant over two seasons and in interaction with seasons. The partitioning of the sums of squares indicated the greater importance of GCA in the inheritance of the resistance. Reciprocal effects were not significant. The estimates of narrow-sense heritability in the two seasons were 0.899 ± 0.056 and 0.603 ± 0.065.     

Genetic mapping of two genes conferring resistance to powdery mildew in common bean (Phaseolus vulgaris L.)

Powdery mildew (PM) is a serious disease in many legume species, including the common bean (Phaseolus vulgaris L.). This study investigated the genetic control behind resistance reaction to PM in the bean genotype, Cornell 49242. The results revealed evidence supporting a qualitative mode of inheritance for resistance and the involvement of two independent genes in the resistance reaction. The location of these resistance genes was investigated in a linkage genetic map developed for the XC RIL population. Contingency tests revealed significant associations for 28 loci out of a total of 329 mapped loci. Fifteen were isolated or formed groups with less than two loci. The thirteen remaining loci were located at three regions in linkage groups Pv04, Pv09, and Pv11. The involvement of Pv09 was discarded due to the observed segregation in the subpopulation obtained from the Xana genotype for the loci located in this region. In contrast, the two subpopulations obtained from the Xana genotype for the BM161 locus, linked to the Co-3/9 anthracnose resistance gene (Pv04), and from the Xana genotype for the SCAReoli locus, linked to the Co-2 anthracnose resistance gene (Pv11), exhibited monogenic segregations, suggesting that both regions were involved in the genetic control of resistance. A genetic dissection was carried out to verify the involvement of both regions in the reaction to PM. Two resistant recombinant lines were selected, according to their genotypes, for the block of loci included in the Co-2 and Co-3/9 regions, and they were crossed with the susceptible parent, Xana. Linkage analysis in the respective F₂ populations supported the hypothesis that a dominant gene (Pm1) was located in the linkage group Pv11 and another gene (Pm2) was located in the linkage group Pv04. This is the first report showing the localization of resistance genes against powdery mildew in Phaseolus vulgaris and the results offer the opportunity to increase the efficiency of breeding programs by means of marker-assisted selection.     

Environmental response patterns in commercial classes of common bean (Phaseolus vulgaris L.)

Summary The yield data of 39 cultivars of diverse commercial classes of beans (Phaseolus vulgaris L.) planted in seven locations in Michigan were subjected to cluster and canonical variate analyses. The essential findings and conclusions can be summarized as follows: (1) Cluster analysis classified the cultivars into sub-sets or clusters almost identically coinciding with their commercial class designation. Canonical variate analysis completely confirmed the sub-groupings. Within class similarities were attributed to a narrow genetic base resulting from a common genetic relationship, or at least sharing of a common gene pool. (2) It was found that two clusters could possess almost identical mean (cluster mean) yields, and deviate in opposite directions over the same range of environments. (3) When total genotype × environmental interaction variance was partitioned into between and within clusters, the cluster × environment portion constituted 80% of the total. (4) These results imply that if the behavior of a given cultivar across a series of environments is known, the behavior of all other members of the class across a similar range of environments would be predictable.Journal Article No. 10329 of the Michigan Agricultural Experiment Station     

Generation means analysis of climbing ability in common bean (Phaseolus vulgaris L.)

Climbing common bean (Phaseolus vulgaris L.) genotypes have among the highest yield potential of all accessions found in the species. Genetic improvement of climbing beans would benefit from an understanding of the inheritance of climbing capacity (made up of plant height [PH] and internode length [IL] traits). The objective of this study was to determine the inheritance of climbing capacity traits in 3 crosses made within and between gene pools (Andean x Andean [BRB32 x MAC47], Mesoamerican x Mesoamerican [Tío Canela x G2333], and Mesoamerican x Andean [G2333 x G19839]) using generation means analysis. For each population, we used 6 generations (P(1), P(2), F(1), F(2), BC(1)P(1), and BC(1)P(2)) that were evaluated at 2 growth stages (40 and 70 days after planting). Results showed the importance of additive compared with the dominant-additive portion of the genetic model. Broad-sense heritabilities for the traits varied from 62.3% to 85.6% for PH and from 66.5% to 83.7% for IL. The generation means analysis and estimates of heritability suggested that the inheritance of PH and IL in climbing beans is relatively simple.     

Time course of N2 fixation in common bean (Phaseolus vulgaris L.)

Field and greenhouse experiments were conducted to assess the nitrogen fixation rates of four cultivars of common bean (Phaseolus vulgaris L.) at different growth stages. The ¹⁵N isotope dilution technique was used to quantify biological nitrogen fixation. In the greenhouse, cultivars M4403 and Kallmet accumulated 301 and 189 mg N plant^–1, respectively, up to 63 days after planting (DAP) of which 57 and 43% was derived from atmosphere. Under field conditions, cultivars Bayocel and Flor de Mayo RMC accumulated in 77 DAP, 147 and 135 kg N ha^–1, respectively, of which approximately one-half was derived from the atmosphere. The rates of N₂ fixation determined at different growth stages increased as the plants developed, and reached a maximum during the reproductive stage both under field and greenhouse conditions. Differences in translocation of N were observed between the cultivars tested, particularly under field conditions. Thus, the fixed N harvest index was 93 and 60 for cultivars Flor de Mayo and Bayocel, respectively. In early stages of growth, the total content of ureides in the plants correlated with the N fixation rates. The findings reported in the present paper can be used to build a strategy for enhancing biological N₂ fixation in common bean.