scholarly journals Unraveling the Roles of Regulatory Genes during Domestication of Cultivated Camellia: Evidence and Insights from Comparative and Evolutionary Genomics

Genes ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 488 ◽  
Author(s):  
Chao Yan ◽  
Ping Lin ◽  
Tao Lyu ◽  
Zhikang Hu ◽  
Zhengqi Fan ◽  
...  
Keyword(s):  
Complex Traits ◽  
Large Scale ◽  
Genetic Alterations ◽  
Genomic Research ◽  
Economic Traits ◽  
Vast Number ◽  
Scale Population ◽  
Camellia Species ◽  
Flower And Fruit Development ◽  
Future Work

With the increasing power of DNA sequencing, the genomics-based approach is becoming a promising resolution to dissect the molecular mechanism of domestication of complex traits in trees. Genus Camellia possesses rich resources with a substantial value for producing beverage, ornaments, edible oil and more. Currently, a vast number of genetic and genomic research studies in Camellia plants have emerged and provided an unprecedented opportunity to expedite the molecular breeding program. In this paper, we summarize the recent advances of gene expression and genomic resources in Camellia species and focus on identifying genes related to key economic traits such as flower and fruit development and stress tolerances. We investigate the genetic alterations and genomic impacts under different selection programs in closely related species. We discuss future directions of integrating large-scale population and quantitative genetics and multiple omics to identify key candidates to accelerate the breeding process. We propose that future work of exploiting the genomic data can provide insights related to the targets of domestication during breeding and the evolution of natural trait adaptations in genus Camellia.

What Does DNA Tell Us about Past Connections and the Settlement of Sahul?

2021 ◽  
Author(s):  
Elizabeth Matisoo-Smith ◽  
Anna L. Gosling
Keyword(s):  
Indigenous Peoples ◽  
Large Scale ◽  
Human Impacts ◽  
Genomic Research ◽  
Community Consultation ◽  
Sequencing Technology ◽  
Local Fauna ◽  
Population Replacement ◽  
Scale Population ◽  
Early Human

Archaeological evidence indicates that the continent of Sahul has been continuously settled for almost as long as modern humans have lived outside of Africa. The relative isolation of the continent, and the difficulty involved in getting there, have meant that the populations have not been subject to the large-scale population replacement seen in other parts of the world. Recent advances in DNA sequencing technology, including the ability to sequence full genomes in both ancient and modern populations, have revealed that the genomes of the Indigenous peoples of Australia and New Guinea, and the local fauna, can contribute significantly to our understanding of early human migrations from Africa, human impacts on environments, as well as human evolution more broadly. Given the power of genomic data, it is of the utmost importance that genomic research of ancient and modern samples is conducted ethically, with full community consultation and engagement at all stages.

scholarly journals Genome-wide detection of CNV regions and their potential association with growth and fatness traits in Duroc pigs

2020 ◽  
Author(s):  
Yibin Qiu ◽  
Rongrong Ding ◽  
Zhanwei Zhuang ◽  
Jie Wu ◽  
Ming Yang ◽  
...  
Keyword(s):  
Association Analysis ◽  
Complex Traits ◽  
Large Scale ◽  
Average Daily Gain ◽  
Potential Candidate ◽  
Genome Wide ◽  
Potential Association ◽  
Scale Population ◽  
Number Variation ◽  
Genetic Mechanisms

Abstract Background: In the process of pig breeding, the average daily gain (ADG), days to 100 kg (AGE), and backfat thickness (BFT) are directly related to growth rate and fatness. However, the genetic mechanisms involved are not well understood. As an essential source of genetic diversity, copy number variation (CNV) that can affect a variety of complex traits and diseases, has gradually been thrust into the limelight. In this study, we reported the genome-wide CNVs of Duroc pigs by SNP genotyping data of 6,627 Duroc pigs. Moreover, we also performed CNV region (CNVR) based association analysis for growth and fatness traits in two Duroc populations.Results: Our study identified a total of 835 nonredundant CNVRs in American and Canadian Duroc pigs, which covered 226.73 Mb (~ 10.00%) of the pig autosomal genome. Among them, we identified 682 CNVRs in the American Duroc pigs and 424 CNVRs in the Canadian Duroc pigs, and 271 CNVRs were detected in both populations. Experimentally, 77.8% of randomly selected CNVRs were validated by quantitative PCR (qPCR). We also identified 24 significant CNVRs for growth and fatness traits though CNVR-based association analysis. Among these, six and three CNVRs in American and Canadian Duroc pigs were found to be associated with both ADG and AGE traits, respectively. Notably, four CNVRs showed both significant in ADG, AGE, and BFT, indicating that these CNVRs may play a pleiotropic role in regulating pig growth and fat deposition. Besides, further bioinformatics analysis determined a subset of potential candidate genes, such as PDGFRB, INSIG1, GPER1, PDGFA, and LPCAT1.Conclusions: The present study provides a necessary supplement to the CNV map of the Duroc genome through a large-scale population genotyping. Also, the CNVR-based association results provide a meaningful way to elucidate the genetic mechanisms of complex traits. The identified CNVRs can be used as molecular markers for genetic improvement in molecular-guided breeding of modern commercial pigs

scholarly journals Status of perennial tree germplasm resources in India and their utilization in the context of global genome sequencing efforts

2020 ◽  
Author(s):  
Kunasekaran Rajarajan ◽  
◽  
Alka Bharati ◽  
Hirdayesh Anuragi ◽  
Arun Kumar Handa ◽  
...  
Keyword(s):  
Tree Species ◽  
Complex Traits ◽  
Human Life ◽  
Genomic Research ◽  
Diagnostic Tools ◽  
Economic Traits ◽  
Juvenile Period ◽  
High Genetic Diversity ◽  
Widespread Application ◽  
Tree Genomics

Tree species are characterized by their perennial growth habit, woody morphology, long juvenile period phase, mostly outcrossing behaviour, highly heterozygosity genetic makeup, and relatively high genetic diversity. The economically important trees have been an integral part of the human life system due to their provision of timber, fruit, fodder, and medicinal and/or health benefits. Despite its widespread application in agriculture, industrial and medicinal values, the molecular aspects of key economic traits of many tree species remain largely unexplored. Over the past two decades, research on forest tree genomics has generally lagged behind that of other agronomic crops. Genomic research on trees is motivated by the need to support genetic improvement programmes mostly for food trees and timber, and develop diagnostic tools to assist in recommendation for optimum conservation, restoration and management of natural populations. Research on long-lived woody perennials is extending our molecular knowledge and understanding of complex life histories and adaptations to the environment, enriching a field that has traditionally drawn its biological inference from a few short-lived herbaceous species. These concerns have fostered research aimed at deciphering the genomic basis of complex traits that are related to the adaptive value of trees. This review summarizes the highlights of tree genomics and offers some priorities for accelerating progress in the next decade.

Next-Generation Sequencing: An Emerging Tool for Drug Designing

2019 ◽  
Vol 25 (31) ◽  
pp. 3350-3357 ◽  
Author(s):  
Pooja Tripathi ◽  
Jyotsna Singh ◽  
Jonathan A. Lal ◽  
Vijay Tripathi
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput ◽  
Large Scale ◽  
Massively Parallel Sequencing ◽  
Genomic Research ◽  
Biological Research ◽  
Next Generation ◽  
Human Welfare ◽  
Drug Designing ◽  
Generation Sequencing

Background: With the outbreak of high throughput next-generation sequencing (NGS), the biological research of drug discovery has been directed towards the oncology and infectious disease therapeutic areas, with extensive use in biopharmaceutical development and vaccine production. Method: In this review, an effort was made to address the basic background of NGS technologies, potential applications of NGS in drug designing. Our purpose is also to provide a brief introduction of various Nextgeneration sequencing techniques. Discussions: The high-throughput methods execute Large-scale Unbiased Sequencing (LUS) which comprises of Massively Parallel Sequencing (MPS) or NGS technologies. The Next geneinvolved necessarily executes Largescale Unbiased Sequencing (LUS) which comprises of MPS or NGS technologies. These are related terms that describe a DNA sequencing technology which has revolutionized genomic research. Using NGS, an entire human genome can be sequenced within a single day. Conclusion: Analysis of NGS data unravels important clues in the quest for the treatment of various lifethreatening diseases and other related scientific problems related to human welfare.

scholarly journals ‘CTRL’: an online, Dynamic Consent and participant engagement platform working towards solving the complexities of consent in genomic research

2021 ◽  
Author(s):  
Matilda A. Haas ◽  
Harriet Teare ◽  
Megan Prictor ◽  
Gabi Ceregra ◽  
Miranda E. Vidgen ◽  
...  
Keyword(s):  
Large Scale ◽  
Genomic Medicine ◽  
International Standards ◽  
Security And Privacy ◽  
Genomic Research ◽  
Return Of Results ◽  
Future Research ◽  
Design And Development ◽  
Participant Engagement ◽  
Dynamic Consent

AbstractThe complexities of the informed consent process for participating in research in genomic medicine are well-documented. Inspired by the potential for Dynamic Consent to increase participant choice and autonomy in decision-making, as well as the opportunities for ongoing participant engagement it affords, we wanted to trial Dynamic Consent and to do so developed our own web-based application (web app) called CTRL (control). This paper documents the design and development of CTRL, for use in the Australian Genomics study: a health services research project building evidence to inform the integration of genomic medicine into mainstream healthcare. Australian Genomics brought together a multi-disciplinary team to develop CTRL. The design and development process considered user experience; security and privacy; the application of international standards in data sharing; IT, operational and ethical issues. The CTRL tool is now being offered to participants in the study, who can use CTRL to keep personal and contact details up to date; make consent choices (including indicate preferences for return of results and future research use of biological samples, genomic and health data); follow their progress through the study; complete surveys, contact the researchers and access study news and information. While there are remaining challenges to implementing Dynamic Consent in genomic research, this study demonstrates the feasibility of building such a tool, and its ongoing use will provide evidence about the value of Dynamic Consent in large-scale genomic research programs.

scholarly journals Social Collective Attack Model and Procedures for Large-Scale Cyber-Physical Systems

Sensors ◽  
2021 ◽  
Vol 21 (3) ◽  
pp. 991
Author(s):  
Peidong Zhu ◽  
Peng Xun ◽  
Yifan Hu ◽  
Yinqiao Xiong
Keyword(s):  
Smart Grid ◽  
Collective Behavior ◽  
Physical System ◽  
Large Scale ◽  
Public Utility ◽  
Modeling Framework ◽  
Vast Number ◽  
Attack Model ◽  
The Social ◽  
Social Collective

A large-scale Cyber-Physical System (CPS) such as a smart grid usually provides service to a vast number of users as a public utility. Security is one of the most vital aspects in such critical infrastructures. The existing CPS security usually considers the attack from the information domain to the physical domain, such as injecting false data to damage sensing. Social Collective Attack on CPS (SCAC) is proposed as a new kind of attack that intrudes into the social domain and manipulates the collective behavior of social users to disrupt the physical subsystem. To provide a systematic description framework for such threats, we extend MITRE ATT&CK, the most used cyber adversary behavior modeling framework, to cover social, cyber, and physical domains. We discuss how the disinformation may be constructed and eventually leads to physical system malfunction through the social-cyber-physical interfaces, and we analyze how the adversaries launch disinformation attacks to better manipulate collective behavior. Finally, simulation analysis of SCAC in a smart grid is provided to demonstrate the possibility of such an attack.

scholarly journals Adaptation of Random Binomial Graphs for Testing Network Flow Problems Algorithms

Mathematics ◽  
2021 ◽  
Vol 9 (15) ◽  
pp. 1716
Author(s):  
Adrian Marius Deaconu ◽  
Delia Spridon
Keyword(s):  
Network Flow ◽  
Large Scale ◽  
Random Network ◽  
Minimum Cost ◽  
Maximum Flow ◽  
Network Flow Problems ◽  
Commodity Flow ◽  
Vast Number ◽  
Flow Problems ◽  
Execution Speed

Algorithms for network flow problems, such as maximum flow, minimum cost flow, and multi-commodity flow problems, are continuously developed and improved, and so, random network generators become indispensable to simulate the functionality and to test the correctness and the execution speed of these algorithms. For this purpose, in this paper, the well-known Erdős–Rényi model is adapted to generate random flow (transportation) networks. The developed algorithm is fast and based on the natural property of the flow that can be decomposed into directed elementary s-t paths and cycles. So, the proposed algorithm can be used to quickly build a vast number of networks as well as large-scale networks especially designed for s-t flows.

scholarly journals Publisher Correction: A link between appendectomy and gastrointestinal cancers: a large-scale population-based cohort study in Korea

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Youn Young Park ◽  
Kil‑yong Lee ◽  
Seong Taek Oh ◽  
Sang Hyun Park ◽  
Kyung Do Han ◽  
...  
Keyword(s):  
Cohort Study ◽  
Large Scale ◽  
Population Based ◽  
Gastrointestinal Cancers ◽  
Scale Population

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

scholarly journals Using Bus Ticketing Big Data to Investigate the Behaviors of the Population Flow of Chinese Suburban Residents in the Post-COVID-19 Phase

2021 ◽  
Vol 18 (11) ◽  
pp. 6066
Author(s):  
Yanbing Bai ◽  
Lu Sun ◽  
Haoyu Liu ◽  
Chao Xie
Keyword(s):  
Travel Behavior ◽  
Large Scale ◽  
Behavior Patterns ◽  
Population Movements ◽  
Economic Level ◽  
Passenger Travel ◽  
Scale Population ◽  
Travel Behaviors ◽  
Railway Passenger ◽  
And Control

Large-scale population movements can turn local diseases into widespread epidemics. Grasping the characteristic of the population flow in the context of the COVID-19 is of great significance for providing information to epidemiology and formulating scientific and reasonable prevention and control policies. Especially in the post-COVID-19 phase, it is essential to maintain the achievement of the fight against the epidemic. Previous research focuses on flight and railway passenger travel behavior and patterns, but China also has numerous suburban residents with a not-high economic level; investigating their travel behaviors is significant for national stability. However, estimating the impacts of the COVID-19 for suburban residents’ travel behaviors remains challenging because of lacking apposite data. Here we submit bus ticketing data including approximately 26,000,000 records from April 2020–August 2020 for 2705 stations. Our results indicate that Suburban residents in Chinese Southern regions are more likely to travel by bus, and travel frequency is higher. Associated with the economic level, we find that residents in the economically developed region more likely to travel or carry out various social activities. Considering from the perspective of the traveling crowd, we find that men and young people are easier to travel by bus; however, they are exactly the main workforce. The indication of our findings is that suburban residents’ travel behavior is affected profoundly by economy and consistent with the inherent behavior patterns before the COVID-19 outbreak. We use typical regions as verification and it is indeed the case.

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