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The nature of spontaneous mutational variation for fitness in Chlamydomonas

Reference	BB/L00237X/1
Principal Investigator / Supervisor	Professor Peter Keightley
Co-Investigators / Co-Supervisors	Professor Nick Colegrave, Dr Robert Ness
Institution	University of Edinburgh
Department	Sch of Biological Sciences
Funding type	Research
Value (£)	620,248
Status	Completed
Type	Research Grant
Start date	30/04/2014
End date	31/03/2018
Duration	47 months

Abstract

New mutations are the ultimate source of genetic variation. Furthermore, the joint actions of new mutations, selection, genetic drift and recombination have been implicated in many important biological phenomena, including the evolution of recombination, the evolution of senescence and inbreeding depression. However, understanding the role of mutation in genetics has been hampered by a lack of knowledge of the genetic basis of variation from new mutations, especially the distribution of fitness effects (DFE) for new mutations and the mechanisms linking genotype with phenotype. In the proposed project, we will capitalize on complete genome sequence data from 90 mutation accumulation (MA) lines of Chlamydomonas that we have generated within an existing BBSRC project. We will make precise fitness measures by competing recombinant lines produced by backcrossing the MA lines to their ancestral strains against marked strains, and by efficient genotyping of the recombinant lines to identify the precise complement of mutations carried by each line. This information will enable us to estimate directly the fitness effects of each mutation and the extent of their epistatic interactions. We will thereby estimate the properties of the DFE in an unbiased manner and at an unprecedented level of detail. We will combine phenotypic and genotypic information to accurately infer the amount of fitness change and genetic variation produced by mutations in different kinds of sites in the genome, including protein-coding versus regulatory, the net effect of epistasis, and the relative frequencies of deleterious and advantageous mutations. We will integrate this information with detailed expression data from the MA lines and their ancestors, which will enable us to mechanistically link the genetic change induced at the DNA level with phenotypic change.

Summary

Many traits, including the ability to survive and reproduce (fitness), vary amongst individuals within a species. Much of this variation for fitness and other traits has a heritable genetic basis. Heritable variation in fitness fuels evolution by natural selection and it is through this process that the staggering diversity of biological form has arisen. Importantly, the origin of genetic variation is ultimately from new mutations, which alter the DNA sequence. However, only a small fraction of mutations are believed to be advantageous and lead to adaptation. A high proportion of new mutations are harmful, as they damage well adapted genes and therefore are continually purged from populations by natural selection. Understanding the impact of both harmful and beneficial mutations is crucially important for a range of unresolved phenomena in biology. For example, rare and recurrent mutations are responsible for many complex genetic disorders. Moreover, sexual reproduction may persist because it allows populations to rid themselves of harmful mutations. Otherwise, these harmful mutations may build up in inbred or asexual populations and potentially leave them vulnerable to extinction. Despite the central role of mutation in these important processes, we know relatively little about it, mostly because new mutations are very rare, occurring at only about one to ten per billion DNA positions in a generation. As a result, neither the relative frequency of harmful and beneficial mutations nor the strength of their effects on fitness has been well described. Without this information, we cannot begin to investigate the underlying causes of mutational effects and ultimately predict the consequences of mutations across the genome. In the proposed project, we will investigate the nature of new spontaneous mutations in the microscopic alga, Chlamydomonas reinhardtii. This single-celled plant is widely used as a model for the study of photosynthesis, cell biology, and increasingly for its potential to generate green energy or biofuel. Emerging technologies in the field of genomics will allow us to study new mutations in unprecedented detail. We are now able to sequence the complete genomes of many individuals and therefore to identify rare mutational events. Other techniques allow us to simultaneously monitor the expression of every gene in the genome to assess the impact of mutation on genetic regulation. Our project can be divided into three complementary sections: (1) First, we plan to look at what kinds of mutations the lines carry and how these different types of mutations affect fitness. This will help us gain insights into what parts of the genome are, on average, most important to fitness and prone to mutation. (2) We will then measure the individual effects of hundreds of mutations. This will be achieved by comparing the growth of many mutant-bearing lines with their non-mutated ancestors and statistically disentangling the effect of each individual mutation. Unlike earlier attempts to estimate the effects of mutations, our study will be the first to directly capture the complexity of spontaneous mutational effects. (3) Lastly, we will compare how genes are regulated amongst our mutant-bearing lines and their non-mutated ancestors. We will then test a number of hypotheses about the importance of gene regulation for fitness, including how sensitive organisms are to changes in gene regulation, whether more highly expressed genes are more important and whether the interconnectedness amongst genes predicts their significance or susceptibility to mutation. This research, describing the fundamental process of mutation, will help biological researchers to address important questions pertaining to disease, conservation and evolution.

Impact Summary

Who will benefit from this research? Wider Public: Our research underpins many areas of science that are of great interest to the general public, such as the genetic risks to endangered species and small populations, the ultimate and proximate causes of ageing, senescence and congential disease, and the evolution of sex and recombination. Medicine: Much complex disease is now believed to be a consequence of the action of the combined effects of many allelic variants with small effects. It is likely that part of the variation among individuals in susceptibility to disease has its origin in recent, slightly deleterious mutations. Understanding the genetic basis of this variation will therefore be beneficial for understanding the nature of variation in susceptibility. It is also increasingly apparent that many genetic diseases manifest through disruption of gene expression networks, so basic science exploring the response of such networks to mutational perturbation has a great potential for downstream impact in this field. Commercial private sector: Our study organism is being developed as a potential biofuel producer and as a bioremediation agent. An understanding of its basic biology and the genetic basis of evolutionary change via fixation of new mutations will offer potentially important insights into these applications. How will they benefit from this research? Wider Public: Maximising the public engagement with science and increasing the public's knowledge skills in this area has the potential not only to enrich their individual lives (with consequent effects on health and wellbeing), but to also advertise the benefits to society of high quality science (paid for by the taxpayer). Benefits in this area can be realised within the lifetime of the grant. Medicine: It is difficult to predict in any detail how the results of our research could impact on the field of medicine. However, an understanding of the effects of naturally occurring mutations on the behaviour of gene regulation networks, and the consequences for the functioning of the organism as a whole may provide important insights into the nature of complex genetic disease. This in turn may provide longer term opportunities to develop effective treatments to target disease whilst minimising side-effects. Due to the nature of our proposal, impacts in this area are considerably downstream and beyond the end point of the research itself. Commercial private sector: A major challenge in developing any organism for an industrial role is causing it to maximise production of the desired molecule or trait, without simultaneously reducing its growth or viability or increasing the production of other undesired substances. Similarly, producing organisms that can robustly express desired characteristics under a variety of environmental perturbations is challenging. A better understanding of the patterns of co-regulation of genes within this organism coupled with a clearer picture of network robustness to local or global perturbation offers the potential to guide the production of better designed organisms for industrial applications. Due to the nature of our proposal, however, impacts in this area are considerably downstream and beyond the end point of the research itself.

Committee	Research Committee C (Genes, development and STEM approaches to biology)
Research Topics	Microbiology, Plant Science, Systems Biology
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

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