Progress 10/01/14 to 09/30/18
Outputs
Target Audience:Target audiences include scientists in the same research area, veterinarians, graduate and undergraduate students and swine producers. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project provided substantial training opportunities to junior technicians, graduate and undergraduate students. During the time of the grant there were 4 graduate students (4 MS and 2 PhD) and 2 junior technicians directly involved in this research project. How have the results been disseminated to communities of interest?Journal articles, presentations and posters were presented to regional, national and international conferences as well as meetings with producers. We collaborate closely with two commercial companies involved in this study. We plan to provide technical support for the transfer to commercial production of the knowledge and technologies developed during this research. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Objective (1). Advance the status of reference genomes for all species, including basic annotation of worldwide genetic variation, by broad sequencing among different lines and breeds of animals. Whole genome and RNA sequencing was performed to dissect and annotate genomic regions associated with economically important phenotypic traits, such as sow age at puberty and viral disease susceptibility. For example, our research uncovered that age at puberty is the earliest indicator of reproductive longevity in sows, an important economic trait for the swine industry. To discover potential pleiotropic loci associated with sow fertility we combined whole genome sequencing of representative sires with RNA sequencing of hypothalamic nuclei of gilts with different puberty status. We also performed RNA sequencing of peripheral blood samples collected from pigs that exhibited high and low viral load during experimentally infection with PCV2. All these data was used for annotation of the QTL regions inferring gene's structure, isoform variation and sequence variants. These data will benefit the entire research community by providing an improved genome assembly and novel sequence variants. Objective (2) Develop strategies to identify and exploit genes and allelic variation that contribute to economically relevant phenotypes and traits, in part through improving functional annotation of the genomes of our species. At University of Nebraska we developed population resources that combines commercial and experimental lines to dissect the genetic sources associated with sow fertility and age at puberty and susceptibility to viral diseases. As part of this objective the following important activities were performed: - Development of population resources. Population resources used in our studies were gradually expanded, as well as the phenotypic and genetic information. - QTL mapping. Progress was made in the dissection of potential functional variants associated with PCVAD susceptibility, age at puberty and reproductive longevity. Genome and RNA sequencing, high- and low-density genotyping were integrated to uncover functional polymorphisms that influence the variation of targeted traits such as PCV2 viremia, immune response and growth during PCV2 challenge. For example, a novel missense polymorphism identified in SYNGR2 gene was associated with variation in PCV2 replication and subsequent immune response. Important progress was also made in the dissection of age at puberty in sows. Novel genetic variants identified by transcriptomic and genomic sequencing and genome-wide associations were integrated into SowPro90, a custom Affymetrix SNP array. This array includes SNPs located in genes overlapping major QTL for age at puberty, SNPs located in other fertility related genes, and potential loss of function SNPs identified in the UNL and USMARC populations. Using SowPro90 genotypes of UNL gilts representing extremes of the distribution for genomic prediction values for age at puberty (early, n=154; late, n=129) we made progress in the dissection of two major QTL associated with age at puberty. For example, in a QTL initially mapped on chromosome 2 (SSC2), a SNP located in the proximal promoter of the UBE2L6 gene (SSC2, 13.3Mb; F=13.39; P=0.0003) was associated with the largest effect on age at puberty, exceeding the effect of the original top SNP (DIAS0004771; F=6.98). UBE2L6 is known to catalyze the binding of ISG15, a marker for pregnancy. The proportion of phenotypic variance explained by this SNPs was 6.8%. - Development of translational genomics tools. A new custom SNP chip (SowPro90 produced by Affymetrix, 103,476 SNPs) was developed in collaboration with USMARC to assist in the dissection of the genetic variation associated with age at puberty in gilts and in other economically important traits. The chip included a large number of genetic variants overlapping major QTLs for age at puberty, one of the earliest indicators of sow fertility. The genetic variants were identified using multiple genomic approaches including deep genomic and transcriptomic sequencing and genome wide-association studies. Quality assessment of data and specific thresholds for quality parameters for this new platform were established in a variety of commercial and research samples (n = 2,586). The impact of this work is substantial: this newly developed research and translational tool is characterized by substantial flexibility assisting UNL and USMARC groups in transferring newly developed markers to swine industry. This information will be used by industry in phenotypic prediction and genomic selection.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Wijesena, H.R., C.A. Lents, B.N. Keel, J.-J. Riethoven, M.L. Spangler, S. D. Kachman and D.C Ciobanu, Integration of gene expression profiling of hypothalamic arcuate nucleus with genome-wide associations to discover functional variants associated with age at puberty in gilts. Plant and Animal Genome Conference, San Diego, January 13-17, 2018.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Wijesena, H.R., D.J. Nonneman, B.N. Keel, J.-J. Riethoven, G.A. Rohrer, S.D. Kachman, and D.C. Ciobanu, Fine Mapping of QTL Associated with Age at Puberty in Gilts Using a Novel Affymetrix SNP Array (SowPro90). Plant and Animal Genome Conference, San Diego, January 12-16, 2019.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2019
Citation:
Garrett M. See G.M., , M.D. Trenhaile-Grannemann, M.L. Spangler, D.C. Ciobanu, and B.E. Mote, A genome-wide association study for gestation length in swine, Submitted Animal Genetics.
- Type:
Conference Papers and Presentations
Status:
Submitted
Year Published:
2019
Citation:
Garrett M. See G.M., , M.D. Trenhaile-Grannemann, D.C. Ciobanu, M.L. Spangler and B.E. Mote, A genome-wide association study for gestation length in swine, 2019 Midwest ASAS Conference, Omaha, NE.
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Walker LR, Engle TB, Vu H, Tosky ER, Nonneman DJ, Smith TPL, Borza T, Burkey TE, Plastow GS, Kachman SD, Ciobanu DC. Synaptogyrin-2 influences replication of Porcine circovirus 2. PLoS Genet. 2018 Oct 31;14(10):e1007750.
|
Progress 10/01/16 to 09/30/17
Outputs
Target Audience:Target audiences include scientists in the same research area, veterinarians, graduate and undergraduate students and swine producers. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Both graduate and undergraduate students are involved in this project that provides great training opportunities. How have the results been disseminated to communities of interest?Journal articles, presentations and posters were presented to regional, national and international meetings. What do you plan to do during the next reporting period to accomplish the goals?The activities for 2018 will continue in the following research areas: - Evaluate the results generated by the novel Affymetrix chip for genomic prediction of important productive traits - Explore in vitro models for validating genes involved in innate immune response following infection with viral pathogens
Impacts
What was accomplished under these goals?
Our main results were generated in the area of gene, genome annotation and dissection of QTL associated with important productive traits such as susceptibility to Porcine Circovirus 2 (PCV2) and age at puberty. Using a combination of genome and RNA sequencing and advanced statistical models we discovered DNA polymorphisms with phenotypic predictive potential to be used across different populations of swine. The impact of these results has potential to improve these economical important traits and positively affect the swine industry. (1) Advance the status of reference genomes for all species, including basic annotation of worldwide genetic variation, by broad sequencing among different lines and breeds of animals. Objective 1: Activity ii. Improve draft genome assemblies to close gaps and improve assembly order. In this activity we made improvements in the annotation of the proximal end of SSC12. - Integration of GWAS, RNA-seq and gene annotation in the QTL region located on SSC12 uncovered a potential gene and a functional polymorphism that explain some of the variation in PCV2 viremia. Objective 1: Activity iii. Coordinate analysis of re-sequencing data to identify SNPs, CNVs, and insertion-deletions, and better annotate gene models within the reference assemblies. Using NIFA funding we sequenced the genome of 20 boars (coverage > 20X) representative of both ends of the distribution - late and early expression of puberty. This information was used to identify polymorphisms outside the limited capability of Illumina Porcine SNP60K BeadArray. Using the same funding, we generated RNA-seq data from hypothalamic arcuate and ventromedial nuclei, anterior hypothalamic and preoptic areas of gilts with different puberty status; age at puberty is an indicator of reproductive longevity, an important economic trait for the swine industry. RNA-seq was also performed on peripheral blood samples collected from pigs that exhibited high and low viral load during experimentally infection with PCV2. RNA-seq alignments were used for annotation of the QTL regions for multiple traits by inferring gene's structure, isoform variation and sequence variants. These data will benefit the entire research community by providing an improved genome assembly and novel sequence variants. (2) Develop strategies to identify and exploit genes and allelic variation that contribute to economically relevant phenotypes and traits, in part through improving functional annotation of the genomes of our species. Objective 2. Activity i) Utilize low, medium, and high-resolution SNP-chips, as well as genome re-sequencing data in genome-wide association studies to identify loci, genes and allelic variants associated with economically important phenotypes. At University of Nebraska we developed population resources that combines genetics of commercial and experimental lines to dissect reproductive longevity and genetic susceptibility to disease. As part of this objective the following activities were performed: - QTL mapping. Using funding from UNL, NIFA and ARD we made progresses in the dissection of potential functional variants associated with PCVAD susceptibility, age at puberty and reproductive longevity. Population resources used in our studies are gradually expanded, as well as the phenotypic information. In this activity we used genome re-sequencing, RNA-seq, high- and low-density genotyping to uncover functional polymorphisms that influence the variation of targeted traits such as PCV2 viremia, immune response and growth during PCV2 challenge but also age at puberty and sow fertility. Also, using an in house newly developed Affymetrix SNP Chip, a subset of UNL gilts with divergent age at puberty were genotyped in order to dissect putative functional genes and genetic variants. - Genome and RNA sequencing provide polymorphisms outside the limited capability of the commercial SNP array/chips. An Affymetrix SNP chip (SowPro90) including 103K SNPs was designed and manufactured. This chip includes generic SNPs from the Illumina Porcine SNP60 BeadArray but also SNPs located in genes/QTL associated with age at puberty and SNPs located in genes involved in innate and adaptive immunity. The majority of the initial samples genotyped with this chip (n~2,600) were represented by commercial samples (n ~2,300). This commercial dataset will be used for the validation of DNA markers associated with fertility phenotypes in the UNL resource population.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Wijesena HR, CA Lents, J-J. Riethoven, MD Trenhaile-Grannemann, JF Thorson, BN Keel, PS Miller, ML Spangler, SD Kachman, DC Ciobanu, Integration of Genomic Approaches to Uncover Sources of Variation in Age at Puberty and Reproductive Longevity in Sows, J Anim Sci. 2017 Sep;95(9):4196-4205. doi: 10.2527/jas2016.1334.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2017
Citation:
Wijesena, H. R., Lents, C. A., Keel, B. N., Thorson, J. F., Sullivan, G., Kachman, S., Ciobanu, D. Variation In Gene Expression In The Hypothalamic Arcuate Nucleus of Gilts With Differences in Pubertal Status and Subjected To Dietary Energy Restriction. Plant and Animal Genome Conference, San Diego, January 14-18, 2017.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2017
Citation:
Ciobanu, D., Wijesena, H. R., Lents, C. A., Trenhaile-Grannemann, M. D., Riethoven, J.-J., Thorson, J. F., Keel, B. N., Miller, P., Spangler, M., Kachman, S. Integration of genomic resources to uncover pleiotropic regions associated with age at puberty and reproductive longevity in sows. Plant and Animal Genome Conference, San Diego, January 14-18, 2017.
- Type:
Conference Papers and Presentations
Status:
Submitted
Year Published:
2018
Citation:
H.R Wijesena, C.A. Lents, B.N. Keel, J.-J. Riethoven, M.L. Spangler, S. D. Kachman and D.C Ciobanu, Integration of gene expression profiling of hypothalamic arcuate nucleus with genome-wide associations to discover functional variants associated with age at puberty in gilts. Plant and Animal Genome Conference, San Diego, January 13-17, 2018.
|
Progress 10/01/15 to 09/30/16
Outputs
Target Audience:Target audiences include scientists in the same research area, veterinarians, graduate and undergraduate students and swine producers. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Both graduate and undergraduate students are involved in this project that provides great training opportunities. How have the results been disseminated to communities of interest?Journal articles, presentations and posters were presented to regional, national and international meetings. What do you plan to do during the next reporting period to accomplish the goals?The activities for 2017 will continue in the following research areas: - QTL mapping, design of a SNP chip for genomic prediction of important productive traits - Explore the phenotypic and genetic variation of novel phenotypes
Impacts
What was accomplished under these goals?
Our main results were generated in the area of gene, genome annotation and dissection of QTL associated with important productive traits such as susceptibility to Porcine Circovirus 2 (PCV2) and reproductive longevity. Using a combination of genome and RNA sequencing and advanced statistical models we discovered DNA markers with predictive potential to be used across different populations of swine. The impact of these results has potential to improve these economical important traits and positively affect the swine industry. (1) Advance the status of reference genomes for all species, including basic annotation of worldwide genetic variation, by broad sequencing among different lines and breeds of animals. Objective 1: Activity ii. Improve draft genome assemblies to close gaps and improve assembly order. In this activity we made improvements in the transcriptome annotation of the proximal end of SSC12. This improvement was driven by the need to fine map a QTL associated with viremia and immune response following experimental challenges with PCV2b. US-MARC provided access to a novel 19Mb scaffold assembled based on Pacific Biosciences long DNA sequencing reads. Using ~ 600 SNPs aligned to the scaffold using BLAT we were able to refine the position of the QTL. Detailed characterization of the QTL region, including protein coding genes prediction algorithms, comparative sequencing, gene ontologies and RNAseq data provided important information for QTL dissection. The potential role of several candidate genes, isoforms and sequence polymorphism were evaluated in subsets of high/low viremic pigs. Objective 1: Activity iii. Coordinate analysis of re-sequencing data to identify SNPs, CNVs, and insertion-deletions, and better annotate gene models within the reference assemblies. Using NIFA funding we sequence the genome of 20 boars (coverage > 20X) representative of both ends of the distribution - late and early expression of puberty and reproductive longevity. This information was used to identify polymorphisms outside the limited capability of Porcine SNP60K Bead Array. Using the same funding, we generated RNAseq data from hypothalamic arcuate nucleus of gilts with different puberty status; age at puberty is an indicator of reproductive longevity, an important economic trait for the swine industry. RNAseq was also performed on alternate homozygote genotypes for the QTL located on SSC12 and exhibited high and low viral load during experimentally infection with PCV2. Alignment results were used for annotation of the QTL region, gene's structure, isoform variation and sequence variation. These data will benefit the entire research community by providing an improved genome assembly and novel sequence variants. (2) Develop strategies to identify and exploit genes and allelic variation that contribute to economically relevant phenotypes and traits, in part through improving functional annotation of the genomes of our species. Objective 2. Activity i) Utilize low, medium, and high-resolution SNP-chips, as well as genome re-sequencing data in genome-wide association studies to identify loci, genes and allelic variants associated with economically important phenotypes. At University of Nebraska we developed population resources that combines genetics of commercial and experimental lines to dissect reproductive longevity and genetic susceptibility to disease. As part of this objective the following activities were performed: - QTL mapping. Using funding from UNL, NIFA and ARD we made improvements in the dissection of genetic variation associated with PCVAD susceptibility and reproductive longevity. Population resources used in our studies are gradually expanded, as well as the phenotypic information. In this activity we used genome re-sequencing, RNAseq, high- and low-density genotyping to uncover functional polymorphisms that influence the variation of targeted traits. - Genome and RNA sequencing provided polymorphisms outside the limited capability of the commercial SNP array/chips. The design of a chip that will include a large number of functional polymorphisms resulted from these projects was initiated. The chip will contain ~90K polymorphisms and will include functional polymorphisms uncovered in these projects but also SNPs represented in common commercial arrays. This chip will be evaluated in different populations.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Trenhaile MD, Petersen JL, Kachman SD, Johnson RK, Ciobanu DC., 2016, Long-term selection for litter size in swine results in shifts in allelic frequency in regions involved in reproductive processes.
Anim Genet. 2016 Oct;47(5):534-42. doi: 10.1111/age.12448.
- Type:
Journal Articles
Status:
Submitted
Year Published:
2017
Citation:
Wijesena HR, CA Lents, J-J. Riethoven, MD Trenhaile-Grannemann, JF Thorson, BN Keel, PS Miller, ML Spangler, SD Kachman, DC Ciobanu, Integration of Genomic Approaches to Uncover Sources of Variation in Age at Puberty and Reproductive Longevity in Sows, Submitted to Journal of Animal Science.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2016
Citation:
E.R. Tosky, T.P.L. Smith, T.B. Engle, E.H. Davis, T.W. Moural, D.J. Nonneman, J. Chin, T.E. Burkey, G.S. Plastow, S.D.
Kachman, D.C. Ciobanu, Investigation and validation of the role of a QTL on SSC12 in PCV2b viremia, Plant and Animal
Genome Conference, January 9 - 13, 2016, San Diego, CA.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2016
Citation:
D.C. Ciobanu, E.R. Tosky, S. Olson, M.D. Trenhaile, C.A. Lents, T.P.L. Smith, D.J. Nonneman, G. Rohrer, J. Chin, P.S.
Miller, T.E. Burkey, M.L. Spangler, J.J. Riethoven, G.S. Plastow, S.D. Kachman, Development of resources and tools for
mapping genetic sources of phenotypic variation, Plant and Animal Genome Conference, January 9 - 13, 2016, San
Diego, CA.
- Type:
Conference Papers and Presentations
Status:
Submitted
Year Published:
2017
Citation:
Hiruni R. Wijesena, Clay A. Lents, Melanie D. Trenhaile - Grannemann, Jean-Jack Riethoven, Brittney N. Keel, Jennifer F. Thorson, Phillip S. Miller, Rodger K. Johnson, Matthew L. Spangler, Stephen D. Kachman, Daniel C. Ciobanu, 2017, The roles of age at puberty and energy restriction in sow reproductive longevity: a genomic perspective, Midwest ASAS Annual Meeting, March 13-15, 2017.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2017
Citation:
H.R. Wijesena, C.A. Lents, B.N. Keel, J.F. Thorson, G.A. Sullivan, M.L. Spangler, S.D. Kachman and D.C. Ciobanu, 2017, Variation In Gene Expression In The Hypothalamic Arcuate Nucleus of Gilts With Differences in Pubertal Status and Subjected To Dietary Energy Restriction, Plant and Animal Genome Conference, San Diego, January 14-18, 2017.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2017
Citation:
D.C. Ciobanu, H.R. Wijesena, C.A. Lents, M.D. Trenhaile - Grannemann, J.J. Riethoven, J.F. Thorson, B.N. Keel, P.S. Miller, M.L. Spangler, S.D. Kachman., 2017, Integration of genomic resources to uncover pleiotropic regions associated with age at puberty and reproductive longevity in sows. Plant and Animal Genome Conference, San Diego, January 14-18, 2017.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2016
Citation:
Daniel C. Ciobanu, Stephen D. Kachman, Sean Olson, Matthew L. Spangler, Melanie Trenhaile, Hiruni R. Wijesena, Phillip Miller, Jean-Jack Riethoven, Clay A. Lents, Jennifer Thorson, Raymond Massey, Timothy J. Safranski, 2016, Translational Genomics for Improving Sow Reproductive Longevity, ADSA ASAS Joint Annual Meetings, Salt Lake City, July 19-23, 2016.
|
Progress 10/01/14 to 09/30/15
Outputs
Target Audience:Target audiences include scientists in the same research area, veterinarians, graduate and undergraduate students and swine producers. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Both graduate and undergraduate students are involved in this project that provides great training opportunities. How have the results been disseminated to communities of interest?Journal articles, presentations and posters were presented to regional, national and international meetings. What do you plan to do during the next reporting period to accomplish the goals?The activities for 2016 will continue in the following research areas: - QTL mapping and genomic prediction of important productive traits - Explore the phenotypic and genetic variation of novel disease phenotypes
Impacts
What was accomplished under these goals?
Our main results were generated in the area of gene, genome annotation and dissection of QTL associated with important productive traits such as susceptibility to Porcine Circovirus 2 (PCV2) and reproductive longevity. We discovered DNA markers with predictive potential to be used across different populations of swine. The impact of these results has potential to improve these economical important traits and positively affect the swine industry. The major accomplishements of 2015 are: Objective 1: Activity ii. Improve draft genome assemblies to close gaps and improve assembly order. In this activity we made substantial improvements in the annotation of the proximal end of SSC12. This improvement was driven by the need to fine map a QTL associated with viremia and immune response following experimental challenges with PCV2b. US-MARC provided access to a novel 19Mb scaffold assembled based on Pacific Biosciences long DNA sequencing reads. Approximately 600 SNPs, previously unmapped or mapped to SSC12 build 10.2, were assigned to the scaffold using BLAT, including the sequence associated with the original QTL. Detailed characterization of the QTL region, including protein coding genes prediction algorithms, gene ontologies and RNAseq data provided initial gene annotation of this scaffold. One of the genes uncovered has a role in innate immune response and represents a candidate for the QTL for viral load mapped previously. Activity iii. Coordinate analysis of re-sequencing data to identify SNPs, CNVs, and insertion-deletions, and better annotate gene models within the reference assemblies. Using NIFA funding we sequence the genome of 20 boars (coverage > 20X) representative of both ends of the distribution - late and early expression of puberty and reproductive longevity. This information is currently used to identify polymorphisms outside the limited capability of Porcine SNP60K Bead Array. Using the same funding, we generated RNAseq data from hypothalamic arcuate nucleus of gilts with different age at puberty; age at puberty is an indicator of reproductive longevity, a great economic trait of swine industry. These data will benefit the entire research community by providing an improved genome assembly and novel sequence variants. Objective 2. Activity i) Utilize low, medium, and high-resolution SNP-chips, as well as genome re-sequencing data in genome-wide association studies to identify loci, genes and allelic variants associated with economically important phenotypes. At University of Nebraska we developed population resources that combines genetics of commercial and experimental lines to dissect reproductive longevity and genetic susceptibility to disease. As part of this objective the following activities were performed: - QTL mapping. Using funding from UNL, NIFA and Genome Canada we made improvements in the dissection of genetic variation associated with PCVAD susceptibility and reproductive longevity. Population resources used in our studies are gradually expanded, as well as the phenotypic information. In this activity we used genome re-sequencing, RNAseq, high- and low-density genotyping to uncover functional polymorphisms that influence the variation of targeted traits. - Genome analysis of the selection sweeps for litter size. Regions that displayed substantial changes in SNP heterozygosity and allelic frequency between populations and haplotypes that are likely under selection in Nebraska Index Line (NIL) were identified. The NIL originated from commercial crossbreds and was selected for increased litter size for many generations. Some of these regions overlapped major QTL for litter size identified by genome-wide association studies. One of these regions included P2X3R, a gene that plays a role in implantation and sustained release of hormones associated with reproductive processes. SNPs identified in this gene were fixed in NIL and polymorphic with nearly equal frequencies in other populations; initial association study underlined suggestive relationship between the genotypes of these SNPs and litter size. - Explore the phenotypic and genetic variation of novel disease phenotypes. We collected the first set of DNA tissue samples from pigs affected by scrotal/umbilical hernias. This condition has important economic impact on the swine industry and due to its complex nature is a good candidate trait for genome-wide association studies. - Dissect diet-dependent associations between DNA markers and economically important traits. Interactions between energy intake and SNPs were analyzed using genome-wide association based on a Bayes B model, and diet-dependent effects of genotypes on age at puberty were identified. Diet-dependent SNPs were responsible for a minor portion of the phenotypic variation (0.29%) in age at puberty compared to the variation explained by the whole SNP panel (28.5%). The eight top diet-dependent SNP effects were identified on SSC6, 7, 8, 11, 14, and 16. Subsequent single-SNP analyses of these markers showed no additive, but SNP x energy intake interaction (P < 0.001) on age at puberty. These SNPs were associated with a specific diet or the direction of the effects were opposite in the two dietary treatments.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
C.A. Kreikemeier, T.B. Engle, K.L. Lucot, S.D. Kachman, T.E. Burkey, D.C. Ciobanu, Genome-wide Analysis of TNF-alpha Response in Pigs Challenged with Porcine Circovirus 2b, Animal Genetics, Aug;46(4):403-9.
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Lucot KL, Spangler ML, Trenhaile MD, Kachman SD, Ciobanu DC., Evaluation of reduced subsets of single nucleotide polymorphisms for the prediction of age at puberty in sows.Anim Genet. 2015 Aug;46(4):403-9
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Morota G, Pe�agaricano F, Petersen JL, Ciobanu DC, Tsuyuzaki K, Nikaido I., An application of MeSH enrichment analysis in livestock. Anim Genet. 2015 Aug;46(4):381-7.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
E.R. Tosky, T.B. Engle, E.H. Davis, S.A. Premaraj, G.S. Plastow, S.D. Kachman, D.C. Ciobanu, SLAII region is associated with variation in Porcine circovirus 2 susceptibility, Plant and Animal Genome Conference, January 10 - 14, 2015, San Diego, CA.
- Type:
Conference Papers and Presentations
Status:
Submitted
Year Published:
2016
Citation:
E.R. Tosky, T.P.L. Smith, T.B. Engle, E.H. Davis, T.W. Moural, D.J. Nonneman, J. Chin, T.E. Burkey, G.S. Plastow, S.D. Kachman, D.C. Ciobanu, Investigation and validation of the role of a QTL on SSC12 in PCV2b viremia, Plant and Animal Genome Conference, January 9 - 13, 2016, San Diego, CA.
- Type:
Conference Papers and Presentations
Status:
Submitted
Year Published:
2016
Citation:
D.C. Ciobanu, E.R. Tosky, S. Olson, M.D. Trenhaile, C.A. Lents, T.P.L. Smith, D.J. Nonneman, G. Rohrer, J. Chin, P.S. Miller, T.E. Burkey, M.L. Spangler, J.J. Riethoven, G.S. Plastow, S.D. Kachman, Development of resources and tools for mapping genetic sources of phenotypic variation, Plant and Animal Genome Conference, January 9 - 13, 2016, San Diego, CA.
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