Selection Footprints and Mapping
Lead Research Organisation:
Roslin Institute
Department Name: UNLISTED
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
The research funded by this grant explores a relatively new approach to gene mapping. The selection (or hitchhiking) mapping approach exploits the fact that genetic diversity will be reduced near a gene under strong selection, due to statistical associations that develop along a chromosome. The recent increase in availability of genetic diversity data, due to technical improvements and reductions in cost of genome-wide sequencing, have made such techniques feasible. So far, this approach has primarily been applied to human data sets, with the goal of understanding the selective processes that have acted on the human genome over the course of evolution. An important issue is that while there has been a large effort applied to data generation and analysis (including the publication of some controversial conclusions regarding human evolution), the power and limitations of this approach have not been seriously addressed by researchers. The importance of our work is that it focuses on genes for which there is strong historical evidence of selection, allowing us to characterize the diversity patterns generated by selection. In most wild species and humans, this would not be possible since it is rare that a gene or genetic region is definitely known to have been under selection. However, in domesticated species, where the selection pressure has been strong and often on well-defined traits, there are more opportunities for implementation of this approach to identify genes related to the domestication process. This research has examined the diversity patterns at neutral markers in the region of three cattle genes with strong evidence of selection as well as for simulated genotypic data, generated under specific selection regimes.
Planned Impact
unavailable
People |
ORCID iD |
| John Woolliams (Principal Investigator) |
Publications
Daetwyler HD
(2007)
Inbreeding in genome-wide selection.
in Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie
Lewis T
(2007)
Genotype by mating type interaction for litter size in Landrace and Large White sows
in Animal Science
Pong-Wong R
(2007)
Optimisation of contribution of candidate parents to maximise genetic gain and restricting inbreeding using semidefinite programming ( Open Access publication )
in Genetics Selection Evolution
Woolliams J
(2009)
The long-term accumulation and depletion of copper in the liver of different breeds of sheep fed diets of differing copper content
in The Journal of Agricultural Science
Woolliams J
(2009)
The copper content of wool in relation to breed and the concentrations of copper in the liver and plasma
in The Journal of Agricultural Science
Bovine HapMap Consortium
(2009)
Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds.
in Science (New York, N.Y.)
Woolliams J
(2009)
Prediction of long-term contributions and inbreeding in populations undergoing mass selection
in Genetical Research
Field A
(2009)
The effect of dietary intake of calcium and phosphorus on the absorption and excretion of phosphorus in chimaera-derived sheep
in The Journal of Agricultural Science
Wiener G
(2009)
Breed differences in copper metabolism in sheep
in The Journal of Agricultural Science
Woolliams J
(2009)
Analysis of factors affecting superovulatory responses in ruminants
in The Journal of Agricultural Science
Woolliams J
(2010)
Modifications to MOET nucleus breeding schemes to improve rates of genetic progress and decrease rates of inbreeding in dairy cattle
in Animal Science
Woolliams J
(2010)
A note on the growth and food consumption of crossbred lambs of five sire breeds
in Animal Science
Wiener G
(2010)
Effects of rapid inbreeding and of crossing of inbred lines on conception rate, prolificacy and ewe survival in sheep
in Animal Science
Wiener G
(2010)
Effects of rapid inbreeding and of crossing inbred lines on the growth of linear body dimensions of sheep
in Animal Science
Woolliams J
(2010)
Embryo manipulation in cattle breeding and production
in Animal Production
Woolliams J
(2010)
The effect of breed of sire on the accumulation of copper in lambs, with particular reference to copper toxicity
in Animal Science
Wiener G
(2010)
Genetic selection to produce lines of sheep differing in plasma copper concentrations
in Animal Science
Woolliams J
(2010)
The value of cloning in MOET nucleus breeding schemes for dairy cattle
in Animal Production
Field A
(2010)
The effect of breed of sire on the urinary excretion of phosphorus and magnesium in lambs
in Animal Science
Villanueva B
(2010)
Genetic progress and inbreeding for alternative nucleus breeding schemes for beef cattle
in Animal Science
Woolliams J
(2010)
Studies on lambs from lines genetically selected for low and high copper status 2. Incidence of hypocuprosis on improved hill pasture
in Animal Science
Woolliams C
(2010)
Studies on lambs from lines genetically selected for low and high copper status 1. Differences in mortality
in Animal Science
Woolliams J
(2010)
The value of indicator traits in the genetic improvement of dairy cattle
in Animal Production
Sinnett-Smith P
(2010)
Genetic variations in subcutaneous adipose tissue metabolism in sheep
in Animal Science
Bishop S
(2010)
Utilization of the sex-determining region Y gene in beef cattle breeding schemes
in Animal Science
Sinnett-Smith P
(2010)
Adipose tissue metabolism and cell size: variation between subcutaneous sites and the effect of copper supplementation
in Animal Science
Woolliams J
(2010)
The effect of breed type and inbreeding on characteristics of the fleece and skin of 12-week-old lambs
in Animal Science
Wiener G
(2010)
Effects of breed, rapid inbreeding, crossbreeding and environmental factors on fleece weight and fleece shedding in sheep
in Animal Science
Woolliams J
(2010)
Decision rules and variance of response in breeding schemes
in Animal Science
Wiener G
(2010)
Effects of rapid inbreeding and of crossing of inbred lines on the body weight growth of sheep
in Animal Science
Sinnett-Smith P
(2010)
Effects of recombinant DNA-derived bovine somatotropin on growth, carcass characteristics and meat quality in lambs from three breeds
in Animal Science
Woolliams J
(2010)
The effects of breed, crossbreeding and other factors on variation in fleece and skin traits
in Animal Science
Sinnett-Smith P
(2010)
Biochemical and physiological responses to metabolic stimuli in Friesian calves of differing genetic merit for milk production
in Animal Science
Woolliams J
(2010)
Genetic contributions of Finnish Ayrshire bulls over four generations
in Animal Science
Wiener G
(2010)
Consequences of inbreeding for financial returns from sheep
in Animal Science
Woolliams J
(2010)
Retention of copper in the liver of sheep genetically selected for high and low concentrations of copper in plasma
in Animal Science
Luo Z
(2010)
Controlling inbreeding in dairy MOET nucleus schemes
in Animal Science
Woolliams J
(2010)
The effect of dietary protein on metabolite concentrations during fasting in calves differing genetically in dairy merit
in Animal Science
Woolliams J
(2010)
Get off my land
in New Scientist
Meuwissen T
(2010)
Responses of multi-trait selection in open nucleus schemes for dairy cattle breeding
in Animal Science
Woolliams J
(2010)
Endogenous pulsing and stimulated release of growth hormone in dairy calves of high and low genetic merit
in Animal Science
Eaglen S
(2011)
Phenotypic effects of calving ease on the subsequent fertility and milk production of dam and calf in UK Holstein-Friesian heifers
in Journal of Dairy Science
Lipschutz-Powell D
(2012)
Bias, accuracy, and impact of indirect genetic effects in infectious diseases.
in Frontiers in genetics
Sánchez-Molano E
(2015)
Genomic prediction of traits related to canine hip dysplasia.
in Frontiers in genetics
Cooper TA
(2016)
Genomic evaluation, breed identification, and population structure of Guernsey cattle in North America, Great Britain, and the Isle of Guernsey.
in Journal of dairy science
Canela-Xandri O
(2016)
Improved Genetic Profiling of Anthropometric Traits Using a Big Data Approach
in PLOS ONE
| Description | The major finding was that the regression method developed in the project was able to detect the positive selection near the selected genes and furthermore was able to detect new putative QTL. However the regression methodology proved relatively sensitive to the variability of the markers in the dataset. The greatest power of detection of the selection footprint was shown to be when the favoured allele had reached high frequency and had moved beyond intermediate frequencies. |
| Exploitation Route | In evolutionary studies and, in livestock, understanding the functional consequences of domestication, and recent natural and artificial selection. |
| Sectors | Agriculture Food and Drink |
| Description | The development of new software to identify segments of DNA that can be used directly for genetic improvement or the removal of deleterious effects by breeding organisations. |
| First Year Of Impact | 2013 |
| Sector | Agriculture, Food and Drink |
| Impact Types | Societal Economic |
| Description | Membership of Drafting Group for UK Country Report on Farm Animal Genetic Resources, 2002 |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Impact | UK Country Report on Farm Animal Genetic Resources 2002. This was the first time this policy area was addressed and formed an international report to FAO. |
| URL | https://www.gov.uk/government/publications/uk-country-report-on-farm-animal-genetic-resources-2002 |
| Description | INIA |
| Organisation | National Institute for Agricultural and Food Research and Technology |
| Country | Spain |
| Sector | Public |
| PI Contribution | Training, design and interpretation of studies, writing papers for journals |
| Collaborator Contribution | Personnel, funding for personnel, scientific discussion, writing papers. |
| Impact | Scientific papers. New PhDs and trained post-docs in Spain. |
| Start Year | 2008 |
| Description | Norwegian University of Life Sciences (NMBU), Aas, Norway |
| Organisation | Norwegian University of Life Sciences (NMBU) |
| Country | Norway |
| Sector | Academic/University |
| PI Contribution | Supervised and lectured to postgraduate students. Provided intellectual input into science proposals, ongoing projects and outputs, including research papers. |
| Collaborator Contribution | Facilities, students, intellectual stimulation, new project ideas, data, and other academic outputs such as scientific papers. |
| Impact | Joint scientific papers. Joint scientific projects (UoE/NMBU). |
| Description | University of Leon |
| Organisation | University of Leon |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | Training, design and interpretation of studies. |
| Collaborator Contribution | Personel. Funding for personnel. |
| Impact | Training, papers, new PhDs. |
| Start Year | 2008 |