Use of microsatellite markers for the assessment of bambara groundnut breeding system and varietal purity before genome sequencing

Genome ◽  
2016 ◽  
Vol 59 (6) ◽  
pp. 427-431 ◽  
Author(s):  
Wai Kuan Ho ◽  
Alice Muchugi ◽  
Samuel Muthemba ◽  
Robert Kariba ◽  
Busiso Olga Mavenkeni ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Genome Sequencing ◽  
Research Output ◽  
Bambara Groundnut ◽  
Agricultural System ◽  
Drought Tolerant ◽  
Single Plant Selection ◽  
Low Levels ◽  
Species Specific ◽  
Varietal Purity

Maximizing the research output from a limited investment is often the major challenge for minor and underutilized crops. However, such crops may be tolerant to biotic and abiotic stresses and are adapted to local, marginal, and low-input environments. Their development through breeding will provide an important resource for future agricultural system resilience and diversification in the context of changing climates and the need to achieve food security. The African Orphan Crops Consortium recognizes the values of genomic resources in facilitating the improvement of such crops. Prior to beginning genome sequencing there is a need for an assessment of line varietal purity and to estimate any residual heterozygosity. Here we present an example from bambara groundnut (Vigna subterranea (L.) Verdc.), an underutilized drought tolerant African legume. Two released varieties from Zimbabwe, identified as potential genotypes for whole genome sequencing (WGS), were genotyped with 20 species-specific SSR markers. The results indicate that the cultivars are actually a mix of related inbred genotypes, and the analysis allowed a strategy of single plant selection to be used to generate non-heterogeneous DNA for WGS. The markers also confirmed very low levels of heterozygosity within individual plants. The application of a pre-screen using co-dominant microsatellite markers is expected to substantially improve the genome assembly, compared to a cultivar bulking approach that could have been adopted.

Species Specific Immunoassays to Measure Blood Platelet and Coagulation Activation in the Rat

1996 ◽  
Vol 76 (06) ◽  
pp. 1090-1095 ◽  
Author(s):  
C Ravanat ◽  
M Freund ◽  
S Schuhler ◽  
P Grunert ◽  
L Meyer ◽  
...  
Keyword(s):  
Antithrombin Iii ◽  
Plasma Concentrations ◽  
Simultaneous Detection ◽  
Blood Platelet ◽  
Coagulation Activation ◽  
Platelet Factor ◽  
Prethrombotic State ◽  
Low Levels ◽  
Species Specific ◽  
Higher Sensitivity

SummaryThe purpose of this study was to develop specific and sensitive immunoassays to detect early indices of hypercoagulability in the rat. Rat platelet factor 4 (rPF4) and rat fibrinopeptide A (rFPA) assays, tools for the detection of activation of platelets and coagulation respectively, were designed using antibodies raised against purified rPF4 and against synthetic rFPA. The relevance of these new assays and of the commercially available ELISA kit for thrombin-antithrombin III (TAT) complexes was demonstrated in a rat model of a prethrombotic state induced by intravenous infusion of varying doses of thromboplastin (90 to 2400 μl/kg/h). In this model, the immunoassays allowed simultaneous detection of low levels of rFPA and rPF4 which were correlated with fibrinogen and platelet consumption and TAT generation and further proved to be of higher sensitivity than the classical methods of platelet count or measurement of fibrinogen levels. Plasma concentrations of rFPA, rPF4 and TAT were dependent on infusion time and thromboplastin dose, while hirudin (1 mg/kg) prevented their appearance. Thus the new specific immunoassays for rPF4 and rFPA and the commercial human TAT assay represent useful tools for pathophysiological studies or the screening of antithrombotic drugs in rats.

scholarly journals Advances in Cereal Crop Genomics for Resilience under Climate Change

Life ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 502
Author(s):  
Tinashe Zenda ◽  
Songtao Liu ◽  
Anyi Dong ◽  
Huijun Duan
Keyword(s):  
Climate Change ◽  
Genome Sequencing ◽  
Gene Editing ◽  
Agronomic Traits ◽  
Cereal Crops ◽  
Agricultural System ◽  
Plant Genomics ◽  
Crop Species ◽  
Underutilized Species ◽  
Recent Developments

Adapting to climate change, providing sufficient human food and nutritional needs, and securing sufficient energy supplies will call for a radical transformation from the current conventional adaptation approaches to more broad-based and transformative alternatives. This entails diversifying the agricultural system and boosting productivity of major cereal crops through development of climate-resilient cultivars that can sustainably maintain higher yields under climate change conditions, expanding our focus to crop wild relatives, and better exploitation of underutilized crop species. This is facilitated by the recent developments in plant genomics, such as advances in genome sequencing, assembly, and annotation, as well as gene editing technologies, which have increased the availability of high-quality reference genomes for various model and non-model plant species. This has necessitated genomics-assisted breeding of crops, including underutilized species, consequently broadening genetic variation of the available germplasm; improving the discovery of novel alleles controlling important agronomic traits; and enhancing creation of new crop cultivars with improved tolerance to biotic and abiotic stresses and superior nutritive quality. Here, therefore, we summarize these recent developments in plant genomics and their application, with particular reference to cereal crops (including underutilized species). Particularly, we discuss genome sequencing approaches, quantitative trait loci (QTL) mapping and genome-wide association (GWAS) studies, directed mutagenesis, plant non-coding RNAs, precise gene editing technologies such as CRISPR-Cas9, and complementation of crop genotyping by crop phenotyping. We then conclude by providing an outlook that, as we step into the future, high-throughput phenotyping, pan-genomics, transposable elements analysis, and machine learning hold much promise for crop improvements related to climate resilience and nutritional superiority.

Drought-tolerant Bambara groundnuts as future food: a comprehensive review of its properties and applications in food

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Liew-Phing Pui ◽  
Wen-Chian Tan ◽  
Ianne Kong ◽  
Choon-Hui Tan
Keyword(s):  
Positive Impact ◽  
Food Products ◽  
Essential Amino Acids ◽  
Fermented Milk ◽  
Bambara Groundnut ◽  
Bulking Agents ◽  
Chemical Compositions ◽  
Content Type ◽  
Nutrient Density ◽  
Drought Tolerant

PurposeThis review provides an overview of the applications of Bambara groundnuts in various food products. The genetic diversity, physical properties and chemical compositions of the crop are also elucidated.Design/methodology/approachThis paper critically reviewed the physicochemical properties and applications of Bambara groundnuts from recent literature.FindingsBambara groundnut (Vigna subterranea) is a drought-tolerant crop from West Africa that contains not only carbohydrates and fats but is also high in protein. The cultivars of Bambara groundnut can be distinguished by the colours of seeds, which range from red, blue-eye, brown and black-eye. Bambara groundnuts contain carbohydrate (57–67%), protein (15–25%), fat (4–8%), fibre (1.4–1.5%) and ash (2.9–4%). As a percentage of protein, the essential amino acids, lysine, methionine and cysteine are relatively high in Bambara groundnuts. Meanwhile, linoleic, palmitic and linolenic acids are the fatty acids present in this crop.Practical implicationsSeveral studies have shown that Bambara groundnuts can be used as fat substitutes, emulsifiers, water binders, bulking agents and thickeners due to its water and oil absorption properties, gelling, pasting, emulsifying and foaming abilities. Bambara groundnuts are used in the development of many intermediate or final products like flour blend, cookies, bread and fermented milk. It has a positive impact on the overall proximate, functional, mineral and amino acid profiles of the food products.Originality/valueDespite its high nutrient density, Bambara groundnuts are an underutilised legume due to unavailability and lack of knowledge among consumers on its benefits. There is a need to promote the use of Bambara groundnuts as a future food.

Differential binding of gold-labeled zona pellucida glycoproteins mZP2 and mZP3 to mouse sperm membrane compartments

Development ◽  
1991 ◽  
Vol 113 (1) ◽  
pp. 141-149 ◽  
Author(s):  
S. Mortillo ◽  
P.M. Wassarman
Keyword(s):  
Plasma Membrane ◽  
Zona Pellucida ◽  
Transmission Electron ◽  
Acrosomal Membrane ◽  
Membrane Compartments ◽  
Sperm Membrane ◽  
Differential Binding ◽  
Inner Acrosomal Membrane ◽  
Low Levels ◽  
Species Specific

Egg zona pellucida glycoproteins mZP3 and mZP2 serve as primary and secondary sperm receptors, respectively, during initial stages of fertilization in mice [Wassarman (1988) A. Rev. Biochem. 57, 415–442]. These receptors interact with complementary egg-binding proteins (EBPs) located on the sperm surface to support species-specific gamete adhesion. Results of whole-mount autoradiographic experiments suggest that purified egg mZP3 and mZP2 bind preferentially to acrosome-intact (AI) and acrosome-reacted (AR) sperm heads, respectively [Bleil and Wassarman (1986) J. Cell Biol. 102, 1363–1371]. Here, we used purified egg mZP2, egg mZP3 and fetuin, which were coupled directly to colloidal gold (‘gold-probes’), to examine binding of these glycoproteins to membrane compartments of AI and AR sperm by transmission electron microscopy. mZP3 gold-probes were found associated primarily with plasma membrane overlying the acrosomal and post-acrosomal regions of AI sperm heads. They were also found associated with plasma membrane overlying the post-acrosomal region of AR sperm heads. mZP2 gold-probes were found associated primarily with inner acrosomal membrane of AR sperm heads, although some gold was associated with outer acrosomal membrane of AI sperm that had holes in plasma membrane overlying the acrosome. Fetuin gold-probes, used to assess background levels of binding, were bound at relatively low levels to plasma membrane and inner acrosomal membrane of AI and AR sperm, respectively. None of the gold-probes exhibited significant binding to sperm tails, or to red blood cells and residual bodies present in sperm preparations. These results provide further evidence that mZP2 and mZP3 bind preferentially to heads of AR and AI sperm, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)

scholarly journals Some Mechanisms Modulating the Root Growth of Various Wheat Species under Osmotic-Stress Conditions

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1545
Author(s):  
Nina V. Terletskaya ◽  
Tamara E. Lee ◽  
Nazira A. Altayeva ◽  
Nataliya O. Kudrina ◽  
Irina V. Blavachinskaya ◽  
...  
Keyword(s):  
Osmotic Stress ◽  
Water Deficit ◽  
Apical Meristem ◽  
Primary Root ◽  
Triticum Aestivum L ◽  
Root Diameter ◽  
Wheat Species ◽  
Drought Tolerant ◽  
Primary Roots ◽  
Species Specific

The role of the root in water supply and plant viability is especially important if plants are subjected to stress at the juvenile stage. This article describes the study of morphophysiological and cytological responses, as well as elements of the anatomical structure of primary roots of three wheat species, Triticum monococcum L., Triticum dicoccum Shuebl., and Triticum aestivum L., to osmotic stress. It was shown that the degree of plasticity of root morphology in water deficit affected the growth and development of aboveground organs. It was found that in conditions of osmotic stress, the anatomical root modulations were species-specific. In control conditions the increase in absolute values of root diameter was reduced with the increase in the ploidy of wheat species. Species-specific cytological responses to water deficit of apical meristem cells were also shown. The development of plasmolysis, interpreted as a symptom of reduced viability apical meristem cells, was revealed. A significant increase in enzymatic activity of superoxide dismutase under osmotic stress was found to be one of the mechanisms that could facilitate root elongation in adverse conditions. The tetraploid species T. dicoccum Shuebl. were confirmed as a source of traits of drought tolerant primary root system for crosses with wheat cultivars.

scholarly journals Evaluation of Seed Yield of Nigerian Bambara Groundnut [Vigna subterranea (L.) Verdc.] Landraces under Varying Water Conditions

2018 ◽  
Vol 10 (2) ◽  
pp. 233-239 ◽  
Author(s):  
Dorcas Ropo ABEJIDE ◽  
Olamide A. FALUSI ◽  
Andrew S. GANA ◽  
Matthew O. ADEBOLA ◽  
Oladipupo A.Y. DAUDU ◽  
...  
Keyword(s):  
Water Stress ◽  
Seed Yield ◽  
Block Design ◽  
Bambara Groundnut ◽  
High Yield ◽  
Stressed Condition ◽  
Drought Tolerant ◽  
University Of Technology ◽  
Water Conditions ◽  
Breeding Programmes

Seed yield of selected Nigerian Bambara Groundnut landraces under two varying water conditions was evaluated. Twenty eight (28) Bambara groundnut accessions were planted in a randomized complete block design with two treatments (Non-water stressed and Water stressed) and replicated five times. The experiment was conducted at the Experimental Garden of the Department of Biological Sciences, Federal University of Technology, Minna, Niger State. The accessions were planted in planting bags during the cropping season of 2016 between July and October. The two treatments were rain fed until maturity except during the period of exposure to water stress where the water stressed plants were transferred to a screen house made with polyvinyl ceiling to prevent water during the flowering stage for two weeks. It was observed that water stress reduced the yield of the Bambara groundnut landraces by 47%. Accessions NGB-01646-B, NGR-NI-20-H  and NGB-01491 which had relatively high yield in the stressed and non- water stressed condition were considered  the most drought tolerant accessions and accession NGR-KG-02-C with low yield both in stressed and non-stressed conditions was identified as the most susceptible accession. Accessions which had high yield only in water stressed conditions could serve as elite line for Bambara groundnut for areas which have problem of drought. These drought tolerant accessions identified in the research can serve as potential parent lines in breeding programmes aimed at the development of drought tolerant varieties of Bambara groundnut.

Fast identification of scallop adductor muscles using species-specific microsatellite markers

2007 ◽  
Vol 227 (2) ◽  
pp. 353-359 ◽  
Author(s):  
Aibin Zhan ◽  
Jingjie Hu ◽  
Xiaoli Hu ◽  
Wei Lu ◽  
Mingling Wang ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Fast Identification ◽  
Adductor Muscles ◽  
Species Specific

Evaluation of maize microsatellite markers for genetic diversity analysis and fingerprinting in sugarcane

Genome ◽  
2003 ◽  
Vol 46 (3) ◽  
pp. 394-403 ◽  
Author(s):  
A Selvi ◽  
N V Nair ◽  
N Balasundaram ◽  
T Mohapatra
Keyword(s):  
Microsatellite Markers ◽  
Cost Effective ◽  
Diversity Analysis ◽  
Phenetic Analysis ◽  
Potential Cost ◽  
Banding Patterns ◽  
Genomic Libraries ◽  
Cost Effective Method ◽  
Low Diversity ◽  
Species Specific

The use of maize microsatellite markers as a potential cost-effective method for molecular analysis of sugarcane was evaluated. Of the 34 primer pairs obtained from maize genomic libraries, 14 showed repeatable amplifications in Saccharum species clones, commercial hybrids, and the related genera Erianthus, accounting for 41.17% cross transferability. Complex banding patterns were encountered in sugarcane with the number of amplified fragments ranging from 7 to 14 with an average of 10 per primer, indicating the high polyploidy and heterozygosity existing in sugarcane. Phenetic analysis of the SSR polymorphisms produced by nine primers could clearly differentiate the different species of Saccharum and Erianthus and revealed the relationships that existed between them. Genetic similarity co-efficient indicated low diversity existing among the S. officinarum clones (82%) and a relatively higher level of diversity in the S. spontaneum clones (69.7%). Higher level of divergence of Erianthus from Saccharum was also clearly estabilished. Five primers produced genus- and species-specific fragments for Erianthus, S. spontaneum, S. officinarum, and S. barberi. The polymorphic primers, when tested on a panel of 30 commercial sugarcane cultivars, revealed a broad range (32.4–83.3%) of pair-wise similarity values, indicating their ability to detect high levels of polymorphism. A combination of two primers could differentiate all the varieties, further emphasizing their potential in fingerprinting and varietal identification.Key words: maize microsatellites, Saccharum, Erianthus, diversity analysis, fingerprinting.

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