Source: UNIVERSITY OF ARIZONA submitted to
INTERPRETING CATTLE GENOMIC DATA: BIOLOGY, APPLICATIONS AND OUTREACH
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
Reporting Frequency
Annual
Accession No.
0168402
Grant No.
(N/A)
Project No.
ARZT-137005-R-24-122
Proposal No.
(N/A)
Multistate No.
NC-1010
Program Code
(N/A)
Project Start Date
Oct 1, 2002
Project End Date
Jun 30, 2006
Grant Year
(N/A)
Project Director
Henderson, D.
Recipient Organization
UNIVERSITY OF ARIZONA
(N/A)
TUCSON,AZ 85721
Performing Department
ANIMAL SCIENCE
Non Technical Summary
Identification of genes involved in the phenotypic expression of adaptation traits are often difficult to identify and are of great economic importance. This project develops statistical methods capable of identifying mRNA dosage differences between adapted and non-adapted beef and dairy cattle.
Animal Health Component
25%
Research Effort Categories
Basic
50%
Applied
25%
Developmental
25%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3063310102025%
3063310104025%
3063410102025%
3063410104025%
Goals / Objectives
1. Determine the location, structure, function and expression of genes affecting health, reproduction, production, and product quality in cattle. 3. Develop and deliver educational materials about bovine genomics research to consumers and stakeholders.
Project Methods
Techniques to address Objective 1 will focus on Bayesian statistical methods with an emphasis on methods to account for multiple hypothesis testing and heterogeneous gene expression variances. Unique aspects of this research include variable selection approaches for data of high dimensionality. Rather than adjust significance levels post-analysis, these Bayesian methods account for multiple hypothesis testing by providing summaries of evidence (posterior probabilities) for the alternative in the presence of all other tests performed. Experiments aimed at identifying genes responsible for arid adaptation in beef and dairy cattle will be designed using facilities at the University of Arizona capable of providing a controlled environment simulating desert conditions. Additional effort will be expended to assist in the development of new microarrays from cDNA clones. Objective 3 will addressed by providing posters at producer meetings and assisting in the development of a consumer / producer oriented web-site.

Progress 10/01/02 to 06/30/06

Outputs
Dr. Henderson is no longer with the University of Arizona.

Impacts
none

Publications

  • No publications reported this period


Progress 01/01/03 to 12/31/03

Outputs
Development of statistical software for the analysis of cDNA, long oligo, and short oligo microarrays. The investigator has recently been added to the project and this research is still in progress. As of March 1, 2004, a beta prototype of the software using a shrinkage estimator for individual gene varainces is under review within the Henderson lab and at the Danish Institute of Agricultural Science in Foulum. A final working version of this part of the software is expected by the end of Summer 2004. An alpha version of a new and novel application of an existing statistical tool for the detection of differential expression using Bayesian Stochastic Search Variable Selection (SSVS) is still under development. A graduate student is currently writing computer code for a basic implementation of SSVS and is working on deriving a variant of SSVS that will also utilize a shrinkage estimator for individual gene variances. A beta prototype is expected by the end of calendar 2004.

Impacts
These two statistical methods should increase power of detection of differential expression while limiting the probability of a Type I error. Additionally, the implementation of these methods in a single software package should enable a broader number of researchers to use these tools in their own research.

Publications

  • Henderson, D. A., Maiti, T., and Nettleton D. 2003. The effect of heterogeneous variances on Type I error rate in statistical analyses of microarray data. Intl. PAG XI: P212. San Diego, CA


Progress 01/01/01 to 12/31/01

Outputs
Heat Shock Protein Genes code for molecules that maintain normal cellular metabolism during heat stress by maintaining proper 3-dimensional structure of peptides which is essential to their activity. Objective of this study was to evaluate seasonal patterns of heat shock protein gene expression in warm and cold adapted horses over a one year period. Cold adapted horses included two Percheron mares and four Belgian Mares. Six Thoroughbred mares comprised the heat-adapted breed population. Blood samples were collected weekly for 1 year from the Thoroughbred mares and monthly from the Draft mares. The blood was split into two equal aliquots of which one was subjected to heat stress in a water bath at 42 C for 1 hour. Leukocytes from both samples were then isolated by erythrocyte lysis followed by centrifugation and total RNA extracted using RNAeasy (Qiagen). RNA is then concentrated by salt/ethanol extraction and stored at -80 C until analysis for heat shock mRNA. The partial equine heat shock CDNA's produced include HSP 90, HSP 70, HSP 70-cognate and Heat shock Factor 2. Future work will involve analysis of total RNA samples for these heat shock protein mRNA's.

Impacts
This study will provide the first data set in the horse on basal and heatshock gene expression response in warm and cold-adapted horses over a year. In particular, it will provide solid data on whether acclimation to warm weather involves up-regulation of basal and heat-shock induced expression of these genes. It will also provide good basal information on expression of these genes in horses.

Publications

  • Collier, R.J., J.C. Byatt, S.C. Denham, P.J. Eppard, A.C. Fabellar, R.L. Hintz, M.F. McGrath. C.L. McLaughlin, J.K. Shearer, J.J. Veenhuizen and J.L. Vicini. 2001. Effects of sustained release bovine somatotropin (Sometribove) on animal health in commercial dairy herds. J. Dairy Sci. 84:1098-1108.
  • Kesiter,Z.O., R.J. Collier and R.L. AX.2001. Follicular growth in lactating cows receiving recombinant bovine somatotropin, gonadotropin releasing hormone and prostaglandins, contrasts between winter and summer months. J. Dairy Sci. 84: Suppl 1 p. 268. (abstract)


Progress 01/01/00 to 12/31/00

Outputs
Eight bovine microsatellite markers have been used to develop haplotypes for carriers of Progressive Degenerative Myeloencephalopathy (PDME; commonly known as Weaver Syndrome) within the Brown Swiss Breed. These markers include TGLA116 (the original marker for PDME), BMS2172, BMS885, DIK8, BM1224, BM6437, BMS495 and INRA072, that encompass a 12.7 cM region of bovine chromosome 4. Haplotypes have been developed for all progeny-tested carrier sires, resulting in a high probability of determining carrier status of progeny from these sires. Using the haplotype test, we have identified a recombinant bull that is a known PDME heterozygote. This bull places the PDME locus telomeric of BM1224, 4.7 cM from the original microsatellite marker of TGLA116. We have superovulated 2 cows with recombination events in the region between BM1224 and BM6437 and mated them to known carrier bulls. Calves will be born beginning in January and immediately genotyped. We will monitor any calves that inherit the Weaver haplotype from their sire for development of disease symptoms. We hope to identify a Weaver bull calf that can produce semen for future progeny testing. Shotgun sequencing of a BAC clone containing BMS495 (TAMU BAC library) isolated a human EST (Hs. 29002) that has been mapped to a region of chromosome 7 in the interval D7484-D7S528. All STS within the microsatellites that map in the region were blasted against the GenBank databases. Only BMS6437 matched an EST that bins to H72758. These sequences align well between the bovine and human maps. We have mapped 7 of the microsatellites (BMS2172, BMS885, DIK8, BM1224, BM6437, BMS495 and INRA072) in the 12,000 rad radiation hybrid panel (12KRHP). Retention frequencies ranged from .133 to .206 for the microsatellites with an average retention of .159. Breakage probability and distance estimates place 6 microsatellites within a linkage group with a LOD score of 6, removing DIK8. BMS2172, BMS885, BM1224, BM6437, and BMS495 are placed in a linkage group with a LOD score of 8, putting DIK 8 and INRA072 in their own linkage groups. The reelin gene (RELN) has been shown to control neuronal migration in the developing brain in mice; and mutations in the gene have shown similar symptoms to PDME. It maps to the long arm of human chromosome 7, which is homologous to BTA4. Primers developed from human studies were used to amplify a 159-bp fragment, which encompasses positions 1136-1295 of the human RELN sequence. After initial sequencing of direct PCR product, the fragment had a 90.06% homology score with human RELN. Sixteen animals representing nine breeds: Guernsey, Angus, Holstein, Jersey, Brown Swiss, Hereford, Gelbvieh, Limousin and Simmental, were PCR amplified and direct sequenced (accession number: AF232904). RELN was mapped in the 12KRHP, but is not linked to the microsatellite markers used in the analysis of Weaver Syndrome.

Impacts
We have used the information to develop a powerful marker test for Weaver Syndrome that is used by the industry.

Publications

  • DeNise, S.K., and E. Oberg. 2000. Genetic analysis of Bovine Progressive Degenerative Myeloencephalopathy (PDME) or Weaver Syndrome in Brown Swiss Cattle. J. Dairy Sci. 83 (1).
  • Lagziel, A., S. DeNise, O. Hanotte, S. Dhara, V. Glazko, A. Broadhead, R. Davoli, V. Russo, and M. Soller. 2000. Geographic and breed distribution of an MspI PCR-RFLP in the bovine growth hormone (bGH) gene. Anim. Genet. 31:1-4.
  • Speidel, S., E. Oberg, M. Ben Abdallah, S. K. DeNise. 2000. Genetic analysis of candidate gene (RELN) for Weaver Syndrome in Brown Swiss Cattle. J. Dairy Sci.83 (1).
  • Woodward, B.W., S.K. DeNise and J.A. Marchello. 2000. Evaluation of calpastatin activity measures in ante- and postmortem muscle from half-sib bulls and steers. J. Anim. Sci. 78:804-809.


Progress 01/01/99 to 12/31/99

Outputs
There are 3 neurological genetic diseases found in Brown Swiss cattle: Weaver Syndrome (progressive degenerative myeloencephalopathy, PDME), Spinal Muscular Atrophy (SMA) and Spinal Dysmyelination (SDM). We have developed a haplotype test with 8 markers that flank the PDME locus to determine heterozygous carriers of the the gene. We have screened the TAMU BAC library for the 8 markers that flank the PDME locus (TGLA116 (48.9), BMS2172 (49.6), BMS885 (50.2), DIK8, BM1224 (51.2), BMS6437 (52.9), BMS495 (55.5) and INRA072 (59.3)). One clone was identified that contains BMS495. We have randomly sequenced 37, 300-500 bp fragments from the BAC clone and identified a human EST that pulls 2 sequences together. This EST maps between IGFBP-3 and GHRHR in humans; but would map centromeric of GHRHR in bovine due to its physical location near BMS495. This information comparatively maps the PDME region to the human map. We have identified a recombinant bull that places the PDME locus telomeric to BM1224. We have amplified and sequenced a 158 bp fragment of the bovine RELN gene, a positional candidate for PDME (GenBank accession number: AF232904). We have collected DNA samples from pedigrees segregating the SMA locus and will begin a genome screen to identify the causative gene.

Impacts
We became the official screening lab for Weaver Syndrome for the Brown Swiss Association, January 2000. We will be able to identify carriers within families at a high success rate allowing the breeders to remove the genetic disease from their populations.

Publications

  • N. Vukasinovic, S.K. DeNise and A.E. Freeman. 1999. Association of growth hormone loci and milk production traits in Holstein bulls. J. Dairy Sci. 82:788-794.


Progress 01/01/98 to 12/31/98

Outputs
Fourteen markers were used to develop a framework map of chromosome 4 using the TAMU 5000 rad radiation hybrid panel. Only two markers were retained in the panel up to panel number 22. Panel number 22 and 24 have incorporated all of chromosome 4. Retention rates were far below those reported by TAMU group last year, but consistent across the chromosome, ranging from 11 to 22 %. Phenotypic data were collected on seven half-sib Angus families and a marker analysis performed on chromosomes 2 and 11. A QTL associated with KPH (LOD score of 4.97) was found on chromosome 2, and two markers on chromosome 11 We continue to work with AI companies to develop marker-assisted selection programs for the dairy industry.

Impacts
(N/A)

Publications

  • Du, F.X., B.W. Woodward and S.K. DeNise. 1998. Haplotype construction of sires with progeny genotypes based on an exact likelihood. J. Dairy Sci. 81(5):1462-1468.
  • Du, F.X., B.W. Woodward and S.K. DeNise. 1998. Evaluating sire's heterozygosity for genes controlling a quantitative trait based on within-family additive genetic variance. J. Anim. Sci. 76(1): 75.
  • Davis, G. and S. DeNise. 1998. The impact of genetic markers on selection. J. Anim. Sci. 76:2331-2339.
  • Freeman, A.E., Vukasinovic, N., and S.K. DeNise. 1998. Association of growth hormone polymorphism with milk production traits in Holsteins. Proc. World Congress on Genetics Applied to Livestock Production. 23:471.
  • Woodward, W., F.-X. Du, H. Montaldo, K. J. Andersen and S. K. DeNise. 1998. Preliminary evidence for major genes controlling beef carcass traits in Limousin cattle. Proc. World Congress on Genetics Applied to Livestock Production. 25:157. Woodward, B.W., F.X. Du, H. Montaldo, and S.K. DeNise. 1998. Evidence for major genes controlling beef carcass traits in Angus cattle. J. Anim. Sci. 76(1):55.


Progress 01/01/97 to 12/31/97

Outputs
We have continued to evaluate 6 half-sib families of current outstanding bulls in active AI for marker-assisted selection using the daughter design. Data have been analyzed with ANIMAP, an interval mapping procedure testing for QTL position and magnitude. Significant marker effects on percent protein have been found on chromosomes 6 and 10. The marker on chromosome 10 is also associated with deviations of protein and contributions to sire proof for protein. A marker on chromosome 21 was associated with a size trait: measured as type traits of stature, strength, body depth and dairy form. DNA from young sires have been collected and we will evaluate the QTL-marker effects found in the daughters. A maximum likelihood method to construct parental haplotypes based on progeny genotypes has been developed (Du et al. In press). Results show that two markers that are tightly linked (<10 cM) with intermediate allele frequencies require a difference of one half-sib progeny between those receiving parental and recombinant gametes to construct sire linkage phase, a difference of two or more progeny is required with two markers 30 cM apart. When two adjacent markers have two alleles with equal allelic frequencies, genotyping 10 and 50 progeny are needed to achieve a power of .85 for constructing a sire linkage phase of two tightly (10 cM) and moderately linked (30 cM) markers, respectively. The family size is reduced to approximately half when both markers have 3 alleles with equal frequencies. Data on 300 Holstein bulls, both young sires in progeny testing programs and active AI bulls, were used to evaluate the effects of 3 growth hormone (bGH) polymorphisms: exon V, at position 2141, intron C at position 1547, and in the 3' region probably at position 2637 (Vukasinovic et al., 1998). Phenotypic traits measured on bulls were daughter yield deviations for milk, fat and protein yield, and fat and protein percentage, obtained in the national evaluation from February 1997. A putative QTL may be located upstream of the bGH gene: milk yield and protein percentage the highest likelihood of the pedigrees was obtained assuming the recombination fraction of 0, and indicating close linkage between the bGH gene and the QTL. However, the obtained LOD scores were low and did not reach the conventional critical value of 3. The low LOD score values (< 1) can be explained by the relatively large proportion of missing information and unknown phases.

Impacts
(N/A)

Publications

  • Maciulla, J.H., S.K. DeNise and H.M. Zhang. 1997. A HaeIII RFLP at the bovine insulin-like growth factor binding protein-3 (bIGFBP-3) locus. An. Genet. 28(5):375.


Progress 01/01/96 to 12/30/96

Outputs
We have three primary populations for studying characteristics that contribute to production in dairy cattle. DNA samples from six dairy bull families in the daughter design have now been collected and stored to study the utility of using marker-assisted selection in young sire selection programs. These samples include daughters in production and sons in sampling programs. Family size ranges from 50 to 150 daughters. We will continue to study these families for quantitative trait loci that contribute to production characteristics in dairy cattle. The second population, in collaboration with scientists at Iowa State University, is a group of 60 young bulls owned by 21st Century Genetics that have been immunosuppressed to study the relationship of response to challenge and future health characteristics of progeny. Dr. Kehrli has completed the cellular immunology evaluation of the 60 bulls to be studied, and Dr. Freeman has estimated breeding values for these young bulls based on neutrophil iodination tests. We have begun screening the six high ranking and seven low ranking bulls for markers on chromosome 23. Samples from progeny of these bulls will be collected this year so that we will be able to study marker associations with health characteristics. The final population is a herd of Brown Swiss cows leased by the University of Arizona. These cows are segregating the Weaver gene (progressive degenerative myeloencephalopathy gene, PDME).

Impacts
(N/A)

Publications

  • ZHANG, H. M., S.K. DENISE and R.L. AX. 1996. Rapid communication: A novel DNA polymorphism of the bovine calpain gene detected by PCR-RFLP analysis. J. AnimalSci. 74:1441.
  • DU, F.-X., B.W. WOODWARD and S.K. DENISE. 1996. A likelihood ratio test to evaluate the linkage phase of a sire with genotyped progeny. J. Anim. Sci. 74(1):110.
  • WOODWARD, B. W., S.K. DENISE and J.M. GESKE. 1996. Evaluation of calpastatin activity measures on live-animal tissue for genetically improving beef tenderness. J. Anim. Sci. 74(1):113.


Progress 01/01/95 to 12/30/95

Outputs
DNA is isolated from sperm cells or leukocytes to serve as a template for polymerase chain reaction (PCR). Following PCR, genotypic differences are assigned after hydrolysis of DNA with appropriate restriction endonuclease enzymes and electrophoretic separation of DNA fragments. Quantitative traits are available from phenotypic data and are used to test for differences among genotypes assigned to individual animals. Quantitative traits are available from phenotypic data are used to test for differences among genotypes assigned to individual animals. Quantitative traits loci (QTL) are being analyzed within a single locus or as combinations of loci, particularly those that may be linked on an individual chromosome. Results from QTL are being used to select bulls for sampling programs in artificial insemination.

Impacts
(N/A)

Publications

  • ZHANG, H.M., DENISE, S.K., CARPENTER, R.T., BROWN, D.R., and AX, R.L. 1995. Molecular cloning and sequencing a segment of the bovine calpain II regulatory subunit gene. J. Anim. Sci. 73:115.
  • AVENDONO, L., ZHANG, H.M., DENISE, K., and CORREA, A. 1995. Heritability for milk yields of Holstein cows located in the Baja California, Mexico. J. Anim. Sci. 73: 111.