Naslov
Genomic admixture: investigation and application

Autori
Frkonja, Anamarija

Vrsta, podvrsta i kategorija rada
Ocjenski radovi, doktorska disertacija

Fakultet
University of Natural Resources and Applied Life Sciences

Mjesto
Beč

Datum
12.04

Godina
2013

Stranica
92

Mentor
Sölkner, Johann & Čurik, Ino

Ključne riječi
admixture, SNP, chromosom, breed

Sažetak
Methods for admixture estimation and application of admixture analysis for different purposes related to livestock are presented. Conventional genomic selection schemes were adapted to admixture analysis. Number of single nucleotide polymorphisms (SNPs) and size of ancestral populations is investigated. A part of thesis copes with selective sweeps which were found with a difference among differentiation index in Simmental and Red Holstein Friesian. Best levels of crossing related to tolerance of some animals to trypanosomosis were enquired. Prediction of breed composition was performed with 54001 SNP markers of 500 Swiss Fleckvieh animals with their ancestral populations. Admixture of a full SNP set and subsets of SNPs was analysed. Best levels of crosses in trypanotolerant Baoule and Zebu were investigated with 25 microsatellites across the genome and 155 SNPs in 23 trypantolerance candidate regions. Breed composition was analysed by different software employing Hidden Markov Model and procedures used in genomic selection. Results of a full set of SNPs indicate that almost all methods performed very similar with a high correlation of ~0.97 to pedigree admixture. Down to ~ 5000 SNPs in a set, the correlations of genomic and pedigree admixture were very similar. Strongest signal of selective sweep investigated among Simmental and Red Holstein Friesian animals was found on chromosome 6. Region found had fixed allele frequencies for 22 SNPs in Simmental animals. Average Baoule admixture in the complete genomes of the Baoule-Zebu composites was 0.31, and in the trypanotolerance candidate regions, 0.37. Regions with highest Baoule proportion in the composites were region on chromosome 7 and region on chromosome 22. Chromosome 22 showed greatest admixture deviation in Baoule favour when compared to the overall genome admixture. Rapid and cheap prediction of breed composition in livestock breeds will be worthwhile in case of none or incomplete pedigrees and the search for the best type of cross or composite of breeds. The results of this thesis show that with currently available SNP chips with 50000 to 60000 markers, accurate prediction is possible, even with small numbers of individuals selected from the pure ancestral populations.

Izvorni jezik
Engleski

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