Zenger, K.R., Khatkar, M.S., Tier, B., Hobbs, M., Cavanagh, J.A.L., Solkner, J., Hawken, R.J., Barris, W., and Raadsma, H.W. (2007) QC analyses of SNP array data: experience from a large population of dairy sires with 23.8 million data points. In: Proceedings of the AAABG 17th Conference 2007 (17) pp. 123-126. From: 17th AAABG Conference 2007, 23-26 September 2007, Armidale, NSW, Australia.

PDF (Published Version) Restricted to Repository staff only

Abstract

The use of a high throughput SNP genotyping platform with 15,380 bovine SNP assays, across 1546 dairy bulls resulted in a data set of approximately 23.8 M SNP data points. Stringent control measures based around low polymorphic content, sample failure, deviation from HWE, low call rate, non-Mendelian inheritance, tri-allelic SNP, and incompatible clustering of data, resulted in removal of 4321 SNPs. The majority (2973) were due to low polymorphic content (MAF<0.01), with the remaining features consistent with assay quality. Despite the need for removal of some SNP, repeatability of SNP call rate was extremely high (>99%) across repeat samples, and between platforms. SNP technology has now matured where comprehensive genome-wide analyses can be conducted in cattle with a high degree of robustness.

Item ID:	10140
Item Type:	Conference Item (Research - E1)
ISBN:	978-1-921208-13-3
ISSN:	1328-3227
Keywords:	quantitative genetics; dairy cattle; selective breeding; genetics; QTL; genomics
Additional Information:	Conference theme "Genetic Improvement - Making it Happen"
Date Deposited:	20 Jul 2010 03:44
FoR Codes:	06 BIOLOGICAL SCIENCES > 0604 Genetics > 060408 Genomics @ 90% 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060412 Quantitative Genetics (incl Disease and Trait Mapping Genetics) @ 10%
SEO Codes:	97 EXPANDING KNOWLEDGE > 970107 Expanding Knowledge in the Agricultural and Veterinary Sciences @ 100%
Downloads:	Total: 5
	More Statistics