Genome-wide association study for feed efficiency and growth traits in U.S. beef cattle

Christopher M. Seabury, David L. Oldeschulte, Mahdi Saatchi, Jonathan E. Beever, Jared E. Decker, Yvette A. Halley, Eric K. Bhattarai, Maral Molaei, Harvey C. Freetly, Stephanie L. Hansen, Helen Yampara-Iquise, Kristen A. Johnson, Monty S. Kerley, Jae Woo Kim, Daniel D. Loy, Elisa Marques, Holly L. Neibergs, Robert D. Schnabel, Daniel W. Shike, Matthew L. SpanglerRobert L. Weaber, Dorian J. Garrick, Jeremy F. Taylor

Research output: Contribution to journalArticle

Abstract

Background: Single nucleotide polymorphism (SNP) arrays for domestic cattle have catalyzed the identification of genetic markers associated with complex traits for inclusion in modern breeding and selection programs. Using actual and imputed Illumina 778K genotypes for 3887 U.S. beef cattle from 3 populations (Angus, Hereford, SimAngus), we performed genome-wide association analyses for feed efficiency and growth traits including average daily gain (ADG), dry matter intake (DMI), mid-test metabolic weight (MMWT), and residual feed intake (RFI), with marker-based heritability estimates produced for all traits and populations. Results: Moderate and/or large-effect QTL were detected for all traits in all populations, as jointly defined by the estimated proportion of variance explained (PVE) by marker effects (PVE≥1.0%) and a nominal P-value threshold (P≤5e-05). Lead SNPs with PVE≥2.0% were considered putative evidence of large-effect QTL (n=52), whereas those with PVE≥1.0% but<2.0% were considered putative evidence for moderate-effect QTL (n=35). Identical or proximal lead SNPs associated with ADG, DMI, MMWT, and RFI collectively supported the potential for either pleiotropic QTL, or independent but proximal causal mutations for multiple traits within and between the analyzed populations. Marker-based heritability estimates for all investigated traits ranged from 0.18 to 0.60 using 778K genotypes, or from 0.17 to 0.57 using 50K genotypes (reduced from Illumina 778K HD to Illumina Bovine SNP50). An investigation to determine if QTL detected by 778K analysis could also be detected using 50K genotypes produced variable results, suggesting that 50K analyses were generally insufficient for QTL detection in these populations, and that relevant breeding or selection programs should be based on higher density analyses (imputed or directly ascertained). Conclusions: Fourteen moderate to large-effect QTL regions which ranged from being physically proximal (lead SNPs≤3Mb) to fully overlapping for RFI, DMI, ADG, and MMWT were detected within and between populations, and included evidence for pleiotropy, proximal but independent causal mutations, and multi-breed QTL. Bovine positional candidate genes for these traits were functionally conserved across vertebrate species.

Original languageEnglish (US)
Article number386
JournalBMC genomics
Volume18
Issue number1
DOIs
StatePublished - May 18 2017

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Genome-Wide Association Study
Growth
Genotype
Population
Single Nucleotide Polymorphism
Weights and Measures
Breeding
Mutation
Genetic Markers
Vertebrates
Genes

Keywords

  • Beef Cattle
  • Feed efficiency and growth
  • GWAS
  • QTL

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Seabury, C. M., Oldeschulte, D. L., Saatchi, M., Beever, J. E., Decker, J. E., Halley, Y. A., ... Taylor, J. F. (2017). Genome-wide association study for feed efficiency and growth traits in U.S. beef cattle. BMC genomics, 18(1), [386]. https://doi.org/10.1186/s12864-017-3754-y

Genome-wide association study for feed efficiency and growth traits in U.S. beef cattle. / Seabury, Christopher M.; Oldeschulte, David L.; Saatchi, Mahdi; Beever, Jonathan E.; Decker, Jared E.; Halley, Yvette A.; Bhattarai, Eric K.; Molaei, Maral; Freetly, Harvey C.; Hansen, Stephanie L.; Yampara-Iquise, Helen; Johnson, Kristen A.; Kerley, Monty S.; Kim, Jae Woo; Loy, Daniel D.; Marques, Elisa; Neibergs, Holly L.; Schnabel, Robert D.; Shike, Daniel W.; Spangler, Matthew L.; Weaber, Robert L.; Garrick, Dorian J.; Taylor, Jeremy F.

In: BMC genomics, Vol. 18, No. 1, 386, 18.05.2017.

Research output: Contribution to journalArticle

Seabury, CM, Oldeschulte, DL, Saatchi, M, Beever, JE, Decker, JE, Halley, YA, Bhattarai, EK, Molaei, M, Freetly, HC, Hansen, SL, Yampara-Iquise, H, Johnson, KA, Kerley, MS, Kim, JW, Loy, DD, Marques, E, Neibergs, HL, Schnabel, RD, Shike, DW, Spangler, ML, Weaber, RL, Garrick, DJ & Taylor, JF 2017, 'Genome-wide association study for feed efficiency and growth traits in U.S. beef cattle', BMC genomics, vol. 18, no. 1, 386. https://doi.org/10.1186/s12864-017-3754-y
Seabury CM, Oldeschulte DL, Saatchi M, Beever JE, Decker JE, Halley YA et al. Genome-wide association study for feed efficiency and growth traits in U.S. beef cattle. BMC genomics. 2017 May 18;18(1). 386. https://doi.org/10.1186/s12864-017-3754-y
Seabury, Christopher M. ; Oldeschulte, David L. ; Saatchi, Mahdi ; Beever, Jonathan E. ; Decker, Jared E. ; Halley, Yvette A. ; Bhattarai, Eric K. ; Molaei, Maral ; Freetly, Harvey C. ; Hansen, Stephanie L. ; Yampara-Iquise, Helen ; Johnson, Kristen A. ; Kerley, Monty S. ; Kim, Jae Woo ; Loy, Daniel D. ; Marques, Elisa ; Neibergs, Holly L. ; Schnabel, Robert D. ; Shike, Daniel W. ; Spangler, Matthew L. ; Weaber, Robert L. ; Garrick, Dorian J. ; Taylor, Jeremy F. / Genome-wide association study for feed efficiency and growth traits in U.S. beef cattle. In: BMC genomics. 2017 ; Vol. 18, No. 1.
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T1 - Genome-wide association study for feed efficiency and growth traits in U.S. beef cattle

AU - Seabury, Christopher M.

AU - Oldeschulte, David L.

AU - Saatchi, Mahdi

AU - Beever, Jonathan E.

AU - Decker, Jared E.

AU - Halley, Yvette A.

AU - Bhattarai, Eric K.

AU - Molaei, Maral

AU - Freetly, Harvey C.

AU - Hansen, Stephanie L.

AU - Yampara-Iquise, Helen

AU - Johnson, Kristen A.

AU - Kerley, Monty S.

AU - Kim, Jae Woo

AU - Loy, Daniel D.

AU - Marques, Elisa

AU - Neibergs, Holly L.

AU - Schnabel, Robert D.

AU - Shike, Daniel W.

AU - Spangler, Matthew L.

AU - Weaber, Robert L.

AU - Garrick, Dorian J.

AU - Taylor, Jeremy F.

PY - 2017/5/18

Y1 - 2017/5/18

N2 - Background: Single nucleotide polymorphism (SNP) arrays for domestic cattle have catalyzed the identification of genetic markers associated with complex traits for inclusion in modern breeding and selection programs. Using actual and imputed Illumina 778K genotypes for 3887 U.S. beef cattle from 3 populations (Angus, Hereford, SimAngus), we performed genome-wide association analyses for feed efficiency and growth traits including average daily gain (ADG), dry matter intake (DMI), mid-test metabolic weight (MMWT), and residual feed intake (RFI), with marker-based heritability estimates produced for all traits and populations. Results: Moderate and/or large-effect QTL were detected for all traits in all populations, as jointly defined by the estimated proportion of variance explained (PVE) by marker effects (PVE≥1.0%) and a nominal P-value threshold (P≤5e-05). Lead SNPs with PVE≥2.0% were considered putative evidence of large-effect QTL (n=52), whereas those with PVE≥1.0% but<2.0% were considered putative evidence for moderate-effect QTL (n=35). Identical or proximal lead SNPs associated with ADG, DMI, MMWT, and RFI collectively supported the potential for either pleiotropic QTL, or independent but proximal causal mutations for multiple traits within and between the analyzed populations. Marker-based heritability estimates for all investigated traits ranged from 0.18 to 0.60 using 778K genotypes, or from 0.17 to 0.57 using 50K genotypes (reduced from Illumina 778K HD to Illumina Bovine SNP50). An investigation to determine if QTL detected by 778K analysis could also be detected using 50K genotypes produced variable results, suggesting that 50K analyses were generally insufficient for QTL detection in these populations, and that relevant breeding or selection programs should be based on higher density analyses (imputed or directly ascertained). Conclusions: Fourteen moderate to large-effect QTL regions which ranged from being physically proximal (lead SNPs≤3Mb) to fully overlapping for RFI, DMI, ADG, and MMWT were detected within and between populations, and included evidence for pleiotropy, proximal but independent causal mutations, and multi-breed QTL. Bovine positional candidate genes for these traits were functionally conserved across vertebrate species.

AB - Background: Single nucleotide polymorphism (SNP) arrays for domestic cattle have catalyzed the identification of genetic markers associated with complex traits for inclusion in modern breeding and selection programs. Using actual and imputed Illumina 778K genotypes for 3887 U.S. beef cattle from 3 populations (Angus, Hereford, SimAngus), we performed genome-wide association analyses for feed efficiency and growth traits including average daily gain (ADG), dry matter intake (DMI), mid-test metabolic weight (MMWT), and residual feed intake (RFI), with marker-based heritability estimates produced for all traits and populations. Results: Moderate and/or large-effect QTL were detected for all traits in all populations, as jointly defined by the estimated proportion of variance explained (PVE) by marker effects (PVE≥1.0%) and a nominal P-value threshold (P≤5e-05). Lead SNPs with PVE≥2.0% were considered putative evidence of large-effect QTL (n=52), whereas those with PVE≥1.0% but<2.0% were considered putative evidence for moderate-effect QTL (n=35). Identical or proximal lead SNPs associated with ADG, DMI, MMWT, and RFI collectively supported the potential for either pleiotropic QTL, or independent but proximal causal mutations for multiple traits within and between the analyzed populations. Marker-based heritability estimates for all investigated traits ranged from 0.18 to 0.60 using 778K genotypes, or from 0.17 to 0.57 using 50K genotypes (reduced from Illumina 778K HD to Illumina Bovine SNP50). An investigation to determine if QTL detected by 778K analysis could also be detected using 50K genotypes produced variable results, suggesting that 50K analyses were generally insufficient for QTL detection in these populations, and that relevant breeding or selection programs should be based on higher density analyses (imputed or directly ascertained). Conclusions: Fourteen moderate to large-effect QTL regions which ranged from being physically proximal (lead SNPs≤3Mb) to fully overlapping for RFI, DMI, ADG, and MMWT were detected within and between populations, and included evidence for pleiotropy, proximal but independent causal mutations, and multi-breed QTL. Bovine positional candidate genes for these traits were functionally conserved across vertebrate species.

KW - Beef Cattle

KW - Feed efficiency and growth

KW - GWAS

KW - QTL

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