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Title: Detecting ancestral junctions in inbred populations
Author: MacLeod, Andrew Keith
Awarding Body: University of Edinburgh
Current Institution: University of Edinburgh
Date of Award: 2005
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This thesis presents theoretical results on the number of junctions on chromosomes in partially inbred populations, and addresses problems posed by locating these junctions using markers in both simulated populations and recombinant inbred lines (RILs). Chapter 1 presents a general introduction to the concept of junctions, and reviews previous work on the theory. Chapter 2 confirms by simulation some of the results presented in chapter 1, and shows that in a population of size N where selfing is excluded, but otherwise mating at random, the expected number of junctions per Morgan on a chromosome is linearly related to the inbreeding coefficient of that population, until complete inbreeding where 2(N+1) junctions are expected. Chapter 2 investigates the efficiency of using markers to detect junctions in inbred populations. Even with a highly dense map of fully informative markers, not all of the junctions present are detected, with the actual detection rate lower than expected if junctions were distributed at random. An approximate expression for the proportion of junctions detected 1/(1+1.4γ), where γ = J/B, the ratio of junctions to marker brackets Chapter 3 applies the theory of junctions to RILs. Theoretical analysis suggests a density of 4 junctions per Morgan in a RIL. The observed counts of junctions detected using microsatellite markers in multiple RILs are found to be slightly lower than this expectation. In the analysis of junctions detected, “cross” and “line” were found to have significant effects in the analysis. Chapter 5 attempts to further elucidate the factors affecting observed junction counts in RILs by looking at the effects of individual markers on the junction count to locate specific regions of the genome that affect junction formation.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available