Research Project: Identifying Genomic Solutions to Improve Efficiency of Swine Production

Location: Genetics and Animal Breeding

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

PigSense: Structural vibration-based activity and health monitoring system for pigs - (Peer Reviewed Journal)
Dong, Y., Bonde, A., Codling, J.R., Bannis, A., Cao, J., Macon, A., Rohrer, G., Miles, J., Sharma, S., Brown-Brandl, T., Sangpetch, A., Sangpetch, O., Zhang, P., Noh, H. 2023. PigSense: Structural vibration-based activity and health monitoring system for pigs. ACM Transactions on Sensor Networks. 20(1):1-43. https://doi.org/10.1145/3604806.

A review of swine heat production: 2003 to 2020 - (Peer Reviewed Journal)
Ramirez, B.C., Hoff, S.J., Hayes, M.D., Brown-Brandl, T.M., Harmon, J.D., Rohrer, G.A. 2022. A review of swine heat production: 2003 to 2020. Frontiers in Animal Science. 3. Article 908434. https://doi.org/10.3389/fanim.2022.908434.

Thermal comfort evaluation of three genetic lines of nursery pigs using thermal images - (Peer Reviewed Journal)
Brown-Brandl, T.M., Hayes, M.D., Rohrer, G.A., Eigenberg, R.A. 2022. Thermal comfort evaluation of three genetic lines of nursery pigs using thermal images. Biosystems Engineering. 225:1-12. https://doi.org/10.1016/j.biosystemseng.2022.11.002.

Recent developments and future directions in meta-analysis of differential gene expression in livestock RNA-Seq - (Review Article)
Keel, B.N., Lindholm-Perry, A.K. 2022. Recent developments and future directions in meta-analysis of differential gene expression in livestock RNA-Seq. Frontiers in Genetics. 13. Article 983043. https://doi.org/10.3389/fgene.2022.983043.

Behavioral time budgets for sows before and after farrowing - (Proceedings)
Macon, A., Brown-Brandl, T., Lee, B., Vander Woude Jr, E., Markvicka, E., Sharma, S., Rohrer, G.A. 2022. Behavioral time budgets for sows before and after farrowing. In: Proceedings of the American Society of Agricultural and Biological Engineers International (ASABE). July 17-20, 2022, Houston, TX. pg. 64. Paper 2200950.

Functional genomics of reproduction in pigs: Are we there yet? - (Review Article)
Nonneman, D.J., Lents, C.A. 2022. Functional genomics of reproduction in pigs: Are we there yet?. Molecular Reproduction and Development. 90(7): 436-444. https://doi.org/10.1002/mrd.23625.

Lameness detection in sows using few-shot approach - (Proceedings)

Posture detection of sows housed in farrowing crates using composite image models - (Proceedings)

Sow posture and feeding activity monitoring in a farrowing pen using ground vibration - (Proceedings)

Automatic phenotyping of activity traits utilizing NUtrack to enhance gilt selection - (Proceedings)

Determining the heat and moisture production rate in group housed gestating sows with esf system - (Abstract Only)
Hong, M., Brown-Brandl, T.M., Ramirez, B.C., Hoff, S.J., Rohrer, G.A., Sharma, R., Hayes, M.D., Harmon, J.D. 2022. Determining the heat and moisture production rate in group housed gestating sows with esf system [abstract]. In: Proceedings of the American Society of Agricultural and Biological Engineers. July 17-20,2022, Houston, Texas. Paper 2201038. pg. 64.

Factors affecting pre-weaning mortality of piglets - (Abstract Only)
Rahman, M.T., Brown-Brandl, T.M., Rohrer, G.A., Shi, Y., Sharma, S.R., Manthena, V. 2022. Factors affecting pre-weaning mortality of piglets [abstract]. In: Proceedings of the American Society of Agricultural and Biological Engineers. July 17-20, 2022, Houston, Texas. Paper 220581. pg. 23.

Transcriptomic analysis for pork color – The ham halo effect in biceps femoris - (Peer Reviewed Journal)
Nonneman, D.J., Keel-Mercer, B.N., Lindholm-Perry, A.K., Rohrer, G.A., Wheeler, T.L., Shackelford, S.D., King, D.A. 2022. Transcriptomic analysis for pork color – The ham halo effect in biceps femoris. Meat and Muscle Biology. 6(1):1-8. Article 13050. https://doi.org/10.22175/mmb.13050.

Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities - (Peer Reviewed Journal)
Keel, B.N., Lindholm-Perry, A.K., Oliver, W.T., Wells, J.E., Jones, S.A., Rempel, L.A. 2021. Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities. BMC Genomic Data. 22. Article 25. https://doi.org/10.1186/s12863-021-00980-5.

Characterizing lactating sow posture in farrowing crates utilizing automated image capture and wearable sensors - (Proceedings)
Macon, A., Sharma, S., Lee, B., Markvicka, E., Rohrer, G.A., Miles, J.R., Brown-Brandl, T. 2021. Characterizing lactating sow posture in farrowing crates utilizing automated image capture and wearable sensors. Proceedings of the European Conference on Agricultural Engineering AgEng 2021, July 4-8, 2021, Evora, Portugal. p. 634-642.

Effects of farrowing stall layout and number of heat lamps on sow and piglet behavior - (Peer Reviewed Journal)
Leonard, S.M., Xin, H., Brown-Brandl, T.M., Ramirez, B.C., Johnson, A.K., Dutta, S., Rohrer, G.A. 2021. Effects of farrowing stall layout and number of heat lamps on sow and piglet behavior. Applied Animal Behaviour Science. 239. Article 105334. https://doi.org/10.1016/j.applanim.2021.105334.

Potential functional variants in AHR signaling pathways are associated with age at puberty in swine - (Peer Reviewed Journal)
Nonneman, D.J., Lents, C.A., Rempel, L.A., Rohrer, G.A. 2021. Potential functional variants in AHR signaling pathways are associated with age at puberty in swine. Animal Genetics. 52(3):284-291. Article 13051. https://doi.org/10.1111/age.13051.

Activity and bone lesion analysis on gilt retention to the breeding herd - (Abstract Only)
Hauxwell, K., Ostrand, L.M., Schmidt, T.B., Psota, E., Mote, B.E., Rohrer, G.A. 2021. Activity and bone lesion analysis on gilt retention to the breeding herd [abstract]. Journal of Animal Science. 99(Supplement 1):154. https://doi.org/10.1093/jas/skab054.264.

Utilization of NUtrack to assess variance components and heritability of activity traits - (Abstract Only)
Ostrand, L.M., Tranhaile-Grannemann, M.D., See, G., Schmidt, T.B., Psota, E., Rohrer, G.A., Mote, B.E. 2021. Utilization of NUtrack to assess variance components and heritability of activity traits [abstract]. Journal of Animal Science. 99(Supplement 1):17. https://doi.org/10.1093/jas/skab054.030.

Evaluation of transcript assembly in multiple porcine tissues suggests optimal sequencing depth for RNA-Seq using total RNA library - (Peer Reviewed Journal)
Keel, B.N., Oliver, W.T., Keele, J.W., Lindholm-Perry, A.K. 2020. Evaluation of transcript assembly in multiple porcine tissues suggests optimal sequencing depth for RNA-Seq using total RNA library. Animal Gene. 17-18. Article 200105. https://doi.org/10.1016/j.angen.2020.200105.

Effects of farrowing stall layout and number of heat lamps on sow and piglet production performance - (Peer Reviewed Journal)
Leonard, S.M., Xin, H., Brown-Brandl, T.M., Ramirez, B.C., Dutta, S., Rohrer, G.A. 2020. Effects of farrowing stall layout and number of heat lamps on sow and piglet production performance. Animals. 10(2).Article 348. https://doi.org/doi:10.3390/ani10020348.

Developmental and allele-specific methylation patterns in fetal liver of pigs derived from White Composite x Meishan reciprocal crosses - (Abstract Only)
Corbett, R.J., Liu, H., Nonneman, D., Smith, T.P.L., Raney, N.E., Tuggle, C.K., Ernst, C.W. 2020. Developmental and allele-specific methylation patterns in fetal liver of pigs derived from White Composite x Meishan reciprocal crosses [abstract]. In proceedings: Plant and Animal Genome Conference, San Diego, CA, 11-15 Jan 2020. W034. Available: https://plan.core-apps.com/pag_2020/abstract/b96984cc-5afc-4dce-b908-9c79e4ac4e85.

The porcine muscle thanatotranscriptome - (Abstract Only)
Nonneman, D.J., Dickey, A.M., King, D.A. 2020. The porcine muscle thanatotranscriptome [abstract]. In: Proceedings of XXVIII Plant and Animal Genome Conference, Swine Workshop. San Diego, CA, 11-15 Jan 2020. W1030.

Using SNP weights derived from gene expression modules to improve GWAS power for feed efficiency in pigs - (Abstract Only)
Keel, B.N., Snelling, W.M., Lindholm-Perry, A.K., Oliver, W.T., Kuehn, L.A., Rohrer, G.A. 2020. Using SNP weights derived from gene expression modules to improve GWAS power for feed efficiency in pigs [abstract]. In proceedings: Plant and Animal Genome Conference Proceedings, San Diego, CA, 11-15 Jan 2020. W222. Available: https://plan.core-apps.com/pag_2020/abstract

Using SNP weights derived from gene expression modules to improve GWAS power for feed efficiency in pigs - (Peer Reviewed Journal)
Keel, B.N., Snelling, W.M., Lindholm-Perry, A.K., Oliver, W.T., Kuehn, L.A., Rohrer, G.A. 2020. Using SNP weights derived from gene expression modules to improve GWAS power for feed efficiency in pigs. Frontiers in Genetics. 10:1339. https://doi.org/10.3389/fgene.2019.01339.

Evaluation of transcript assembly in multiple porcine tissues suggests optimal sequencing depth for RNA-Seq using total RNA library - (Abstract Only)
Keel, B.N., Oliver, W.T., Keele, J.W., Lindholm-Perry, A.K. 2020. Evaluation of transcript assembly in multiple porcine tissues suggests optimal sequencing depth for RNA-Seq using total RNA library. In: Proceedings of Plant and Animal Genome XXVIII Conference, January 11-15, 2020, San Diego, California. Poster No. PE0128. Available: https://plan.core-apps.com/pag_2020/abstract

Genome-wide associations for fatty acid composition of pork identifies novel candidate SNP on chromosome 14 - (Abstract Only)
Nonneman, D.J., Clancy, M.D., Rohrer, G.A., Arkfeld, E., Boler, D.D., Dilger, A.C., King, A., Wheeler, T.L., Shackelford, S.D. 2020. Genome-wide associations for fatty acid composition of pork identifies novel candidate SNP on chromosome 14 [abstract]. In proceedings: Plant and Animal Genome Conference XXVIII, San Diego, CA, January 11-15, 2020. Abstract PE0396. Available: https://plan.core-apps.com/pag_2020/abstract/60658e794c2a6d06f3aa20dcfb5c9f80

A survey of copy number variation in the porcine genome detected from whole-genome sequence - (Peer Reviewed Journal)
Keel, B.N., Nonneman, D.J., Lindholm-Perry, A.K., Oliver, W.T., Rohrer, G.A. 2019. A survey of copy number variation in the porcine genome detected from whole-genome sequence. Frontiers in Genetics. 10:737. https://doi.org/10.3389/fgene.2019.00737.

Evaluation of genotype quality parameters for SowPro90, a new genotyping array for swine - (Peer Reviewed Journal)
Wijesena, H.R., Rohrer, G.A., Nonneman, D.J., Keel, B.N., Petersen, J.L., Kachman, S.D., Ciobanu, D.C. 2019. Evaluation of genotype quality parameters for SowPro90, a novel genotyping platform for swine. Journal of Animal Science. 97(8):3262-3273. https://doi.org/10.1093/jas/skz185.

A survey of genomic variants in commercial swine germplasm identified from whole-genome sequence - (Abstract Only)

Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data - (Peer Reviewed Journal)
Beiki, H., Liu, H., Manchanda, N., Nonneman, D.J., Smith, T.P.L., Reecy, J., Tuggle, C. 2019. Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data. BMC Genomics. 20:344-362. https://doi.org/10.1186/s12864-019-5709-y.

From phenotype to gene discovery: A case study of host genetics influencing porcine circovirus 2 susceptibility - (Abstract Only)
Walker, L., Wijesena, H., Sutton, K., Vu, H., Nonneman, D., Smith, T., Plastow, G., Kachman, S., Ciobanu, D. 2019. From phenotype to gene discovery: A case study of host genetics influencing porcine circovirus 2 susceptibility [abstract]. In proceedings: 37th International Society for Animal Genetics (ISAG). 7-12 July 2019, Lleida, Spain. p. 7. Abstract OP25.

Characterization of A-to-I editing events in fetal pig tissues - (Abstract Only)
Corbett, R.J., Funkhouser, S.A., Nonneman, D.J., Smith, T.P.L., Ernst, C.W. 2019. Characterization of A-to-I editing events in fetal pig tissues [abstract]. In Proceedings: 37th International Society for Animal Genetics (ISAG). 7-12 July 2019, Lleida, Spain. pg. 24. Abstract OP86.

Host synaptogyrin-2 facilitates replication of PCV2b - (Abstract Only)
Walker, L., Engle, T., Vu, H., Tosky, E., Nonneman, D., Smith, T., Borza, T., Burkey, T., Plastow, G., Kachman, S., Ciobanu, D. 2019. Host synaptogyrin-2 facilitates replication of PCV2b [abstract]. In proceedings: 37th International Society for Animal Genetics (ISAG). 7-12 July 2019, Lleida, Spain. pg. 119. Abstract P208.

The enigmatic role of host genetics in disease susceptibility: a case study of Porcine circovirus 2 - (Abstract Only)
Walker, L.R., Engle, T.B., Vu, H., Tosky, E.R., Nonneman, D.J., Smith, T.P.L., Borza, T., Burkey, T.E., Plastow, G.S., Kachman, S.D., Ciobanu, D.C. 2019. The enigmatic role of host genetics in disease susceptibility: a case study of Porcine circovirus 2 [abstract]. In: Plant and Animal Genome Conference Proceedings XXVII, 12-16 January 2019, San Diego, CA. pg. 232. W1128. Available: https://www.intlpag.org/2019/images/pdf/2019/PAGXXVII-abstracts-workshops.pdf

Cataloguing genetic variants in commercial swine - (Abstract Only)
Keel, B.N., Nonneman, D.J., Rohrer, G.A. 2019. Cataloguing genetic variants in commercial swine [abstract]. In: Plant & Animal Genome Conference Proceedings XXVII, 12-16 January 2019, San Diego, CA. pg. 216. W1046. Available: https://www.intlpag.org/2019/images/pdf/2019/PAGXXVII-abstracts-workshops.pdf

Genetic factors associated with changes in feeding behavior due to elevated temperature - (Abstract Only)

Functional annotation of the porcine genome and ISAFG update - (Abstract Only)
Tuggle, C.K., Zhou, H., Ernst, C.W., Loving, C.L., Koltes, J.E., Reecy, J.M., Ross, P.J., Nonneman, D.J., Smith, T.P.L., Steibel, J.P., Huang, W. 2019. Functional annotation of the porcine genome and ISAFG update [abstract]. In: Plant and Animal Genome Conference XXVII Proceedings, 12-16 Jan 2019, San Diego, CA. pg. 96. W448. Available: https://www.intlpag.org/2019/images/pdf/2019/PAGXXVII-abstracts-workshops.pdf

Fine mapping of QTL associated with age at puberty in gilts using a novel Affymetrix SNP (SowPro90) - (Abstract Only)
Wijesena, H.R., Nonneman, D.J., Keel, B.N., Riethoven, J.J., Rohrer, G.A., Kachman, S.D., Ciobanu, D.C. 2019. Fine mapping of QTL associated with age at puberty in gilts using a novel Affymetrix SNP (SowPro90) [abstract]. In: Plant and Animal Genome Conference Proceedings XXVII, 12-16 January 2019, San Diego, CA. pg. 116. PE0404. Available: https://www.intlpag.org/2019/images/pdf/2019/PAGXXVII-abstracts-posters.pdf

Host genetics influences replication of porcine circovirus 2b - (Abstract Only)
Walker, L.R., Engle, T.B., Vu, H., Tosky, E.R., Nonneman, D.J., Smith, T.P.L., Borza, T., Burkey, T.E., Plastow, G.S., Kachman, S.D., Ciobanu, D.C. 2019. Host genetics influences replication of porcine circovirus 2b [abstract]. In: Plant and Animal Genome Conference XXVII Proceedings, 12-16 January 2019, San Diego, CA. pg. 233. W1136. Available: https://www.intlpag.org/2019/images/pdf/2019/PAGXXVII-abstracts-workshops.pdf

Transcriptome and genome-wide histone modifications in swine fetal liver - (Abstract Only)
Niu, B., Liu, H., Nonneman, D.J., Tuggle, C.K. 2019. Transcriptome and genome-wide histone modifications in swine fetal liver [abstract]. Plant and Animal Genome Conference Proceedings, San Diego, CA, 12-16 January 2019. pg. 212, PE0420. Available: https://www.intlpag.org/2019/images/pdf/2019/PAGXXVII-abstracts-posters.pdf

Deciphering the dynamics of porcine circovirus associated diseases using gene silencing and editing - (Abstract Only)
Walker, L., Engle, T., Vu, H., Tosky, E., Nonneman, D.J., Smith, T.P.L., Borza, T., Burkey, T., Plastow, G.S., Kachman, S.D., Ciobanu, D.C. 2019. Deciphering the dynamics of porcine circovirus associated diseases using gene silencing and editing [abstract]. In: Plant and Animal Genome Conference Proceedings XXVII, 12-16 Jan. 2019, San Diego, CA. pg. 216, W1045. Available: https://www.intlpag.org/2019/images/pdf/2019/PAGXXVII-abstracts-workshops.pdf

Porcine single nucleotide polymorphisms and their functional effect: an update - (Peer Reviewed Journal)
Keel, B.N., Nonneman, D.J., Lindholm-Perry, A.K., Oliver, W.T., Rohrer, G.A. 2018. Porcine single nucleotide polymorphisms and their functional effect: an update. BMC Research Notes. 11:860. https://doi.org/10.1186/s13104-018-3973-6.

Evolution of the commercial sow - (Abstract Only)
Rohrer, G.A. 2019. Evolution of the commercial sow [abstract]. Journal of Animal Science. 97 (Supplement 2):14. Abstract 25. https://doi.org/10.1093/jas/skz122.025.

Transcriptome profiling of olfactory epithelium in normal cycling and acyclic gilts - (Abstract Only)
Nonneman, D.J., Dickey, A.M., Lents, C.A. 2019. Transcriptome profiling of olfactory epithelium in normal cycling and acyclic gilts [abstract]. Journal of Animal Science. 97(Supplement 2):125. Abstract 213. https://doi.org/10.1093/jas/skz122.222.

Synaptogyrin-2 influences replication of porcine circovirus 2 - (Peer Reviewed Journal)
Walker, L.R., Engle, T.B., Vu, H., Tosky, E.R., Nonneman, D.J., Smith, T.P.L., Borza, T., Burkey, T.E., Plastow, G.S., Kachman, S.D., Ciobanu, D.C. 2018. Synaptogyrin-2 influences replication of porcine circovirus 2. PLoS Genetics. 14(10):e1007750. https://doi.org/10.1371/journal.pgen.1007750.

Long-term effects of lactocrine-deficiency on the global porcine endometrial transcriptome and the microRNA-mRNA interactome at pregnancy day 13 - (Abstract Only)
George, A.F., Ho, T., Prasad, N., Keel, B.N., Miles, J.R., Vallet, J.L., Bartol, F.F., Bagnell, C.A. 2018. Long-term effects of lactocrine-deficiency on the global porcine endometrial transcriptome and the microRNA-mRNA interactome at pregnancy day 13 [abstract]. In proceedings: Society for the Study of Reproduction 51st Annual Meeting, 10-13 July 2018, New Orleans, LA. p. 23-24. Available: https://www.ssr.org/sites/ssr.org/files/2018_annual_meeting_abstracts_updated.pdf