Progress 11/01/09 to 09/30/13
Outputs
Target Audience: The research was presented to scientists working in the same area, graduate and undergraduate students and producers. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? There are two MS students and one undergraduate (UCARE) involved in this project that provides tremendous opportunities for development and training. How have the results been disseminated to communities of interest? Abstracts and posters were presented at Regional, National and International meetings. What do you plan to do during the next reporting period to accomplish the goals? Continue to expand the population, fine mapping of the functional variants and transfer the knowledge into commercial applications.
Impacts
What was accomplished under these goals?
SNPs located in AVPR1A gene such as G31E and G256D have the potential to reduce age at puberty and improve reproductive longevity, leading to an increase in sow net values in the commercial herds. Genomic prediction results showed that a limited number of SNPs were able to explain proportions of phenotypic variation in AP similar to that obtained from high-density SNP panels.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2013
Citation:
Daniel C. Ciobanu, Stephen D. Kachman, Clay A. Lents, and Timothy J. Safranski (2013) Translational Genomics for Improving Sow Reproductive Longevity, SSR Annual Meeting, Montr�al, Qu�bec, 2226 July 2013.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2013
Citation:
Tart, J. K., Lucot, K. L., Bundy, J. W., Miller, P., Rothschild, M. F., Spangler, M., Garrick, D. J., Johnson, R., Kachman, S., Ciobanu, D. (2013) Genome-wide prediction of pleiotropic regions that influence age.
- Type:
Conference Papers and Presentations
Status:
Submitted
Year Published:
2014
Citation:
Lucot K.L, M.L. Spangler, S.D. Kachman, and D.C. Ciobanu (2014) Genomic prediction of age at puberty in sows using Bayesian methods, ASAS Midwest Meeting, March 17-19, 2014, Des Moines, IA.
- Type:
Conference Papers and Presentations
Status:
Submitted
Year Published:
2014
Citation:
Trenhaile M.D., K.L. Lucot, J.K. Tart, J.W. Bundy, J. F. Thorson, E.M. Keuter, J.R. Wood, M.F. Rothschild, G.A. Rohrer, P.S. Miller, M.L. Spangler, C.A. Lents, R.K. Johnson, S.D. Kachman, and D.C. Ciobanu
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Progress 10/01/11 to 09/30/12
Outputs
OUTPUTS: Traditional selection for sow reproductive longevity results is ineffective due to low heritability and late expression of the trait. The goal of this project was to identify genetic markers associated with puberty, lifetime reproductive and productive traits using a resource population developed at UNL. The gilts were produced in replicates of approximately 90-120 gilts per replicate. Females were maintained through four parities. Females that did not conceive or farrow a litter and those with structural problems were culled. The first seven replicates are completed and three replicates are in various stages of progress (R8-R11). In all replications, gilts received same diet and management until 123 d of age when half of the gilts are placed on experimental energy restricted diet (80% of the ad libitum diet) until breeding. The DNA of the first 10 replicates was isolated and genotyped using Porcine 60K SNP BeadArray. Using this resource population of crossbred gilts, in 2012 we explored pleiotropic sources of variation that influence age at puberty and reproductive longevity. PARTICIPANTS: Individuals working in the project: D. C. Ciobanu (PI), S.D. Kachman (Co-PI), P. S. Miller (Co-PI), D. Garrick (Co-PI), and R. K. Johnson (Co-PI). Graduate students: J. K. Tart, K. Lucot. Research technicians: J Bundy. TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
Of the traits recorded before breeding, only age at puberty significantly affected the probability that females would produce a first parity litter. The genetic variance explained by 1 Mb windows of the sow genome, compared across traits, uncovered regions that influence both age at puberty and lifetime number of parities. Allelic variants of SNPs located on SSC5 (27-28 Mb), SSC 8 (36-37 Mb) and SSC12 (1.2-2 Mb) exhibited additive effects and were associated with both early expression of puberty and a greater than average number of lifetime parities. Combined analysis of these SNPs showed that an increase in the number of favorable alleles had positive impact on reproductive longevity, increasing number of parities with up to 1.36. The region located on SSC5 harbors non-synonymous alleles in arginine vasopressin receptor 1A (AVPR1A) gene, a G-protein coupled receptor associated with social and reproductive behaviors in voles and humans and a candidate for the observed effects. This region is characterized by high levels of linkage disequilibrium in different lines and could be exploited in marker assisted selection programs across populations to increase sow reproductive longevity.
Publications
- Tart J.K., R.K. Johnson, J.W. Bundy, N.N. Ferdinand, A.M. McKnite, J.R. Wood, P.S. Miller, M.F. Rothschild, M.L. Spangler, D.J. Garrick, S.D. Kachman, D.C. Ciobanu (2012) Genome-wide prediction of age at puberty and reproductive longevity in sows (accepted, Animal Genetics).
- Genomic Analysis of Characteristics in Swine Contributing to Sow Longevity, Julie Kathleen Tart (MSc Thesis, University of Nebraska - Lincoln, May 2012)
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Progress 10/01/10 to 09/30/11
Outputs
OUTPUTS: The goal of this project was to identify genetic markers associated with development, reproductive and lifetime productive traits using a resource population developed at UNL. The females used in the experiment are from two genetic line combinations that display differences in lean growth and reproductive rates. Dams of the gilts were either a rotational cross of commercial Landrace x Large White or Nebraska Index Line (L45). Females of both genetic types were inseminated with semen from individual boars with known identities of an unrelated industry maternal line to produce half-sib families of project gilts. The gilts were produced in replicates of approximately 90-120 gilts per replicate. Females were maintained through four parities. Females that did not conceive or farrow a litter and those with structural problems were culled. The first six replicates are completed, two replicates are in various stages of progress (R7-8) and one (R9) will be generated early in 2012. In all replications, gilts received same diet and management until 123 d of age when half of the gilts are placed on an experimental energy restricted diet (80% of the ad libitum diet) until breeding. Genome wide association analysis was performed between marker genotypes and reproductive and lifetime productivity phenotypes using the first four replicates for total number born (TNB), number born alive, number of mummies (MUM) and stillborn (SB) and the first 7 replicated for age at puberty. Proportion of variance for each reproductive and developmental trait accounted for by the 59,608 SNPs was estimated using Bayes C and Bayes B approaches. The probability of a particular SNP to have an effect on a trait was set to 0.005 (1- pi). Line, replicate and diet were used as covariates in the analyses. The genes located in regions associated with clusters of SNPs associated with the largest effects were further characterized using gene ontology information available for human orthologs. The DNA of replicates 6-8 was isolated from tail clips using the DNeasy blood and tissue kit. DNA quantity and quality was assessed by NanoDrop Spectrophotometer and agarose electrophoresis. The DNA samples were genotyped for 62,183 Single Nucleotide Polymorphisms (SNP) using the Porcine 60K SNP BeadArray. A paper was published in UNL Swine Report and several abstracts were submitted, presented and published at ASAS Midwest Conference (Des Moines, March, 2011, 2012) and Plant and Animal Genome Conference (San Diego, CA, January, 2011, 2012). The results were communicated at the NSRP-8 2011 annual meeting during Plant and Animal Genome Conference. PARTICIPANTS: Individuals working in the project: D. C. Ciobanu (PI), S.D. Kachman (Co-PI), P. S. Miller (Co-PI), D. Garrick (Co-PI), and R. K. Johnson (Co-PI). Graduate students: J. K. Tart, J. Bundy. Research technicians: A.M. McKnite TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Variation in age (AP) at puberty in the first 7 replicates (n=852) was associated with the largest marker effects. Tight clusters of SNPs packed in less than 1 Mb and associated with large effects on puberty onset were located on SSC1 (88 Mb and 269 Mb regions), SSC2 (64 Mb), SSC3 (15 Mb), SSC5 (27Mb), SSC6 (85 and 111 Mb), SSC8 (30 Mb), SSC9 (119 Mb), SSC11 (46 Mb) and SSC12 (1 Mb). Some of these regions overlap QTLs previously reported in different populations. Lower marker effects were identified for TNB, NBA, MUM and SB from parity 1 to 4. Most of the regions that had major effects on litter size impacted multiple parities. This is particularly true for the first two parities where the number of analyzed individuals is the largest and provides the best mapping power. Rich clusters of SNPs (>6 windows of 5 SNPs closely packed, usually in less than 1Mb) located on SSC8 (32.9-33.8 Mb), SSC9 (22.0-22.2, 30.4-30.7 Mb), SSC12 (15.9-16.2 Mb) and SSC15 (117.0-117.5 Mb) explained the largest amount of variation of TNB of the first two parities (top 0.5 %). The same regions also influenced the variation in NBA. Clusters of SNPs located on SSC4 (96.4-102.5 Mb), SSC14 (106.3-109.9 Mb) and SSC17 (55.2-57.3 Mb) had a large effect on TNB of three of the four parities analyzed. Major SNP clusters associated with SB at parity 1 were located on multiple regions on SSC1, SSC3, and SSC13 and individual regions on SSC7, SSC14, and SSC15. Variation in MUM at parity 1 was influenced by multiple regions on SSC1, SSC8, SSC9, SSC14 and SSC15 and individual regions on SSC17 and SSC18. A region located on SSC1 appeared to influence the variation of both SB (78.4-79.5 Mb) and MUM (77.9-78.5 Mb) at parity 1. Selection for sow lifetime productivity is difficult due to long generation intervals and the inability to identify, with precision, superior animals early in life. Age at puberty is a trait with moderate heritability and large variance that can serve as an early indicator of lifetime productivity. A significant relationship was detected between genomic prediction of AP and number of parities produced by each sow during lifetime (r=-0.24, p<0.0001). A significant genetic relationship was detected between AP and lifetime litter size: gilts that expressed puberty early in life have an increased lifetime TNB (-0.33, p<0.0001) and NBA (-0.32, p<0.0001). However, detection of puberty onset is labor intensive and cannot be used as a selection tool in commercial herds. Detection of genetic markers for age at puberty has potential to improve sow lifetime productivity and significantly reduce the production cost to swine industry.
Publications
- Julie K. Tart, Nichelle N. Ferdinand, Stephen D. Kachman, Autumn M. McKnite, Xusheng Wang, Phillip S. Miller, Rodger K. Johnson, Daniel C. Ciobanu (2011) Genome-wide association study for puberty onset and lifetime productivity in sows, ASAS Midwest Meeting, Des Moines, IA, March 2011.
- Daniel C. Ciobanu, Nichelle N. Ferdinand, Stephen D. Kachman, Autumn M. McKnite, Simon C. Brewer, Phillip S. Miller, Rodger K. Johnson (2011) Genome-Wide Association Studies of Sow Lifetime Productivity, UNL Swine Report.
- J. K. Tart, N. N. Ferdinand, S. D. Kachman, A. M. McKnite, X. Wang, P. S. Miller, R. K. Johnson, D. C. Ciobanu (2011), Identification of molecular markers associated with puberty onset and sow lifetime productivity using genome wide association studies, Plant and Animal Genome Meeting, San Diego, CA, January 2011.
- D. C. Ciobanu, S.D. Kachman, A.M. McKnite, T.P. Bohnert, N. N. Ferdinand, J. K. Tart, J.A. Galeota, T.W. Moural, S.P. Harris, R. Moreno, X. Wang, S. Brewer, M.F. Rothschild, P. S. Miller and R. K. Johnson (2011), Genome-wide association analyses of reproduction and disease susceptibility in swine, Plant and Animal Genome Meeting, San Diego, CA, January 2011.
- J. K. Tart, J. W. Bundy, N. N. Ferdinand, A. M. McKnite, M. F. Rothschild, P. S. Miller, S. D. Kachman, D. J. Garrick, R. K. Johnson, D. C. Ciobanu, Genome-wide association study of age at puberty and reproductive longevity in two maternal lines of crossbred gilts, Plant and Animal Genome Meeting, San Diego, CA, January 2012 (submitted)
- J. K. Tart, J. W. Bundy, N. N. Ferdinand, A.M. McKnite, M F. Rothschild, D. J. Garrick, P. S. Miller, S. D. Kachman, R. K. Johnson, D. C. Ciobanu, Genome-Wide Association Study for Age at Puberty in Maternal Line Gilts, ASAS Midwest Meeting, Des Moines, IA, March 2012 (submitted).
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Progress 10/01/09 to 09/30/10
Outputs
OUTPUTS: The goal of this project was to identify genetic markers associated with development, reproductive and lifetime productive traits using a resource population developed at UNL. The females used in the experiment are from two genetic line combinations that differ in lean growth and reproductive rates. Dams of the gilts were either a rotational cross of commercial Landrace x Large White or Nebraska Index Line (L45). Females of both genetic types were inseminated with semen of an unrelated industry maternal line to produce half-sib families of project gilts designated as LWxLR or L45X. Semen was collected and packaged from individual boars with known identities. The gilts were produced in replicates and selected randomly for this research at approximately 50 d of age. Females were maintained through four parities. Females that did not conceive or farrow a litter and those with structural problems were culled. The first four replicates are completed, three replicates are in various stages of progress (R5-7) and one (R8) will be generated early 2011. In all replications, gilts received, or will receive, the same diet and management until 123 d of age when half of the gilts were, or will be, placed on an experimental energy restricted diet (80% of the ad libitum diet) until they are moved to the breeding barn. To address the goal of the research a genome based association analysis was performed between marker genotypes and developmental, reproductive and lifetime productivity phenotypes using the first four replicates. Proportion of variance for each reproductive and developmental trait accounted for by the 59,608 SNPs was estimated using a Bayes C approach. The probability of a particular SNP to have an effect on a trait was set to 0.005. Line, replicate and diet were used as covariates in the analyses. Combined analysis of the SNP effects was performed to uncover evidence of pleiotropy. The majority of the SNPs (55,427) are mapped on the latest assemble (build 9) of the porcine reference genome. The location of the remaining SNPs will be identified at the release of the new sequence assemble. The DNA of the Replicate 5 (n=91) was isolated from tail clips using the DNeasy blood and tissue kit DNA quantity and quality was assessed by NanoDrop Spectrophotometer and agarose electrophoresis. The DNA samples were genotyped for 62,183 Single Nucleotide Polymorphisms (SNP) using the Porcine 60K SNP BeadArray that includes 62,183 SNP assays. GenCall data analysis software was used to assign quality scores (GeneCall) for each genotype. A GeneCall genotype quality score of 0.15 was used as a cutoff threshold for removing low quality genotypes. A report of the research was presented during a genomics meeting at National Pork Board. A paper was submitted to UNL Swine Report and several abstracts were submitted to ASAS Midwest Conference (Des Moines, March, 2010) and Plant and Animal Genome Conference (San Diego, CA, January, 2010). The results will be communicated at the NSRP-8 annual meeting during Plant and Animal Genome Conference. PARTICIPANTS: Individuals working at the project: D. C. Ciobanu (PI), S.D. Kachman (Co-PI), P. S. Miller (Co-PI) and R. K. Johnson (Co-PI). Graduate students: N. N. Ferdinand and J. K. Tart. Research technicians: A.M. McKnite TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
Variation in age at puberty was associated with the largest marker effects from all the reproductive traits. Clusters of SNPs associated with large effects on puberty onset were located on SSC1 (21 to 29 Mb and 269 Mb regions), SSC2 (56 and 80 Mb), SSC10 (3 and 61 Mb) and SSC14 (27 Mb). Additional regions with clusters of SNPs associated with lower effects were also detected on two other regions of SSC1 and on SSC3, SSC4, SSC6, SSC8, SSC9, SSC10, SSC11 and SSC18. As expected, lower marker effects were identified for litter size from parity 1 to 4 and lifetime productive traits. Variation of lifetime number of live-born piglets is affected by many environmental factors and potentially influenced by genes located on many swine chromosomes. Clusters of SNPs clearly associated with the largest effects are located on SSC1 (291 Mb), SSC2 (132 Mb), SSC6 (105 Mb), SSC8 (62 Mb), SSC13 (97 Mb), SSC16 (22 and 67 Mb) and SSC17 (55 Mb). Similarly, lifetime number of weaned piglets is affected by several chromosomes but clear clusters of SNPs associated with major effects are located on 7 chromosomes, each with a relatively low effect. Common major loci that affect lifetime number of live-born and number of weaned piglets include those located on SSC1 and SSC17. SNPs located on two regions SSC1 that were associated with variation in age at puberty also appeared to influence lifetime productivity traits, such as total number of live born pigs and total weaning weights. Main clusters of SNPs associated with gilt weaning weights were located on proximal SSC8 and distal SSC11. Loci that potentially influence growth from weaning to treatment initiation (123 d) are located on SSC1, SSC2, SSC3, SSC4, SSC16 and SSC18. Growth during the developmental phase (treatment, from 123 d till breeding) when the gilts were subjected to two feeding regimens appeared to be influenced by regions located on most chromosomes. Loci that potentially influence variation in growth during both developmental phases were identified on distal SSC2 and proximal SSC3. SNPs located on proximal SSC3 appear to influence also lifetime number of weaned pigs. Selection for sow lifetime productivity is difficult due to long generation intervals and the inability to identify, with precision, superior animals at an early age. Discovery of genetic markers associated with lifetime productivity is hampered by the characteristics of the trait, which is measured during the lifetime of the animal, incorporates several traits, and includes significant environmental variation. Age at puberty is a trait with moderate heritability and large variance that can serve as an early indicator of lifetime productivity. However, detection of puberty onset is labor intensive and therefore not used as a selection tool in most herds. Incorporation of the discovered SNP markers associated with puberty onset into breeding programs has the potential to improve sow lifetime productivity and overall swine production. Similarly, identification of genetic markers associated with gilt development could have an impact on sow reproductive longevity and ultimately on lifetime productivity.
Publications
- 1. Julie K. Tart, Nichelle N. Ferdinand, Stephen D. Kachman, Autumn M. McKnite, Xusheng Wang, Phillip S. Miller, Rodger K. Johnson, Daniel C. Ciobanu, Genome-wide association study for puberty onset and lifetime productivity in sows, ASAS Midwest Meeting, Des Moines, IA, March 2011, (accepted). 2. Daniel C. Ciobanu, Nichelle N. Ferdinand, Stephen D. Kachman, Autumn M. McKnite, Simon C. Brewer, Phillip S. Miller, Rodger K. Johnson, Genome-Wide Association Studies of Sow Lifetime Productivity, UNL Swine Report (submitted). 3. J. K. Tart, N. N. Ferdinand, S. D. Kachman, A. M. McKnite, X. Wang, P. S. Miller, R. K. Johnson, D. C. Ciobanu, Identification of molecular markers associated with puberty onset and sow lifetime productivity using genome wide association studies, Plant and Animal Genome Meeting, San Diego, CA, January 2011 (submitted). 4. D. C. Ciobanu, S.D. Kachman, A.M. McKnite, T.P. Bohnert, N. N. Ferdinand, J. K. Tart, J.A. Galeota, T.W. Moural, S.P. Harris, R. Moreno, X. Wang, S. Brewer, M.F. Rothschild, P. S. Miller and R. K. Johnson, Genome-wide association analyses of reproduction and disease susceptibility in swine, Plant and Animal Genome Meeting, San Diego, CA, January 2011 (submitted).
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