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dc.contributor.advisorHouston, Ross
dc.contributor.authorTsai, Hsin Yuan
dc.date.accessioned2018-03-22T11:31:09Z
dc.date.available2018-03-22T11:31:09Z
dc.date.issued2017-07-08
dc.identifier.urihttp://hdl.handle.net/1842/28918
dc.description.abstractBackground Atlantic salmon (Salmo Salar) is a key aquaculture species in several countries. Since its critical role in economic sector and scientific research, this species has been relatively extensively investigated, in comparison with other farmed and wild aquatic species. However, the genetic components associated with growth and fillet-related traits are lack consistency, and the issue of sea louse disease in both wild and famed salmon is still unsolved. Objectives Overall aim of this project was to understand the genetic basis of growth-related traits and host resistance to sea lice using three large commercial farmed salmon populations. Specifically, the method of quantitative trait loci (QTL) mapping, genome-wide association study (GWAS), and genomic prediction (GS) were utilized to dissect the genetic architectures associated with traits of interest in our experimental populations. Prior to this, linkage mapping was performed to construct a high-density linkage map for Atlantic salmon. Results Linkage map A linkage map was firstly constructed underlying a SNP array containing 132 K validated SNPs. 96,396 SNPs were successfully assigned to 29 chromosomes that correspond to the linkage group number of European Atlantic salmon. 6.5 % of unassigned contigs, which was equal to 1 % of recent whole genome reference assembly (GCA_000233375.4) anchored to exist chromosomes by referring to linkage mapping result. Genetic components associated with growth traits Heritabilities of growth-related traits were about 0.5 to 0.6 in adult and juvenile farmed salmon. The QTL mapping and GWAS suggested the growth-related traits are likely a polygenic genetic architecture with no major QTL segregating. The prediction accuracy estimated by genomic prediction showed that approximately 5,000 SNP markers could achieve the highest accuracy in body weight and length in juvenile salmon within population. Genetic components associated with lice resistance The heritability of lice resistance was 0.22 to 0.33 using pedigree and genetic relationship matrices respectively. GWAS indicated that the host resistance to sea lice was likely polygenic with no individual SNP surpassed the genome-wide significance threshold. Genomic prediction showed that about 5 to 10 K SNPs was able to achieve the asymptote of accuracy in closely related animals, while the greatest advantage of genomic prediction was observed in non-sibling test within population. Conclusions As the growth-related traits and lice resistance are both likely polygenic and population-specific, the genomic prediction is an efficient approach to capture the genetic variances of the traits in selection candidates in experimental population, especially for traits with low heritability such as flesh colour and lice resistance. Family-based selection method is the better choice than mass selection to accumulate the genetic effects in corresponding SNP platform. Given the high cost of genotyping and field data collection, the genotyping-by-sequencing and genotype imputation are likely the way to make significant improvements in relevant research.en
dc.language.isoenen
dc.publisherThe University of Edinburghen
dc.relation.hasversionTsai H.Y., Robledo, D., Lowe, N.R., Bekaert, M., Taggart, J.B., Bron, J.E., Houston, R.D., 2016. Construction and annotation of a high density SNP linkage map of the Atlantic salmon (Salmo salar) genome. G3: Genes Genomes Genet. 6, 2173–2179.en
dc.relation.hasversionTsai H.Y., Hamilton, A., Guy, D.R., Tinch, A.E., Bishop, S.C., Houston, R.D., 2015. The genetic architecture of growth and fillet traits in farmed Atlantic salmon (Salmo salar). BMC Genet. 16, 51.en
dc.relation.hasversionTsai H.Y., Hamilton, A., Tinch, A.E., Guy, D.R., Gharbi, K., Stear, M.J., Oswald, M., Bishop, S.C., Houston, R.D., 2015. Genome wide association and genomic prediction for growth traits in juvenile farmed Atlantic salmon using a high density SNP array. BMC Genomics 16, 969.en
dc.relation.hasversionTsai H.Y., Hamilton, A., Guy, D.R., Tinch, A.E., Bishop, S.C., Houston, R.D., 2015. Verification of SNPs associated with growth traits in two populations of farmed atlantic salmon. Int. J. Mol. Sci. 17, 1–10.en
dc.relation.hasversionTsai H.Y., Hamilton, A., Tinch, A.E., Guy, D.R., Bron, J.E., Taggart, J.B., Gharbi, K., Stear, M., Matika, O., Pong-Wong, R., Bishop, S.C., Houston, R.D., 2016. Genomic prediction of host resistance to sea lice in farmed Atlantic salmon populations. Genet. Sel. Evol. 48, 1–11.en
dc.relation.hasversionTsai H.Y., Bishop S.C., Houston R.D. The genetic regulation of growth and sea lice resistance in farmed Atlantic salmon (S. Salar). Hendrix Genetics Academics, Eindhoven, Netherlands. May 2015.en
dc.relation.hasversionTsai H.Y., Hamilton A., Guy D.R., Tinch A.E., Bishop S.C., & Houston R.D. Genome wide association study identifies SNPs associated with early growth performance in Atlantic salmon (S. Salar). The International Symposium on Genetics in Aquaculture XII, Santiago de Compostela, Spain. June 2015.en
dc.relation.hasversionTsai H.Y., A. Hamilton, D.R. Guy, A.E. Tinch, K. Gharbi, M.J. Stear, O. Matika, S.C. Bishop, R.D. Houston. GWAS and genomic selection of growth traits and host resistance to sea lice in Atlantic salmon. British Society of Animal Sciences, Edinburgh, U.K. October 2015.en
dc.relation.hasversionTsai H.Y., A. Hamilton, D.R. Guy, A.E. Tinch, J.E. Bron, K. Gharbi, M.J. Stear, O. Matika, S.C. Bishop, R.D. Houston. Genomic Prediction of Host Resistance to Sea Lice (L. salmonis) in Atlantic Salmon (S. salar). International Plant and Animal Genome XXIV, San Diego, CA, U.S.A. January 2016.en
dc.relation.hasversionTsai H.Y., A. Hamilton, D.R. Guy, A.E. Tinch, J.E. Bron, J.B. Taggart, K. Gharbi, M.J. Stear, O. Matika, R. Pong-Wong, J.M. Hickey, S.C. Bishop, R.D. Houston. Genomic selection for breeding improved resistance to sea lice in Farmed Atlantic Salmon. Aquaculture Europe 2016, Edinburgh, U.K. September 2016.en
dc.subjectAtlantic salmonen
dc.subjectsea louse diseaseen
dc.subjecthost resistanceen
dc.subjectquantitative trait locien
dc.subjectgenomic predictionen
dc.titleGenomic basis of growth traits and host resistance against sea lice (L. Salmonis) in Atlantic salmon (S. Salar)en
dc.typeThesis or Dissertationen
dc.type.qualificationlevelDoctoralen
dc.type.qualificationnamePhD Doctor of Philosophyen
dc.rights.embargodate2018-07-08


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