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United States Department of Agriculture

Agricultural Research Service

Related Topics

Amanda Kay Lindholm-Perry
Nutrition and Environmental Management Research
Research Geneticist
Amanda.Lindholm@ars.usda.gov
Phone: (402) 762-4189
Fax: (402) 762-4209
P.O. BOX 166
CLAY CENTER, NE, 68933-0166

Projects
Improved Nutrient Efficiency of Beef Cattle and Swine
Appropriated (D)
  Accession Number: 422392

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Profile of the spleen transcriptome in beef steers with variation in gain and feed intake - (Peer Reviewed Journal) - (05-Jul-16)
Ruminal expression of the NQO1, RGS5, and ACAT1 genes may be indicators of feed efficiency in beef steers - (Peer Reviewed Journal) - (08-Jun-16)
Transcriptome profile of genes differentially expressed in the mesenteric adipose tissue of beef cattle with variation in feed intake and gain - (Abstract Only) - (25-May-16)
Transcriptome differences in the rumen of beef steers with variation in feed intake and gain Reprint Icon - (Peer Reviewed Journal)
Kern, R.J., Lindholm-Perry, A.K., Freetly, H.C., Snelling, W.M., Kern, J.W., Keele, J.W., Miles, J.R., Foote, A.P., Oliver, W.T., Kuehn, L.A., Ludden, P.A. 2016. Transcriptome differences in the rumen of beef steers with variation in feed intake and gain. Gene. 586:12-26.
Rumen papillae morphology of beef steers relative to gain and feed intake and the association of volatile fatty acids with kallikrein gene expression Reprint Icon - (Peer Reviewed Journal)
Kern, R.J., Lindholm-Perry, A.K., Freetly, H.C., Kuehn, L.A., Rule, D.C., Ludden, P.A. 2016. Rumen papillae morphology of beef steers relative to gain and feed intake and the association of volatile fatty acids with kallikrein gene expression. Livestock Science. 187:24-30.
Differential gene expression in the duodenum, jejunum and ileum among crossbred beef steers with divergent gain and feed intake phenotypes - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Butler, A.R., Kern, R.J., Hill, R., Kuehn, L.A., Wells, J., Oliver, W.T., Hales, K.E., Foote, A.P., Freetly, H.C. 2016. Differential gene expression in the duodenum, jejunum and ileum among crossbred beef steers with divergent gain and feed intake phenotypes. Animal Genetics. 47(4):408-427. doi: 10.1111/age.12440.
Differential expression of genes in the liver associated with gain and intake in beef steers - (Abstract Only)
Zarek, C.M., Lindholm-Perry, A.K., Freetly, H.C. 2016. Differential expression of genes in the liver associated with gain and intake in beef steers [abstract]. Journal of Animal Science. 94(Supplement 2):185.
Potential metabolic pathways associated with differences in weight maintenance and gain in mature cow skeletal and adipose tissue - (Abstract Only)
Cunningham, H.C., Cammack, K.M., Austin, K.J., Freetly, H.C., Lindholm-Perry, A.K. 2015. Potential metabolic pathways associated with differences in weight maintenance and gain in mature cow skeletal and adipose tissue. Plant & Animal Genome XXIV Conference, January 9-13, 2016, San Diego, CA. Poster P0270.
Relationship of glucocorticoids and hematological measures with feed intake, growth, and efficiency of finishing beef cattle Reprint Icon - (Peer Reviewed Journal)
Foote, A.P., Hales, K.E., Tait Jr, R.G., Berry, E.D., Lents, C.A., Wells, J. E., Lindholm-Perry, A.K., Freetly, H.C. 2016. Relationship of glucocorticoids and hematological measures with feed intake, growth, and efficiency of finishing beef cattle. Journal of Animal Science. 94(1):275-283. doi: 10.2527/jas2015-9407
Differences in transcript abundance of genes on BTA15 located within a region associated with gain in beef steers Reprint Icon - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Kern, R.J., Kuehn, L.A., Snelling, W.M., Miles, J.R., Oliver, W.T., Freetly, H.C. 2015. Differences in transcript abundance of genes on BTA15 located within a region associated with gain in beef steers. Gene. 572(1):42-48. doi: dx.doi.org/10.1016/j.gene.2015.06.076
Methane production and methanogen levels in steers that differ in residual gain Reprint Icon - (Peer Reviewed Journal)
Freetly, H.C., Lindholm-Perry, A.K., Hales, K.E., Brown-Brandl, T.M., Kim, M.S., Myer, P.R., Wells, J. 2015. Methane production and methanogen levels in steers that differ in residual gain. Journal of Animal Science. 93(5):2375-2381.
Genomewide association study of lung lesions in cattle using sample pooling - (Peer Reviewed Journal)
Keele, J.W., Kuehn, L.A., McDaneld, T.G., Tait Jr., R.G., Jones, S., Smith, T.P., Shackelford, S.D., King, D.A., Wheeler, T.L., Lindholm-Perry, A.K., McNeel, A.K. 2015. Genomewide association study of lung lesions in cattle using sample pooling. Journal of Animal Science. 93(3):956-964. DOI: 10.2527/jas.2014-8492.
Differential expression of genes in the jejunum of steers with feed efficiency phenotypes - (Abstract Only)
Butler, A.R., Lindholm-Perry, A.K., Freetly, H.C. 2015. Differential expression of genes in the jejunum of steers with feed efficiency phenotypes [abstract]. Journal of Animal Science. 93(Supplement 2):179.
A polymorphism in myostatin influences puberty but not fertility in beef heifers, whereas µ-calpain affects first calf birth weight Reprint Icon - (Peer Reviewed Journal)
Cushman, R.A., Tait Jr, R.G., McNeel, A.K., Forbes, E.D., Amundson, O.L., Lents, C.A., Lindholm-Perry, A.K., Perry, G.A., Wood, J.A., Cupp, A.S., Smith, T.P., Freetly, H.C., Bennett, G.L. 2015. A polymorphism in myostatin influences puberty but not fertility in beef heifers, whereas µ-calpain affects first calf birth weight. Journal of Animal Science. 93(1):117-126.
Genetic markers that influence feed efficiency phenotypes also affect cattle temperament as measured by flight speed Reprint Icon - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Kuehn, L.A., Freetly, H.C., Snelling, W.M. 2015. Genetic markers that influence feed efficiency phenotypes also affect cattle temperament as measured by flight speed. Animal Genetics. 46(1):60-64.
RNA-Seq detection of differential gene expression in the rumen of beef steers associated with feed efficiency phenotypes - (Abstract Only)
Kern, R.J., Lindholm-Perry, A.K., Freetly, H.C., Snelling, W.M., Kern, J.W., Miles, J.R., Ludden, P.A. 2014. RNA-Seq detection of differential gene expression in the rumen of beef steers associated with feed efficiency phenotypes [abstract]. Journal of Animal Science. 92(E-Supplement 2):918.
Gentic improvement in cattle -- are we sacrificing reproduction in favor of production? - (Literature Review)
Cushman, R.A., McNeel, A.K., Tait Jr, R.G., Lindholm-Perry, A.K., Perry, G.A., Snelling, W.M., Bennett, G.L. 2014. Gentic improvement in cattle -- are we sacrificing reproduction in favor of production?. In: Juengel, J. L., Miyamoto, A., Price, C., Reynolds, L. P., Smith, W. F., and Webb, R., editors. Reproduction in Domestic Ruminants VIII. Leicestershire, England: Context Products Ltd. p. 27-36.
DNA polymorphisms and transcript abundance of PRKAG2 and phosphorylated AMP-activated protein kinase in the rumen are associated with gain and feed intake in beef steers Reprint Icon - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Kuehn, L.A., Oliver, W.T., Kern, R.J., Cushman, R.A., Miles, J.R., McNeel, A.K., Freetly, H.C. 2014. DNA polymorphisms and transcript abundance of PRKAG2 and phosphorylated AMP-activated protein kinase in the rumen are associated with gain and feed intake in beef steers. Animal Genetics. 45(4):461-472.
Surface enlargement factor of rumen papillae and expression of genes involved in dermatological diseases and their relationships with feed intake in beef steers - (Abstract Only)
Kern, R.J., Lindholm-Perry, A.K., Freetly, H.C., Snelling, W.M., Miles, J.R., Ludden, P.A. 2014. Surface enlargement factor of rumen papillae and expression of genes involved in dermatological diseases and their relationships with feed intake in beef steers [abstract]. Journal of Animal Science. 92(Supplement 2):32.
An evaluation of the differences in the rumen transcriptome among beef steers with extreme feed efficiency phenotypes - (Abstract Only)
Lindholm-Perry, A.K., Kern, R.J., Kuehn, L.A., Miles, J.R., Freetly, H.C., Snelling, W.M., Ludden, P.A. 2014. An evaluation of the differences in the rumen transcriptome among beef steers with extreme feed efficiency phenotypes. Plant & Animal Genome XXII Conference, January 11-15, 2014, San Diego, CA. Abstract No. W155.
Adipose and muscle tissue gene expression of two genes (NCAPG and LCORL) located in a chromosomal region associated with cattle feed intake and gain Reprint Icon - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Kuehn, L.A., Oliver, W.T., Sexten, A.K., Miles, J.R., Rempel, L.A., Cushman, R.A., Freetly, H.C. 2013. Adipose and muscle tissue gene expression of two genes (NCAPG and LCORL) located in a chromosomal region associated with cattle feed intake and gain. PLoS One. 8(11):e80882.
Ruminal and adipose gene expression in beef steers selected for diverse feed intake and gain phenotypes - (Abstract Only)
Lindholm-Perry, A.K., Rempel, L.A., Hales, K.E., Oliver, W.T., Freetly, H.C., Kuehn, L.A. 2013. Ruminal and adipose gene expression in beef steers selected for diverse feed intake and gain phenotypes [abstract]. Journal of Animal Science Supplement. 91(E-Supplement 2):629.
Lipogenic-associated gene activity of adipose tissue from beef heifers and relation to production and reproductive traits - (Abstract Only)
Rempel, L.A., Cushman, R.A., McDaneld, T.G., Miles, J.R., Kuehn, L.A., Lindholm-Perry, A.K. 2013. Lipogenic-associated gene activity of adipose tissue from beef heifers and relation to production and reproductive traits. Journal of Animal Science. 91 (E-Supplement 2):466 (Abstract #510).
Ruminal methanogens in steers that are negative or positive for residual gain - (Abstract Only)
Freetly, H., Wells, J., Kim, M., Hales, K., Lindholm-Perry, A. 2013. Ruminal methanogens in steers that are negative or positive for residual gain [abstract]. Journal of Animal Science. 91(E-Supplement 2):437.
Prioritizing sequence polymorphisms for potential association with phenotype - (Abstract Only)
Snelling, W.M., Bennett, G.L., Thallman, R.M., Lindholm-Perry, A.K., Kuehn, L.A., McDaneld, T.G., Kachman, S.D., Spangler, M.L., Koshinsky, H., Kalbfleisch, T.S., Pollak, E.J. 2013. Prioritizing sequence polymorphisms for potential association with phenotype [abstract]. Journal of Animal Science. 91(E-Supplement 2):74-75.
Development and applications of low-cost, high-throughput genotyping - (Abstract Only)
Thallman, R.M., Lindholm-Perry, A.K., Curry, J.D., Fofanov, V.Y., Koshinsky, H. 2013. Development and applications of low-cost, high-throughput genotyping [abstract]. Journal of Animal Science. 91(Supplement 2):20. Abstract No. O063.
Low-cost genotyping by next generation sequencing: Next generation genotyping - (Abstract Only)
Curry, J.D., Snelling, W.M., Lindholm-Perry, A.K., Dier, P., Shin, M., Nguyen, J., Bulsara, N., Thallman, R.M., Fofanov, V.Y., Koshinsky, H. 2013. Low-cost genotyping by next generation sequencing: Next generation genotyping [abstract]. Plant and Animal Genome XXI Conference. Poster Abstract No. P0525.
Use of single nucleotide polymorphisms (SNP) to fine-map quantitative trait loci (QTL) in swine - (Abstract Only)
Rohrer, G.A., Lindholm-Perry, A.K., Shackelford, S.D., King, D.A., Wheeler, T.L., Nonneman, D. 2013. Use of single nucleotide polymorphisms (SNP) to fine-map quantitative trait loci (QTL) in swine [abstract]. Plant and Animal Genome XXI Conference Proceedings. Abstract #W047.
Development of low-cost, high-throughput genotyping to complement SNP discovery by individual animal whole-genome sequencing - (Abstract Only)
Thallman, R.M., Snelling, W.M., Curry, J.D., Smith, T.P., Kalbfleisch, T.S., Kuehn, L.A., McDaneld, T.G., Bennett, G.L., Lindholm-Perry, A.K., Fofanov, V.Y., Koshinsky, H., Pollak, E.J. 2013. Development of low-cost, high-throughput genotyping to complement SNP discovery by individual animal whole-genome sequencing [abstract]. Plant and Animal Genome XXI Conference. Workshop Abstract No. W146.
Adipose and muscle tissue expression of two genes (NCAPG and LCORL) located in a chromosomal region associated with cattle feed intake and gain - (Abstract Only)
Lindholm-Perry, A.K., Sexten, A.K., Kuehn, L.A., Rempel, L.A., Miles, J.R., Cushman, R.A., Freetly, H.C. 2012. Adipose and muscle tissue expression of two genes (NCAPG and LCORL) located in a chromosomal region associated with cattle feed intake and gain [abstract]. Journal of Animal Science. 90(Suppl. 3):453.
Evaluation of bovine chemerin (RARRES2) gene variation on beef cattle production traits - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Kuehn, L.A., Rempel, L.A., Smith, T.P., Cushman, R.A., McDaneld, T.G., Wheeler, T.L., Shackelford, S.D., King, D.A., Freetly, H.C. 2012. Evaluation of bovine chemerin (RARRES2) gene variation on beef cattle production traits. Frontiers in Genetics. 3:39.
Association, effects and validation of polymorphisms within the NCAPG - LCORL locus located on BTA6 with feed intake, gain, meat and carcass traits in beef cattle - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Sexten, A.K., Kuehn, L.A., Smith, T.P., King, D.A., Shackelford, S.D., Wheeler, T.L., Ferrell, C.L., Jenkins, T.G., Snelling, W.M., Freetly, H.C. 2011. Association, effects and validation of polymorphisms within the NCAPG - LCORL locus located on BTA6 with feed intake, gain, meat and carcass traits in beef cattle. BioMed Central (BMC) Genetics. 12:103.
Mass genotyping by sequencing technology - (Abstract Only)
Curry, J.D., Lindholm-Perry, A.K., Shin, M., Liu, J.T., Bulsara, N., Dier, P., Thallman, R.M., Fofanov, V.Y., Koshinsky, H. 2012. Mass genotyping by sequencing technology. Plant & Animal Genome XX Conference, January 14-18, 2012, San Diego, California. Poster No. P0182.
Genetic markers on BTA14 predictive for residual feed intake in beef steers and their effects on carcass and meat quality traits - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Kuehn, L.A., Snelling, W.M., Smith, T.P., Ferrell, C.L., Jenkins, T.G., King, D.A., Shackelford, S.D., Wheeler, T.L., Freetly, H.C. 2012. Genetic markers on BTA14 predictive for residual feed intake in beef steers and their effects on carcass and meat quality traits. Animal Genetics. 43:599-603.
Genetic markers in bovine chromosome 14 are significant for residual feed intake in steers - (Abstract Only)
Lindholm-Perry, A.K., Kuehn, L.A., Smith, T.P., Snelling, W.M., Freetly, H.C. 2011. Genetic markers in bovine chromosome 14 are significant for residual feed intake in steers. Journal of Animal Science. 89(E-Suppl. 1):422-423.
A region on BTA14 that includes the positional candidate genes LYPLA1, XKR4 and TMEM68 is associated with feed intake and growth phenotypes in cattle - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Kuehn, L.A., Smith, T.P., Ferrell, C.L., Jenkins, T.G., Freetly, H.C., Snelling, W.M. 2012. A region on BTA14 that includes the positional candidate genes LYPLA1, XKR4 and TMEM68 is associated with feed intake and growth phenotypes in cattle. Animal Genetics. 43(2):216-219.
Predictive markers in calpastatin for tenderness in commercial pig populations Reprint Icon - (Peer Reviewed Journal)
Nonneman, D.J., Lindholm-Perry, A.K., Shackelford, S.D., King, D.A., Wheeler, T.L., Rohrer, G.A., Bierman, C.D., Schneider, J.F., Miller, R.K., Zerby, H., Moeller, S.J. 2011. Predictive markers in calpastatin for tenderness in commercial pig populations. Journal of Animal Science. 89:2663-2672.
Evaluation of polymorphisms within the genes GSHR and SLC2A2 that are within a region on bovine chromosome 1 (BTA1) previously associated with feed intake and weight gain - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Kuehn, L.A., Snelling, W.M., Smith, T.P., Ferrell, C.L., Jenkins, T.G., Freetly, H.C. 2012. Evaluation of polymorphisms within the genes GSHR and SLC2A2 that are within a region on bovine chromosome 1 (BTA1) previously associated with feed intake and weight gain. Animal Genetics. 43(1):112.
Genomic regions associated with kyphosis in swine Reprint Icon - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Rohrer, G.A., Kuehn, L.A., Keele, J.W., Holl, J.W., Shackelford, S.D., Wheeler, T.L., Nonneman, D.J. 2010. Genomic regions associated with kyphosis in swine. BMC Genetics. 11:112.
The effects of genetic markers on BTA6 significant for steer feed intake and gain traits on carcass and meat traits - (Abstract Only)
Lindholm-Perry, A.K., Sexten, A.K., Kuehn, L.A., Smith, T.P., King, D.A., Shackelford, S.D., Wheeler, T.L., Snelling, W.M., Freetly, H.C. 2011. The effects of genetic markers on BTA6 significant for steer feed intake and gain traits on carcass and meat traits. Plant & Animal Genome XIX Conference. Poster No. P531. p. 230
Polymorphisms in POMC are not associated with dry matter intake and average daily gain phenotypes in beef cattle Reprint Icon - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Kuehn, L.A., Snelling, W.M., Smith, T.P.L., Ferrell, C.L., Jenkins, T.G., Freetly, H.C. 2010. Polymorphisms in POMC are not associated with dry matter intake and average daily gain phenotypes in beef cattle. Animal Genetics. 41(6):669-670.
Using growth traits and adipose function to identify indicators of heifer fertility - (Abstract Only)
Cushman, R.A., Allan, M.F., Mcdaneld, T.G., Kuehn, L.A., Rempel, L.A., Lindholm-Perry, A.K., Snelling, W.M., Freetly, H.C. 2010. Using growth traits and adipose function to identify indicators of heifer fertility [abstract]. Proceedings of 8th International Ruminant Reproduction Symposium. p. 130 (Abstract # M43).
A Region on BTA6 Is Associated with Feed Intake and Gain in Beef Cattle - (Abstract Only)
Sexten, A.K., Kuehn, L.A., Smith, T.P., Freetly, H.C., Snelling, W.M., Lindholm-Perry, A.K. 2010. A Region on BTA6 Is Associated with Feed Intake and Gain in Beef Cattle [abstract]. Journal of Animal Science. 88 (E-Supplement 2):185.
Evaluation of Two Positional Candidate Genes on BTA14 for Association with Dry Matter Intake in Beef Cattle - (Abstract Only)
Lindholm-Perry, A.K., Kuehn, L.A., Smith, T.P., Freetly, H.C., Snelling, W.M. 2010. Evaluation of Two Positional Candidate Genes on BTA14 for Association with Dry Matter Intake in Beef Cattle [abstract]. Plant & Animal Genome XVIII Conference. Poster No. P553. p. 216.
Allele-Specific Transcription Factor Binding in Pig Calpastatin Promoter Regions Reprint Icon - (Abstract Only)
Nonneman, Dan J., Lindholm-Perry, Amanda K., Shackelford, Steven D., King, D.Andy, Wheeler, Tommy L., Rohrer, Gary A. 2010. Allele-Specific Transcription Factor Binding in Pig Calpastatin Promoter Regions. Plant and Animal Genome Conference Proceedings XVIII. 1/9-13/2010. San Diego, CA. Abstract #P607.
Association of Functional SNPs in Pig Calpastatin Regulatory Regions with Tenderness Reprint Icon - (Abstract Only)
Nonneman, D.J., Lindholm-Perry, A.K., Shackelford, S.D., King, D.A., Wheeler, T.L., Rohrer, G.A., Bierman, C., Miller, R.K., Zerby, H., Moeller, S.J. 2010. Association of Functional SNPs in Pig Calpastatin Regulatory Regions with Tenderness. Proc., Midwestern Section of the American Society of Animal Science Meeting. March 15-17, 2010. Des Moines, IA. Abstract #34. p. 11-12.
Relationships among calpastatin single nucleotide polymorphisms, calpastatin expression and tenderness in pork longissimus Reprint Icon - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Rohrer, G.A., Holl, J.W., Shackelford, S.D., Wheeler, T.L., Koohmaraie, M., Nonneman, D.J. 2009. Relationships among calpastatin single nucleotide polymorphisms, calpastatin expression and tenderness in pork longissimus. Animal Genetics. 40(5):713-721.
Positional candidate genes for kyphosis in commercial swine populations Reprint Icon - (Abstract Only)
Lindholm-Perry, A.K., Rohrer, G.A., Keele, J.W., Holl, J.W., Shackelford, S.D., Wheeler, T.L., Koohmaraie, M., Nonneman, D.J. 2009. Positional Candidate Genes for Kyphosis in Commercial Swine Populations. Proc., Plant and Animal Genome Conference XVII. 1/10-14/2009, San Diego, CA. P529.
Update on genetic markers for pork quality - (Proceedings)
Rohrer, G.A., Holl, J.W., Lindholm-Perry, A.K., Nonneman, D.J., Shackelford, S.D., Wheeler, T.L., Koohmaraie, M. 2007. Update on genetic markers for pork quality. Conference Proc., National Swine Improvement Federation Conference & Ann. Mtg., Dec. 5-7, 2007. Kansas City, MO, NSIF Volume 32, www.nsif.com
Last Modified: 7/25/2016