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United States Department of Agriculture

Agricultural Research Service


Location: Range and Livestock Research

Title: Using single nucleotide polymorphism to detect selection signature in Hereford beef cattle

item Huang, Y
item Maltecca, C
item Macneil, Michael
item Cassady, J

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 3/13/2011
Publication Date: 7/9/2011
Citation: Huang, Y., Maltecca, C., MacNeil, M.D., Cassady, J.P. 2011. Using single nucleotide polymorphism to detect selection signature in Hereford beef cattle. Meeting Abstract. J. Anim. Sci. 89(E-Suppl. 1):166. Abstract #40.

Interpretive Summary: n/a

Technical Abstract: The objective of this study was to investigate selection signature in 2 sources of purebred Hereford beef cattle. Data were available from 240 Line 1 Herefords (L1) born between 1953 to 2008, and 311 Industry Herefords (IH) born between 1970 and 2008. Line 1 Herefords were sampled from a closed line mainly selected for post weaning gain. Industry Herefords were a sample of registered US purebred Herefords. A genome-wide scan using 52,156 SNPs revealed different characteristics in L1 and IH. Average minor allele frequency of SNPs was 0.19 ± 0.168 in L1 and 0.23 ± 0.161 in IH. Number of homozygous markers was of 11,382 in L1 and 5,745 in IH. The fixation index was 0.260 and 0.031 for L1 and IH, respectively. To detect differences in selection between the 2 populations, pooled heterozygosity (Hp) was calculated for sliding windows of 6 SNPs across the genome. Low Hp values are indicative of a high degree of fixation and putative selective sweeps. High Hp values can be the result of ongoing selection sweeps, balancing selection, or selection for multiple traits. Average Hp was 0.26 ± 0.10 for L1 and 0.29 ± 0.08 for IH. 225 low Hp windows (Hp <0.05) were identified in L1 while only 25 in IH. Fiftyfour known QTLs were previously found to be associated with traits including birth weight and weaning weight, co-localized with low Hp windows that were common in L1 and IH on BTA 1, 3, 6, 13, 14, 15, 16, 18, and 25. Fifty-six known QTLs associated with growth traits such as average daily gain and yearling weight co-localized with low Hp windows that were only found in L1 in BTA 2, 5, 14, 17, 21, and 26. Number of high Hp windows (Hp >0.46) was of 155 in L1 and 78 in IH. This might reflect that L1 being selected for only one trait, while IH was selected on several traits with multiple concurring sweeps. Differences in number of high Hp windows might also indicate regional balancing selection. Based on these results it was concluded that there had been a loss of heterozygosity in Line 1 Herefords. The low Hp windows indicated putative selective sweeps in L1. Further investigations are needed to explain the high Hp windows across the genome.

Last Modified: 06/26/2017
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