Genetic diversity and relationships among 192 public common bean inbred lines assessed by SSR markers.

Knowledge of germplasm diversity and of relationships among elite breeding materials has a significant impact on the improvement of crop plants and on the development of strategies for genetic resources management and exploration. The present study was conducted to determine the level of genetic variation and relatedness among some selected common bean varieties by using microsatellite markers. In this investigation, we used 61 SSRs to fingerprint 192 common bean inbred public lines released over the last 50 years in the U.S.A. All the lines are commercial seed type classes that are grown in the USA and include both dry bean classes and snap beans for the fresh and processing markets.The 344 alleles identified were used as raw data for estimating the amount of diversity and to describe the genetic structure of the commercial bean gene pool. A model-based clustering analysis placed the varieties in six clusters that correspond to major breeding groups plus a set of lines showing evidence of mixed origins. Neighbor-joining tree was constructed to further assess the genetic structure of common bean lines, showing good agreement with the pedigree information and the cluster analysis. A significant fixation index FST, also revealed genetic substructure within the U.S. common bean gene pool with Kidney and Pinto-Great Northern beans being the most different from the other varietal groups.The results of this study - based on a much larger number of SSRs -confirm a previous observation indicating a relatively low level of genetic variation and a molecular variability that parallels phenotypic characters distinguishing different commercial groups. Our results indicate also a strong subpopulation structure and provide additional tools for breeding and breeder’s rights implementation

Identification and characterization in common bean of a putative homologue to the Arabidopsis Indehiscent gene.

Pod shattering represents a key component of the domestication syndrome in common bean, because it makes this species dependent upon the farmer for seed dispersal. Attempts to elucidate the genetic control of this process have led to the identification of a major gene(St) linked to the presence of pod suture fibers involved in pod shattering. Although St has been placed on the common bean genetic map, the sequence and the specific functions of this gene remain unknown. The purpose of the current study was to identify a candidate gene for St. Arabidopsis thaliana INDEHISCENT gene (IND) is the primary factory required for silique shattering. A sequence homologous to IND was successfully amplified in Phaseolus vulgaris and mapped on the common bean map using two recombinant inbred population (BAT93 x Jalo EEP558; Midas x G12873). Although PvIND maps near the St locus, the lack of complete co-segregation between PvIND and St and the lack of polymorphisms at the PvIND locus correlating with the dehiscent/indehiscent phenotype suggests that PvIND may be not directly involved in pod shattering and may not be the gene underlying the St locus. Alternatively, a more precise phenotyping method needs to be developed to more accurately map the St locus

Beans ( Phaseolus spp.) - model food legumes

Globally, 800 million people are malnourished. Heavily subsidised farmers in rich countries produce sufficient surplus food to feed the hungry, but not at a price the poor can afford. Even donating the rich world's surplus to the poor would not solve the problem. Most poor people earn their living from agriculture, so a deluge of free food would destroy their livelihoods. Thus, the only answer to world hunger is to safeguard and improve the productivity of farmers in poor countries. Diets of subsistence level farmers in Africa and Latin America often contain sufficient carbohydrates (through cassava, corn/maize, rice, wheat, etc.), but are poor in proteins. Dietary proteins can take the form of scarce animal products (eggs, milk, meat, etc.), but are usually derived from legumes (plants of the bean and pea family). Legumes are vital in agriculture as they form associations with bacteria that 'sfix-nitrogen' from the air. Effectively this amounts to internal fertilisation and is the main reason that legumes are richer in proteins than all other plants. Thousands of legume species exist but more common beans (Phaseolus vulgaris L.) are eaten than any other. In some countries such as Mexico and Brazil, beans are the primary source of protein in human diets. As half the grain legumes consumed worldwide are common beans, they represent the species of choice for the study of grain legume nutrition. Unfortunately, the yields of common beans are low even by the standards of legumes, and the quality of their seed proteins is sub-optimal. Most probably this results from millennia of selection for stable rather than high yield, and as such, is a problem that can be redressed by modern genetic techniques. We have formed an international consortium called Phaseomics' to establish the necessary framework of knowledge and materials that will result in disease-resistant, stress-tolerant, high-quality protein and high-yielding beans. Phaseomics will be instrumental in improving living conditions in deprived regions of Africa and the Americas. It will contribute to social equity and sustainable development and enhance inter- and intra-cultural understanding, knowledge and relationships. A major goal of Phaseomics is to generate new common bean varieties that are not only suitable for but also desired by the local farmer and consumer communities. Therefore, the socio-economic dimension of improved bean production and the analysis of factors influencing the acceptance of novel varieties will be an integral part of the proposed research (see Figure 1). Here, we give an overview of the economic and nutritional importance of common beans as a food crop. Priorities and targets of current breeding programmes are outlined, along with ongoing efforts in genomics. Recommendations for an international coordinated effort to join knowledge, facilities and expertise in a variety of scientific undertakings that will contribute to the overall goal of better beans are given. To be rapid and effective, plant breeding programmes (i.e., those that involve crossing two different 'sparents') rely heavily on molecular 'smarkers'. These genetic landmarks are used to positio

Pod indehiscence is a domestication and aridity resilience trait in common bean.

Plant domestication has strongly modified crop morphology and development. Nevertheless, many crops continue to display atavistic characteristics that were advantageous to their wild ancestors but are deleterious under cultivation, such as pod dehiscence (PD). Here, we provide the first comprehensive assessment of the inheritance of PD in the common bean (Phaseolus vulgaris), a major domesticated grain legume. Using three methods to evaluate the PD phenotype, we identified multiple, unlinked genetic regions controlling PD in a biparental population and two diversity panels. Subsequently, we assessed patterns of orthology among these loci and those controlling the trait in other species. Our results show that different genes were selected in each domestication and ecogeographic race. A chromosome Pv03 dirigent-like gene, involved in lignin biosynthesis, showed a base-pair substitution that is associated with decreased PD. This haplotype may underlie the expansion of Mesoamerican domesticates into northern Mexico, where arid conditions promote PD. The rise in frequency of the decreased-PD haplotype may be a consequence of the markedly different fitness landscape imposed by domestication. Environmental dependency and genetic redundancy can explain the maintenance of atavistic traits under domestication

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

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

Genetic diversity analysis of common beans based on molecular markers

A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation

Tagging the Signatures of Domestication in Common Bean (Phaseolus vulgaris) by Means of Pooled DNA Samples

-Background and Aims: The main aim of this study was to use an amplified fragment length polymorphism (AFLP)-based, large-scale screening of the whole genome of Phaseolus vulgaris to determine the effects of selec- tion on the structure of the genetic diversity in wild and domesticated populations. -Methods: Using pooled DNA samples, seven each of wild and domesticated populations of P. vulgaris were studied using 2506 AFLP markers (on average, one every 250 kb). About 10% of the markers were also analysed on indi- -Key Results: The most important outcome is that a large fraction of the genome of the common bean (16 %; P, 0.01) appears to have been subjected to effects of selection during domestication. Markers obtained in indivi- vidual genotypes and were used to infer allelic frequencies empirically from bulk data. In both data sets, tests were made to determine the departure from neutral expectation for each marker using an FST-based method. dual genotypes were also mapped and classified according to their proximities to known genes and quantitative trait loci (QTLs) of the domestication syndrome. Most of the markers that were found to be potentially under the effects of selection were located in the proximity of previously mapped genes and QTLs related to the domestication syndrome. - Conclusions: Overall, the results indicate that in P. vulgaris a large portion of the genome appears to have been subjected to the effects of selection, probably because of linkage to the loci selected during domestication. As most of the markers that are under the effects of selection are linked to known loci related to the domestication syndrome, it is concluded that population genomics approaches are very efficient in detecting QTLs. A method based on bulk DNA samples is presented that is effective in pre-screening for a large number of markers to determine selection signatures

Genetically engineered organisms and the environment: Current status and recommendations

The Ecological Society of America has evaluated the ecological effects of current and potential uses of field-released genetically engineered organisms (GEOs), as described in this Position Paper. Some GEOs could play a positive role in sustainable agriculture, forestry, aquaculture, bioremediation, and environmental management, both in developed and developing countries. However, deliberate or inadvertent releases of GEOs into the environment could have negative ecological effects under certain circumstances. Possible risks of GEOs could include: (1) creating new or more vigorous pests and pathogens; (2) exacerbating the effects of existing pests through hybridization with related transgenic organisms; (3) harm to nontarget species, such as soil organisms, non-pest insects, birds, and other animals; (4) disruption of biotic communities, including agroecosystems; and (5) irreparable loss or changes in species diversity or genetic diversity within species. Many potential applications of genetic engineering extend beyond traditional breeding, encompassing viruses, bacteria, algae, fungi, grasses, trees, insects, fish, and shellfish. GEOs that present novel traits will need special scrutiny with regard to their environmental effects. The Ecological Society of America supports the following recommendations. (1) GEOs should be designed to reduce environmental risks. (2) More extensive studies of the environmental benefits and risks associated with GEOs are needed. (3) These effects should be evaluated relative to appropriate baseline scenarios. (4) Environmental release of GEOs should be prevented if scientific knowledge about possible risks is clearly inadequate. (5) In some cases, post-release monitoring will be needed to identify, manage, and mitigate environmental risks. (6) Science-based regulation should subject all transgenic organisms to a similar risk assessment framework and should incorporate a cautious approach, recognizing that many environmental effects are GEO- and site-specific. (7) Ecologists, agricultural scientists, molecular biologists, and others need broader training and wider collaboration to address these recommendations. In summary, GEOs should be evaluated and used within the context of a scientifically based regulatory policy that encourages innovation without compromising sound environmental management. The Ecological Society of America is committed to providing scientific expertise for evaluating and predicting the ecological effects of field-released transgenic organisms

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