Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/28838
Title: Genomic evaluation based on selected variants from imputed whole-genome sequence data in Australian sheep populations
Contributor(s): Moghaddar, N  (author)orcid ; MacLeod, I M (author); Duijvesteijn, N  (author); Bolormaa, S (author); Khansefid, M (author); Al-Mamun, H (author); Clark, S  (author)orcid ; Swan, A A  (author); Daetwyler, H D (author); van der Werf, J H J  (author)orcid 
Publication Date: 2018
Open Access: Yes
Handle Link: https://hdl.handle.net/1959.11/28838
Open Access Link: http://www.wcgalp.org/system/files/proceedings/2018/genomic-evaluation-based-selected-variants-imputed-whole-genome-sequence-data-australian-sheep.pdfOpen Access Link
Abstract: This study investigates improvement in accuracy of genomic prediction for growth and eating quality traits in Australian sheep populations based on selected variants from imputed whole genome sequence (WGS) data combined with a 50k-SNP array. Selection of SNP variants was based on single trait multi-breed genome wide association studies (GWAS) on WGS data in an independent data subset. Genomic prediction was based on genomic best linear unbiased prediction (GBLUP) using training sets of between 6,353 and 11,067 multi-breed purebred and crossbred animals. Four different genotype sets were compared: 50k SNP genotypes, WGS variants, selected sequence variants from GWAS and selected sequence variants combined with 50k genotypes. The latter set was modeled as either one or as two subsets with different variance components. Results showed a substantial improvement in prediction accuracy when selected sequence variants from GWAS were added to the standard 50k-SNP array. Absolute value of increase in accuracy across different traits was on average 6.2% and 4.1% for purebred and crossbred Merino sheep, respectively, when selected sequence variants and 50k genotypes were fitted as two variance components simultaneously. The improvement in prediction accuracy across different traits was on average 4.4% and 3.8% for purebred and crossbred Merino sheep, respectively, when selected sequence variants combined with 50k SNP arrays were fitted as one variance component.
Publication Type: Conference Publication
Conference Details: World Congress on Genetics Applied to Livestock Production, Auckland, New Zealand
Source of Publication: Proceedings of the World Congress on Genetics Applied to Livestock Production, v.11, p. 1-7
Field of Research (FOR): 070201 Animal Breeding
060412 Quantitative Genetics (incl. Disease and Trait Mapping Genetics)
060408 Genomics
Socio-Economic Objective (SEO): 830310 Sheep - Meat
830311 Sheep - Wool
Peer Reviewed: Yes
HERDC Category Description: E1 Refereed Scholarly Conference Publication
Other Links: http://www.wcgalp.org/proceedings/2018
Description: These proceedings are only published online. As such, there is no front matter per se. Therefore, the proceedings list from the website has been included here as front matter (i.e. evidence the article was published).
An alternative website with the title "11th World Congress on Genetics Applied to Livestock Production" is located here: https://royalsociety.org.nz/events/11th-world-congress-on-genetics-applied-to-livestock-production/
Appears in Collections:Animal Genetics and Breeding Unit (AGBU)
Conference Publication
School of Environmental and Rural Science

Files in This Item:
2 files
File Description SizeFormat 
Show full item record
Google Media

Google ScholarTM

Check


Items in Research UNE are protected by copyright, with all rights reserved, unless otherwise indicated.