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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Livestock Bio-Systems » Research » Research Project #426415

Research Project: Genetic and Genomic Approaches to Improve Swine Reproductive Efficiency

Location: Livestock Bio-Systems

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

RNA-seq meta-analysis identifies genes in skeletal muscle associated with gain and intake across a multi-season study of crossbred beef steers Reprint Icon - (Peer Reviewed Journal)
Keel, B.N., Zarek, C.M., Keele, J.W., Kuehn, L.A., Snelling, W.M., Oliver, W.T., Freetly, H.C., Lindholm-Perry, A.K. 2018. RNA-seq meta-analysis identifies genes in skeletal muscle associated with gain and intake across a multi-season study of crossbred beef steers. BMC Genomics. 19:430. https://doi.org/10.1186/s12864-018-4769-8.

Genome-wide association of myoglobin concentrations in pork loins Reprint Icon - (Peer Reviewed Journal)
Cross, A.J., King, D.A., Shackelford, S.D., Wheeler, T.L., Nonneman, D.J., Keel, B.N., Rohrer, G.A. 2018. Genome-wide association of myoglobin concentrations in pork loins. Meat and Muscle Biology. 2(1):189-196. https://doi.org/10.22175/mmb2017.08.0042.

Genome-wide association of changes in swine feeding behaviour due to heat stress - (Peer Reviewed Journal)
Cross, A.J., Keel, B.N., Brown-Brandl, T.M., Cassady, J.P., Rohrer, G.A. 2018. Genome-wide association of changes in swine feeding behaviour due to heat stress. Genetics Selection Evolution. 50:11. https://doi.org/10.1186/s12711-018-0382-1.

Feed-forward and generalised regression neural networks in modelling feeding behaviour of pigs in the grow-finish phase Reprint Icon - (Peer Reviewed Journal)
Cross, A.J., Rohrer, G.A., Brown-Brandl, T.M., Cassady, J.P., Keel, B.N. 2018. Feed-forward and generalised regression neural networks in modelling feeding behaviour of pigs in the grow-finish phase. Biosystems Engineering. 173:124-133. https://doi.org/10.1016/j.biosystemseng.2018.02.005.

Comparison of Burrows-Wheeler transform-based mapping algorithms used in high-throughput whole-genome sequencing: application to Illumina data for livestock genomes Reprint Icon - (Peer Reviewed Journal)
Keel, B.N., Snelling, W.M. 2018. Comparison of Burrows-Wheeler transform-based mapping algorithms used in high-throughput whole-genome sequencing: application to Illumina data for livestock genomes. Frontiers in Genetics. 9:35. https://doi.org/10.3389/fgene.2018.00035.

Transcriptome analysis for pork color – the ham halo effect in biceps femoris - (Abstract Only)
Nonneman, D.J., Keel, B.N., King, D.A. 2018. Transcriptome analysis for pork color – the ham halo effect in biceps femoris [abstract]. Journal of Animal Science. 96(Supplement 2):102. Abstract 192.

A survey of copy number variation in the porcine genome detected from whole-genome sequence - (Abstract Only)
Keel, B.N., Nonneman, D.J., Rohrer, G.A. 2018. A survey of copy number variation in the porcine genome detected from whole-genome sequence [abstract]. Journal of Animal Science. 96(Supplement 2):17-18. Abstract 32.

Additional annotation of the pig transcriptome using integrated Iso-seq and Illumina RNA-seq analysis - (Abstract Only)
Beiki, H., Liu, H., Huang, J., Manchanda, N., Nonneman, D.J., Smith, T.P.L., Tuggle, C.K. 2018. Additional annotation of the pig transcriptome using integrated Iso-seq and Illumina RNA-seq analysis. [abstract] In proceedings: Plant and Animal Genome Conference XXVI, San Diego, CA, 13-17 Jan 2018. Poster abstract P0439. Available: pag.confex.com/pag/xxvi/meetingapp.cgi/paper/30999.

MOCASSIN-prot: A multi-objective clustering approach for protein similarity networks Reprint Icon - (Peer Reviewed Journal)
Keel, B.N., Deng, B., Moriyama, E.N. 2018. MOCASSIN-prot: A multi-objective clustering approach for protein similarity networks. Bioinformatics. 34(8):1270-1277. https://doi.org/10.1093/bioinformatics/btx755.

MOCASSIN-prot software - (Other)
Keel, B.N., Deng, B., Moriyama, E.N. 2018. MOCASSIN-prot software [computer program]. Version 1. Lincoln, Nebraska: University of Nebraska-Lincoln. Available: http://bioinfolab.unl.edu/emlab/MOCASSINprot.

Incorporating deep learning into the analysis of diverse livestock data - (Abstract Only)
Keel, B.N. 2017. Incorporating deep learning into the analysis of diverse livestock data. [Abstract]. In Proceedings: Livestock High-Throughput Phenotyping and Big Data Analytics (Livestock HTP and Big Data), Nov. 13-14, 2017, Beltsville, MD. www.animalgenome.org/share/meetings/LivestockHTP.

A feed-forward neural network for modeling feeding behavior of group-housed grow-finish pigs with respect to thermal conditions - (Proceedings)
Keel, B.N., Cross, A.J., Brown-Brandl, T.M., Cassady, J.P., Rohrer, G.A. 2018. A feed-forward neural network for modeling feeding behavior of group-housed grow-finish pigs with respect to thermal conditions. In proceedings: World Congress of Genetics Applied in Livestock Production, 11-16 Feb 2018, Auckland, New Zealand. Volume Species-Porcine 1, 240. Available: https://www.wcgalp.org/proceedings/2018

Genome-wide association of myoglobin concentrations in pork loins - (Abstract Only)
Cross, A.J., King, D.A., Shackelford, S.D., Wheeler, T.L., Cassady, J.P., Nonneman, D.J., Rohrer, G.A. 2017. Genome-wide association of myoglobin concentrations in pork loins. [abstract] In proceedings: South Dakota State University Swine Day Proceedings. Brookings, SD. Oct. 11, 2017. pg. 12.

Polymorphism in the intron 20 of porcine O-linked N-acetylglucosamine transferase Reprint Icon - (Peer Reviewed Journal)
Kim, J.G., Nonneman, D.J., Kim, D., Shin, S., Rohrer, G.A. 2017. Polymorphism in the intron 20 of porcine O-linked N-acetylglucosamine transferase. Asian-Australasian Journal of Animal Sciences. 30(8):1086-1092. doi:10.5713/ajas.17.0143.

Meta-analysis of RNA-Seq data across cohorts in a multi-season feed efficiency study of crossbred beef steers accounts for biological and technical variability within season - (Abstract Only)
Keel, B.N., Zarek, C.M., Keele, J.W., Kuehn, L.A., Snelling, W.M., Oliver, W.T., Freetly, H.C., Lindholm-Perry, A.K. 2017. Meta-analysis of RNA-Seq data across cohorts in a multi-season feed efficiency study of crossbred beef steers accounts for biological and technical variability within season [abstract]. Journal of Animal Science Supplement. 95(Suppl4):98. doi:10.2527/asasann.2017/198.

Genome wide association of changes in feeding behavior due to heat stress in pigs - (Abstract Only)
Cross, A.J., Keel, B.N., Brown-Brandl, T.M., Rohrer, G.A. 2017. Genome wide association of changes in feeding behavior due to heat stress in pigs [abstract]. International Society for Animal Genetics (ISAG). Abstract #MT279 (Abstract book p. 138-139). Available: http://www.isag.us/2017/docs/ISAG2017_Proceedings.pdf.

A survey of single nucleotide polymorphisms identified from whole-genome sequencing and their functional effect in the porcine genome Reprint Icon - (Peer Reviewed Journal)
Keel, B.N., Nonneman, D.J., Rohrer, G.A. 2017. A survey of single nucleotide polymorphisms identified from whole-genome sequencing and their functional effect in the porcine genome. Animal Genetics. 48(4):404-411. doi:10.1111/age.12557.

USMARC update on swine reproduction research - (Abstract Only)
Nonneman, D.J., Lents, C.A., Keel, B.N., Rohrer, G.A. 2017. USMARC update on swine reproduction research. Plant and Animal Genome Conference. [Abstract] In Proceedings: Plant and Animal Genome XXV Conference, Jan. 14-18, 2017. San Diego, CA. W914.

Evaluation of functional variation in candidate genes for pork quality - (Abstract Only)
Nonneman, D.J., Rohrer, G.A., Kalbfleisch, T.S., Shackelford, S.D., King, D.A., Wheeler, T.L. 2017. Evaluation of functional variation in candidate genes for pork quality [abstract]. Journal of Animal Science. 95(supplement 2):19-20. https://doi.org/10.2527/asasmw.2017.041.

Genetic analysis of teat number in pigs reveals some developmental pathways independent of vertebra number and several loci which only affect a specific side Reprint Icon - (Peer Reviewed Journal)
Rohrer, G.A., Nonneman, D.J. 2017. Genetic analysis of teat number in pigs reveals some developmental pathways independent of vertebra number and several loci which only affect a specific side. Genetics Selection Evolution. 49:4. doi:10.1186/s12711-016-0282-1.

Genome-wide association of myoglobin concentrations in pork loins - (Abstract Only)
Cross, A.J., King, D.A., Shackelford, S.D., Wheeler, T.L., Cassady, J.P., Nonneman, D.J., Rohrer, G.A. 2017. Genome-wide association of myoglobin concentrations in pork loins [abstact]. Journal of Animal Science. 95(Suppl2):20. doi:10.2527/asasmw.2017/042.

Swine transcriptome characterization by combined Iso-Seq and RNA-seq for annotating the emerging long read-based reference genome - (Abstract Only)
Liu, H., Manchanda, N., Nonneman, D.J., Smith, T.P., Tuggle, C. 2017. Swine transcriptome characterization by combined Iso-Seq and RNA-seq for annotating the emerging long read-based reference genome [abstract]. In proceedings: Plant and Animal Genome Conference, Jan. 14-18, 2017, San Diego, CA. P1162.

Genetic improvement of sow lifetime productivity - (Abstract Only)
Rohrer, G.A., Cross, A.J., Lents, C.A., Miles, J.R., Nonneman, D.J., Rempel, L.A. 2017. Genetic improvement of sow lifetime productivity. [Abstract] In proceedings: Midwestern Section of the American Society of Animal Science. March 13-15, 2017. Omaha, NE. Journal of Animal Science Supplement 95(Suppl 2):11-12 doi:10.2527/asasmw.2017.026.

Evolutionary and functional features of copy number variation in the cattle genome - (Peer Reviewed Journal)
Keel, B.N., Lindholm-Perry, A.K., Snelling, W.M. 2016. Evolutionary and functional features of copy number variation in the cattle genome. Frontiers in Genetics. 7:207. doi:10.3389/fgene.2016.00207.

Genome-wide copy number variation in the bovine genome detected using low coverage sequence of popular beef breeds - (Abstract Only)
Keel, B.N., Snelling, W.M., Keele, J.W. 2016. Genome-wide copy number variation in the bovine genome detected using low coverage sequence of popular beef breeds [abstract]. International Society for Animal Genetics (35th ISAG). Abstract Book. p. 83 (Abstract # P4008).

A GWAS of teat number in pigs - (Abstract Only)
Rohrer, G.A., Nonneman, D.J. 2016. A GWAS of teat number in pigs [abstract]. International Society for Animal Genetics (35th ISAG). Abstract Book. p. 131-132 (Abstract # P5033).

Genome-wide association and identification of candidate genes for age at puberty in swine Reprint Icon - (Peer Reviewed Journal)
Nonneman, D.J., Schneider, J.F., Lents, C.A., Wiedmann, R.T., Vallet, J.L., Rohrer, G.A. 2016. Genome-wide association and identification of candidate genes for age at puberty in swine. BMC Genetics. 17(1):50.

Segregation of naturally occurring mitochondrial DNA variants in a mini-pig model Reprint Icon - (Peer Reviewed Journal)
Cagnone, G., Tsai, T.-S, Srirattana, K., Rossello, F., Powell, D.R., Rohrer, G., Cree, L., Trounce, I.A., St. John, J.C. 2016. Segregation of naturally occurring mitochondrial DNA variants in a mini-pig model. Genetics. 202(3):931-944.

Potential functional variants associated with age at puberty in a validation population of swine - (Abstract Only)
Nonneman, D.J., Lents, C.A., Kalbfleisch, T.S., Vallet, J.L., Rohrer, G.A. 2016. Potential functional variants associated with age at puberty in a validation population of swine [abstract]. Plant and Animal Genome Conference Proceedings. XXIV Conference:Abstract #P0619.

Investigation and validation of the role of a QTL on SSC12 in PCV2b viremia - (Abstract Only)
Tosky, E., Smith, T.P.L., Engle, T., Davis, E., Moural, T., Nonneman, D., Chin, J., Burkey, T., Plastow, G.S., Kachman, S.D., Ciobanu, D.C. 2016. Investigation and validation of the role of a QTL on SSC12 in PCV2b viremia [abstract]. Plant and Animal Genome XXIV Conference Proceedings. Abstract #P0638.

Do you really know where this SNP goes? - (Abstract Only)
Rohrer, G.A., Nonneman, D., Schroeder, S.G., Chin, J., Koren, S., Phillippy, A., Green, R., Putnam, N., Smith, T.P.L. 2016. Do you really know where this SNP goes? [abstract] Plant and Animal Genome XXIV Conference Proceedings. Abstract #W909.

A study of vertebra number in pigs confirms the association of vertnin and reveals additional QTL Reprint Icon - (Peer Reviewed Journal)
Rohrer, G.A., Nonneman, D.J., Wiedmann, R.T., Schneider, J.F. 2015. A study of vertebra number in pigs confirms the association of vertnin and reveals additional QTL. BMC Genetics. 16(1):129.

Implementing meta-analysis from genome-wide association studies for pork quality traits Reprint Icon - (Peer Reviewed Journal)
Bernal Rubio, Y.L., Gualdrón Duarte, J.L., Bates, R.O., Ernst, C.W., Nonneman, D., Rohrer, G.A., King, D.A., Shackelford, S.D., Wheeler, T.L., Cantet, R.J.C., Steibel, J.P. 2015. Implementing meta-analysis from genome-wide association studies for pork quality traits. Journal of Animal Science. 93(12):5607-5617.

Genome-wide copy number variations using SNP genotyping in a mixed breed swine population Reprint Icon - (Peer Reviewed Journal)
Wiedmann, R.T., Nonneman, D.J., Rohrer, G.A. 2015. Genome-wide copy number variations using SNP genotyping in a mixed breed swine population. PLoS One. 10(7):e0133529. DOI: 10.1371/journal.pone.0133529.

Porcine models of muscular dystrophy Reprint Icon - (Review Article)
Selsby, J.T., Ross, J.W., Nonneman, D., Hollinger, K. 2015. Porcine models of muscular dystrophy. ILAR Journal. 56(1):116-126.

Research on gilt first estrus and pubertal development at USMARC - (Abstract Only)
Nonneman, D., Lents, C.A., Schneider, J.F., Vallet, J.L., Rohrer, G.A. 2015. Research on gilt first estrus and pubertal development at USMARC [abstract]. Plant and Animal Genome XXIII Conference Proceedings. Abstract #W827.

A study of vertebra number in pigs confirms the effect of vertnin and reveals additional QTL - (Abstract Only)
Rohrer, G.A., Nonneman, D., Schneider, J.F. 2015. A study of vertebra number in pigs confirms the effect of vertnin and reveals additional QTL [abstract]. Plant and Animal Genome XXIII Conference Proceedings. Abstract #P0370.