Gene function, gene networks and the fate of duplicated genes

1999 ◽  
Vol 10 (5) ◽  
pp. 549-553 ◽  
Author(s):  
Sebastian M. Shimeld
Keyword(s):  
Gene Function ◽  
Gene Networks ◽  
Duplicated Genes

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 Regulatory divergence of flowering time genes in the allopolyploid Brassica napus

2017 ◽  
Author(s):  
D. Marc Jones ◽  
Rachel Wells ◽  
Nick Pullen ◽  
Martin Trick ◽  
Judith A. Irwin ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Flowering Time ◽  
Gene Networks ◽  
Regulatory Elements ◽  
Duplicated Genes ◽  
Crop Species ◽  
Gene Copies ◽  
Gene Expression Dynamics ◽  
Flowering Time Gene ◽  
In Cis

AbstractPolyploidy is a recurrent feature of eukaryotic evolution and has been linked to increases in complexity, adaptive radiation and speciation. Within angiosperms, such events occur repeatedly in many plant lineages. We investigated the role of duplicated genes in the regulation of flowering in Brassica napus. This relatively young allotetraploid represents a snapshot of evolution and artificial selection in progress. In line with the gene balance hypothesis, we find preferential retention of expressed flowering time genes relative to the whole genome. Furthermore, gene expression dynamics across development reveal diverged regulation of many flowering time gene copies. This finding supports the concept of responsive backup circuits being key for the retention of duplicated genes. A case study of BnaTFL1 reveals differences in cis-regulatory elements downstream of these genes that could explain this divergence. Such differences in the regulatory dynamics of duplicated genes highlight the challenges for translating gene networks from model to more complex polyploid crop species.

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.

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 How often do duplicated genes evolve new functions?

Genetics ◽  
1995 ◽  
Vol 139 (1) ◽  
pp. 421-428 ◽  
Author(s):  
J B Walsh
Keyword(s):  
Gene Function ◽  
Null Alleles ◽  
Duplicated Genes ◽  
Effective Population ◽  
The Road ◽  
Large Populations ◽  
New Gene ◽  
On The Road ◽  
Duplicate Locus ◽  
Linkage Effects

Abstract A recently duplicated gene can either fix a null allele (becoming a pseudogene) or fix an (advantageous) allele giving a slightly different function, starting it on the road to evolving a new function. Here we examine the relative probabilities of these two events under a simple model. Null alleles are assumed to be neutral; linkage effects are ignored, as are unequal crossing over and gene conversion. These assumptions likely make our results underestimates for the probability that an advantageous allele is fixed first. When new advantageous mutations are additive with selection coefficient s and the ratio of advantageous to null mutations is rho, the probability an advantageous allele is fixed first is ([1 - e-s]/[rho S] + 1)-1, where S = 4Nes with Ne the effective population size. The probability that a duplicate locus becomes a pseudogene, as opposed to evolving a new gene function, is high unless rhoS > 1. However, even if advantageous mutations are very rare relative to null mutations, for sufficiently large populations rhoS > 1 and new gene function, rather than pseudogene formation, is the expected fate of most duplicated genes.

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