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Selection of SNPs from 50K and 777K arrays to predict breed-of-origin in cattle.
MedLine Citation:
PMID:  24045484     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
Reliable breed assignment can be performed with SNPs. Currently high density SNP-chips are available with large numbers of SNPs from which the most informative SNPs can be selected for breed assignment. Several methods have been published to select the most informative SNPs to distinguish between breeds. Here we evaluated Delta, Wright's FST and Weir and Cockerham's FST and extended these methods by adding a rule to avoid selection of sets of SNPs in high LD providing the same information; SNPs that had a r(2) value > 0.3 with any of the SNPs already selected were discarded. The different selection methods were evaluated both for the 50K SNP and the 777K Bovine BeadChip. Animals from four cattle breeds (989 Holstein Friesian, 97 Groningen White headed, 137 Meuse-Rhine-Yssel and 64 Dutch Friesian) were genotyped. After editing 30,447 and 452,525 SNPs were available for the 50K and 777K SNP chip, respectively. All selection methods showed that only a small set of SNPs is needed to differentiate among the four Dutch cattle breeds, while comparison of the selection methods showed small differences only. In general the 777K performed marginally better than the 50K BeadChip, especially at higher confidence thresholds. The rule to avoid selection of SNPs in high LD reduced the required number of SNPs to achieve correct breed assignment. The Global W&C FST performed marginally better than other selection methods. There was little overlap in the SNPs selected from the two BeadChips, while the number of SNPs selected was about the same.
Authors:
B Hulsegge; M P L Calus; J J Windig; A H Hoving-Bolink; M H T Maurice-van Eijndhoven; S J Hiemstra
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2013-9-17
Journal Detail:
Title:  Journal of animal science     Volume:  -     ISSN:  1525-3163     ISO Abbreviation:  J. Anim. Sci.     Publication Date:  2013 Sep 
Date Detail:
Created Date:  2013-9-18     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  8003002     Medline TA:  J Anim Sci     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Affiliation:
Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, P.O. Box 65, 8200 AB Lelystad, The Netherlands.
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