Award details

Signatures of Domestication and Adaptation

Reference	BBS/E/T/000PR9818
Principal Investigator / Supervisor	Dr Wilfried Haerty
Co-Investigators / Co-Supervisors	Professor Anthony Hall, Professor Neil Hall, Dr Tamas Korcsmaros
Institution	Earlham Institute
Department	Earlham Institute Department
Funding type	Research
Value (£)	7,379,492
Status	Current
Type	Institute Project
Start date	01/04/2017
End date	31/03/2023
Duration	59 months

Abstract

Uncovering genetic variation of natural and domesticated populations, quantifying gene flow between them and understanding diversification mechanisms operating in both environments is vital for sustainability of agriculture and aquaculture in the face of climate change, as well as increased vulnerability to diseases. We will apply our expertise in animal and plant genomics to identify domestication and adaptation diversification hotspots and bottlenecks in key systems: crops and wild relatives in Poaceae and Brassicaceae and aquaculture fish species (both farmed and wild Tilapia populations). For each of these systems, we will scan genomes of domesticated and cultivated species, and those of their wild relatives, to assess genetic diversity in these populations and identify patterns of selection that are linked to environmental adaptation, speciation, and evolution under domestication. Using improved genome annotations, we will identify and characterise variants segregating at high frequency within protein coding sequences, their regulatory regions, and conserved noncoding elements in domesticated species in comparison to their wild relatives. We will compare the pattern of intraspecies diversity between wild and cultivated lines to assess the impact of artificial selection on the loss of heterozygosity and the fixation of weakly deleterious variants. We will assess the selective constraints acting on regulatory elements and gene regulation through evolutionary analyses to provide demographic and genetic data necessary to model interactions between farmed and wild species, and predict population character and abundance. This information will ultimately contribute to the improvement and expansion of breeding programs. We will also utilise natural and synthetic hybrids to investigate the immediate and long-term effects of hybridisation and polyploidy on genome architecture and evolution. We will focus our investigations on Triticeae species (tetraploid: Triticum turgidum, T. dicoccum; diploid: T. urartu, T. monococcum) and their hybrids. We will apply sequence-based approaches to assay transcriptional activity (RNA-seq, smRNA-seq), and interrogate existing public data and data available through the Designing Future Wheat ISP WP4 (ATAC-Seq, ChIP-Seq, DNA methylation), to define the epigenome of natural and synthetic hybrids and the wild progenitors. The widespread use and misuse of antimicrobials in our general environment has allowed bacteria to be frequently exposed to sub-inhibitory concentrations, favouring the evolution and spread of resistance to the most commonly used antimicrobial molecules. The effects of these low antibacterial concentrations on pathogenic bacteria leading to the selection of variants associated with resistance are currently not fully understood despite their implications for the effectiveness of antimicrobial drugs in the future. Using machine learning approaches to mine currently available data, we will investigate the genetic changes responsible for adaptation of Salmonella to certain hosts and environments as well as changes in virulence or drug resistance. We aim to characterise the fitness effects of resistance mutations and how they can be maintained in a population with and without antimicrobial selection. Using experimental selection (performed by QI collaborators) and genome sequencing (performed by EI), we will assess whether the trajectory of mutations and allele frequency changes at different antimicrobial concentrations can be predicted and modelled.

Summary

unavailable

Committee	Not funded via Committee
Research Topics	Animal Health, Crop Science, Plant Science
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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