Genome wide association studies for temperament in New Zealand dairy cattle : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Animal Science in Animal Breeding and Genetics at Massey University, Palmerston North, New Zealand

Simple item page
dc.contributor.authorChan, Fei Yi
dc.date.accessioned2013-05-10T01:24:51Z
dc.date.available2013-05-10T01:24:51Z
dc.date.issued2012
dc.description.abstractThe aim of this thesis was to identify genomic regions associated with cow temperament in New Zealand dairy cattle. The data set used was provided by the Livestock Improvement Corporation, and contains estimated breeding values (EBV) for temperament of 3140 bulls of three breeds; Holstein-Friesian (HF), Jersey (JE) and Crossbreed (XB) born between 1994 and 2006. Biallelic genotype data were also provided containing 700,000 single nucleotide polymorphism (SNP) markers. Estimated breeding values for cow temperament were adjusted (Adj-EBVtemp) for age, percentage of North American Holstein genes (NAH%), percentage of New Zealand Holstein-Friesian (HF%) and percentage of Jersey (JE%). Using PLINK, the association between individual markers and temperament was investigated. PLINK was also used to produce output with genomic corrected p-values (GC) which adjusts for inflation based on the median chi-square statistic. Suggestive and genome-wide significance thresholds were set at -log10 (1e-4) and -log10 (5e-5) respectively. From literature review, the average estimate of heritability of temperament was 0.17, and average genetic correlation with milk yield was 0.165. JE bulls had the highest average EBV for temperament (0.0352 ± 0.239) followed by XB (0.0079 ± 0.217) and HF bulls (-0.0402 ± 0.256). PLINK analysis show BTA 4 to contain genome-wide significant genomic regions across all three breeds for Adj-EBVtemp. Further investigation on individual chromosomes provided no further information on significant genomic regions affecting temperament. A closer look at many of these regions show they are in domains known as “Junk DNA”. Results suggest that although genomic selection for temperament in dairy cattle is plausible, genetic gain via direct selection for this trait will be slow and desired effects may not be immediate.en
dc.identifier.urihttp://hdl.handle.net/10179/4401
dc.language.isoenen
dc.publisherMassey Universityen_US
dc.rightsThe Authoren_US
dc.subjectDairy cattleen
dc.subjectCowsen
dc.subjectGeneticsen
dc.subjectGenomeen
dc.subjectBreedingen
dc.subjectTemperamenten
dc.subjectAnimal behaviouren
dc.subjectNew Zealanden
dc.titleGenome wide association studies for temperament in New Zealand dairy cattle : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Animal Science in Animal Breeding and Genetics at Massey University, Palmerston North, New Zealanden
dc.typeThesisen
massey.contributor.authorChan, Fei Yien
thesis.degree.disciplineAnimal Breeding and Geneticsen
thesis.degree.grantorMassey Universityen
thesis.degree.levelMastersen
thesis.degree.nameMaster of Science (M.Sc.)en
Files
Original bundle
Now showing 1 - 2 of 2
Thumbnail Image
Name:
01_front.pdf
Size:
103.56 KB
Format:
Adobe Portable Document Format
Description:
Download
Thumbnail Image
Name:
02_whole.pdf
Size:
3.04 MB
Format:
Adobe Portable Document Format
Description:
Download
License bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
license.txt
Size:
804 B
Format:
Item-specific license agreed upon to submission
Description:
Download
Collections
Theses and Dissertations