Source: UNIVERSITY OF FLORIDA submitted to
IMPROVEMENT OF BEEF CATTLE IN MULTIBREED POPULATIONS: PHASE V
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
0228512
Grant No.
(N/A)
Project No.
FLA-ANS-005150
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Oct 1, 2012
Project End Date
Sep 30, 2017
Grant Year
(N/A)
Project Director
Elzo, MA, AG.
Recipient Organization
UNIVERSITY OF FLORIDA
G022 MCCARTY HALL
GAINESVILLE,FL 32611
Performing Department
Animal Sciences
Non Technical Summary
The structure of the beef cattle industry in the United States in general, and in Florida in particular, is primarily based on crossbreeding. Although official figures are unavailable, it could be conservatively estimated that over 80% of beef cattle marketed in the US are crossbred. National beef cattle genetic improvement programs are still largely based on phenotypic and pedigree information, and continue to be the responsibility of breed associations. Genomic information has begun to be used as a complementary source of information, but it has yet to be fully incorporated into national beef cattle evaluation procedures. Although current national beef cattle multibreed genetic evaluation procedures utilize records from purebred and crossbred animals, genetic prediction models consider only fixed additive and nonadditive genetic effects and random additive genetic effects. Because random nonadditive genetic effects are not included, individual sires cannot be compared for their crossbred combining ability. On the other hand, the development of low and high density marker chips such as the Illumina GoldenGate Bovine3K and the IlluminaSNP50 Beadchips have made possible the use of genomic information for genetic predictions. The current high cost of these high density chips has prevented their widespread use, but their cost is expected to decrease in the future. These chips have the potential to revolutionize genetic evaluation. Models and procedures that allow the use of genotypes, phenotypes and pedigree information have been developed and evaluated primarily using additive models in single-breed cattle populations, or in multibreed populations treated as single-breed populations. Comprehensive analyses of multibreed populations that include a variety of economically relevant traits, and population structures and sizes both within and across countries have yet to be conducted. This project intends to develop models and procedures that utilize genomic, phenotypic, and pedigree information for the evaluation of animals in simple and complex multibreed populations. Because computations can increase substantially in complex multibreed populations, alternative simplifying assumptions will be explored, among them grouping of base breeds, evaluation of animals for functions of traits resulting from the combination of several individual traits, and assumptions relative to homogeneity of genetic parameters across breed groups. The genomic and genomic-polygenic models to be developed are expected to improve our ability to identify the best animals for purebred and crossbred matings for single traits and for multiple economically relevant traits under a variety of environmental conditions.
Animal Health Component
(N/A)
Research Effort Categories
Basic
(N/A)
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3033310108030%
3033320108015%
3033399108055%
Knowledge Area
303 - Genetic Improvement of Animals;

Subject Of Investigation
3320 - Meat, beef cattle; 3310 - Beef cattle, live animal; 3399 - Beef cattle, general/other;

Field Of Science
1080 - Genetics;
Goals / Objectives
Objectives: 1)Development of models and procedures to improve the genomic and polygenic ability, accuracy of prediction, selection, and mating strategies of straightbred and crossbred cattle in national and international multibreed populations for economically important traits under multiple environmental conditions. 2)Development of applied genomic and polygenic economic indicators to determine the value of straightbred and crossbred cattle from national and international multibreed populations for functions of traits under multiple environmental conditions. Expected Outputs: New models and computational procedures for the prediction of additive and nonaddive polygenic and genomic effects in multibreed populations. Refereed and non-refereed publications. Presentations to meeetings and conferences. Development of software. Training of graduate students.
Project Methods
The research procedure during Phase V will, as in previous phases of this project, integrate theoretical, computational, experimental, biological and applied aspects. Phenotypic information on reproduction, growth, carcass, meat palatability, and health will be obtained from existing accumulated multibreed data sets, and newly collected experimental and field data. Multibreed field data will be from national and international organizations as part of collaborative agreements. Datasets currently available include Brangus phenotypic (growth), pedigree, and genomic information from New Mexico State University, Montana multibreed cattle population dataset from Brazil (growth, ultrasound), Colombian beef, dairy, and buffalo populations (ASOCEBU, Antioquia, Narino, Monteria), and Thai dairy and beef cattle populations (DPO, 3 cooperatives, private herds; health, reproduction, management, nutrition, growth, carcass, dairy, socio-economic data). Datasets from other national and international organizations will be requested as needed. National experimental phenotypic data will come primarily from the Angus-Brahman multibreed herd of the University of Florida. Additional phenotypic information will be obtained from national and international populations involved in research collaborations with the University of Florida (e.g., Colorado State University, Texas A&M University, the Meat Animal Research Center). Genomic data will be obtained from animals in the Angus-Brahman multibreed herd of the University of Florida as funding permits. In addition, genomic information will be obtained from other multibreed populations as part of national and international collaborative projects (e.g., Colorado State University, the Meat Animal Research Center, Kasetsart University in Thailand). Models and computational strategies for the prediction of genetic, genomic, and combined genetic-genomic values and estimation of covariance components in completely diallel and incompletely diallel multibreed populations of any number base breeds will be developed. The general form of genetic models will be similar to those used in previous phases of this project, i.e., it will contain multibreed contemporary group, group environmental effects, additive group genetic effects, nonadditive group genetic effects, additive animal genetic effects, nonadditive animal genetic effects, permanent environmental effects, and residual. The general form of multibreed genomic models will be similar to the general form of multibreed genetic models, but it will contain multibreed additive and nonadditive random genomic effects instead of additive and nonadditive random animal genetic effects. The general form of multibreed genetic-genomic models will be a combination of the general form for genetic and genomic models. Direct and maternal effects will be considered for additive and nonadditive genetic and genomic effects, and for permanent environmental effects. Models will account for heterogeneity of variances and covariances across breeds and breed group combinations for additive and nonadditive genetic and genomic, and environmental random effects.

Progress 10/01/16 to 09/30/17

Outputs
Target Audience:Scientists Graduate Students Producers Industry Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?These activities increased the level of national and international cooperation, and contributed to the training of 9 PhD and 1 MS national and international students. How have the results been disseminated to communities of interest?Refereed and non-refereed publications, presentations at scientific conferences and meetings with stakeholders and producers. What do you plan to do during the next reporting period to accomplish the goals?Continue with the workplan for each of the research areas in beef cattle and dairy cattle in the US and Thailand. Increase the scope of national and international collaborations. Train additional graduate students and research scholars. Continue efforts to secure additional funding for these various activities.

Impacts
What was accomplished under these goals? 1) Phenotypes: Beef (reproduction, growth, ultrasound, carcass, meat palatability) and dairy (reproduction and production) data collection and editing from multibreed populations in Thailand, and USA; 2) Updating of UF MAB and Brahman databases for reproduction, survival, growth, ultrasound, carcass, and meat palatability with 2017 information; 3) Construction of a Florida Brahman database with growth, ultrasound, carcass, and meat palatability traits with information from 8 Brahman breeders and data from the American Brahman breeders Association; 4) Tissue samples from 320 calves and sires from the multibreed Angus-Brahman (MAB) and Brahman (BRA) herds, and 797 calves, sires, and dams from 6 Florida Brahman breeders; 5) Extraction of DNA from 3592 MAB and Brahman calves, sires, and dams to be genotyped with either GeneSeek GGPHD250k or GeneSeek50k; 6) Upgrading of FORTRAN software for beef and dairy cattle editing of phenotypes, genotypes, and pedigree data and construction of input data files for imputation (3k, 9k, 20k, 26k, 80k, 150k, 250k; Findhap; FImpute) and for genomic-polygenic evaluation (BLUPF90); 7) Upgrading of SAS programs for editing of reproduction, growth, ultrasound, carcass, and meat palatability traits; 8) Estimation of genetic parameters and genomic-polygenic predictions for 4 reproduction traits, 9 ultrasound and carcass traits, and 2 tenderness traits for animals in the UF MAB, UF BRA, and Florida Brahman herds represented in the accumulated Florida MAB-BRA dataset; 9) Theoretical research on statistical genomics to improve the estimation of allele frequencies, breed composition, variance components, and prediction of additive genetic values; 10) Collaboration with Thai researchers on: a) Genomic-polygenic predictions, SNP marker associations, enriched pathway analyses, and protein-protein networks in multibreed dairy populations using GeneSeek GGPLD 9k, 20k, 26k, and GGPHD80k chips; b) Semen characteristics and growth traits of AI sires in the Thai multibreed dairy cattle population. Products of these collaborations: 1) Estimation of genetic parameters, genomic-polygenic predictions, SNP predictions, and SNP variances for three sets of traits in the Florida MAB-BRA population. Sets and traits were: a) Reproduction set (yearling weight adjusted to 305 days of age (YW), reproductive tract score (RTS), age at first calving (AFC), and calving interval (FCI); b) Ultrasound-carcass set (ultrasound weight (UW), ultrasound ribeye area (UREA), ultrasound fat (UBF), ultrasound percent intramuscular fat (UPIMF), slaughter age (SLA), hot carcass weight (HCW), ribeye area (REA), backfat thickness (FAT), and marbling score (MAR)); and c) Tenderness set (Warner-Bratzler shear force (WBSF) and tenderness score (TEND)). Number of animals with one or more phenotypic records was 15,637 (9,327 Brahman and 6,310 Angus and Brahman-Angus crossbreds), and the number of animals in the pedigree files was 23,750 (16,818 Brahman and 6,932 Angus and Brahman-Angus crossbreds). Genotypic data were from 782 Brahman, Brahman-Angus, and Angus cattle from the UF MAB and Brahman herds genotyped with GeneSeek GGP F250k chip. As expected for quantitative traits determined by large numbers of genes, most SNP markers had small effects and variances for all traits. 2) Development of novel statistical methods for point estimation and prediction that incorporate genomic information into a series of relevant genetics problems. First, decision theory was used to derive admissible-minimax estimators of allele frequencies with appealing statistical and biological properties. In particular, it was proven that some of them have uniformly smaller variance than the maximum likelihood estimator. The next problem was the development of statistical models to carry out simultaneous prediction of additive genetic values in several populations accounting for heterogeneity of marker allele substitution affects and allele frequencies as well as randomness of genotypes. A hierarchical Bayes approach was adopted. To address the adequacy of accounting for heterogeneity across populations, approximate algebraic expressions for Bayes factors and fractional Bayes factors were derived using the Laplace approximation. Subsequently, the theory of concentration and covariance graph models was introduced in the context of genome-wide prediction as a means of modelling correlated marker allele substitution effects partially (concentration graph models) or marginally (covariance graph models). This theory was developed to estimate the covariance or the precision matrix of an observable p-dimensional vector-valued random variable using a sample of size N. However, in genome-wide prediction the target is to estimate the covariance or the precision matrix of an unobservable p-dimensional vector-valued random variable, typically using a single vector containing phenotypes. Thus, methods to overcome this problem were developed; the outputs were Bayesian and frequentist formulations to account for correlated marker effects in genomic prediction. 3) Association between significant SNP for first-lactation 305-d milk (MY) and fat yields (FY) and genes accounting for population structure using all additive relationships and constructing genetic groups with either SNP genotypic information or expected breed composition in the Thai multibreed dairy cattle population. Significant SNP markers were used to identify genes using R package Map2NCBI. Molecular function and biological processes of genes identified by significant SNP markers located inside or within 2,500 bp of these genes were obtained via program PANTHER. Both models yielded identically high correlations between number of significant SNP and number of genes per chromosome for MY (r = 0.97) and FY (r = 0.99). Genes associated with MY and FY were primarily involved in binding and catalytic activities as well as in cellular and metabolic processes. 4) Effect of percent Brahman genetics on Warner-Bratzler shear force (WBSF), desmin and troponin-T (TnT) degradation, hydroxylysyl pyridinoline (HP) crosslink content, and perimysial collagen melting temperature. Steers (n = 131) were harvested at 1.27 cm of backfat thickness and assigned to 4 groups: 6/32 or less, 12/32, 14/32 to 18/32, and 23/32 to 32/32 Brahman. As Brahman % increased: a) WBSF increased (linear, P = 0.01); b) tenderness score decreased (less tender) and connective tissue score increased (more connective tissue) (linear, P = 0.01); c) amount of degraded desmin (38 kDa) and TnT (34 and 30 kDa) decreased (linear, P < 0.03), and amount of immunoreactive 36 kDa TnT increased (linear, P = 0.04). Brahman % had no effect (P = 0.14) on HP crosslink content, but tended to increase (P = 0.07) perimysial collagen melting temperature as the percent Brahman increased. The percentage of Brahman genetic influence was positively correlated to WBSF (r = 0.25), 36 kDa immunoreactive TnT (r = 0.26), and perimysial collagen melting temperature (r = 0.25; P = 0.01). Sensory panel tenderness (r = -0.44), juiciness (r = -0. 26), and connective tissue scores (r = -0.63), 38 kDa degraded desmin (r = -0.34), 34 (r = -0.36) and 30 (r = -0.29) kDa degraded TnT, and HP collagen crosslinks (r = -0.20) were negatively correlated to percent Brahman % (P < 0.03). Increasing Brahman % in steers negatively affected tenderness partially through a reduction in degradation of desmin and TnT.

Publications

  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Jaichansukkit, T.?, T. Suwanasopee, S. Koonawootrittriron, P. Tummaruk, and M. A. Elzo. 2017. Effect of daily fluctuations in ambient temperature on reproductive failure traits of Landrace and Yorkshire sows under Thai tropical environmental conditions. Trop. Anim. Health Prod. 49:503-508.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Laodim, T. *, M. A. Elzo, S. Koonawootrittriron, T. Suwanasopee, and D. Jattawa. 2017. Identification of SNP markers associated with milk and fat yields in multibreed dairy cattle using two genetic group structures. Livest. Sci. 2016:95-104.
  • Type: Books Status: Published Year Published: 2017 Citation: Koonawootrittriron, S., M. Elzo, T. Suwanasopee, C. Chaimongkol, T. Sainui, T. Tongprapi, and T. Ralukmun. 2017. D.P.O. Sire & Dam Summary 2017. Dairy Farming Promotion Organization, Ministry of Agriculture and Cooperatives of Thailand, Bangkok. p 1- 106.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Elzo, M. A., R. G. Mateescu, D. D. Johnson, T. L. Scheffler, J. M. Scheffler, C. Carr, D. O. Rae, J. G. Wasdin, M. D. Driver and J. D. Driver. 2017. Genomic-polygenic and polygenic predictions for nine ultrasound and carcass traits in Angus-Brahman multibreed cattle using three sets of genotypes. Livest. Sci. 202:58-66.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Martinez, C. A. *, K. Khare, S. Rahman, and M. A. Elzo. 2017. Modelling correlated marker effects in genome-wide prediction via Gaussian concentration graph models. J. Theor. Biol. 437:67-78.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Martinez, C. A. *, K. Khare, A. Banerjeee, and M. A. Elzo. 2017. Joint genome-wide prediction in several populations accounting for randomness of genotypes: A hierarchical Bayes approach. II: Multivariate spike and slab priors for marker effects and derivation of approximate Bayes and fractional Bayes factors. J. Theor. Biol. 417:131-141.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Martinez, C. A. *, K. Khare, A. Banerjeee, and M. A. Elzo. 2017. Joint genome-wide prediction in several populations accounting for randomness of genotypes: A hierarchical Bayes approach. I: Multivariate Gaussian priors for marker effects and derivation of the joint probability mass function of genotypes. J. Theor. Biol. 417:8-19.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Martinez, C. A.*, K. Khare, S. Rahman, and M. A. Elzo. 2017. Gaussian covariance graph models accounting for correlated marker effects in genome-wide prediction. J. Anim. Breed. Genet. 134:412-421.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Noppibool, U.*, M. A. Elzo, S. Koonawootrittriron, and T. Suwanasopee. 2017. Genetic correlations between first parity and accumulated second to last parity reproduction traits as selection aids to improve sow lifetime productivity. Asian-Australasian J. Anim. Sci. 30:320-327.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Wang, J., Y. Hu, M. A. Elzo, Y. Shi, A. Jia, S. Chen, and S. Lai. 2017. Genetic effect of Myf5 in rabbit meat quality traits. J. Genet. 96:673-679.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Wang, J., Y. Shi, M. A. Elzo, Y. Su, X. Jia, S. Chen, and S. Lai. 2017. Myopalladin gene polymorphism is associated with rabbit meat quality traits. Italian J. Anim. Sci. 16:400-404.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Wongpom, B.*, S. Koonawootrittriron, M. A. Elzo, and T. Suwanasopee. 2017. Milk Yield, Fat Yield and Fat Percentage associations in a Thai Multibreed Dairy Population. Agric. Nat. Res. 51:218-222.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Yodklaew, P. ?, M. A. Elzo, S. Koonawootrittriron, and T. Suwanasopee. 2017. Genome-wide association study for lactation characteristics, milk yield, and age at first calving of dairy cattle in Thailand. Agric. Nat. Res. 51:223-230.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Jattawa, D. *, S. Koonawootrittriron, M. A. Elzo, and T. Suwanasopee. 2017. Genomic Evaluation using different Pedigree records in Thai dairy Population. Proc. Sixth National Animal Science Conference. Agricultural Sci. J. 48 (Suppl. 2): 344-351.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Sarakul, M. *, S, Koonawootrittriron, T. Suwanasopee, and M. A. Elzo, 2017. Factors affecting semen quantity and quality of dairy bulls raised under Thai tropical conditions. Proc. Sixth National Animal Science Conference. Agricultural Sci. J. 48 (Suppl. 2): 292-299.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Fan, P. *, C. Nelson, M. A. Elzo, K. C. Jeong. 2017. Understanding cross-talk between host and gut microflora to enhance health and growth performance. 10th Int. Conf. Nutraceut. & Func. Foods, Gunsan, Jeonbuk, South Korea, October 22-25, 2017.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Hamblen, H. M. *, J. D. Leal, M. A. Elzo, D. D. Johnson, C. C. Carr, T. Scheffler, J. M. Scheffler, and R. G. Mateescu. 2017. Association of a single nucleotide polymorphism in ?-calpain gene with Warner-Bratzler shear force in a crossbred Brahman-Angus population. Amer. Meat Sci. Assoc., Texas A&M University, College Station, TX, June 16-21, 2017.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Elzo, M. A., R. Mateescu, D. D. Johnson, T. L. Scheffler, J. M. Scheffler, C. Carr, D. O. Rae, J. G. Wasdin, M. D. Driver, and J. D. Driver. 2017. Multibreed Angus-Brahman genetic parameters and predictions for nine ultrasound and carcass traits using three genomic-polygenic models and one polygenic model. J. Anim. Sci. 95:96-96.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Jattawa, D. ?, S. Koonawootrittriron, M. A. Elzo, and T. Suwanasopee. 2017. Comparison of Genomic-Polygenic Evaluations Using Random Regression Models with Legendre Polynomials and Splines for Milk Yield and Fat Percentage in Thai Multibreed Dairy Cattle. J. Anim. Sci. 95:79-80.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Laodim, T. *, M. A. Elzo, S. Koonawootrittriron, and T. Suwanasopee. 2017. Population structure in a Thai multibreed dairy cattle population. J. Anim. Sci. 95:79-79.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Noppibool, U.*, S. Koonawootrittriron, M. A. Elzo, and T. Suwanasopee. 2017. Genetic Analysis of Production Traits in Different Parities Using Multiple Trait Animal Models in a Thai Landrace-Yorkshire Swine Population. J. Anim. Sci. 95:104-104.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Sae-tiao, T. *, S. Koonawootrittriron. T. Suwanasopee and M.A. Elzo. 2017. Trend for Diurnal Temperature Variation and Relative Humidity and Their Impact on Milk Yield of Dairy Cattle in Tropical Climates. J. Anim. Sci. 95:248-248.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Jattawa, D. *, S. Koonawootrittriron, T. Suwanasopee and M. A. Elzo. 2017. Genomic estimated breeding values of Thai and foreign sires for the improvement of milk production potential of dairy cattle in Thailand. Proc. Animal Genetic Improvement and Biotechnology Conference, Thailand, July 13-14, 2017, p 30.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Konkruea, T. *, S. Koonawootrittriron, T. Suwanasopee and M. A. Elzo. 2017. Accuracy of genomic-polygenic breeding values for age at first calving and milk yield in Thai multibreed dairy cattle population. Animal Genetic Improvement and Biotechnology Conference, Thailand, July 13-14, 2017, p 29.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Sae-tiao, T. *, S. Koonawootrittriron, T. Suwanasopee and M. A. Elzo. 2017. Milk production response to changes in ambient temperature and humidity of multibreed dairy cattle in Thailand. Animal Genetic Improvement and Biotechnology Conference, Thailand, July 13-14, 2017, p 26.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Sarakul, M. *, S. Koonawootrittriron, T. Suwanasopee and M. A. Elzo. 2017. Genetic Parameter for Semen production traits of artificial insemination bulls raised under Thai tropical conditions. Animal Genetic Improvement and Biotechnology Conference, Thailand, July 13-14, 2017, p 27.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Wongpom, B. *, S. Koonawootrittriron, T. Suwanasopee and M. A. Elzo. 2017. Genomic parameters for milk yield and fat yield in a multibreed dairy cattle population in Central Thailand. Animal Genetic Improvement and Biotechnology Conference, Thailand, July 13-14, 2017, p 28.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Gobena, M.*, J. D. Leal, M. A. Elzo, and R. G. Mateescu. 2017. Predicting breed composition in an Angus-Brahman crossbred population using genomic data. P0044 25th Plant and Animal Genome Conference, San Diego, CA, January 14-18, 2017.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Leal, J. D.*, M. A. Elzo, D. D. Johnson and R. G. Mateescu. 2017. Polymorphism association in �-calpain and calpastatin genes with tenderness in a crossbred Brahman-Angus population. P0428 25th Plant and Animal Genome Conference, San Diego, CA, January 14-18, 2017.


Progress 10/01/12 to 09/30/17

Outputs
Target Audience:Scientists Graduate Students Producers Industry Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?These activities increased the level of national and international cooperation, and contributed to the training of 16PhD and 3MS national and international students. How have the results been disseminated to communities of interest?Over 250 refereed and non-refereed publications, presentations at scientific conferences and meetings with stakeholders and producers. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? 1) System of beef (reproduction, growth, ultrasound, carcass, meat palatability) and dairy (reproduction and production) phenotypecollection and editing from multibreed populations; 2) UF Multibreed Angus-Brahman (MAB)and Brahman (BRA) databases for reproduction, survival, growth, ultrasound, carcass, and meat palatability; 3)Florida Brahman database with growth, ultrasound, carcass, and meat palatability traits with information from eight Brahman breeders and data from the American Brahman breeders Association; 4) Tissue samples from 4,488 animals from the UF MAB, UF BRA, and eight Florida Brahman breeder herds; 5) DNA from 3592 MAB and Brahmancalves, sires, and damsgenotyped with either GeneSeek GGPHD250k or GeneSeek50k; 6) FORTRAN software for beef and dairy cattle editing of phenotypes, genotypes, and pedigree data and construction of input data files for imputation (3k, 9k, 20k, 26k, 80k, 150k, 250k; Findhap; FImpute) and for genomic-polygenic, genomic, and polygenic evaluation (BLUPF90) and variance component estimation (AIREMLF90); 7) SAS programs for editing of reproduction, growth, ultrasound, carcass, and meat palatability traits; 8) Estimation of genetic parameters and genomic-polygenic and polygenicpredictions for growth traits, reproduction traits,ultrasound, carcass traits, andtenderness traits for animals in US Multibreed Angus-Brahman and Brahman populations; 9) Theoretical research on statistical genomics to improve the estimation of allele frequencies, breed composition, variance components, and prediction of additive genetic values; 10) Genomic-polygenic, genomic, and polygenic predictions and variance components, genetic trends, SNP marker associations, enriched pathway analyses, and protein-protein networks in multibreed beef populations in the US and dairy populations in Thailand using GeneSeek GGP9k, GGP20k, GGP26k, GGPHD80k, and GGPHD250k chips; 11) Genetic and genomic research collaborations (predictions, variance components) for a variety of reproduction and production traits in beef cattle, dairy cattle, buffaloes, sheep, and pigs with researchers in Colombia, Ethiopia, Mexico, Pakistan, Thailand; 12) Collaboration with UF researchers from meat science, veterinary medicine, and microbiology to conduct genomic-polygenic analyses for growth, ultrasound, carcass, meat palatability, and E. Coli O157 using animals from the UF MAB and Brahman herds.

Publications


    Progress 10/01/15 to 09/30/16

    Outputs
    Target Audience:Scientists Graduate Students Producers Industry Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?These activities increased the level of national and international cooperation, and contributed to the training of 7 PhD and 1 MS national and international students. How have the results been disseminated to communities of interest?Refereed and non-refereed publications, presentations at scientific conferences and meetings with stakeholders and producers. What do you plan to do during the next reporting period to accomplish the goals?Continue with the workplan for each of the research areas in beef cattle, dairy cattle, and swine in the US, Colombia, and Thailand. Increase the scope of national and international collaborations. Train additional graduate students and research scholars. Continue efforts to secure additional funding for these various activities.

    Impacts
    What was accomplished under these goals? 1) Phenotypes: Beef (reproduction, growth, ultrasound, carcass, meat palatability), dairy (reproduction and production), and swine data collection and editing from multibreed populations in Colombia, Thailand, and USA; 2) Tissue samples: a) Blood samples from 314 calves from the multibreed Angus-Brahman (MAB) population, and semen from 15 sires; b) Genotypes from 785 MAB sires and calves with GeneSeek GGPHD250k; 3) Collaboration with Colombian researchers on genomic-polygenic evaluation of dairy cattle at high altitudes in Colombia; 4) Upgrading of FORTRAN software for beef and dairy cattle editing of phenotypes, genotypes, and pedigree data and construction of input data files for imputation (3k, 9k, 20k, 26k, 80k, 150k, 250k; Findhap; FImpute) and for genomic-polygenic evaluation (BLUPF90, GS3, QXPAK); 5) Upgrading of SAS programs for editing of reproduction, growth, ultrasound, carcass, and meat palatability traits; 6) Maintenance and updating of MAB and Brahman databases for reproduction, survival, growth, ultrasound, carcass, and meat palatability with 2016 information; 7) Collaboration with Thai researchers on imputation accuracy, genomic-polygenic, genomic, and polygenic evaluation of Thai multibreed dairy populations using GeneSeek GGPLD 9k, 20k, 26k, and GGPHD80k chips; 8) Collaboration with Thai researchers on genetic parameter estimation and evaluation in swine for length of productive live, lifetime production, and lifetime efficiency in Thailand; 9) Collaboration with researchers from meat science, veterinary medicine, and microbiology to conduct genomic-polygenic analyses for reproduction, growth, ultrasound, carcass, meat palatability, and E. Coli O157 in UF MAB and Brahman cattle populations. Products of these collaborations: 1) Genomic-polygenic and polygenic parameters and estimates of variance components for 365-d yearling weight (YW), yearling reproductive tract score (RTS), age at first calving (AFC), and first calving interval (FCI) in an Angus-Brahman multibreed population using single-step genomic-polygenic (GPM) and polygenic models (PM). Numbers of phenotypic records were 1,758 for YW, 381 for RTS, 1,385 for AFC, and 985 for FCI. The pedigree file had 6,869 calves, sires, and dams, and genotype file contained 115,711 actual and imputed GGPHD150k SNP markers from 1,547 animals. Heritabilities were slightly higher for GPM than PM (0.47 vs. 0.45 for YW, 0.31 vs. 0.30 for RTS, 0.14 vs. 0.12 for AFC, and 0.31 vs. 0.29 for FCI). Genetic correlations were positive between YW and RTS (GPM: 0.55; PM: 0.60), negative between RTS and AFC (GPM: -0.22; PM: -0.55) and between AFC and FCI (GPM: -0.68; PM: -0.67), and near zero for all other trait pairs. The similarity between GPM and PM heritabilities and genetic correlations indicated that the 115,711 GGPHD150k SNP markers added little additional information to that contained in the pedigree. 2) Variance components, genetic parameters, EBV, accuracies, and rankings for nine ultrasound and carcass traits in a multibreed Angus-Brahman population using three genomic-polygenic models and one polygenic model (PM). The genomic-polygenic models used the complete GeneSeek GPF250k SNP set (GPM), top 5% SNP (GPMR1), and 5% SNP evenly spread across the genome (GPMR2). Yearling ultrasound traits were weight (UW), ribeye area (UREA), backfat (UFAT), and percent intramuscular fat (UPIMF). Carcass traits were slaughter age (SLA), hot carcass weight (HCW), ribeye area (REA), backfat thickness (FAT), and marbling score (MAR). Comparable heritabilities were obtained with GPM and PM for UW (GPM: 0.54 ± 0.05; PM: 0.51 ± 0.05), UREA (GPM: 0.36 ± 0.03; PM: 0.34 ± 0.03), UFAT (GPM: 0.12 ± 0.02; PM: 0.11 ± 0.02), UMPIMF (GPM: 0.34 ± 0.03; PM: 0.30 ± 0.03), SLA (GPM: 0.59 ± 0.07, PM: 0.61 ± 0.06), HCW (GPM: 0.58 ± 0.06, PM: 0.52 ± 0.07), REA (GPM: 0.48 ± 0.04, PM: 0.45 ± 0.05), FAT (GPM: 0.41 ± 0.05, PM: 0.30 ± 0.05), and MAR (GPM: 0.56 ± 0.07, PM: 0.51 ± 0.08). Additive genetic correlations between pairs of ultrasound and carcass traits were all between -0.31 and 0.81. High similarity existed among predicted EBV and accuracies from GPM, GPMR1, and GPMR2 as well as high-rank correlations for sires, dams, and progenies. This indicated that the two reduced genotype sets were appropriate alternatives to the complete GPF250k set for genomic-polygenic evaluation and selection in this multibreed Angus-Brahman population. 3) Accuracy of imputation from low density (LDC) to moderate density SNP chips (MDC) in a Thai Holstein-Other multibreed dairy cattle population. Dairy cattle with complete pedigree information (n = 1,244) from 145 dairy farms were genotyped with GeneSeek GGP20K (n = 570), GGP26K (n = 540) and GGP80K (n = 134) chips. After checking for single nucleotide polymorphism (SNP) quality, 17,779 SNP markers in common between the GGP20K, GGP26K, and GGP80K were used to represent MDC. Imputation accuracy for the three software packages ranged from 76.79% to 93.94%. FImpute had higher imputation accuracy (93.94%) than Findhap (84.64%) and Beagle (76.79%). 4) Estimates of variance components, genetic parameters, prediction accuracies, and rankings of animals for 305-d milk yield (305-d MY) and 305-d fat percentage (305-d FP) from random regression genomic-polygenic (RRGM) and random regression polygenic (RRPM) models. In addition, RRGM and RRPM prediction accuracies and rankings were compared with those from a standard cumulative 305-d genomic-polygenic model (SCGM). The dataset contained first-lactation monthly test-day records (69,029 for MY and 29,878 for FY) from 7206 Holstein-upgraded cows located in 761 Thai farms.The RRGM yielded higher additive genetic variances and heritabilities for 305-d MY and 305-d FP than RRPM, whereas correlations between MY and FY were similar in both models. The highest prediction accuracies for both traits were for RRGM, followed by RRPM, and the lowest ones were from SCGM. The higher heritability estimates and higher prediction accuracies for RRGM than for RRPM and SCGM indicated that higher selection responses for 305-d MY and 305-d FP may be achieved in this Thai dairy population by utilizing a random-regression model and genotypic information in addition to phenotypes and pedigree. 5) Estimates of genetic parameters and trends for length of productive life (LPL), lifetime number of piglets born alive (LBA), lifetime number of piglets weaned (LPW), lifetime litter birth weight (LBW), and lifetime litter weaning weight (LWW) in a commercial swine farm in Northern Thailand. Data consisted of 3,109 phenotypic records from 2,271 Landrace (L) and 838 Yorkshire sows (Y) collected from July 1989 to August 2013. heritabilities were medium for all five traits (0.17±0.04 for LPL and LBA to 0.20±0.04 for LPW). Genetic correlations among these traits were high, positive, and favorable (p<0.05), ranging from 0.93±0.02 (LPL-LWW) to 0.99±0.02 (LPL-LPW). Sow genetic trends were non-significant for LPL and all lifetime production traits.Sire genetic trends were negative and significant for LPL (−2.54±0.65 d/yr; p = 0.0007), LBA (−0.12±0.04 piglets/yr; p = 0.0073), LPW (−0.14±0.04 piglets/yr; p = 0.0037), LBW (−0.13±0.06 kg/yr; p = 0.0487), and LWW (−0.69±0.31 kg/yr; p = 0.0365). Dam genetic trends were positive, small and significant for all traits (1.04±0.42 d/yr for LPL, p = 0.0217; 0.16±0.03 piglets/yr for LBA, p<0.0001; 0.12±0.03 piglets/yr for LPW, p = 0.0002; 0.29±0.04 kg/yr for LBW, p<0.0001 and 1.23±0.19 kg/yr for LWW, p<0.0001).

    Publications

    • Type: Journal Articles Status: Published Year Published: 2016 Citation: Mir, R. A., T. A. Weppelmann, M. A. Elzo, S. Ahn, and K. C. Jeong. 2016. Colonization of beef cattle by Shiga toxin-producing Escherichia coli during the first year of life: a cohort study. PLoS One 12(2): e0148518.
    • Type: Journal Articles Status: Awaiting Publication Year Published: 2016 Citation: Noppibool, U.*, S. Koonawootrittriron, M. A. Elzo, and T. Suwanasopee. 2016. Genetic Relationships between Length of Productive Life and Lifetime Production Efficiency in a Commercial Swine Herd in Northern Thailand. Anim. Sci. J. (In Press) [http://dx.doi.org/10.1111/asj.12647]
    • Type: Journal Articles Status: Published Year Published: 2016 Citation: Noppibool, U., M. A. Elzo, S. Koonawootrittriron, and T. Suwanasopee. 2016. Estimation of genetic parameters and trends for length of productive life and lifetime production traits in a commercial Landrace and Yorkshire swine population in Northern Thailand. Asian-Australasian J. Anim. Sci. 29:1222-1228.
    • Type: Journal Articles Status: Published Year Published: 2016 Citation: Royer, A. M., C. Shivers, D. Riley, M. A. Elzo, and M. D. Garcia. 2016. Single nucleotide polymorphisms associated with carcass traits in a population of Brahman and Brahman influenced steers. Gen. Mol. Res. 15(2): gmr.15028280.
    • Type: Journal Articles Status: Published Year Published: 2016 Citation: Wang, J., G. Li, M. A. Elzo, X. Jia, S. Chen, and S. Lai. 2016. Calpastatin gene polymorphism is associated with rabbit meat quality traits. J. Appl. Anim. Res. 45:342-345.
    • Type: Journal Articles Status: Published Year Published: 2016 Citation: Wang, J., P. Xu, S. Li, L. Yan, M. A. Elzo, X. Jia, S. Chen, M. Zhang, and S. Lai. 2016. A single nucleotide polymorphism in CAST gene is associated with meat quality traits in rabbits. Anim. Sci. Pap. Rep. 34: 269-278.
    • Type: Journal Articles Status: Published Year Published: 2016 Citation: Wang, J., Y. Su, M. A. Elzo, X. Jia, S. Chen, and S. Lai. 2016. Comparison of carcass and meat quality traits among three rabbit breeds. Korean J. Food Sci. Anim. Res. 36:84-89.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Phelps, K. J., D. D. Johnson, M. A. Elzo, C. B. Paulk, and J. M. Gonzalez. 2016. Effect of Brahman genetics on myofibrillar protein degradation, collagen crosslinking, and meat tenderness. AMSA 69th Recip. Meat Conf., Angelo State Univ., San Angelo, TX, June 19-22, 2016.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Wright, S., Scheffler, T., Scheffler, J., D. Johnson, M. A. Elzo. 2016. Relating muscle fiber morphometrics and protein degradation to meat quality in a multibreed herd. AMSA 69th Recip. Meat Conf., Angelo State Univ., San Angelo, TX, June 19-22, 2016.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Martinez, C. A., K. Khare, A. Banerjee, and M. A. Elzo. 2016. Accounting for randomness of genotypes in across and single population genome-enabled prediction: A hierarchical Bayes approach. Fifth Int. Conf. Quant. Genet., Madison, WI, June 12-17, 2016.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Leal, J., D. Johnson, M. A. Elzo, and R. Mateescu. 2016. Association of SNPs in calpain and calpastatin genes with meat tenderness in an Angus-Brahman population. Proc. 14th Annual Res. Symp. Anim. Mol. Cell. Biol. Grad. Prog. Univ. Florida, Brooksville, FL, April 15-16, 2016, p 22.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Martinez, C. A.?, K. Khare, A. Banerjee, and M. A. Elzo. 2016. New statistical methods to account for correlated marker effects in genome-wide prediction through Gaussian concentration graph models: Bayesian and Frequentist formulations. 2nd Anim. Sci. Symp., Saint Augustine, FL, October 21-22, 2016.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Elzo, M. A., R. Mateescu, M. G. Thomas, D. D. Johnson, D. O. Rae, J. G. Wasdin, M. D. Driver, and J. D. Driver. 2016. Genomic-polygenic and polygenic parameters and prediction trends for growth and reproduction traits in an Angus-Brahman multibreed population. J. Anim. Sci. 94 (Suppl. 5):151.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Jattawa, D., S. Koonawootrittriron, M. A. Elzo, and T. Suwanasopee. 2016. Genomic and polygenic evaluations for milk and fat yields in Holstein upgraded Thai dairy cattle. J. Anim. Sci. 94 (Suppl. 5):328.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Noppibool, U., S. Koonawootrittriron, M. A. Elzo, and T. Suwanasopee. 2016. Genetic parameters and trends for length of productive life and lifetime production efficiency traits in Thai Landrace and Yorkshire sows. J. Anim. Sci. 94 (Suppl. 5):174.
    • Type: Journal Articles Status: Published Year Published: 2016 Citation: Elzo, M. A., R. Mateescu, M. G. Thomas, D. D. Johnson, C. A. Martinez, D. O. Rae, J. G. Wasdin, M. D. Driver and J. D. Driver. 2016. Growth and reproduction genomic-polygenic and polygenic parameters and prediction trends as Brahman fraction increases in an Angus-Brahman multibreed population. Livest. Sci. 190:104-112.
    • Type: Journal Articles Status: Published Year Published: 2016 Citation: Gebreyohannes, G.*, S. Koonawootrittriron, M. A. Elzo, and T. Suwanasopee. 2016. Estimation of covariance components and genetic parameters using a random regression monthly test-day model in an Ethiopian dairy cattle population. Agric. Nat. Res. 50:64-70.
    • Type: Journal Articles Status: Published Year Published: 2016 Citation: Jattawa, D., M. A. Elzo, S. Koonawootrittriron, and T. Suwanasopee. 2016. Genomic-polygenic and polygenic evaluations for milk yield and fat percentage using random regression models with Legendre polynomials in a Thai multibreed dairy population. Livest. Sci. 188:133-141.
    • Type: Journal Articles Status: Published Year Published: 2016 Citation: Jattawa, D., M. A. Elzo, S. Koonawootrittriron, and T. Suwanasopee. 2016. Imputation Accuracy from Low to Moderate Density Single Nucleotide Polymorphism Chips in a Thai Multibreed Dairy Cattle Population. Asian Australas. J. Anim. Sci. 29:464-470.
    • Type: Journal Articles Status: Published Year Published: 2016 Citation: Kaniyamattam, K., M. A. Elzo, J. B. Cole, and A. De Vries. 2016. A stochastic dynamic dairy model with multi-trait genetics. J. Dairy Sci. 99:8187-8202.


    Progress 10/01/14 to 09/30/15

    Outputs
    Target Audience:Scientists Graduate Students Producers Industry Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?These activities increased the level of national and international cooperation, and contributed to the training of 9 PhD and 2 MS national and international students. How have the results been disseminated to communities of interest?Refereed and non-refereed publications, presentations at scientific conferences and meetings with stakeholders and producers. What do you plan to do during the next reporting period to accomplish the goals?Continue with the workplan for each of the research areas in beef cattle, dairy cattle, and swine in the US, Colombia, and Thailand. Increase the scope of national and international collaborations. Train additional graduate students and research scholars. Continue efforts to secure additional funding for these various activities.

    Impacts
    What was accomplished under these goals? 1) Phenotypes: Beef (reproduction, growth, ultrasound, carcass, meat palatability), dairy (reproduction and production), and swine data collection and editing from multibreed populations in Colombia, Thailand, and USA; 2) Tissue samples: a) Blood and hair samples from 324 calves from the multibreed Angus-Brahman (MAB) population, and semen from 11 sires; b) Genotypes from 238 MAB sires and calves; 3) Collaboration with Colombian researchers on Genomic-polygenic evaluation of dairy cattle at high altitudes in Colombia; 4) Upgrading of FORTRAN software for beef and dairy cattle editing of phenotypes, genotypes, and pedigree data and construction of input data files for imputation (3k, 9k, 20k, 26k, 80k; Findhap2, 3, 4; FImpute) and for genomic-polygenic evaluation (BLUPF90, GS3, QXPAK); 5) Upgrading of SAS programs for editing of growth, ultrasound, carcass, and meat palatability traits; 12) Maintenance and updating of MAB and Brahman databases for reproduction, survival, growth, ultrasound, carcass, and meat palatability information with 2015 information; 4) Collaboration with Libyan researchers on genetic parameter estimation, genetic evaluation, and genetic trends for dairy traits in Libyan Holstein; 5) Collaboration with Thai researchers on imputation accuracy, genomic-polygenic, genomic, and polygenic evaluation of Thai multibreed dairy populations using GeneSeek GGP-LD 9k, 20k, 26k, and GGP-HD (80k) chips; 6) Collaboration with Thai researchers on genetic parameter estimation and genetic evaluation in swine for length of productive live, lifetime production, and lifetime efficiency in Northern Thailand; 7) Collaboration with researchers from meat science, veterinary medicine, and microbiology to conduct genomic-polygenic analyses for growth, ultrasound, carcass, meat palatability, and E. Coli O157 UF MAB and Brahman cattle populations. Products of these collaborations: 1) Multibreed genomic-polygenic and polygenic evaluation of Bos taurus-Bos indicus cattle for growth traits in an Angus-Brahman multibreed population under subtropical conditions. Dataset included 5,300 calves, 293 sires, 1,725 dams. Similar estimates of variance components and genetic parameters with both models. Higher percent Brahman tended to yield higher EBV values for direct birth and weaning weight traits, but lower EBV for postweaning gain direct and birth and weaning weight maternal. Animals with high and low EBV for all traits existed across the Angus-Brahman expected composition spectrum; 2) Genomic-polygenic evaluation of multibreed Angus-Brahman cattle for postweaning ultrasound and weight traits with actual and imputed Illumina50k SNP genotypes. Additive genomic to total genetic variance fractions for postweaning ultrasound traits explained by 46,909 actual and imputed Illumina50k SNP genotypes were 0.17 for ultrasound ribeye area, 0.32 for ultrasound fat thickness, 0.25 for ultrasound percent intramuscular fat, and 0.19 for postweaning weight. Rank correlations between genomic-polygenic and polygenic EBV were higher (0.93 to 0.96) than between genomic-polygenic and genomic EBV (0.81 to 0.94), and between genomic and polygenic EBV (0.66 to 0.81); 3) Evaluation of Animal and Microbial Factors Affecting Prevalence of Shiga Toxin Producing E. coli (STEC) and Cefotaxime Resistance (CefR). Preliminary results based on data from one year indicated that: a) STEC prevalence decreased from birth to yearling across all Angus-Brahman breed groups; b) Bulls, heifers, and steers had similar shedding of Stx1 and Stx2 until one year of age; c) CefR prevalence tended to increase until weaning, then it dropped in yearlings; and d) CefR genes in commensal bacteria were identical to those from human pathogens (bla CTX-M 1, bla CTX-M 15); 4) Studies on statistical genomics to improve genome-wide prediction and variance components estimation in high dimensional problems. Derivation of estimators of allelic frequencies using Bayes and minimax decision rules that were more precise than the usual maximum likelihood estimator. Estimators accounted for random variation in allele frequencies. Development of a series of hierarchical Bayesian models for simultaneous prediction of breeding values and phenotypes as well as estimation of allelic frequencies using data from several populations. Models accounted for random variation of genotypes and allelic frequencies. Bayes factors to compare the proposed models with standard hierarchical Bayesian models were obtained; 5) Genome-Wide Linkage Disequilibrium in a Thai Multibreed Dairy Cattle Population. High levels of LD 16 were found in autosomes, particularly between SNP pairs at distances shorter than 50 kb. The mean of D′ (linkage disequilibrium relative to its maximum) and the square of the correlation coefficient for SNPs separated by 40 to 50 kb were 0.694 and 0.202. The minimum sample size required to obtain accurate measures of LD was 177; 6) Comparison of genetic evaluations for milk yield and fat yield using a polygenic model and 2 three genomic-polygenic models with different sets of SNP genotypes in Thai multibreed 3 dairy cattle. Estimates of variance components, heritabilities and prediction accuracies for milk and fat yields from genomic-polygenic models using actual plus imputed 80k genotypes with Findhap or FImpute were similar and higher than genomic-polygenic models using actual 7k genotypes, and the lowest ones were those from the polygenic model. Similarly, the highest rank correlations were between 80k genomic-polygenic models, followed by rank correlations between 7k and 80k models, and the lowest ones were between the three genomic-polygenic models and the polygenic model. These activities increased the level of national and international cooperation, and contributed to the training of 9 PhD and 2 MS national and international students.

    Publications

    • Type: Books Status: Published Year Published: 2015 Citation: Koonawootrittriron, S., M. Elzo, T. Suwanasopee, C. Chaimongkol, T. Sainui, T. Tongprapi, and T. Ralukmun. 2015. D.P.O. Sire & Dam Summary 2015. Dairy Farming Promotion Organization, Ministry of Agriculture and Cooperatives of Thailand, Bangkok.
    • Type: Journal Articles Status: Published Year Published: 2015 Citation: Elzo, M. A., M. G. Thomas, D. D. Johnson, C. A. Martinez, G. C. Lamb, D. O. Rae, J. G. Wasdin, and J. D. Driver. 2015. Genetic parameters and predictions for direct and maternal growth traits in a multibreed Angus-Brahman cattle population using genomic-polygenic and polygenic models. Livest. Sci. 178:43-51.
    • Type: Journal Articles Status: Published Year Published: 2015 Citation: Elzo, M. A., M. G. Thomas, C. A. Martinez, G. C. Lamb, D. D. Johnson, I. Misztal, D. O. Rae, J. G. Wasdin, and J. D. Driver. 2015. Genomic-polygenic evaluation of multibreed Angus-Brahman cattle for postweaning ultrasound and weight traits with actual and imputed Illumina50k SNP genotypes. Livest. Sci. 175:18-26.
    • Type: Journal Articles Status: Published Year Published: 2015 Citation: Laodim, T., S. Koonawootrittriron, T. Suwanasopee, and M. A. Elzo. 2015. Genome-wide linkage disequilibrium in a Thai multibreed dairy population. Livest. Sci. 180:27-33.
    • Type: Journal Articles Status: Published Year Published: 2015 Citation: Martinez, C. A., K. Khare, and M. A. Elzo. 2015. On the Bayesness, minimaxity and admissibility of point estimators of allelic frequencies. J. Theor. Biol. 383:106-115.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Abdalla-Bozrayda, S., E. A. E. Abdalla, and M. A. Elzo. 2015. Genetic parameters and trends for dairy traits in Holstein Friesian under North-African conditions. J. Anim. Sci. 93 (Suppl. S3):348.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Elzo, M. A., M. G. Thomas, D. D. Johnson, C. A. Martinez, G. C. Lamb, D. O. Rae, J. G. Wasdin, and J. D. Driver. 2015. Genomic-polygenic and genomic predictions of direct and maternal effects for growth traits in a multibreed Angus-Brahman cattle population. J. Anim. Sci. 93 (Suppl. S3):643.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Jaichansukkit, T. *, T. Suwanasopee , S. Koonawootrittriron, and M. A. Elzo. 2015. Genetic parameters of lifetime characteristics of pre-weaning production traits of Landrace sows raised under tropical conditions. J. Anim. Sci. 93 (Suppl. S3): 34.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Jattawa, D., S. Koonawootrittriron, M. A. Elzo, and T. Suwanasopee. 2015. Accuracy of genomic imputation in a Thai multibreed dairy cattle population. J. Anim. Sci. 93 (Suppl. S3):650.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Kaniyamattam, K., M. A. Elzo, and A. De Vries. 2014. Development of a daily stochastic dynamic dairy simulation model including the 12 traits in the Net Merit Index. J. Anim. Sci. 93 (Suppl. S3):351.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Khemsawat, J., S. Koonawootrittriron, T. Suwanasopee , and M. A. Elzo. 2015. Cow-calf production performance under different management systems in Thailand. J. Anim. Sci. 93 (Suppl. S3):400.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Konkruea, T., S. Koonawootrittriron, T. Suwanasopee , and M. A. Elzo. 2015. Genetic and phenotypic trends for age at first calving and milk yield in daughters from imported and Thai Holstein sires. J. Anim. Sci. (Suppl. S3):345.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Laodim, T., S. Koonawootrittriron, M. A. Elzo, and T. Suwanasopee. 2015. Linkage disequilibrium in a Thai dairy cattle population with different Holstein fractions. J. Anim. Sci. 93 (Suppl. S3):651.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Royer, A., C. Shivers, D. Riley, M. Elzo, and M. Garcia. 2015. An SNP association study evaluating Brahman and Brahman-influenced steers for growth and carcass traits. J. Anim. Sci. 93 (Suppl. S3):644.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Sae-tiao, T., S. Koonawootrittriron, T. Suwanasopee, and M. A. Elzo. 2015. Changes in temperature-humidity index and number of hot days related to heat stress of dairy cattle in Thailand. J. Anim. Sci. 93 (Suppl. S3):98.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Wongpom, B., S. Koonawootrittriron, M. A. Elzo, and T. Suwanasopee. 2015. Genomic-polygenic evaluation for milk yield and fat yield in a multibreed dairy cattle population in Central Thailand. J. Anim. Sci. 93 (Suppl. S3):345.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Mart�nez, C. A., K. Khare, and M. A. Elzo. 2015. Revisiting allelic frequencies estimation: A decision theory approach to derive Bayes, minimax and admissible estimators. J. Anim. Sci. 93 (Suppl. S3):579.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Mir, R., T. A. Weppelmann, M. A. Elzo, K. C. Jeong. 2015. Animal factors that influence the prevalence of Shiga toxin-producing Escherichia coli in beef cattle. Verocytotoxin-producing Escherichia coli (VTEC) Conference, September 13-16, 2015, Boston, MA.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Noppibool, U. ?, S. Koonawootrittriron, M. A. Elzo, and T. Suwanasopee. 2015. Genetic parameters for length of productive life and lifetime production traits of purebred Landrace and Yorkshire sows in Northern Thailand. J. Anim. Sci. 93 (Suppl. S3): 32.


    Progress 10/01/13 to 09/30/14

    Outputs
    Target Audience: Scientists Graduate Students Producers Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest? Refereed and nonrefereed publications Conference presentations Tutorial classes to graduate students In person and electronic meetings (Skype) What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

    Impacts
    What was accomplished under these goals? 1) Phenotypes: Beef (reproduction, growth, ultrasound, carcass, meat palatability), dairy (reproduction and production) data collection and editing from multibreed populations in Colombia, Libya, Thailand, and USA; 2) Tissue samples: a) Blood and hair samples from 280 calves from the multibreed Angus-Brahman (MAB) population, and semen from 14 sires; b) Blood samples on 559 Thai dairy cattle; c) Fecal samples for E. Coli O157 analysis: 60 MAB calves; 3) Collaboration with Colombian researchers on Genomic-polygenic evaluation of dairy cattle at high altitudes in Colombia; 4) Collaboration with Mexican researchers on estimation of genetic parameters and trends in Mexican Holstein dairy populations; 5) Collaboration with Pakistani researchers on environmental factors affecting wool yield in Pakistani Buchi sheep; 6) Collaboration with Libyan researchers on genetic evaluation and genetic parameter estimation in two Libyan dairy populations; 7) Collaboration with Thai researchers on genomic-polygenic evaluation of Thai multibreed dairy populations; Genotyping of 540 dairy samples with the GGPv3 (26k) and 19 with the GGP-HD (80k) chips; 8) Collaboration with Thai and Ethiopian researchers on genotype by environment interaction and genetic evaluation in multibreed Ethiopian dairy populations using random regression models; 9) Genomic-polygenic evaluation of multibreed Angus-Brahman cattle for postweaning ultrasound and weight traits with actual and imputed Illumina50k SNP genotypes; 10) Comparison of genetic parameters and predictions for direct and maternal growth traits in a multibreed Angus-Brahman cattle population using genomic-polygenic and polygenic models; 11) Updated FORTRAN software for editing of phenotypes, genotypes, and pedigree data and construction of input data files for imputation (findhap2) and for genomic-polygenic evaluation (GS3, BLUPF90, QXPAK); SAS programs for editing growth, ultrasound, carcass, and meat palatability traits; 12) a) Constructed 2014 sire, dam, and calf files with reproduction, survival, growth, ultrasound, carcass, and meat palatability information for the Angus-Brahman multibreed and Brahman herds of the University of Florida; b) Added reproduction, survival, growth, ultrasound, carcass, and meat palatability information to the accumulated Angus-Brahman multibreed and Brahman databases (1987 to 2014); 13) Collaboration with researchers from meat science, veterinary medicine, and microbiology to conduct genomic-polygenic analyses for growth, ultrasound, carcass, meat palatability, and E. Coli O157 using animals from the UF MAB and Brahman herds. Products of these collaborations: 1) Additive genomic to total genetic variance fractions for postweaning ultrasound traits explained by 46,909 actual and imputed Illumina50k SNP genotypes were 0.17 for ribeye area, 0.32 for fat thickness, 0.25 for percent intramuscular fat, and 0.19 for weight in a multibreed Angus-Brahman population. Heritabilities were 0.33 for UREA, 0.22 for UBF, 0.43 for UPIMF, and 0.54 for UW. The additive genomic to total genetic variance ratios were 1.8, 1.0, 4.4, and 2.1 times whereas heritabilities were 1.0, 1.2, 1.0, and 1.2 times those obtained for these traits with 2,899 Illumina3k SNP. Rank correlations between genomic-polygenic and polygenic EBV were the highest (0.93 to 0.96), followed by those between genomic-polygenic and genomic EBV (0.81 to 0.94), and by those between genomic and polygenic EBV (0.66 to 0.81); 2) Comparison of three genomic-polygenic and one polygenic model indicated that the complete genomic-polygenic and the polygenic model yielded similar estimates of variance components and genetic parameters for direct and maternal growth traits in an Angus-Brahman multibreed population (293 sires, 1,725 dams, and 5,264 calves). Ignoring pedigree information for genotyped animals increased differences in variance components and lowered rank correlations relative to the complete genomic-polygenic and polygenic models. Ignoring pedigree information for both ungenotyped and genotyped animals yielded the worst estimates of variance components and the lowest rank correlations particularly for maternal growth traits. 3) Genome-wide association analysis of a Thai multibreed Holstein-Other Breeds dairy population (1,305 first-lactation cows, 291 sires, 1,192 dams) with the GeneSeek GGP-LD chip identified 7 markers (CDK15, LDB2, LOC100294777, LOC524269, MAP3K5, SLC24A4, and ZNF154) associated with 5 traits (milk yield, initial yield, peak yield, persistency, and age at first calving); 4) Linkage disequilibrium (LD) analysis in a Thai Holstein-Other Breeds dairy population (n = 1,413 cows) found high levels of LD in autosomes, particularly between SNP separated by 50 kb or less. The mean of D′ (linkage disequilibrium relative to its maximum) and r2 (coefficient of correlation squared) for SNPs separated by 40 to 50 kb were 0.694 and 0.202; 5) Annual dairy genetic evaluation summary (DPO, Thailand); 6) Sire by location interaction existed at two geographic locations in Ethiopia (Bako and Holetta). Correlations between sire rankings in Bako and Holetta were 0.86 for milk yield and initial yield and 0.87 for milk yield per day indicating that substantial re-ranking occurred across locations. All these activities increased the level of national and international cooperation, and contributed to the training of 9 PhD and 3 MS national and international students.

    Publications

    • Type: Journal Articles Status: Published Year Published: 2014 Citation: Toledo, H. O., J. M. Berruecos, C. G. Vasquez, F. J. Ruiz, and M. A. Elzo. 2014. Genetic and phenotypic trends for milk production under two data recording systems in Holstein cattle in Mexico. Mexican J. Anim. Sci. 5:471-485.
    • Type: Journal Articles Status: Published Year Published: 2014 Citation: Toledo, H. O., J. M. Berruecos, C. G. Vasquez, F. J. Ruiz, and M. A. Elzo. 2014. Estimation of genetic parameters for milk production under two data recording systems in Holstein cattle in Mexico. Mexican J. Anim. Sci. 5:443-457.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Elzo, M. A., M. G. Thomas, D. D. Johnson, C. A. Martinez, G. C. Lamb, D. O. Rae, J. G. Wasdin, and J. D. Driver. 2014. Genomic-Polygenic Evaluation of Multibreed Angus-Brahman Cattle for Postweaning Ultrasound and Weight Traits with Actual and Imputed Illumina50k SNP Genotypes. Proc. 10th World Congress of Genetics Applied to Livestock Production, Vancouver, BC, Canada, p 1-3.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Hermas, S. A., and M. A. Elzo. 2014. Estimation of Genetic Parameters and Trends for Milk Production in a Libyan Holstein Population under Arid Mediterranean Subtropical Conditions. Proc. 10th World Congress of Genetics Applied to Livestock Production, Vancouver, BC, Canada, p 1-3.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Jattawa, D., S. Koonawootrittriron, T. Suwanasopee, M. A. Elzo, P. Ritsawai, T. Laodim, T. Konkruea, B. Wongpom, P. Yodklaew, and J. Khemsawat. 2014. Problems and obstacles in blood sampling for dairy breeding research in Thailand. Thai J. Anim. Sci. 1 (Suppl. 1):321-324.
    • Type: Conference Papers and Presentations Status: Published Year Published: 20147 Citation: Laodim, T., S. Koonawootrittriron, T. Suwanasopee, and M. A. Elzo. 2014. Genome Patterns of SNP Variation in a Thai Multibreed Dairy Population. Pages 17-24 in Proc. Kasetsart University Conference, Animals, Bangkok, Thailand.
    • Type: Conference Papers and Presentations Status: Published Year Published: 20147 Citation: Noppibool, U., S. Koonawootrittriron, M. A. Elzo, and T. Suwanasopee. 2014. Effect of Breed Group and Age at First Farrowing on Length of Productive Life of Sows. Proc. Royal Golden Jubilee Congress, Pattaya, Thailand.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Raies M., M. Y. Kang, T. Bliss, M. A. Elzo, K. C. Jeong. 2014. Animal risk that modulate the prevalence and persistence of Shiga toxin-producing Escherichia coli in cattle. Pages 88-89 in EPI Research Day Book of Abstracts.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Ritsawai, P., S. Koonawootrittriron, D. Jattawa, T. Suwanasopee and M. A. Elzo. 2014. Fraction of cattle breeds and their influence on milk production of Thai dairy cattle. Pages 25-32 in Proc. Kasetsart University Conference, Animals, Bangkok, Thailand.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Yodklaew, P., S. Koonawootrittriron, M. A. Elzo, and T. Suwanasopee. 2014. Genome-wide Association Study for Milk Production and Age at First Calving of Dairy Cattle in Thailand. Thai J. Anim. Sci. 1 (Suppl. 1):302-304.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Elzo, M. A., M. G. Thomas, D. D. Johnson, C. A. Martinez, G. C. Lamb, D. O. Rae, J. G. Wasdin, and J. D. Driver. 2014. Genomic-Polygenic Evaluation of Multibreed Angus-Brahman Cattle for Postweaning Ultrasound and Weight Traits with Actual and Imputed Illumina50k SNP Genotypes. Poster 709 at World Congress of Genetics Applied to Livestock Production, Vancouver, BC, Canada, August 17-22, 2014.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Hermas, S. A., and M. A. Elzo. 2014. Estimation of Genetic Parameters and Trends for Milk Production in a Libyan Holstein Population under Arid Mediterranean Subtropical Conditions. Poster 800 at World Congress of Genetics Applied to Livestock Production, Vancouver, BC, Canada, August 17-22, 2014.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Kaniyamattam, K., M. A. Elzo, and A. De Vries. 2014. Development of a stochastic dynamic dairy simulation model incorporating multi-trait genetics. Florida Genetics Symposium, University of Florida, Gainesville, FL, October 29-30, 2014.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Martinez, C. A., K. Khare, and M. A. Elzo. 2014. Derivation of Bayes and Minimax decision rules for allelic frequencies estimation in biallelic loci. J. Anim. Sci. 92 (E-Suppl. 2):470.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Raies M., M. Y. Kang, T. Bliss, M. A. Elzo, K. C. Jeong. 2014. Animal risk that modulate the prevalence and persistence of Shiga toxin-producing Escherichia coli in cattle. EPI Research Day, University of Florida, Gainesville, FL, February 21, 2014.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Laodim, T., S. Koonawootrittriron, T. Suwanasopee, and M. A. Elzo. 2014. Genome Patterns of SNP Variation in a Thai Multibreed Dairy Population. Kasetsart University Annual Conference, Bangkok, Thailand, February 4-7, 2014.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Noppibool, U., S. Koonawootrittriron, M. A. Elzo, and T. Suwanasopee. 2014. Effect of Breed Group and Age at First Farrowing on Length of Productive Life of Sows. Royal Golden Jubilee Congress, Pattaya, Thailand, May 28-30, 2014.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Yodklaew, P., S. Koonawootrittriron, M. A. Elzo, and T. Suwanasopee. 2014. Genome-wide Association Study for Milk Production and Age at First Calving of Dairy Cattle in Thailand. Third National Animal Science Conference, Chiang Mai, Thailand, April 8-14, 2014.
    • Type: Books Status: Published Year Published: 2014 Citation: Koonawootrittriron, S., M. Elzo, T. Suwanasopee, C. Chaimongkol, T. Sainui, T. Tongprapi, and T. Ralukmun. 2014. D.P.O. Sire & Dam Summary 2013. Dairy Farming Promotion Organization, Ministry of Agriculture and Cooperatives of Thailand, Bangkok. p 1-56.
    • Type: Journal Articles Status: Published Year Published: 2014 Citation: Akhtar, M., K. Javed, H. M. Abdullah, N. Ahmad, and M. A. Elzo. 2014. Environmental factors affecting greasy wool yield traits of Buchi sheep in Pakistan. J. Anim. Plant Sci. 24:685-692.
    • Type: Journal Articles Status: Published Year Published: 2014 Citation: Elzo, M. A., M. G. Thomas, C. A. Martinez, G. C. Lamb, D. D. Johnson, I. Misztal, D. O. Rae, J. G. Wasdin, and J. D. Driver. 2014. Genomic-polygenic evaluation of multibreed Angus-Brahman cattle for postweaning feed efficiency and growth using actual and imputed Illumina50k SNP genotypes. Livest. Sci. 159:1-10.
    • Type: Journal Articles Status: Published Year Published: 2014 Citation: Gebreyohannes, G., S. Koonawootrittriron, M. A. Elzo, and T. Suwanasopee. 2014. Genotype by Environment Interaction Effect on Lactation Pattern and Milk Production Traits in an Ethiopian Dairy Cattle Population. Kasetsart J. Nat. Sci. 48:38-51.
    • Type: Journal Articles Status: Published Year Published: 2014 Citation: Gonzalez, J. M., D. D. Johnson, M. A. Elzo, M. C. White, A. M. Stelzleni, and S. E. Johnson. 2014. Effect of Brahman genetic influence on collagen enzymatic crosslinking gene expression and meat tenderness. Anim. Biotech. 25:165-178.


    Progress 10/01/12 to 09/30/13

    Outputs
    Target Audience: Scientists Graduate Students Producers Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

    Impacts
    What was accomplished under these goals? 1) Phenotypes: Beef (reproduction, growth, ultrasound, carcass, meat palatability), dairy (reproduction and production) data collection and editing from multibreed populations in Colombia, Thailand, and USA; 2) Tissue samples: a) Blood and hair samples from 318 calves from the multibreed Angus-Brahman (MAB) population, and semen from 29 sires; b) Blood samples on 2,103 Thai dairy cattle; c) Fecal samples: 318 MAB calves; 3) Collaboration with Colombian researchers on: a) Genomic-polygenic evaluation of dairy cattle; b) Genetic parameters and trends in Angus-Brahman multibreed cattle using multibreed models; c) Genetic parameters for body weight in Buffaloes using random regression models; 4) Collaboration with Mexican researchers on estimation of genetic parameters and genetic trends in two Holstein dairy populations in Mexico; 5) Collaboration with Pakistani researchers on genetic and environmental factors affecting Buchi sheep in Pakistan; 6) Collaboration with Thai and Ethiopian researchers on: a) Genetic evaluation and trends in national Bos taurus-Bos indicus multibreed dairy populations; b) Goodness of fit of lactation curves, estimation of variance components, and genetic evaluation of dairy cattle for lactation curve parameters, milk yield and milk composition traits in an Ethiopian multibreed population; c) Genotyping of 1,533 dairy samples with GeneSeek GGP-LD (9k) and GGP-HD (80k) chips; d) Development of SAS programs for statistical description and fixed effect analysis of feed intake, growth, ultrasound, carcass, and meat palatability traits in the MAB population; e) Development of FORTRAN software for editing of phenotypes, genotypes, and pedigree data and construction of input data files for imputation (findhap2) and for polygenic-genomic evaluation (GS3, BLUPF90); 7) Collaboration with researchers from meat science, veterinary medicine, and microbiology to conduct genomic-polygenic analyses for growth, ultrasound, carcass, meat palatability, and E. Coli O157 using animals from the UF MAB and Brahman herds. Products of these collaborations: 1) Fractions of additive variances explained by 46,909 actual and imputed Illumina50k SNP were 0.48 for residual feed intake, 0.36 for daily feed intake, 0.50 for feed conversion ratio, and 0.28 for postweaning weight gain. These fractions were 3.2, 3.2, 2.0, and 1.8 times larger than those previously obtained for these 4 traits using the 2,899 SNP from the Illumina3k chip. This resulted in considerably higher rank correlations between calf additive genetic predictions from genomic, polygenic, and genomic-polygenic, models in this Angus-Brahman multibreed population; 2) Analysis of E. coli O157 fecal data indicated that prevalence and numbers of colonies per sample decreased with age preweaning in MAB 2013 calves; 3) Lactation curve parameters (incomplete gamma function) and milk yield in an Ethiopian Boran-Horro-Friesian-Jersey-Simmental population had medium heritabilities (0.20 to 0.33), and breed group-environment interaction existed at two geographic locations; 4) Sire and cow genetic trends for milk yield in two Mexican Holstein populations were heavily influenced by use of US and Canadian sires; 5) Genetic trends were positive for direct but negative for maternal birth and 270-d weight effects in and Angus-Brahman multibreed population in Colombia; 6) Annual dairy genetic evaluation summary (DPO, Thailand). These activities increased the level of national and international cooperation, and contributed to the training of 8 PhD and 2 MS national and international students.

    Publications

    • Type: Books Status: Published Year Published: 2013 Citation: Koonawootrittriron, S., M. Elzo, T. Suwanasopee, C. Chaimongkol, T. Sainui, T. Tongprapi, and T. Ralukmun. 2013. D.P.O. Sire & Dam Summary 2012. Dairy Farming Promotion Organization, Ministry of Agriculture and Cooperatives of Thailand, Bangkok, p 1-56.
    • Type: Book Chapters Status: Published Year Published: 2013 Citation: Martinez, C. A., M. A. Elzo, and C. Manrique. 2013. Animal genetic evaluation in multibreed populations. In Considerations on genetic improvement and associated factors in Colombian Criollo cattle and multibreed groups, R. Campos and C. V. Duran, Eds. National University of Colombia, Palmira, p 21-78.
    • Type: Journal Articles Status: Published Year Published: 2013 Citation: Akhtar, M. K. Javed, H. M. Abdullah, N. Ahmad, and M. A. Elzo. 2013. Environmental factors affecting postweaning traits of Buchi sheep in Pakistan. J. Anim. Plant Sci. 23:699-704.
    • Type: Journal Articles Status: Published Year Published: 2013 Citation: Elzo, M. A., C. A. Martinez, G. C. Lamb, D. D. Johnson, M. G. Thomas, I. Misztal, D. O. Rae, J. G. Wasdin, and J. D. Driver. 2013. Genomic-polygenic evaluation for ultrasound and weight traits in Angus-Brahman multibreed cattle with the Illumina3k chip. Livest. Sci. 153:39-49.
    • Type: Journal Articles Status: Published Year Published: 2013 Citation: Gebreyohannes, G. S. Koonawootrittriron, M. A. Elzo, and T. Suwanasopee. 2013. Variance Components and Genetic Parameters for Milk Production and Lactation Pattern in an Ethiopian Multibreed Dairy Cattle Population. Asian-Australasian J. Anim. Sci. 26:1237-1246.
    • Type: Journal Articles Status: Published Year Published: 2013 Citation: Gebreyohannes, G, S. Koonawootrittriron, M. A. Elzo, and T. Suwanasopee. 2013. Fitness of lactation curve functions to daily and monthly test-day milk data in an Ethiopian multi-breed dairy cattle population. Kasetsart J. Nat. Sci. 47:60-73.
    • Type: Journal Articles Status: Published Year Published: 2013 Citation: Jeon, S. J., M. A. Elzo, N. DiLorenzo, G. C. Lamb, and K. C. Jeong. 2013. Evaluation of animal genetic and physiological factors that affect the prevalence of Escherichia coli O157 in cattle. PloS One 8:e55728.
    • Type: Journal Articles Status: Published Year Published: 2013 Citation: Mercadante, P. M., K. M. Bischoff, V. R. G. Mercadante, G. C. Lamb, M. A. Elzo, S. E. Johnson, D. O. Rae, J. V. Yelich, and A. D. Ealy. 2013. Subspecies differences in early fetal development and plasma pregnancy associated glycoprotein concentrations in cattle. J. Anim. Sci. 91:3693-3701.
    • Type: Other Status: Published Year Published: 2013 Citation: Riley, D., M. Elzo, M. Garcia, R. Randel, and R. Vann. 2013. Multi-State Research  Four universities collaborate on Brahman research. The Amer. Brahman Rev. 4:44-45.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Coy, B. Y., C. A. Martinez, C. Manrique, and M. A. Elzo. 2013. Genetic analysis of female weights via random regression and multiple trait models in a multibreed beef cattle population. J. Anim. Sci. 91(E-Suppl. 2):65.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Elzo, M. A., M. G. Thomas, C. A. Mart�nez, G. C. Lamb, D. D. Johnson, I. Misztal, D. O. Rae, J. G. Wasdin, and J. D. Driver. 2013. Genomic-polygenic evaluation of multibreed Angus-Brahman cattle for feed efficiency and postweaning growth using actual and imputed Illumina50k SNP genotypes. J. Anim. Sci. 91(E-Suppl. 2):72-73.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Gebreyohannes, G., S. Koonawootrittriron, M. A. Elzo, and T. Suwanasopee. 2013. Genotype by environment interaction effect on lactation pattern and milk production traits in an Ethiopian dairy cattle population. J. Anim. Sci. 91(E-Suppl. 2):289.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Jaichansukkit, T., T. Suwanasopee, M. A. Elzo, S. Koonawootrittriron. 2013. Characteristics of lifetime pre-weaning production traits in Landrace and Yorkshire sows under tropical conditions. J. Anim. Sci. 91(E-Suppl. 2):374.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Noppibool, U., S. Koonawootrittriron, M. A. Elzo, T. Suwanasopee. 2013. Effect of proportion of non-productive sow days on lifetime production traits in swine under Thai tropical conditions. J. Anim. Sci. 91(E-Suppl. 2):374.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Toledo, H. O., F. J. Ruiz, C. G. Vazquez, J. M. Berruecos, and M. A. Elzo. 2013. Genetic and phenotypic trends for milk yield in Holstein populations in Mexico. J. Anim. Sci. 91(E-Suppl. 2):288.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Vergara, O. D., M. A. Elzo, R. M. Patino, A. Calderon, and R. Almanza. 2013. Genetic parameters and genetic trends for preweaning growth in an Angus-Brahman cattle population in the Colombian tropics. J. Anim. Sci. 91(E-Suppl. 2):65-66.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Elzo, M. A. 2013. Multibreed animal model and expected progeny differences as instruments for genetic improvement in cattle. A series of four conferences in four Colombian cities on the role of genetics in livestock competitiveness, July 22-26, 2013.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Elzo, M. A. 2013. A discussion on the Senepol Multibreed Genetic Evaluation System. World Senepol Conference, Bogota, Colombia, July 18, 2013.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Elzo, M. A., D. D. Johnson, D. O. Rae, K. C. Jeong, D. G. Riley, C. A. Martinez, R. A. Mir, J. G. Wasdin, J. D. Driver, and G. E. Dahl. 2013. Brahman Project Update. Brahman Field Day, Gainesville, FL, November 21, 2013.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Martinez, C. A., and M. A. Elzo. 2013. Statistical analysis of multibreed Angus-Brahman microbiological data. Microbiology-Animal Genetics Research Group Meeting, University of Florida, Gainesville, FL, June 10, 2013.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Johnson, D. D., and M. A. Elzo. 2013. Carcass characteristics and meat quality of beef from the Angus-Brahman multibreed project. Florida Beef Cattle Short Course, Gainesville, FL, May 8, 2013.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Wongprom, B., S. Koonawootrittriron, M. A. Elzo, and T. Suwanasopee. 2013. Genetic parameter estimates for rump traits and teat length in a multibreed dairy cattle population in Thailand. J. Anim. Sci. 91(E-Suppl. 2):288-289.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Yodklaew, P., S. Koonawootrittriron, M. A. Elzo, and T. Suwanasopee. 2013. Impact of sire by region interaction on first-lactation traits of dairy cows raised under tropical conditions in Thailand. J. Anim. Sci. 91(E-Suppl. 2):289.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Jeon, S. J. , M. A. Elzo, N. DiLorenzo, G. C. Lamb, and K. C. Jeong. 2013. Animal genetic and physiological factors contribute to the prevalence of E. coli O157 in cattle. In Proc. 11th Annual Res. Symp. Anim. Mol. Cell Biol., p 20.


    Progress 10/01/11 to 09/30/12

    Outputs
    OUTPUTS: 1) Beef, dairy, sheep, swine data collection and editing from multibreed populations in Mexico, Pakistan, Thailand, and USA; 2) Tissue sample collection from Thai dairy populations for genetic-genomic evaluation; 3) Collaboration with Colombian researchers on: a) Genetic evaluation and estimation of genetic parameters for growth and ultrasound carcass traits in a multibreed Bos taurus-Bos indicus cattle in Southern Cesar; b) Genetic-economic evaluation of Holstein farms in Antioquia; c) Performance tests of meat and meat-milk dual-purpose Buffaloes using random regression mixed models; and d) Random regression models and covariance functions in multibreed Bos indicus-Bos taurus multibreed populations; 4) Collaboration with Brazilian researchers on genetic evaluation of the Montana multibreed population for growth and ultrasound carcass traits; 5) Collaboration with Mexican researchers on estimation of genetic parameters and genetic trends in two Holstein dairy populations in Mexico; 6) Collaboration with Pakistani researchers on genetic and environmental factors affecting Buchi sheep in Pakistan; 7) Collaboration with Thai and Ethiopian researchers on: a) dairy production and revenue in privately and cooperative owned farmer organizations in Central Thailand; b) Somatic cell count effects on milk traits in Central Thailand; c) Genetic evaluation and trends in national Bos taurus-Bos indicus multibreed dairy populations; d) Genetic evaluation of dairy cattle for lactation curve and milk yield and composition traits in an Ethiopian multibreed population; 8) Collaboration with researchers from NFREC and the UF Meats Laboratory on feed efficiency using UF multibreed herds. Data collected: a) growth, feed consumption, temperament, ultrasound data (GrowSafe facility; b) steer carcass information; and c) palatability data; 9) Collaboration with CSU to collect and store blood samples at the USDA-NAGP repository in Fort Collins, CO. Products of these collaborations: 1) Higher level of national and international cooperation; 2) Analysis of beef, dairy, sheep, and swine experimental and field data from Brazil, Colombia, Ethiopia, Pakistan, Thailand, and USA; 3) Blood samples from 240 calves born in 2012 plus 250 blood samples from Brahman calves, dams, and sires sent to the USDA_NAGP repository; 4) Genetic-genomic evaluation and estimation of genomic and polygenic parameters for postweaning gain and ultrasound carcass traits in UF multibreed herd; 5) Genetic parametes and trends for Mexican Holstein; 6) Environmental factors affecting Buchi sheep for reproduction, growth, and wool traits in Pakistan; 7) Comparison of two dairy organizations for milk yield and revenues in Thailand; 7) Annual dairy genetic evaluation summary (DPO, Thailand); 8) Publication of Colombian research on cattle growth and ultrasound traits; 9) Publication of genetic and genomic research using data from the UF multibreed herd; 10) Training of 8 PhD and 8 MS national and international students; 11) Twenty five publications; 12) Eleven presentations at national and international meetings. PARTICIPANTS: Mauricio A. Elzo (PI) Department of Animal Sciences University of Florida D. D. Johnson (Co-PI) Department of Animal Sciences University of Florida D. O. Rae (Co-PI) Large Animal Clinical Sciences University of Florida Skorn Koonawootrittriron Department of Animal Science Kasetsart University Thailand Thanathip Suwanasopee Department of Animal Science Kasetsart University Thailand Mario Ceron Faculty of Agricultural Sciences University of Antioquia Colombia Carlos Manrique Department of Animal Sciences National University of Colombia Colombia Carlos Martinez Department of Animal Sciences National University of Colombia Colombia Ignacy Misztal Department of Animal and Dairy Science University of Georgia Clifford Lamb North Florida Research and Education Center University of Florida Milton Thomas Department of Animal and Range Sciences New Mexico State University David Riley Department of Animal Science Texas A&M University Hugo Toledo National Autonomous University of Mexico Mexico Maqsood Akhtar University of Veterinary and Animal Sciences Lahore, Pakistan TARGET AUDIENCES: Scientists Graduate Students Producers PROJECT MODIFICATIONS: Not relevant to this project.

    Impacts
    1) The genomic-polygenic analysis of postweaning gain and ultrasound traits with the Illumina3k chip indicated that SNP from the Illumina3k chip explained only a small fraction of the genetic variance for ultrasound ribeye area (9%), ultrasound backfat (38%), ultrasound percent intramuscular fat (6%), and postweaning weight gain (8%) in the UF Angus-Brahman multibreed population. These fractions were similar to those obtained for feed efficiency traits in this multibreed population. Genomic-polygenic, genomic, and polygenic predicted values tended to decrease as Brahman fraction of calf increased suggesting that calves with higher percentage Brahman grew more slowly and had less desirable ultrasound carcass traits; 2) Fractions of additive genetic variance explained by Illumina3k SNP were 0.08 for hot carcass weight, 0.47 for dressing percent, 0.19 for ribeye area, 0.27 for backfat thickness, and 0.23 for marbling suggesting that genomic-polygenic models would be needed to compute EBV reliably in UF Angus-Brahman multibreed population; 3) Thai farms from a Dairy Cooperative had lower milk yields and revenues than farms from a private organization; 3) Heritability estimates were 0.12 for somatic cell count (SCC), and 0.31 for milk yield, and their genetic correlation was non-significant in Central Thailand suggesting that selection for high milk yield and low SCC would be feasible; 4) The modified incomplete gamma function yielded the best fit for daily data and the inverse polynomial function was the best for test-day milk data in a Boran, Friesian, Jersey, Simmental multibreed Ethiopian dairy population; 5) The association between fraction Holstein and milk yield in Thailand was quadratic; 87.5% Holstein cattle had the highest milk yields. These results stressed the limitations of upgrading adapted local dairy cattle to Holstein as a means of increasing milk production under tropical conditions; 6) Random regression analysis in a nine-breed Colombian Bos indicus-Bos taurus population suggested that selection for additive direct genetic effects based on weight at early age would be effective to obtain heavier animals at later growth stages under tropical pasture conditions; 6) Collected 490 tissue samples from Angus, Brahman, Brangus, and Angus-Brahman animals in Florida; 7) Collected over 800 tissue samples for the genomic analysis of the multibreed dairy cattle population in Thailand; 8) Training of 8 PhD and 8 MS national and international students; 9) Twenty five publications and 6 manuscripts submitted; 10) Eleven presentations at national and international meetings.

    Publications

    • Akhtar, M., K. Javed, H. M. Abdullah, N. Ahmad, and M. A. Elzo. 2012. Environmental factors affecting preweaning growth traits of Buchi sheep in Pakistan. J. Anim. Plant Sci. 22:529-536.
    • Bolivar, D. M., M. F. Ceron, and M. A. Elzo. 2012. Performance tests for buffaloes (Bubalus bubalis) coming from meat and dual-purpose (meat-milk) preweaning management systems in Colombia. Col. J. Anim. Sci. (In press)
    • Elzo, M. A., C. C. Chase, Jr., D. D. Johnson, D. O. Rae, D. G. Riley, R. D. Randel, C. R. Long, J. Block, J. G. Wasdin, J. D. Driver, M. L. Rooks, and G. E. Dahl. 2012. The Brahman Project. Florida Beef Cattle Short Course, Gainesville, FL, May 4, 2012.
    • Elzo, M. A., G. Hu, C. A. Martinez, G. C. Lamb, D. D. Johnson, M. G. Thomas, I. Misztal, D. O. Rae, J. G. Wasdin, and J. D. Driver. 2012. Genomic-polygenic evaluation of Angus-Brahman cattle for carcass traits with the Illumina3K chip. J. Anim. Sci. 90 (E-Suppl. 3):523.
    • Elzo, M. A., D. D. Johnson, D. O. Rae, J. G. Wasdin, and J. D. Driver. 2012. UF Beef Cattle Genetic-Genomic Research. Handout for Honduran Visitors, University of Florida, IFAS, Department of Animal Science Beef Unit; 7 pp; October 18, 2012.
    • Elzo, M. A., S. Koonawootrittriron, and T. Suwanasopee. 2012. Genomic evaluation in cattle: Experiences from UF and KU. Proc. Genetic Improvement of Livestock and Aquatic Animals in the Tropics: Challenge and Reward (GILAAT), Bangkok, Thailand, September 24-26, 2012.
    • Elzo, M. A., S. Koonawootrittriron, and T. Suwanasopee. 2012. Genomic evaluation in cattle: Experiences from UF and KU. Page 27 in GILAAT 2012 Genetic Improvement of Livestock and Aquatic Animals in the Tropics: Challenge and Reward, Bangkok, Thailand, September 24-26, 2012.
    • Elzo, M. A., C. A. Martinez, G. C. Lamb, D. D. Johnson, M. G. Thomas, I. Misztal, D. O. Rae, J. G. Wasdin, and J. D. Driver. 2012. Genomic-polygenic evaluation of postweaning weight and ultrasound carcass traits in an Angus-Brahman multibreed population. J. Anim. Sci. 90 (E-Suppl. 3):522-523.
    • Elzo, M. A. and O. Vergara, Eds. 2012. Statistical modeling applied to animal sciences: II. Genetic Evaluations. Editorial Biogenesis, Medellin, Colombia. http://editorialbiogenesis.udea.edu.co/index.php/biogenesis/article/v iewFile/194/199.
    • Elzo, M. A., G. C. Lamb, D. D. Johnson, M. G. Thomas, I. Misztal, D. O. Rae, C. A. Martinez, J. G. Wasdin, and J. D. Driver. 2012. Genomic-polygenic evaluation of Angus-Brahman multibreed cattle for feed efficiency and postweaning growth using the Illumina3k chip. J. Anim. Sci. 90:2488-2497.
    • Gebreyohannes, G., S. Koonawootrittriron, M. A. Elzo and T. Suwanasopee. 2012. Fitness of lactation curve functions to daily and monthly test-day milk data in an Ethiopian dairy cattle population. J. Anim. Sci. 90 (E-Suppl. 3):302.
    • Toledo, H. O., J. M. Berruecos, C. G. Vazquez, F. J. Ruiz, and M. A. Elzo. 2012. Genetic parameters for milk production in two Holstein dairy populations in Mexico. 48th National Livestock Research Meetings, Queretaro, Mexico, September 10-13, 2012.
    • Gebreyohannes, G., S. Koonawootrittriron, M. A. Elzo and T. Suwanasopee. 2012. Estimation of Genetic Parameters for Lactation Pattern and Milk Production Traits in an Ethiopian Dairy Cattle Population. Genetic Improvement of Livestock and Aquatic Animals in the Tropics: Challenge and Reward, Bangkok, Thailand, September 24-26, 2012.
    • Gebreyohannes, G., S. Koonawootrittriron, M. A. Elzo and T. Suwanasopee. 2012. Impact of crossbreeding on production and reproduction traits in an Ethiopian dairy cattle population. 15th Animal Science Congress of the Asian-Australasian Association of Animal Production Societies, Bangkok, Thailand, November 26-30, 2012.
    • Jattawa, D., S. Koonawootrittriron, M. A. Elzo, and T. Suwanasopee. 2012. Somatic Cells Count and Its Genetic Association with Milk Yield in Dairy Cattle Raised under Thai Tropical Environmental Conditions. Asian-Aust. J. Anim. Sci. 25:1216-1222.
    • Koonawootrittriron, S., M. Elzo, T. Suwanasopee, C. Chaimongkol, T. Sainui, T. Tongprapi, and T. Ralukmun. 2012. D.P.O. Sire & Dam Summary 2011. Dairy Farming Promotion Organization, Ministry of Agriculture and Cooperatives of Thailand, Bangkok. p 1-56.
    • Koonawootrittriron, S., M. A. Elzo, S. Yeamkong, and T. Suwanasopee. 2012. A Comparative Study on Dairy Production and Revenue of the Dairy Farms Supported by a Private Organization with those Supported by a Dairy Cooperative in Central Thailand. Livest. Res. Rural Dev. 24 (4), Article #61. http://www.lrrd.org/lrrd24/4/koon24061.htm.
    • Koonawootrittriron, S., U. Nopibool, M. A. Elzo and T. Suwanasopee. 2012. Length of productive life and lifetime production of Landrace, Yorkshire and crossbred sows raised under Thai tropical conditions. J. Anim. Sci. 90 (E-Suppl. 3):640.
    • Koonawootrittriron, S., P. Yodklaew, M. A. Elzo and T. Suwanasopee. 2012. Association between milk production and Holstein fraction of upgraded dairy cattle in the Thai tropics. J. Anim. Sci. 90 (E-Suppl. 3):266.
    • Martinez, C.A., M. A. Elzo, A. Jimenez, C. Manrique1 and G. Hu. 2012. Covariance functions, genetic parameters and breeding values for longitudinal ultrasound measures of ribeye area in a Colombian multibreed cattle population. J. Anim. Sci. 90 (E-Suppl. 3):267.
    • Martinez, C. A., M. A. Elzo, C. Manrique, L. F. Grajales, and A. Jimenez. 2012. Random regression models for estimation of covariance functions, genetic parameters and prediction of breeding values for rib eye area in a Colombian Bos indicus-Bos taurus multibreed cattle population. Col. J. Stat. 35 (Special Issue, 2):309-330.
    • Martinez, C. A., M. A. Elzo, C. Manrique, and A. Jimenez. 2012. Covariance components, genetic parameters and breeding values for live weight using random regression models in a Bos taurus-Bos indicus multibreed cattle population in Colombia. Col. J. Anim. Sci. (In press)
    • Martinez, C. A., C. Manrique, M. A. Elzo, and A. Jimenez. 2012. Additive genetic group and heterosis effects on growth traits and corporal composition measurements via ultrasound in crossbred animals in Southern Cesar, Colombia. Col. J. Anim. Sci. 25:377-390.
    • Martinez, C. A., C. Manrique, M. A. Elzo, and A. Jimenez. 2012. Cattle genetic evaluation: A historical perception. Col. J. Anim. Sci. 25:293-311.
    • Ramirez-Diaz, J., T. A. Oliveira, A. Zampar, S. F. N. Pertile, M. A. Elzo, J. B. S. Ferraz, G. B. Mourao. 2012. Genetic parameters for carcass traits and weaning weight of composite beef cattle in Brazil. J. Anim. Sci. 90 (E-Suppl. 3):270.