Genetic relationships among seven sections of genus Arachis studied by using SSR markers

<p>Abstract</p> <p>Background</p> <p>The genus <it>Arachis</it>, originated in South America, is divided into nine taxonomical sections comprising of 80 species. Most of the <it>Arachis </it>species are diploids (2<it>n </it>= 2<it>x </it>= 20) and the tetraploid species (2<it>n </it>= 2<it>x </it>= 40) are found in sections <it>Arachis</it>, <it>Extranervosae </it>and <it>Rhizomatosae</it>. Diploid species have great potential to be used as resistance sources for agronomic traits like pests and diseases, drought related traits and different life cycle spans. Understanding of genetic relationships among wild species and between wild and cultivated species will be useful for enhanced utilization of wild species in improving cultivated germplasm. The present study was undertaken to evaluate genetic relationships among species (96 accessions) belonging to seven sections of <it>Arachis </it>by using simple sequence repeat (SSR) markers developed from <it>Arachis hypogaea </it>genomic library and gene sequences from related genera of <it>Arachis</it>.</p> <p>Results</p> <p>The average transferability rate of 101 SSR markers tested to section <it>Arachis </it>and six other sections was 81% and 59% respectively. Five markers (IPAHM 164, IPAHM 165, IPAHM 407a, IPAHM 409, and IPAHM 659) showed 100% transferability. Cluster analysis of allelic data from a subset of 32 SSR markers on 85 wild and 11 cultivated accessions grouped accessions according to their genome composition, sections and species to which they belong. A total of 109 species specific alleles were detected in different wild species, <it>Arachis pusilla </it>exhibited largest number of species specific alleles (15). Based on genetic distance analysis, the A-genome accession ICG 8200 (<it>A. duranensis</it>) and the B-genome accession ICG 8206 (<it>A. ipaënsis</it>) were found most closely related to <it>A. hypogaea</it>.</p> <p>Conclusion</p> <p>A set of cross species and cross section transferable SSR markers has been identified that will be useful for genetic studies of wild species of <it>Arachis</it>, including comparative genome mapping, germplasm analysis, population genetic structure and phylogenetic inferences among species. The present study provides strong support based on both genomic and genic markers, probably for the first time, on relationships of <it>A. monticola </it>and <it>A. hypogaea </it>as well as on the most probable donor of A and B-genomes of cultivated groundnut.</p

\u3ci\u3eAspergillus\u3c/i\u3e and aflatoxin in groundnut (\u3ci\u3eArachis hypogaea\u3c/i\u3e L.) and groundnut cake in Eastern Ethiopia

This study was conducted to assess major Aspergillus species and aflatoxins associated with groundnut seeds and cake in Eastern Ethiopia and evaluate growers’ management practices. A total of 160 groundnut seed samples from farmers’ stores and 50 groundnut cake samples from cafe and restaurants were collected. Fungal isolation was done from groundnut seed samples. Aspergillus flavus was the dominant species followed by Aspergillus parasiticus. Aflatoxin analyses of groundnut seed samples were performed using ultra performance liquid chromatography; 22.5% and 41.3% of samples were positive, with total aflatoxin concentrations of 786 and 3135 ng g−1 from 2013/2014 and 2014/2015 samples, respectively. The level of specific aflatoxin concentration varied between 0.1 and 2526 ng g−1 for B2 and B1, respectively. Among contaminated samples of groundnut cake, 68% exhibited aflatoxin concentration below 20 ng g−1, while as high as 158 ng g−1 aflatoxin B1 was recorded. The study confirms high contamination of groundnut products in East Ethiopia

An Integrated Pipeline of Open Source Software Adapted for Multi-CPU Architectures: Use in the Large-Scale Identification of Single Nucleotide Polymorphisms

The large amounts of EST sequence data available from a single species of an organism as well as for several species within a genus provide an easy source of identification of intra- and interspecies single nucleotide polymorphisms (SNPs). In the case of model organisms, the data available are numerous, given the degree of redundancy in the deposited EST data. There are several available bioinformatics tools that can be used to mine this data; however, using them requires a certain level of expertise: the tools have to be used sequentially with accompanying format conversion and steps like clustering and assembly of sequences become time-intensive jobs even for moderately sized datasets. We report here a pipeline of open source software extended to run on multiple CPU architectures that can be used to mine large EST datasets for SNPs and identify restriction sites for assaying the SNPs so that cost-effective CAPS assays can be developed for SNP genotyping in genetics and breeding applications. At the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), the pipeline has been implemented to run on a Paracel high-performance system consisting of four dual AMD Opteron processors running Linux with MPICH. The pipeline can be accessed through user-friendly web interfaces at http://hpc.icrisat.cgiar.org/PBSWeb and is available on request for academic use. We have validated the developed pipeline by mining chickpea ESTs for interspecies SNPs, development of CAPS assays for SNP genotyping, and confirmation of restriction digestion pattern at the sequence level

Genetic fingerprinting and aflatoxin production of \u3ci\u3eAspergillus\u3c/i\u3e section Flavi associated with groundnut in eastern Ethiopia

Background: Aspergillus species cause aflatoxin contamination in groundnut kernels, being a health threat in agricultural products and leading to commodity rejection by domestic and international markets. Presence of Aspergillus flavus and A. parasiticus colonizing groundnut in eastern Ethiopia, as well as presence of aflatoxins have been reported, though in this region, no genetic studies have been done of these species in relation to their aflatoxin production. Results: In this study, 145 Aspergillus isolates obtained from groundnut kernels in eastern Ethiopia were genetically fingerprinted using 23 Insertion/Deletion (InDel) markers within the aflatoxin-biosynthesis gene cluster (ABC), identifying 133 ABC genotypes. Eighty-four isolates were analyzed by Ultra-Performance Liquid Chromatography (UPLC) for in vitro aflatoxin production. Analysis of genetic distances based on the approximately 85 kb-ABC by Neighbor Joining (NJ), 3D-Principal Coordinate Analysis (3D-PCoA), and Structure software, clustered the isolates into three main groups as a gradient in their aflatoxin production. Group I, contained 98% A. flavus, including L- and non-producers of sclerotia (NPS), producers of B1 and B2 aflatoxins, and most of them collected from the lowland-dry Babile area. Group II was a genetic admixture population of A. flavus (NPS) and A. flavus S morphotype, both low producers of aflatoxins. Group III was primarily represented by A. parasiticus and A. flavus S morphotype isolates both producers of B1, B2 and G1, G2 aflatoxins, and originated from the regions of Darolabu and Gursum. The highest in vitro producer of aflatoxin B1 was A. flavus NPS N1436 (77.98 μg/mL), and the highest producer of aflatoxin G1 was A. parasiticus N1348 (50.33 μg/mL), these isolates were from Gursum and Darolabu, respectively. Conclusions: To the best of our knowledge, this is the first study that combined the use of InDel fingerprinting of the ABC and corresponding aflatoxin production capability to describe the genetic diversity of Aspergillus isolates from groundnut in eastern Ethiopia. Three InDel markers, AFLC04, AFLC08 and AFLC19, accounted for the main assignment of individuals to the three Groups; their loci corresponded to aflC (pksA), hypC, and aflW (moxY) genes, respectively. Despite InDels within the ABC being often associated to loss of aflatoxin production, the vast InDel polymorphism observed in the Aspergillus isolates did not completely impaired their aflatoxin production in vitro

Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping

BACKGROUND: With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow. RESULTS: A laboratory information management system (LIMS) has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat) genotyping data from the legume (chickpea, groundnut and pigeonpea) and cereal (sorghum and millets) crops of importance in the semi-arid tropics. CONCLUSION: A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping laboratory. The application with source code is freely available for academic users and can be downloaded from

A Pipeline Strategy for Grain Crop Domestication

In the interest of diversifying the global food system, improving human nutrition, and making agriculture more sustainable, there have been many proposals to domesticate wild plants or complete the domestication of semidomesticated orphan crops. However, very few new crops have recently been fully domesticated. Many wild plants have traits limiting their production or consumption that could be costly and slow to change. Others may have fortuitous preadaptations that make them easier to develop or feasible as high-value, albeit low-yielding, crops. To increase success in contemporary domestication of new crops, we propose a pipeline approach, with attrition expected as species advance through the pipeline. We list criteria for ranking domestication candidates to help enrich the starting pool with more preadapted, promising species. We also discuss strategies for prioritizing initial research efforts once the candidates have been selected: developing higher value products and services from the crop, increasing yield potential, and focusing on overcoming undesirable traits. Finally, we present new-crop case studies that demonstrate that wild species’ limitations and potential (in agronomic culture, shattering, seed size, harvest, cleaning, hybridization, etc.) are often only revealed during the early phases of domestication. When nearly insurmountable barriers were reached in some species, they have been (at least temporarily) eliminated from the pipeline. Conversely, a few species have moved quickly through the pipeline as hurdles, such as low seed weight or low seed number per head, were rapidly overcome, leading to increased confidence, farmer collaboration, and program expansion.Fil: DeHaan, Lee R.. The Land Institute; Estados UnidosFil: Van Tassel, David L.. The Land Institute; Estados UnidosFil: Anderson, James A.. University of Minnesota; Estados UnidosFil: Asselin, Sean R.. University of Manitoba; CanadáFil: Barnes, Richard. University of Minnesota; Estados UnidosFil: Baute, Gregory J.. University of British Columbia; CanadáFil: Cattani, Douglas J.. University of Manitoba; CanadáFil: Culman, Steve W.. Ohio State University; Estados UnidosFil: Dorn, Kevin M.. University of Minnesota; Estados UnidosFil: Hulke, Brent S.. United States Department of Agriculture. Agriculture Research Service; Estados UnidosFil: Kantar, Michael. University of British Columbia; CanadáFil: Larson, Steve. Forage and Range Research Laboratory; Estados UnidosFil: David Marks, M.. University of Minnesota; Estados UnidosFil: Miller, Allison J.. Saint Louis University; Estados UnidosFil: Poland, Jesse. Kansas State University; Estados UnidosFil: Ravetta, Damián Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Museo Paleontológico Egidio Feruglio; ArgentinaFil: Rude, Emily. University of Wisconsin; Estados UnidosFil: Ryan, Matthew R.. Cornell University; Estados UnidosFil: Wyse, Don. University of Minnesota; Estados UnidosFil: Zhang, Xiaofei. University of Minnesota; Estados Unido

Peanut Consumption in Malawi: An Opportunity for Innovation

Peanuts are a valuable source of nutrients, but peanut consumption patterns, consumption frequencies, and the factors influencing peanut consumption in Malawi are not known. This study surveyed consumers to fill this knowledge gap and to assess Malawian consumers&rsquo; readiness to try new food products. Out of the 489 respondents surveyed, all but three consumed peanuts (in any form). The majority (70.4%) consumed peanuts at least three times in a week. Chi-square test showed that demographic and socioeconomic variables had significant effects (p &lt; 0.05) on peanut product preferences, the frequency of peanut consumption, and readiness to try new foods. For instance, women mostly preferred peanut flour compared to men, and peanut butter was the most preferred form for younger consumers. Logistic regression analysis showed that consumers with high school education or below were 2.35 times more likely to eat peanuts more often than consumers with post high school education. Among the participants that were ready to try new foods (54%), men and those with post high school education were 1.90 and 2.74 times more likely to try new foods than their respective counterparts. In general, the diversity of peanut products on the Malawian market is limited, and socioeconomic restrictions override consumer preferences. Therefore, future peanut-based food products innovations should explore ways to overcome such restrictions

\u3ci\u3eAspergillus\u3c/i\u3e and aflatoxin in groundnut (\u3ci\u3eArachis hypogaea\u3c/i\u3e L.) and groundnut cake in Eastern Ethiopia

This study was conducted to assess major Aspergillus species and aflatoxins associated with groundnut seeds and cake in Eastern Ethiopia and evaluate growers’ management practices. A total of 160 groundnut seed samples from farmers’ stores and 50 groundnut cake samples from cafe and restaurants were collected. Fungal isolation was done from groundnut seed samples. Aspergillus flavus was the dominant species followed by Aspergillus parasiticus. Aflatoxin analyses of groundnut seed samples were performed using ultra performance liquid chromatography; 22.5% and 41.3% of samples were positive, with total aflatoxin concentrations of 786 and 3135 ng g−1 from 2013/2014 and 2014/2015 samples, respectively. The level of specific aflatoxin concentration varied between 0.1 and 2526 ng g−1 for B2 and B1, respectively. Among contaminated samples of groundnut cake, 68% exhibited aflatoxin concentration below 20 ng g−1, while as high as 158 ng g−1 aflatoxin B1 was recorded. The study confirms high contamination of groundnut products in East Ethiopia