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

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

Pancreatic alpha cell mass in European subjects with type 2 diabetes

AIMS/HYPOTHESIS: Type 2 diabetes is a bi-hormonal disease characterised by relative hypoinsulinaemia and hyperglucagonaemia with elevated blood glucose levels. Besides pancreatic beta cell defects, a low number of beta cells (low beta cell mass) may contribute to the insufficient secretion of insulin. In this study our aim was to determine whether the alpha cell mass is also altered. METHODS: Using a point counting method, we measured the ratio of alpha to beta cell areas in pancreas samples obtained at autopsy from 50 type 2 diabetic subjects, whose beta cell mass had previously been found to be 36% lower than that of 52 non-diabetic subjects. RESULTS: The topography of alpha and beta cells was similar in both groups: many alpha cells were localised in the centre of the islets and the ratio of alpha/beta cell areas increased with islet size. The average ratio was significantly higher in type 2 diabetic subjects (0.72) than in non-diabetic subjects (0.42), with, however, a large overlap between the two groups. In contrast, the alpha cell mass was virtually identical in type 2 diabetic subjects (366 mg) and non-diabetic subjects (342 mg), and was not influenced by sex, BMI or type of diabetes treatment. CONCLUSIONS: The higher proportion of alpha to beta cells in the islets of some type 2 diabetic subjects is due to a decrease in beta cell number rather than an increase in alpha cell number. This imbalance may contribute to alterations in the normal inhibitory influence exerted by beta cells on alpha cells, and lead to the relative hyperglucagonaemia observed in type 2 diabete

Identification of a Simple Sequence Repeat molecular-marker set for large-scale analyses of pear germplasm

Simple Sequence Repeats (SSR) are molecular markers suitable to assess the genetic variation of germplasm resources; however, large-scale SSR use requires protocol optimization. The present work aimed to identify SSR markers, developed for pear and other fruit species that are effective in characterizing pear germplasm collections and in demonstrating their use in providing support for genetic breeding programs. From a total of 62 SSR markers investigated, 23 yielding reproducible and polymorphic patterns were used to genotype a sample of 42 pear accessions of the Brazilian Pear Germplasm Bank (PGB). When compared to these 23 SSR markers, a subset of eleven markers, selected based on He, PIC and PId, was used to distinguish individual accessions and perform cluster analysis with similar efficacy. Genetic diversity analysis clustered the European, Japanese and Chinese accessions in distinct groups. This markers subset constitutes a valuable tool for several applications related to pear genetic resources management and breeding

Determinants of exocrine pancreatic function as measured by fecal elastase-1 concentrations (FEC) in patients with diabetes mellitus

<p>Abstract</p> <p>Objective</p> <p>Recently it has been shown that there is not only endocrine insufficiency in diabetic patients, but a frequent co-morbidity of both, the endocrine and exocrine pancreas. The present study was performed to further analyse the determinants of exocrine pancreatic function in patients with diabetes mellitus.</p> <p>Methods</p> <p>The records of 1992 patients with diabetes mellitus who had been treated in our hospital during a 2-year period were re-evaluated. Defined parameters were documented in standardized data sheets. Records were further checked for the results of imaging procedures of the pancreas. In 307 patients FEC had been performed and documented. Only these patients were included in further evaluation.</p> <p>Results</p> <p>FEC was inversely correlated with diabetes duration and HbA1c-levels but not with age. C-peptide levels correlated positively with FEC. BMI and FEC were also significantly correlated. There was no correlation between diabetes therapy and exocrine pancreatic function as there was no correlation with any concomitant medication. The presence of diabetes-associated antibodies was not related to FEC. According to the documented data 38 were classified as type-1 diabetes (12.4%), 167 as type-2 (54.4%), and 88 patients met the diagnostic criteria of type-3 (28.7%). Fourteen patients could not be classified because of lacking information (4.6%).</p> <p>Conclusions</p> <p>Exocrine insufficiency might be explained as a complication of diabetes mellitus. However, it is more likely that type-3 diabetes is much more frequent than previously believed. Consequently the evaluation of exocrine function and morphology should be included into the clinical workup of any diabetic patient at least at the time of manifestation.</p

Extension of the core map of common bean with EST-SSR, RGA, AFLP, and putative functional markers

Microsatellites and gene-derived markers are still underrepresented in the core molecular linkage map of common bean compared to other types of markers. In order to increase the density of the core map, a set of new markers were developed and mapped onto the RIL population derived from the ‘BAT93’ × ‘Jalo EEP558’ cross. The EST-SSR markers were first characterized using a set of 24 bean inbred lines. On average, the polymorphism information content was 0.40 and the mean number of alleles per locus was 2.7. In addition, AFLP and RGA markers based on the NBS-profiling method were developed and a subset of the mapped RGA was sequenced. With the integration of 282 new markers into the common bean core map, we were able to place markers with putative known function in some existing gaps including regions with QTL for resistance to anthracnose and rust. The distribution of the markers over 11 linkage groups is discussed and a newer version of the common bean core linkage map is proposed