Genome changes due to artificial selection in U.S. Holstein cattle

Li Ma, Tad S. Sonstegard, John B. Cole, Curtis P. Vantassell, George R. Wiggans, Brian A Crooker, Cheng Tan, Dzianis Prakapenka, George E. Liu, Yang Da

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Background: The availability of a unique unselected Holstein line since 1964 provided a direct comparison between selected and unselected Holstein genomes whereas large Holstein samples provided unprecedented statistical power for identifying high-confidence SNP effects. Utilizing these unique resources, we aimed to identify genome changes affected by selection since 1964. Results: Direct comparison of genome-wide SNP markers between a Holstein line unselected since 1964 and contemporary Holsteins showed that the 40 years of artificial selection since 1964 resulted in genome landscape changes. Among the regions affected by selection, the regions containing 198 genes with fertility functions had a larger negative correlation than that of all SNPs between the SNP effects on milk yield and daughter pregnancy rate. These results supported the hypothesis that hitchhiking of genetic selection for milk production by negative effects of fertility genes contributed to the unintended declines in fertility since 1964. The genome regions subjected to selection also contained 67 immunity genes, the bovine MHC region of Chr23 with significantly decreased heterozygosity in contemporary Holsteins, and large gene clusters including T-cell receptor and immunoglobulin genes. Conclusions: This study for the first time provided direct evidence that genetic selection for milk production affected fertility and immunity genes and that the hitchhiking of genetic selection for milk production by negative fertility effects contributed to the fertility declines since 1964, and identified a large number of candidate fertility and immunity genes affected by selection. The results provided novel understanding about genome changes due to artificial selection and their impact on fertility and immunity genes and could facilitate developing genetic methods to reverse the declines in fertility and immunity in Holstein cattle.

Original languageEnglish (US)
Article number128
JournalBMC Genomics
Volume20
Issue number1
DOIs
StatePublished - Feb 11 2019

Fingerprint

Fertility
Genome
Immunity
Single Nucleotide Polymorphism
Genetic Selection
Milk
Genes
Fertility Agents
T-Cell Receptor Genes
Immunoglobulin Genes
Pregnancy Rate
Multigene Family

Keywords

  • Fertility
  • Genetic selection
  • Genome landscape
  • Immunity
  • Milk production

PubMed: MeSH publication types

  • Journal Article

Cite this

Ma, L., Sonstegard, T. S., Cole, J. B., Vantassell, C. P., Wiggans, G. R., Crooker, B. A., ... Da, Y. (2019). Genome changes due to artificial selection in U.S. Holstein cattle. BMC Genomics, 20(1), [128]. https://doi.org/10.1186/s12864-019-5459-x

Genome changes due to artificial selection in U.S. Holstein cattle. / Ma, Li; Sonstegard, Tad S.; Cole, John B.; Vantassell, Curtis P.; Wiggans, George R.; Crooker, Brian A; Tan, Cheng; Prakapenka, Dzianis; Liu, George E.; Da, Yang.

In: BMC Genomics, Vol. 20, No. 1, 128, 11.02.2019.

Research output: Contribution to journalArticle

Ma, L, Sonstegard, TS, Cole, JB, Vantassell, CP, Wiggans, GR, Crooker, BA, Tan, C, Prakapenka, D, Liu, GE & Da, Y 2019, 'Genome changes due to artificial selection in U.S. Holstein cattle', BMC Genomics, vol. 20, no. 1, 128. https://doi.org/10.1186/s12864-019-5459-x
Ma L, Sonstegard TS, Cole JB, Vantassell CP, Wiggans GR, Crooker BA et al. Genome changes due to artificial selection in U.S. Holstein cattle. BMC Genomics. 2019 Feb 11;20(1). 128. https://doi.org/10.1186/s12864-019-5459-x
Ma, Li ; Sonstegard, Tad S. ; Cole, John B. ; Vantassell, Curtis P. ; Wiggans, George R. ; Crooker, Brian A ; Tan, Cheng ; Prakapenka, Dzianis ; Liu, George E. ; Da, Yang. / Genome changes due to artificial selection in U.S. Holstein cattle. In: BMC Genomics. 2019 ; Vol. 20, No. 1.
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