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.

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.

Language and life history: A new perspective on the development and evolution of human language

2006 ◽  
Vol 29 (3) ◽  
pp. 259-280 ◽  
Author(s):  
John L. Locke ◽  
Barry Bogin
Keyword(s):  
Life History ◽  
Adult Development ◽  
Homo Sapiens ◽  
Human Life ◽  
Modern Human ◽  
Linguistic Knowledge ◽  
Human Language ◽  
Juvenile Period ◽  
Development Of Language ◽  
New Perspective

It has long been claimed that Homo sapiens is the only species that has language, but only recently has it been recognized that humans also have an unusual pattern of growth and development. Social mammals have two stages of pre-adult development: infancy and juvenility. Humans have two additional prolonged and pronounced life history stages: childhood, an interval of four years extending between infancy and the juvenile period that follows, and adolescence, a stage of about eight years that stretches from juvenility to adulthood. We begin by reviewing the primary biological and linguistic changes occurring in each of the four pre-adult ontogenetic stages in human life history. Then we attempt to trace the evolution of childhood and juvenility in our hominin ancestors. We propose that several different forms of selection applied in infancy and childhood; and that, in adolescence, elaborated vocal behaviors played a role in courtship and intrasexual competition, enhancing fitness and ultimately integrating performative and pragmatic skills with linguistic knowledge in a broad faculty of language. A theoretical consequence of our proposal is that fossil evidence of the uniquely human stages may be used, with other findings, to date the emergence of language. If important aspects of language cannot appear until sexual maturity, as we propose, then a second consequence is that the development of language requires the whole of modern human ontogeny. Our life history model thus offers new ways of investigating, and thinking about, the evolution, development, and ultimately the nature of human language.

scholarly journals Hyrcanian forests-Stable rear-edge populations harbouring high genetic diversity of Fraxinus excelsior, a common European tree species

2018 ◽  
Vol 24 (11) ◽  
pp. 1521-1533 ◽  
Author(s):  
Eva Ortvald Erichsen ◽  
Katharina Birgit Budde ◽  
Khosro Sagheb-Talebi ◽  
Francesca Bagnoli ◽  
Giovanni Giuseppe Vendramin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Tree Species ◽  
Fraxinus Excelsior ◽  
High Genetic Diversity ◽  
Hyrcanian Forests ◽  
Rear Edge ◽  
Edge Populations

scholarly journals Comprehensive detection of recurring genomic abnormalities: a targeted sequencing approach for multiple myeloma

2019 ◽  
Vol 9 (12) ◽  
Author(s):  
Venkata Yellapantula ◽  
Malin Hultcrantz ◽  
Even H. Rustad ◽  
Ester Wasserman ◽  
Dory Londono ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Clinical Trial Design ◽  
High Sensitivity ◽  
Genomic Research ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Genomic Markers ◽  
Next Generation Sequencing Ngs ◽  
New Generation ◽  
Gains And Losses

AbstractRecent genomic research efforts in multiple myeloma have revealed clinically relevant molecular subgroups beyond conventional cytogenetic classifications. Implementing these advances in clinical trial design and in routine patient care requires a new generation of molecular diagnostic tools. Here, we present a custom capture next-generation sequencing (NGS) panel designed to identify rearrangements involving the IGH locus, arm level, and focal copy number aberrations, as well as frequently mutated genes in multiple myeloma in a single assay. We sequenced 154 patients with plasma cell disorders and performed a head-to-head comparison with the results from conventional clinical assays, i.e., fluorescent in situ hybridization (FISH) and single-nucleotide polymorphism (SNP) microarray. Our custom capture NGS panel had high sensitivity (>99%) and specificity (>99%) for detection of IGH translocations and relevant chromosomal gains and losses in multiple myeloma. In addition, the assay was able to capture novel genomic markers associated with poor outcome such as bi-allelic events involving TP53. In summary, we show that a multiple myeloma designed custom capture NGS panel can detect IGH translocations and CNAs with very high concordance in relation to FISH and SNP microarrays and importantly captures the most relevant and recurrent somatic mutations in multiple myeloma rendering this approach highly suitable for clinical application in the modern era.

scholarly journals Transcriptome Analysis in Domesticated Species: Challenges and Strategies

2015 ◽  
Vol 9S4 ◽  
pp. BBI.S29334 ◽  
Author(s):  
Jessica P. Hekman ◽  
Jennifer L Johnson ◽  
Anna V. Kukekova
Keyword(s):  
Complex Traits ◽  
Gene Networks ◽  
Association Studies ◽  
Cultural Value ◽  
Genomic Research ◽  
Model Organisms ◽  
Genome Wide Association Studies ◽  
Rna Seq ◽  
Genome Wide ◽  
Genome Assemblies

Domesticated species occupy a special place in the human world due to their economic and cultural value. In the era of genomic research, domesticated species provide unique advantages for investigation of diseases and complex phenotypes. RNA sequencing, or RNA-seq, has recently emerged as a new approach for studying transcriptional activity of the whole genome, changing the focus from individual genes to gene networks. RNA-seq analysis in domesticated species may complement genome-wide association studies of complex traits with economic importance or direct relevance to biomedical research. However, RNA-seq studies are more challenging in domesticated species than in model organisms. These challenges are at least in part associated with the lack of quality genome assemblies for some domesticated species and the absence of genome assemblies for others. In this review, we discuss strategies for analyzing RNA-seq data, focusing particularly on questions and examples relevant to domesticated species.

Co-ordinated performance of leaf hydraulics and economics in 10 Chinese temperate tree species

2016 ◽  
Vol 43 (11) ◽  
pp. 1082 ◽  
Author(s):  
Ying Jin ◽  
Chuankuan Wang ◽  
Zhenghu Zhou ◽  
Zhimin Li
Keyword(s):  
Resource Use ◽  
Tree Species ◽  
Eastern China ◽  
Hydraulic Conductance ◽  
Economic Traits ◽  
Leaf Economics Spectrum ◽  
Leaf Hydraulic Conductance ◽  
Leaf Hydraulics ◽  
Leaf Economics ◽  
Nutrient Traits

Exploring relationships between leaf hydraulics and economic traits is important in understanding the carbon–water coupling and in extending the leaf economics spectrum. In this study, leaf hydraulics, photosynthesis, structural and nutrient traits and photosynthetic resource use efficiency were measured for 10 temperate tree species in the north-eastern China. Leaf hydraulic conductance was positively correlated with photosynthetic traits, specific leaf area, leaf nitrogen concentration, photosynthetic water and nitrogen use efficiencies, suggesting co-ordination between leaf hydraulics and economic traits. Principal component analysis revealed that significant correlations existed among leaf hydraulic, photosynthetic and resource use traits (axis 1), and axis 2 was strongly associated with leaf structural and nutrient traits. The 10 species were distributed along the diagonal line between axis 1 and axis 2. Species displaying the ‘fast’ strategy tended to have higher photosynthetic rates, leaf hydraulic conductance and photosynthetic water and nutrient use efficiencies; however, they also had lower carbon investment and faced a greater risk of embolism. These findings indicate that leaf hydraulics, economics and resource uses together play an important role in determining species ecological strategies, and provide supports for the ‘fast–slow’ leaf economics spectrum.

scholarly journals The future of genomics for developmentalists

2013 ◽  
Vol 25 (4pt2) ◽  
pp. 1263-1278 ◽  
Author(s):  
Robert Plomin ◽  
Michael A. Simpson
Keyword(s):  
Complex Traits ◽  
Rare Variants ◽  
Behavioral Development ◽  
Genomic Research ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Risk And Resilience ◽  
Polygenic Scores ◽  
Dna Variants ◽  
The Future

AbstractThe momentum of genomic science will carry it far into the future and into the heart of research on typical and atypical behavioral development. The purpose of this paper is to focus on a few implications and applications of these advances for understanding behavioral development. Quantitative genetics is genomic and will chart the course for molecular genomic research now that these two worlds of genetics are merging in the search for many genes of small effect. Although current attempts to identify specific genes have had limited success, known as the missing heritability problem, whole-genome sequencing will improve this situation by identifying all DNA sequence variations, including rare variants. Because the heritability of complex traits is caused by many DNA variants of small effect in the population, polygenic scores that are composites of hundreds or thousands of DNA variants will be used by developmentalists to predict children's genetic risk and resilience. The most far-reaching advance will be the widespread availability of whole-genome sequence for children, which means that developmentalists would no longer need to obtain DNA or to genotype children in order to use genomic information in research or in the clinic.

scholarly journals Significance and management of acetic acid bacteria culture collections

2013 ◽  
Vol 2 (1s) ◽  
pp. 9 ◽  
Author(s):  
Luciana De Vero ◽  
Paolo Giudici
Keyword(s):  
Acetic Acid ◽  
Complex Traits ◽  
Sequence Data ◽  
Human Life ◽  
Acetic Acid Bacteria ◽  
Fermented Food ◽  
Industrial Biotechnology ◽  
Microbial Culture ◽  
Culture Collections ◽  
Functional Studies

Acetic acid bacteria (AAB) are obligate aerobic microorganisms which have large significance in human life. Traditionally, AAB species have been used to produce fermented food and beverages thanks to their ability to oxidize ethanol to acetic acid. Moreover, in the last decades, they have been extensively investigated for other industrial biotechnology applications as the development of processes for highvalue products or biosensors. The potential exploitation of AAB diversity requires the existence of microbial culture collections, which are able to supply not only strains but essential data for fundamental microbial research. Therefore, microbial collections can be helpful to provide critical insights into AAB physiology and metabolism as well as integrate sequence data with transcriptional and functional studies to better define complex traits and develop new potential microbial processes. This article reviews the significance of microbial collections, with an overview of the well-known European Biological Resources Centers (BRCs) collecting AAB, and provides an insight into their cultivability and metabolic activity. It also discusses appropriate techniques in preserving <em>authentic</em> strains, quality control implications, databases and BRC networking as well as connections among collections and stakeholders.

scholarly journals Wheat Genomics: Present Status and Future Prospects

2008 ◽  
Vol 2008 ◽  
pp. 1-36 ◽  
Author(s):  
P. K. Gupta ◽  
R. R. Mir ◽  
A. Mohan ◽  
J. Kumar
Keyword(s):  
Repetitive Sequences ◽  
Genomic Research ◽  
Large Set ◽  
Economic Traits ◽  
Physical Maps ◽  
Gene Space ◽  
Genome Wide ◽  
Genomics Research ◽  
Number Of Genes ◽  
Molecular Maps

Wheat (Triticum aestivum L.), with a large genome (16000 Mb) and high proportion (∼80%) of repetitive sequences, has been a difficult crop for genomics research. However, the availability of extensive cytogenetics stocks has been an asset, which facilitated significant progress in wheat genomic research in recent years. For instance, fairly dense molecular maps (both genetic and physical maps) and a large set of ESTs allowed genome-wide identification of gene-rich and gene-poor regions as well as QTL including eQTL. The availability of markers associated with major economic traits also allowed development of major programs on marker-assisted selection (MAS) in some countries, and facilitated map-based cloning of a number of genes/QTL. Resources for functional genomics including TILLING and RNA interference (RNAi) along with some new approaches like epigenetics and association mapping are also being successfully used for wheat genomics research. BAC/BIBAC libraries for the subgenome D and some individual chromosomes have also been prepared to facilitate sequencing of gene space. In this brief review, we discuss all these advances in some detail, and also describe briefly the available resources, which can be used for future genomics research in this important crop.

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