Genomic prediction and quantitative trait locus discovery in a cassava training population constructed from multiple breeding stages

Open Access Article; Published online: 11 Dec 2019Assembly of a training population (TP) is an important component of effective genomic selection‐based breeding programs. In this study, we examined the power of diverse germplasm assembled from two cassava (Manihot esculenta Crantz) breeding programs in Tanzania at different breeding stages to predict traits and discover quantitative trait loci (QTL). This is the first genomic selection and genome‐wide association study (GWAS) on Tanzanian cassava data. We detected QTL associated with cassava mosaic disease (CMD) resistance on chromosomes 12 and 16; QTL conferring resistance to cassava brown streak disease (CBSD) on chromosomes 9 and 11; and QTL on chromosomes 2, 3, 8, and 10 associated with resistance to CBSD for root necrosis. We detected a QTL on chromosome 4 and two QTL on chromosome 12 conferring dual resistance to CMD and CBSD. The use of clones in the same stage to construct TPs provided higher trait prediction accuracy than TPs with a mixture of clones from multiple breeding stages. Moreover, clones in the early breeding stage provided more reliable trait prediction accuracy and are better candidates for constructing a TP. Although larger TP sizes have been associated with improved accuracy, in this study, adding clones from Kibaha to those from Ukiriguru and vice versa did not improve the prediction accuracy of either population. Including the Ugandan TP in either population did not improve trait prediction accuracy. This study applied genomic prediction to understand the implications of constructing TP from clones at different breeding stages pooled from different locations on trait accuracy

Model-Driven Automatic Question Generation for a Gamified Clinical Guideline Training System

Clinical practice guidelines (CPGs) are a cornerstone of modern medical practice since they summarize the vast medical literature and provide care recommendations based on the current best evidence. However, there are barriers to CPG utilization such as lack of awareness and lack of familiarity of the CPGs by clinicians due to ineffective CPG dissemination and implementation. This calls for research into effective and scalable CPG dissemination strategies that will improve CPG awareness and familiarity. We describe a model-driven approach to design and develop a gamified e-learning system for clinical guidelines where the training questions are generated automatically. We also present the prototype developed using this approach. We use models for different aspects of the system, an entity model for the clinical domain, a workflow model for the clinical processes and a game engine to generate and manage the training sessions. We employ gamification to increase user motivation and engagement in the training of guideline content. We conducted a limited formative evaluation of the prototype system and the users agreed that the system would be a useful addition to their training. Our proposed approach is flexible and adaptive as it allows for easy updates of the guidelines, integration with different device interfaces and representation of any guideline.acceptedVersio

Highly linear microstrip wideband bandpass filter with switchable notched band for wireless applications

This article presents a highly linear reconfigurable bandpass filter embedded with a switchable notch structure to get a band-notched characteristic at a specified frequency.A single PIN diode (BAP65-02) is used for the purpose of switching the notch. An optical switch, comprised of a silicon dice activated using near infrared light is also investigated as an alternative to the PIN diode. While the PIN diode or the optical switch is in the ON state this reconfigurable filter behaves as a bandpass filter with a notch at 2.4 GHz in order to reject WLAN interference while a full band response is obtained in the OFF state. The proposed filter is able to achieve good linearity using PIN diode with IIP3 of 47 dBm and there is no significant loss. A prototype is fabricated, and measured results are compared to simulations. A good agreement has been achieved between simulated and measured results

Compact UWB bandpass filter with reconfigurable notched band

A compact bandpass filter is presented for ultra-wideband (UWB) applications with a reconfigurable notched band to reject unwanted signals from the WiMAX systems. A single pin diode is used for the purpose of switching the notch. An optical switch, comprised of a silicon dice activated using near infrared light is also investigated as an alternative to the pin diode. While the switch is in the ON state this reconfigurable filter behaves as a bandpass filter with a notch at 3.5 GHz and a full band response is obtained in the OFF state. The filter offers excellent performance for the lower-band frequency of a UWB system, ranging from 3.1 to 5.0 GHz and exhibits very low passband insertion loss. Also, transmission zeros are generated at the passband edges to enhance the signal selectivity. A filter sample has been designed and fabricated to provide experimental verification on the proposed filter. A good agreement has been achieved between simulated and measured results with both the pin diode as well as the optical switch. The proposed reconfigurable filter with notched band was able to achieve 40% size reduction as compared to an embedded open-circuited stub

Optically reconfigurable microstrip UWB bandpass filters

This paper presents an optically reconfigurable microstrip ultra-wideband filter. A single optical switch comprised of a silicon wafer is activated using near infra-red light to select between either a bandpass or bandstop response. With the switch in the ON state, the circuit behaves as a bandpass filter while in the OFF state, the circuit behaves as a bandstop filter in the same frequency band. The proposed filter was designed, fabricated and tested. Its performance was evaluated through simulation and measurements

Identification of additional/novel QTL associated with resistance to cassava green mite in a biparental mapping population

Open Access JournalCassava green mite [CGM, Mononychellus tanajoa (Bondar)] is the most destructive dry-season pest in most cassava production areas. The pest is responsible for cassava fresh root yield losses of over 80%. Deployment of CGM resistant cultivars is the most cost-effective and sustainable approach of alleviating such production losses. The purposes of this study were to validate the stability of CGM resistance genes found in previously published results, to identify new genes for CGM resistance in bi-parental mapping population and estimate the heritability of the trait. A total of 109 F1 progeny derived from a cross between CGM resistant parent, TMEB778 and a very susceptible parent, TMEB419 were evaluated under CGM hotspot areas in Nigeria for two cropping seasons. A total of 42,204 SNP markers with MAF ≥ 0.05 were used for single-marker analysis. The most significant QTL (S12_7962234) was identified on the left arm on chromosome 12 which explained high phenotypic variance and harboured significant single nucleotide polymorphism (SNP) markers conferring resistance to CGM and leaf pubescence (LP). Colocalization of the most significant SNP associated with resistance to CGM and LP on chromosome 12 is possibly an indication of a beneficial pleiotropic effect or are physically linked. These significant SNPs markers were intersected with the gene annotations and 33 unique genes were identified within SNPs at 4 – 8MB on chromosome 12. Among these genes, nine novel candidate genes namely; Manes.12077600, Manes.12G086200, Manes.12G061200, Manes.12G083100, Manes.12G082000, Manes.12G094100, Manes.12G075600, Manes.12G091400 and Manes.12G069300 highly expressed direct link to cassava green mite resistance. Pyramiding the new QTL/genes identified on chromosome 12 in this study with previously discovered loci, such on chromosome 8, will facilitate breeding varieties that are highly resistant CGM

Challenges in managing real-time data in health information system (HIS)

© Springer International Publishing Switzerland 2016. In this paper, we have discussed the challenges in handling real-time medical big data collection and storage in health information system (HIS). Based on challenges, we have proposed a model for realtime analysis of medical big data. We exemplify the approach through Spark Streaming and Apache Kafka using the processing of health big data Stream. Apache Kafka works very well in transporting data among different systems such as relational databases, Apache Hadoop and nonrelational databases. However, Apache Kafka lacks analyzing the stream, Spark Streaming framework has the capability to perform some operations on the stream. We have identified the challenges in current realtime systems and proposed our solution to cope with the medical big data streams

Genetic diversity and population structure of cowpea [Vigna unguiculata (L.)Walp.] germplasm collected from Togo based on DArT markers

Open Access Journal; Published online: 20 Sep 2021Crop genetic diversity is a sine qua non for continuous progress in the development of improved varieties, hence the need for germplasm collection, conservation and characterization. Over the years, cowpea has contributed immensely to the nutrition and economic life of the people in Togo. However, the bulk of varieties grown by farmers are landraces due to the absence of any serious genetic improvement activity on cowpea in the country. In this study, the genetic diversity and population structure of 255 cowpea accessions collected from five administrative regions and the agricultural research institute of Togo were assessed using 4600 informative diversity array technology (DArT) markers. Among the regions, the polymorphic information content (PIC) ranged from 0.19 to 0.27 with a mean value of 0.25. The expected heterozygosity (He) varied from 0.22 to 0.34 with a mean value of 0.31, while the observed heterozygosity (Ho) varied from 0.03 to 0.07 with an average of 0.05. The average inbreeding coefficient (FIS) varied from 0.78 to 0.89 with a mean value of 0.83, suggesting that most of the accessions are inbred. Cluster analysis and population structure identified four groups with each comprising accessions from the six different sources. Weak to moderate differentiation was observed among the populations with a genetic differentiation index varying from 0.014 to 0.117. Variation was highest (78%) among accessions within populations and lowest between populations (7%). These results revealed a moderate level of diversity among the Togo cowpea germplasm. The findings of this study constitute a foundation for genetic improvement of cowpea in Togo

Technological innovations for improving cassava production in sub-Saharan Africa

Open Access Journal; Published online: 21 Jan 2021Cassava is crucial for food security of millions of people in sub-Saharan Africa. The crop has great potential to contribute to African development and is increasing its income-earning potential for small-scale farmers and related value chains on the continent. Therefore, it is critical to increase cassava production, as well as its quality attributes. Technological innovations offer great potential to drive this envisioned change. This paper highlights genomic tools and resources available in cassava. The paper also provides a glimpse of how these resources have been used to screen and understand the pattern of cassava genetic diversity on the continent. Here, we reviewed the approaches currently used for phenotyping cassava traits, highlighting the methodologies used to link genotypic and phenotypic information, dissect the genetics architecture of key cassava traits, and identify quantitative trait loci/markers significantly associated with those traits. Additionally, we examined how knowledge acquired is utilized to contribute to crop improvement. We explored major approaches applied in the field of molecular breeding for cassava, their promises, and limitations. We also examined the role of national agricultural research systems as key partners for sustainable cassava production

Genome-wide association study of root mealiness and other texture-associated traits in cassava

Open Access Journal; Published online: 17 Dec 2021Cassava breeders have made significant progress in developing new genotypes with improved agronomic characteristics such as improved root yield and resistance against biotic and abiotic stresses. However, these new and improved cassava (Manihot esculenta Crantz) varieties in cultivation in Nigeria have undergone little or no improvement in their culinary qualities; hence, there is a paucity of genetic information regarding the texture of boiled cassava, particularly with respect to its mealiness, the principal sensory quality attribute of boiled cassava roots. The current study aimed at identifying genomic regions and polymorphisms associated with natural variation for root mealiness and other texture-related attributes of boiled cassava roots, which includes fibre, adhesiveness (ADH), taste, aroma, colour, and firmness. We performed a genome-wide association (GWAS) analysis using phenotypic data from a panel of 142 accessions obtained from the National Root Crops Research Institute (NRCRI), Umudike, Nigeria, and a set of 59,792 high-quality single nucleotide polymorphisms (SNPs) distributed across the cassava genome. Through genome-wide association mapping, we identified 80 SNPs that were significantly associated with root mealiness, fibre, adhesiveness, taste, aroma, colour and firmness on chromosomes 1, 4, 5, 6, 10, 13, 17 and 18. We also identified relevant candidate genes that are co-located with peak SNPs linked to these traits in M. esculenta. A survey of the cassava reference genome v6.1 positioned the SNPs on chromosome 13 in the vicinity of Manes.13G026900, a gene recognized as being responsible for cell adhesion and for the mealiness or crispness of vegetables and fruits, and also known to play an important role in cooked potato texture. This study provides the first insights into understanding the underlying genetic basis of boiled cassava root texture. After validation, the markers and candidate genes identified in this novel work could provide important genomic resources for use in marker-assisted selection (MAS) and genomic selection (GS) to accelerate genetic improvement of root mealiness and other culinary qualities in cassava breeding programmes in West Africa, especially in Nigeria, where the consumption of boiled and pounded cassava is low