Shifting the limits in wheat research and breeding using a fully annotated reference genome

Introduction: Wheat (Triticum aestivum L.) is the most widely cultivated crop on Earth, contributing about a fifth of the total calories consumed by humans. Consequently, wheat yields and production affect the global economy, and failed harvests can lead to social unrest. Breeders continuously strive to develop improved varieties by fine-tuning genetically complex yield and end-use quality parameters while maintaining stable yields and adapting the crop to regionally specific biotic and abiotic stresses. Rationale: Breeding efforts are limited by insufficient knowledge and understanding of wheat biology and the molecular basis of central agronomic traits. To meet the demands of human population growth, there is an urgent need for wheat research and breeding to accelerate genetic gain as well as to increase and protect wheat yield and quality traits. In other plant and animal species, access to a fully annotated and ordered genome sequence, including regulatory sequences and genome-diversity information, has promoted the development of systematic and more time-efficient approaches for the selection and understanding of important traits. Wheat has lagged behind, primarily owing to the challenges of assembling a genome that is more than five times as large as the human genome, polyploid, and complex, containing more than 85% repetitive DNA. To provide a foundation for improvement through molecular breeding, in 2005, the International Wheat Genome Sequencing Consortium set out to deliver a high-quality annotated reference genome sequence of bread wheat. Results: An annotated reference sequence representing the hexaploid bread wheat genome in the form of 21 chromosome-like sequence assemblies has now been delivered, giving access to 107,891 high-confidence genes, including their genomic context of regulatory sequences. This assembly enabled the discovery of tissue- and developmental stage–related gene coexpression networks using a transcriptome atlas representing all stages of wheat development. The dynamics of change in complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. Aspects of the future value of the annotated assembly for molecular breeding and research were exemplarily illustrated by resolving the genetic basis of a quantitative trait locus conferring resistance to abiotic stress and insect damage as well as by serving as the basis for genome editing of the flowering-time trait. Conclusion: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. Importantly, the bioinformatics capacity developed for model-organism genomes will facilitate a better understanding of the wheat genome as a result of the high-quality chromosome-based genome assembly. By necessity, breeders work with the genome at the whole chromosome level, as each new cross involves the modification of genome-wide gene networks that control the expression of complex traits such as yield. With the annotated and ordered reference genome sequence in place, researchers and breeders can now easily access sequence-level information to precisely define the necessary changes in the genomes for breeding programs. This will be realized through the implementation of new DNA marker platforms and targeted breeding technologies, including genome editing

Analysis of WOFDM over LTE 1.25 MHz Band

Orthogonal Frequency Division Multiplexing (OFDM) is the one of the most preferred multiplexing technique for realizing high-speed wireless communication, like Long Term Evolution (LTE) and LTE-Adv. In the era of digital wireless communication, applications of wavelet theory have been favorably applied in many areas of signal processing. Orthogonality, flexible time-frequency analysis, and the ability to characterize signals accurately have attracted the attention of the telecommunication community to use wavelet as a basis function for OFDM. In this paper, discrete wavelet transform (DWT) has been proposed as an alternative signal analysis with multiple merits such as support high-speed applications, immune to distortion, wavelet diversity, better error performance, and efficient bandwidth utilization. A simulative analysis of various wavelets, at different modulation techniques, over OFDM has been presented to demonstrate the improvement in BER performance. Further, in accordance with the LTE parameterization over 1.25 MHz band, the performance of wavelet-based OFDM (WOFDM) is found significantly higher in terms of maximum achievable data rate and system spectral efficiency

Power Spectral Analysis of Short-Term Heart Rate Variability in Healthy and Arrhythmia Subjects by the Adaptive Continuous Morlet Wavelet Transform

Power spectral analysis of short-term heart rate variability (HRV) can provide instant valuable information to understand the functioning of autonomic control over the cardiovascular system. In this study, an adaptive continuous Morlet wavelet transform (ACMWT) method has been used to describe the time-frequency characteristics of the HRV using band power spectra and the median value of interquartile range. Adaptation of the method was based on the measurement of maximum energy concentration. The ACMWT has been validated on synthetic signals (i.e. stationary, non-stationary as slow varying and fast changing frequency with time) modeled as closest to dynamic changes in HRV signals. This method has been also tested in the presence of additive white Gaussian noise (AWGN) to show its robustness towards the noise. From the results of testing on synthetic signals, the ACMWT was found to be an enhanced energy concentration estimator for assessment of power spectral of short-term HRV time series compared to adaptive Stockwell transform (AST), adaptive modified Stockwell transform (AMST), standard continuous Morlet wavelet transform (CMWT) and Stockwell transform (ST) estimators at statistical significance level of 5%. Further, the ACMWT was applied to real HRV data from Fantasia and MIT-BIH databases, grouped as healthy young group (HYG), healthy elderly group (HEG), arrhythmia controlled medication group (ARCMG), and supraventricular tachycardia group (SVTG) subjects. The global results demonstrate that spectral indices of low frequency power (LFp) and high frequency power (HFp) of HRV were decreased in HEG compared to HYG subjects (p<0.0001). While LFp and HFp indices were increased in ARCMG compared to HEG (p<0.00001). The LFp and HFp components of HRV obtained from SVTG were reduced compared to other group subjects (p<0.00001)

Gender Differences in HIV Risk Perception and Sexual Behaviour of Young Adults in Metropolitan Areas of Fiji

This study seeks to understand variations in Human Immunodeficiency Virus (HIV) risk perception and sexual behaviour among male and female adults in Fiji. The Second-Generation Surveillance Report (2006) indicates the median age of first sex within the youth group as 16 years (range 10 – 23 years). Therefore, this study was purposively targeted at individuals of reproductive age, preferably 10 years and above. We utilized convenience sampling to collect 137 self-administered surveys from individuals working in both public and private sector organizations in two highly populated areas of Fiji. Independent samples t-test analyses revealed that men living in urban areas are more likely to experiment with multiple sexual partners, have a higher tendency of engaging in sexual practices, and are highly likely to have unsafe sex with multiple partners. Gender-sensitive interventions may help facilitate and achieve positive behaviour change among males and influence the sexual health of females

Analysis of Energy Efficient Routing Protocols in Wireless Sensor Networks

ABSTRACT Wireless sensor networking is an emerging technology that has a wide range of potential applications including environment monitoring, smart spaces, medical systems and robotic exploration. Such a network normally consists of a large number of distributed nodes that organize themselves into a multi-hop wireless network. Conventional routing protocols may not be optimal for sensor networks. With the development of MEMS (micro-electro-mechanicalsystems), low-power analog and digital electronics, and low-power RF design, the design of wireless sensors has been developed rapidly. In this paper, we look at communication protocols, which can have significant impact on overall energy dissipation of these networks. LEACH (Low-Energy Adaptive Clustering Hierarchy) is a clusteringbased protocol that utilizes randomized rotation of local cluster base stations to evenly distribute the energy load among the sensors in the network. Simulations show that LEACH can achieve as much as a factor of 8 reductions in energy dissipation compared with conventional routing protocols. LEACH also distributes energy dissipation evenly throughout the sensors, increasing the lifetime of the system

BER and PSD Improvement of FBMC with Higher Order QAM Using Hermite Filter for 5G Wireless Communication and beyond

Nowadays, multicarrier modulation schemes are being widely used in wireless communication system than single-carrier modulation techniques. Single-carrier modulation schemes are less capable of dealing with multipath fading channels than multicarrier modulation schemes, which results in lower spectral efficiency. Multicarrier modulation schemes have the ability to overcome multipath fading channels. Multicarrier modulation technique currently used in 4G technology in many countries is OFDM and it is easy for implementation, immune to interference, and provide fast data rate. However, the rising users demand on wireless communication resulted in need for further advancement of wireless communication system. The present OFDM transmission does not fulfill the requirements of 5G wireless communication system and beyond due to major limitations such as out of band emission and usage of cyclic prefix. To overcome the challenges of OFDM, different modulation schemes like Filter Bank Multicarrier with Offset-QAM, Filter Bank Multicarrier with QAM, Universal Filter Multicarrier, Filtered-OFDM, and Weighted Overlap and Added-OFDM are proposed. In this study, the Filter Bank Multicarrier with QAM using Hermite prototype filter is proposed to overcome drawbacks of OFDM and all other proposed waveforms. The performances of each multicarrier technique are analyzed based on power spectral density and bit error rate. Simulation result shows that the power spectral density of FBMC with QAM using Hermite filter resulted in 4.7 dB reduction of out of band emission compared to FBMC with QAM using PHYDYAS filter. The bit error rate is also reduced for Vehicular A, Vehicular B, Pedestrian A, and Pedestrian B channel models

Mechanistic Association of Quantitative Trait Locus with Malate Secretion in Lentil (Lens culinaris Medikus) Seedlings under Aluminium Stress

Aluminium (Al) toxicity acts as a major delimiting factor in the productivity of many crops including lentil. To alleviate its effect, plants have evolved with Al exclusion and inclusion mechanisms. The former involves the exudation of organic acid to restrict the entry of Al3+ to the root cells while latter involves detoxification of entered Al3+ by organic acids. Al-induced secretion of organic acids from roots is a well-documented mechanism that chelates and neutralizes Al3+ toxicity. In this study, F6 recombinant inbred lines (RILs) derived from a cross between L-7903 (Al-resistant) and BM-4 (Al-sensitive) were phenotyped to assess variation in secretion levels of malate and was combined with genotypic data obtained from 10 Al-resistance linked simple sequence repeat (SSRs) markers. A major quantitative trait loci (QTL) was mapped for malate (qAlt_ma) secretion with a logarithm of odd (LOD) value of 7.7 and phenotypic variation of 60.2%.Validated SSRs associated with this major QTL will be useful in marker assisted selection programmes for improving Al resistance in lentil

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Kumar A., Sharma D., Pathak R.K., Tomar R.S.S., Agrawal A., Tripathi M.K. (2021) Science-Led Innovation for Searching and Creating Values in Natural Gene Pool of Millets for Agri-Food Nutrition and Health. In: Kumar A., Tripathi M.K., Joshi D., Kumar V. (eds) Millets and Millet Technology. Springer, SingaporeThe green revolution has increased the quantum of major cereals (wheat and rice), which otherwise would have been substantially low across the developing countries; a significant contribution that one can never undervalue. However, focused monoculture of either crop was realized particularly with respect to loss of agro-biodiversity and sustenance of nutri-rich minor crops resulting in poor food grain diversity. Albeit, these crops provide sufficient calories, they do not make a complete diet resulting in malnutrition of over 2000 million people worldwide. Millets are versatile grains valued for their exceptional nutritional profile. Being the reservoir of essential micronutrients and trace elements they are often termed as nature’s nutraceutical basket. Furthermore, their climate resilient nature and adaptation to low input agriculture makes them “harbingers for evergreen revolution.” The latest advancements in genomics and automate phenotyping techniques for searching genes and metabolites, coupled with high-throughput transformation processes have opened new avenues for product development in millets. Furthermore, various computational biology platforms help us in analyzing big molecular data of crop plants to identify valuable genes hidden in them. In addition, molecular breeding platforms may be utilized to speed up the introgression of value-added genes in high welding and widely adapted genetic backgrounds. This chapter focuses on searching for values in the natural millet gene pool of millets for developing climate smart crops with value-added traits.Not Availabl