scholarly journals From Gene Networks to Gene Function

2003 ◽  
Vol 13 (12) ◽  
pp. 2568-2576 ◽  
Author(s):  
T. Schlitt
Keyword(s):  
Gene Function ◽  
Gene Networks

scholarly journals A roadmap for gene functional characterisation in wheat

2019 ◽  
Author(s):  
Nikolai M Adamski ◽  
Philippa Borrill ◽  
Jemima Brinton ◽  
Sophie Harrington ◽  
Clemence Marchal ◽  
...  
Keyword(s):  
Gene Function ◽  
Gene Networks ◽  
Crop Production ◽  
Crop Improvement ◽  
Basic Research ◽  
Reference Sequence ◽  
Background Information ◽  
World Population ◽  
Putative Gene ◽  
Functional Characterisation

To adapt to the challenges of climate change and the growing world population, it is vital to increase global crop production. Understanding the function of genes within staple crops will accelerate crop improvement by allowing targeted breeding approaches. Despite the importance of wheat, which provides 20 % of the calories consumed by humankind, a lack of genomic information and resources has hindered the functional characterisation of genes in this species. The recent release of a high-quality reference sequence for wheat underpins a suite of genetic and genomic resources that support basic research and breeding. These include accurate gene model annotations, gene expression atlases and gene networks that provide background information about putative gene function. In parallel, sequenced mutation populations, improved transformation protocols and structured natural populations provide rapid methods to study gene function directly. We highlight a case study exemplifying how to integrate these resources to study gene function in wheat and thereby accelerate improvement in this important crop. We hope that this review provides a helpful guide for plant scientists, especially those expanding into wheat research for the first time, to capitalise on the discoveries made in Arabidopsis and other plants. This will accelerate the improvement of wheat, a complex polyploid crop, of vital importance for food and nutrition security.

scholarly journals Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function

2009 ◽  
Vol 10 (9) ◽  
pp. R97 ◽  
Author(s):  
James C Costello ◽  
Mehmet M Dalkilic ◽  
Scott M Beason ◽  
Jeff R Gehlhausen ◽  
Rupali Patwardhan ◽  
...  
Keyword(s):  
Experimental Data ◽  
Drosophila Melanogaster ◽  
Gene Function ◽  
Gene Networks ◽  
Predict Gene Function

scholarly journals A roadmap for gene functional characterisation in wheat

2019 ◽  
Author(s):  
Nikolai M Adamski ◽  
Philippa Borrill ◽  
Jemima Brinton ◽  
Sophie Harrington ◽  
Clemence Marchal ◽  
...  
Keyword(s):  
Gene Function ◽  
Gene Networks ◽  
Crop Production ◽  
Crop Improvement ◽  
Basic Research ◽  
Reference Sequence ◽  
Background Information ◽  
World Population ◽  
Putative Gene ◽  
Functional Characterisation

To adapt to the challenges of climate change and the growing world population, it is vital to increase global crop production. Understanding the function of genes within staple crops will accelerate crop improvement by allowing targeted breeding approaches. Despite the importance of wheat, which provides 20 % of the calories consumed by humankind, a lack of genomic information and resources has hindered the functional characterisation of genes in this species. The recent release of a high-quality reference sequence for wheat underpins a suite of genetic and genomic resources that support basic research and breeding. These include accurate gene model annotations, gene expression atlases and gene networks that provide background information about putative gene function. In parallel, sequenced mutation populations, improved transformation protocols and structured natural populations provide rapid methods to study gene function directly. We highlight a case study exemplifying how to integrate these resources to study gene function in wheat and thereby accelerate improvement in this important crop. We hope that this review provides a helpful guide for plant scientists, especially those expanding into wheat research for the first time, to capitalise on the discoveries made in Arabidopsis and other plants. This will accelerate the improvement of wheat, a complex polyploid crop, of vital importance for food and nutrition security.

What Makes a Weed a Weed? How Virus-mediated Reverse Genetics Can Help to Explore the Genetics of Weediness

2020 ◽  
Vol 31 (5) ◽  
pp. 224-229
Author(s):  
Dana R. MacGregor
Keyword(s):  
Gene Function ◽  
Gene Networks ◽  
Reverse Genetics ◽  
Specific Gene ◽  
Reverse Genetic ◽  
Virus Induced Gene Silencing ◽  
Weed Species ◽  
Genetic Techniques ◽  
Agricultural Weeds ◽  
Insight Into

Reverse genetics investigates what a gene does by testing how the plant responds when the specific gene is changed. These techniques have been in use for decades to assess whether a given gene underpins interesting phenotypes and gain insight into the function of gene networks and families. Weed science has only recently entered the "genomic era" in which genomic and reverse genetics approaches are used to address hypotheses. This review focuses on two reverse genetic techniques used on a variety of plants including agricultural weeds, virus-induced gene silencing (VIGS) and virus-mediated overexpression (VOX), explaining the biology behind them and highlighting how these tools may be used for gene function validation in weed species for which no other transgenic approaches have been developed.

scholarly journals Gene divergence and pathway duplication in the metabolic network of yeast and digital organisms

2009 ◽  
Vol 6 (41) ◽  
pp. 1233-1245 ◽  
Author(s):  
P. Gerlee ◽  
T. Lundh ◽  
B. Zhang ◽  
A. R. A. Anderson
Keyword(s):  
Gene Function ◽  
Degree Distribution ◽  
Gene Networks ◽  
Preferential Attachment ◽  
Bipartite Network ◽  
Scale Free ◽  
Evolving Systems ◽  
Digital Organisms ◽  
Free Gene ◽  
Function Network

We have studied the metabolic gene–function network in yeast and digital organisms evolved in the artificial life platform A vida . The gene–function network is a bipartite network in which a link exists between a gene and a function (pathway) if that function depends on that gene, and can also be viewed as a decomposition of the more traditional functional gene networks, where two genes are linked if they share any function. We show that the gene–function network exhibits two distinct degree distributions: the gene degree distribution is scale-free while the pathway distribution is exponential. This is true for both yeast and digital organisms, which suggests that this is a general property of evolving systems, and we propose that the scale-free gene degree distribution is due to pathway duplication, i.e. the development of a new pathway where the original function is still retained. Pathway duplication would serve as preferential attachment for the genes, and the experiments with A vida revealed precisely this; genes involved in many pathways are more likely to increase their connectivity. Measuring the overlap between different pathways, in terms of the genes that constitute them, showed that pathway duplication also is a likely mechanism in yeast evolution. This analysis sheds new light on the evolution of genes and functionality, and suggests that function duplication could be an important mechanism in evolution.

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