Signature of forty years of artificial selection in U.S. Holstein cattle identified by long-range frequency analyses

Authors: Sonstegard, Tad; WANG, SHENGWEN - University Of Minnesota; Van Tassell, Curtis - Curt; MA, LI - University Of Minnesota; Wiggans, George; CROOKER, BRIAN - University Of Minnesota; Cole, John; MARIANI, BRIAN - Genetics & Ivf Institute; Kim, Eui-Soo; GARBE, JOHN - University Of Minnesota; FAHRENKRUG, SCOTT - University Of Minnesota; Liu, Ge - George; DA, YANG - University Of Minnesota

Submitted to: Meeting Abstract
Publication Type: Proceedings
Publication Acceptance Date: 4/30/2012
Publication Date: 6/17/2012
Citation: Sonstegard, T.S., Wang, S., Van Tassell, C.P., Ma, L., Wiggans, G.R., Crooker, B., Cole, J.B., Mariani, B.D., Kim, E., Garbe, J.R., Fahrenkrug, S., Liu, G., Da, Y. 2012. Signature of forty years of artificial selection in U.S. Holstein cattle identified by long-range frequency analyses. International Conference on Quantitative Genetics: Understanding Variation in Complex Traits, Edinburgh, Scotland, June 17–22, Programme & Book of Abstracts, p. 213, abstr. P-314.

Interpretive Summary:

Technical Abstract: Three groups of U.S. Holstein cattle were analyzed for selection signature of artificial selection since 1964 using long-range frequency measures. The three groups included Holsteins unselected since 1964, contemporary Holsteins, and an elite line of contemporary Holsteins. Long-range frequencies included allele frequency and heterozygosity differences in 1-8Mb sliding windows of SNP markers of the bovine 50K SNP chip between the unselected group and the two contemporary groups subjected to 40 years of artificial selection. The contemporary Holsteins had significantly lower long-range heterozygosity than the unselected group near a large cluster of 90 RNA genes on Chr21. Some of the microRNA genes in that RNA gene cluster had strong interactions (MFE < -30) with the mRNA of several genes in the telomere region of Chr21 that affected protein yield. The most significant RNA interaction was between microRNA bta-mir-370 and the mRNA of TRM61 (MFE = -43.2). Both the centromere and telomere regions of Chr21 had large long-range allele frequency differences between the selected and unselected groups. Allele frequency differences between the selected and unselected groups identified selection signature near PLGF on Chr10 and in the PRKCA-CACNG5-HELZ region of Chr19. Allele frequency and heterozygosity differences between the elite group, the unselected group and the contemproary Holsteins excluding the elite group identified signature of the elite Holsteins on Chr18 and Chr13. The Chr18 region with elite signature coincided with a 15 Mb region that had a large number of SNP effects on dairy functional traits. The elite signature on Chr13 involved two regions. The first region had elevated allele frequency differences between the elite and unselected groups and was previously reported to have highly significant SNP effect for milk yield. The second region was the 25-30 Mb region with striking decreased long-range heterozygosity in the elite group compared to the unselected group.