HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Abstract Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Isler, B. J. Articles by Leymaster, K. A. Search for Related Content PubMed PubMed Citation Articles by Isler, B. J. Articles by Leymaster, K. A.

Evaluation of associations between prion haplotypes and growth, carcass, and meat quality traits in a Dorset x Romanov sheep population^1,2

US Meat Animal Research Center, USDA, ARS, Clay Center, NE 68933-0166

	Abstract

Top Abstract INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION IMPLICATIONS LITERATURE CITED

 
There is concern about potential antagonistic correlated responses due to intensive selection for scrapie-resistant haplotypes of the prion (PRNP) gene in sheep. The objective of the present research was to test for associations of PRNP haplotypes for codons 136, 154, and 171 with growth, carcass, and meat quality traits in an F₂ Dorset x Romanov population (n = 415) segregating the 2 callipyge alleles. Haplotypes of the 3 PRNP codons were determined for each sheep, and breed of origin of each gamete was predicted by genotyping 6 microsatellite markers flanking the PRNP locus. Twenty-five growth, carcass, and meat quality traits were evaluated. Data were analyzed using a basic model consisting of fixed effects of year, sex, and callipyge genotype, the random effect of sire, and 7 covariates corresponding to the probability that a lamb inherited a specific PRNP haplotype of either Dorset or Romanov origin. A fixed effect of litter size was added to the model for growth traits. The model for carcass traits contained the linear and quadratic effects of chilled carcass weight and the interactions among callipyge genotype and linear and quadratic terms. For meat quality traits, the model contained chilled carcass weight as a covariate and the interaction between callipyge genotype and chilled carcass weight. A contrast between the resistant ARR haplotype and the average effect of other PRNP haplotypes was tested to investigate the effects of potential selection for ARR within each breed of origin (Dorset, ARR vs. ARQ, VRQ, and AHQ; Romanov, ARR vs. ARQ and VRQ). There was limited evidence that selecting for scrapie resistance would cause correlated responses due to linkage disequilibrium. Associations of only 3 traits with PRNP haplotypes were detected in either breed of origin. In Romanov, the ARR haplotype was associated with longer carcasses (P < 0.013), narrower rumps (P = 0.038), and less marbling (P = 0.022) than the average of ARQ and VRQ haplotypes. No significant contrasts were detected for Dorset. This study is the first to account for breed of origin while investigating haplotype associations in an F₂ population. This study provided limited evidence of associations between PRNP haplotypes and growth, carcass, and meat quality traits.

Key Words: carcass trait • growth trait • meat quality trait • prion gene • scrapie resistance • sheep

	INTRODUCTION

Top Abstract INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION IMPLICATIONS LITERATURE CITED

 
The existence of transmissible spongiform encephalopathies, such as bovine spongiform encephalopathy in cattle and scrapie in sheep, is a significant hazard to livestock industries. Traditionally, culling of affected animals (and animals sharing the same production area) has been the standard method of scrapie control in the sheep industry. Unfortunately, this method is not effective with prion diseases, due to their long incubation time and unusual method of transmission.

A genetic component to scrapie susceptibility has been known for many years. The 3 most important genetic markers associated with scrapie susceptibility are located at codons 136, 154, and 171 of the prion (PRNP) gene (for review see Baylis and Goldmann, 2004). The PRNP haplotype encoding alanine, arginine, and arginine (ARR) at the respective 136, 154, and 171 positions is associated with increased resistance to scrapie, whereas the valine, arginine, and glutamine haplotype (VRQ) is associated with increased susceptibility to scrapie. The scrapie susceptibility of 3 other common PRNP haplotypes (ARQ, AHQ, and ARH) is intermediate or unknown.

Many countries currently have scrapie eradication plans utilizing these genetic markers (Byrne, 2003). Several researchers have investigated possible antagonistic associations between the PRNP locus and milk (de Vries et al., 2005), performance (Alexander et al., 2005), and growth (Brandsma et al., 2004) traits. However, consistent evidence supporting antagonistic associations has not been found. The objective of this study was to test for associations between PRNP haplotypes and a comprehensive set of growth, carcass, and meat quality traits in an F₂ population of Dorset x Romanov sheep.

	MATERIALS AND METHODS

Top Abstract INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION IMPLICATIONS LITERATURE CITED

 
Animal Populations and Phenotypic Data
Sheep were produced to investigate the chromosomal location, gene action, and phenotypic effects of the callipyge locus (Freking et al., 1998a). Nine Dorset rams were mated with 255 Romanov ewes to produce Dorset x Romanov F₁ lambs. Eight F₁ sires and 138 F₁ dams (from 9 Dorset grandsires and 114 Romanov grand-dams) produced 432 F₂ offspring in 1994 and 1995. Traits included in the current study are listed in Table 1. Weights were recorded at birth and at an average of 8 (weaning), 12, and 20 wk of age. Preweaning ADG was calculated using the weight gain from birth to weaning and age at weaning. Postweaning ADG from 12 to 20 wk of age was calculated in a similar manner.

Carcasses were split along the dorsal midline and the length of the carcass was measured from the anterior edge of the first rib to the anterior edge of the aitchbone. Metacarpal bone length was measured as an additional indicator of skeletal development. Fat depths were measured at the midpoint of the longissimus muscle between the 12th and 13th ribs and at the midline of the fourth sacral vertebra. The left side of the carcass was retained for later use in shear force determination. The right side of the carcass was cut between the fifth and sixth ribs and between the last 2 lumbar vertebrae to produce 3 carcass subsections. Subsections from the right side corresponded to anterior (shoulder, neck, foreshank, and breast), middle (loin, rib, and flank), and posterior (sirloin, leg, and hindshank) portions of the carcass. Each subsection was individually weighed. Longissimus muscle depth, width, surface area, and subjective marbling score (on a scale from 0 = devoid to 600 = moderate) were measured between the 12th and 13th ribs.

Proximate chemical analysis was performed on each of the carcass subsections. Each subsection was frozen and ground separately to measure ash, water, protein, and ether extract (fat) content (AOAC, 1990).

From the left side of the carcass, loin chops (2.5 cm thick) were collected for use in shear force determination. Loin chops were aged at 4°C for 14 d and stored at –20°C until shear force measurement. Storage duration ranged from 2 wk to 5 mo. Before shear force measurement, chops were thawed at 5°C, broiled to an internal temperature of 40°C, and then turned and broiled to an internal temperature of 75°C using an open-hearth electric broiler (Farberware, Bronx, NY). Loin chops were allowed to cool at 4°C for 24 h before 6 cores (1.27 cm diameter each) from 3 chops were obtained, making sure that the cores ran parallel to the muscle fibers. Each core was sheared once using an Instron Universal Testing Machine (model 1132, Instron, Canton, MA) with a Warner-Bratzler shear attachment, a 50-kg load cell, and a cross-head speed of 50 mm/min. Shear force was calculated as the mean shear force of the 6 cores.

Collection of Genotypic Data
Genomic DNA was extracted from blood, liver, or spleen tissue of 9 Dorset grandsires, 8 Romanov grand-dams, and all F₁ parents and F₂ lambs using Gentra Generation Capture kits (Gentra Systems Inc., Minneapolis, MN) or a standard saturated salt procedure (Miller et al., 1988). Sheep were genotyped at 6 microsatellite loci (Figure 1) using the standard PCR protocol of de Gortari et al. (1998). Five of these markers were previously linkage-mapped to ovine chromosome 13 (Maddox et al., 2001; http://rubens.its.unimelb.edu.au/~JILLM/jill.htm). The sixth marker, \PRNP_S11, was not linkage-mapped to chromosome 13, but was identified within the ovine genome sequence (Genbank Accession No. U67922) that contains the PRNP gene (Geldermann et al., 2003).

View larger version (9K): [in this window] [in a new window]   Figure 1. Linkage map of ovine chromosome 13 markers used in the current study. Names of anonymous microsatellite loci are preceded with a backslash symbol, following COGNOSAG nomenclature guidelines (Andresen et al., 1995). Units are in centimorgans.

To account for the effects of callipyge genotypes on carcass and meat quality traits, all sheep were genotyped at the callipyge locus using a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer assay described by Freking et al. (2002). Animals were genotyped as C^MatC^Pat, C^MatN^Pat, N^MatC^Pat, or N^MatN^Pat at the callipyge locus, with C representing the mutant allele and N representing the wild-type allele. Superscripts denoted the maternal (Mat) or paternal (Pat) origin of each allele. The 2 classes of heterozygous sheep (C^MatN^Pat and N^MatC^Pat) were differentiated using flanking marker information for ovine chromosome 18 (Freking et al., 1998a).

Linkage distances for chromosome 13 were calculated using CRIMAP version 2.4 (Washington University, St. Louis, MO), and compared with the reported linkage distances (http://rubens.its.unimelb.edu.au/~JILLM/jill.htm). Genotyping errors and deviations from the reported linkage distances were investigated using the CHROMPIC option of CRIMAP. The lack of genotypic information and the inability to resolve pedigree inconsistencies using genotypic data resulted in deletion of data collected on 13 F₂ lambs. No recombinant gametes were detected within the interval containing PRNP_136, PRNP_154, PRNP_171, and \PRNP_S11 loci (Figure 1), and haplotypes were determined based on phase information. The probability of grandparental origin (Dorset or Romanov) of the PRNP haplotype for each gamete was estimated using Genoprob (Thallman, 2002). Following Genoprob analysis, the \PRNP_S11 locus was no longer considered part of the PRNP haplotypes, because this locus has no known association with scrapie susceptibility.

Five PRNP haplotypes of Dorset origin (ARR, ARQ, VRQ, AHQ, and ARH) and 3 of Romanov origin (ARR, ARQ, and VRQ) were segregating in the F₂ population (Table 2). Because of the low frequency of the Dorset ARH haplotype (n = 4), these data were removed from subsequent analyses. Seven probabilities were calculated for each gamete, each corresponding to the probability of inheriting 1 of the 7 breed-specific PRNP haplotypes. Probabilities summed to 2 within each lamb, as each F₂ lamb contained 2 PRNP haplotypes. Breed of origin probabilities were distributed in a bimodal manner, with the majority of probabilities greater than 0.95 or less than 0.05. The small number of intermediate probabilities was most likely due to incomplete genotypic information or low marker informativeness for some F₂ chromosomes.

Fitting the effect of PRNP haplotype in this manner, rather than including the assumed PRNP haplotype in the statistical model as a class variable (as in other studies), allows the PRNP haplotype to be weighted using the probabilities of breed origin. Probabilities located at the upper and lower extremes of the distribution will be weighted more heavily in the analyses than will intermediate probabilities. The power to detect true effects of the resistant ARR haplotype increases as the contribution of more uncertain genotypes (intermediate probabilities) is reduced.

A single contrast among regression coefficients of PRNP haplotype covariates was constructed within each breed of origin. For Dorset, the ARR coefficient was compared with the average of ARQ, VRQ, and AHQ (1, –0.33, –0.33, –0.33), whereas for Romanov, ARR was compared with ARQ and VRQ (1, –0.5, –0.5). Contrasts tested the difference between the resistant ARR haplotype and the average of the other haplotypes, consistent with the use of haplotype information by sheep industries in many countries.

Freking et al. (1999) discussed the nonnormal distribution of Warner-Braztler shear force residuals in these data. Dispersion of residuals increased with greater values of shear force, indicating a nonnormal distribution. Shear force values were transformed by natural logarithm before statistical analysis to account for the proportional relationship between standard deviations and means of callipyge genotypes.

Meat quality traits were analyzed using a model that included the random effect of sire, fixed effects of birth year, sex, and callipyge genotype, and 7 covariates, as described above. For analysis of transformed Warner-Bratzler shear force data, callipyge genotypes were grouped into 3 categories: N^MatC^Pat, C^MatC^Pat, and NN (which consisted of N^MatN^Pat and C^MatN^Pat sheep). For analysis of longissimus marbling data, callipyge genotypes were grouped into 4 categories (C^MatC^Pat, C^MatN-^Pat, N^MatC^Pat, and N^MatN^Pat). For shear force, a birth year x callipyge genotype interaction was included to account for the differing distributions of shear force values in sheep born in 1994 and 1995 (Freking et al., 1999). A covariate of chilled carcass weight and the interaction between chilled carcass weight and callipyge genotype were included in the model for both meat quality traits. To test for associations between meat quality traits and PRNP haplotypes, breed-specific contrasts were constructed as described above.

	RESULTS

Top Abstract INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION IMPLICATIONS LITERATURE CITED

 
The genotypic distribution of PRNP haplotypes in the F₂ population is presented in Table 2. Frequencies of the most resistant and most susceptible haplotypes (ARR and VRQ, respectively; Baylis and Goldmann, 2004) were 0.333 and 0.216, respectively. Frequency of the AHQ haplotype was only 0.060.

Dorset and Romanov haplotype frequencies differed greatly (Table 3), supporting the decision to include separate covariates for Romanov- and Dorset-derived haplotypes in statistical models. Because of this situation, the precision of estimates of the contrast of the ARR regression coefficient compared with the average of the other coefficients differed between breeds of origin. Using carcass traits as an example, there were 207 gametes of Dorset origin with the ARR haplotype, and 169 Dorset gametes with ARQ, VRQ, or AHQ haplotypes. For Romanov, there were 27 ARR gametes, compared with 305 ARQ or VQR gametes.

	DISCUSSION

Top Abstract INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION IMPLICATIONS LITERATURE CITED

A number of studies have investigated associations between PRNP genotypes and economically important traits (Prokopova et al., 2002; de Vries et al., 2004, 2005; Alexander et al., 2005). However, only a single study (Brandsma et al., 2004) found multiple associations of PRNP genotypes with traits. In the study by Brandsma et al. (2004), associations were detected between the ARR haplotype and breeding values for litter size and 135-d weight in Dutch Texel sheep. Sheep homozygous for the ARR haplotype had greater breeding values for litter size and lesser breeding values for 135-d weight than sheep with zero or one copy of the ARR haplotype. In contrast, the current study did not detect an association between PRNP haplotypes and growth traits. However, the differing breed composition of the 2 studies makes direct comparison difficult. The genetic background (breed) of the population under study may influence associations between PRNP haplotypes and economically important traits.

In general, it is unlikely that detection of unfavorable associations of specific PRNP haplotypes with phenotypic variation of pertinent traits will be a common occurrence in sheep. There are several reasons for this statement. Most traits of economic importance are largely quantitative in nature, although the number of QTL reported in the scientific literature continues to increase. The PRNP locus on chromosome 13 segregates independently of loci on the other 26 ovine chromosomes. Within chromosome 13, associations between loci depend on linkage disequilibrium, a temporary phenomenon. If associations are detected, the PRNP haplotype resistant to scrapie may in fact be favorably, rather than unfavorably, associated with phenotypic variation. Consistent with goals of the US national scrapie eradication program and experimental results to date, increasing the frequency of resistant PRNP haplotypes should be considered a selection goal of breed development programs.

	IMPLICATIONS

Top Abstract INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION IMPLICATIONS LITERATURE CITED

 
With the continuing concern about scrapie and other transmissible spongiform encephalopathies, the application of methods to reduce the incidence of these diseases is crucial to the livestock industry. Genetic markers associated with scrapie resistance are used to reduce the incidence of scrapie in sheep populations worldwide. However, before breeding programs focus on intensive selection for scrapie-resistant haplotypes, it is important to understand relationships between haplotypes and economically important traits. The current study found little evidence of antagonistic relationships between the resistant prion haplotype and growth, carcass, or meat quality traits in crossbred sheep of Dorset and Romanov origin. Within the Dorset and Romanov breeds, advantages of selection for scrapie resistance seem to outweigh any potential adverse correlated responses.

	Footnotes

 
¹ Mention of a trade name, proprietary product, or specified equipment does not constitute a guarantee or warranty by the USDA and does not imply approval to the exclusion of other products that may be suitable.

² The authors thank J. K. Carnahan (US Meat Animal Research Center, Clay Center, NE) for providing genotypes at prion codons 136, 154, and 171.

³ Current address: ASC 2118, Ferris State University, Big Rapids, MI 49307.

⁴ Corresponding author: leymaster{at}email.marc.usda.gov

Received for publication August 22, 2005. Accepted for publication November 13, 2005.

	LITERATURE CITED

Top Abstract INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION IMPLICATIONS LITERATURE CITED

 


Alexander, B. M., R. H. Stobart, W. C. Russell, K. I. O’Rourke, G. S. Lewis, J. R. Logan, J. V. Duncan, and G. E. Moss. 2005. The incidence of genotypes at codon 171 of the PRNP protein gene (PRNP) in five breeds of sheep and production traits of ewes associated with those genotypes. J. Anim. Sci. 83:455–459.[Abstract/Free Full Text]

Andresen, E., T. E. Broad, S. Brown, D. W. Cooper, L. Distasio, C. H. S. Dolling, M. Fleet, D. F. Hill, J. J. Lauvergne, R. S. Lundie. 1995. Revised guidelines for gene nomenclature in ruminants 1993. Genet. Sel. Evol. 27:89–93.

AOAC. 1990. Official Methods of Analysis. 15th ed. Assoc. Off. Anal. Chem., Arlington, VA.

Baylis, M., and W. Goldmann. 2004. The genetics of scrapie in sheep and goats. Curr. Mol. Med. 4:385–396.[Medline]

Brandsma, J. H., L. L. G. Janss, and A. H. Visscher. 2004. Association between PrP genotypes and littersize and 135 d weight in Texel sheep. Livest. Prod. Sci. 85:59–64.

Byrne, D. 2003. Eradication of transmissible spongiform encephalopathy (European Commission Regulation 1915/2003). Off. J. Eur. Union L 283:29–33.

de Gortari, M. J., B. A. Freking, S. M. Kappes, K. A. Leymaster, A. M. Crawford, R. T. Stone, and C. W. Beattie. 1998. A second generation linkage map of the sheep genome. Mamm. Genome 9:204–209.[Medline]

de Vries, F., N. Borchers, H. Hamann, C. Drogenmuller, S. Reinecke, W. Lupping, and O. Distl. 2004. Associations between the PRNP protein genotype and performance traits of meat breeds of sheep. Vet. Rec. 155:140–143.[Abstract/Free Full Text]

de Vries, F., H. Hamann, C. Drogenmuller, M. Ganter, and O. Distl. 2005. Analysis of associations between the PRNP protein genotypes and production traits in East Friesian milk sheep. J. Dairy Sci. 88:392–398.[Abstract/Free Full Text]

Freking, B. A., J. W. Keele, C. W. Beattie, S. M. Kappes, T. P. L. Smith, T. S. Sonstegard, M. K. Nielsen, and K. A. Leymaster. 1998a. Evaluation of the ovine callipyge locus: I. Relative chromosomal position and gene action. J. Anim. Sci. 76:2062–2071.[Abstract/Free Full Text]

Freking, B. A., J. W. Keele, M. K. Nielsen, and K. A. Leymaster. 1998b. Evaluation of the ovine callipyge locus: II. Genotypic effects on growth, slaughter, and carcass traits. J. Anim. Sci. 76:2549–2559.[Abstract/Free Full Text]

Freking, B. A., J. W. Keele, S. D. Shackelford, T. L. Wheeler, M. Koohmaraie, M. K. Nielsen, and K. A. Leymaster. 1999. Evaluation of the ovine callipyge locus: III. Genotypic effects on meat quality traits. J. Anim. Sci. 77:2336–2344.[Abstract/Free Full Text]

Freking, B. A., S. K. Murphy, A. A. Wylie, S. J. Rhodes, J. W. Keele, K. A. Leymaster, R. L. Jirtle, and T. P. L. Smith. 2002. Identification of the single base change causing the callipyge muscle hypertrophy phenotype, the only known example of polar over-dominance in mammals. Genome Res. 12:1496–1506.[Abstract/Free Full Text]

Geldermann, H., S. Pruess, J. Eckert, Y. Han, and K. Ollesch. 2003. Analysis of polymorphic microsatellites within the bovine and ovine PRNP protein (PRNP) genes. Anim. Genet. 34:283–289.[Medline]

Maddox, J. F., K. P. Davies, A. M. Crawford, D. J. Hulme, D. Vaiman, E. P. Cribiu, P. Edmond, B. A. Freking, K. J. Beh, N. E. Cockett, N. Kang, C. D. Riffkin, R. Drinkwater, S. S. Moore, K. G. Dodds, J. M. Lumsden, T. C. van Stijn, S. H. Phua, D. L. Adelson, H. R. Burkin, J. E. Broom, J. Buitkamp, L. Cambridge, W. T. Cushwa, E. Gerard, S. M. Galloway, B. Harrison, R. J. Hawken, S. Hiendleder, H. M. Henry, J. F. Medrano, K. A. Paterson, L. Schibler, R. T. Stone, and B. van Hest. 2001. An enhanced linkage map of the sheep genome comprising more than 1000 loci. Genome Res. 11:1275–1289.[Abstract/Free Full Text]

Miller, S. A., D. D. Dykes, and H. F. Polesky. 1988. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 16:1215.[Free Full Text]

Prokopova, L., R. M. Lewis, W. S. Dingwall, and G. Simm. 2002. Scrapie genotype: A correlation with lean growth rate? CD-ROM Commun. No. 13–44 in Proc. 7th World Congr. Genet. Appl. Livest. Prod., Montpellier, France.

Shackelford, S. D., K. A. Leymaster, T. L. Wheeler, and M. Koohmaraie. 2004. Lamb meat quality progress report number 2. Preliminary results of an evaluation of effects of breed of sire on carcass composition and sensory traits of lamb. http://www.marc.usda.gov/npa/marc Accessed June 13, 2005.

Thallman, R. M. 2002. Users’ manual for GenoProb 2.700. USDA-ARS, Clay Center, NE.

This article has been cited by other articles:

				R. M. Sawalha, S. Brotherstone, N. R. Lambe, and B. Villanueva Association of the prion protein gene with individual tissue weights in Scottish Blackface sheep J Anim Sci, August 1, 2008; 86(8): 1737 - 1746. [Abstract] [Full Text] [PDF]

				S. Salaris, S. Casu, and A. Carta Investigating the relationship between the prion protein locus and udder morphology traits and milk yield in Sardinian sheep J Anim Sci, November 1, 2007; 85(11): 2840 - 2845. [Abstract] [Full Text] [PDF]

				G. D. Snowder, L. D. Van Vleck, L. V. Cundiff, G. L. Bennett, M. Koohmaraie, and M. E. Dikeman Bovine respiratory disease in feedlot cattle: Phenotypic, environmental, and genetic correlations with growth, carcass, and longissimus muscle palatability traits J Anim Sci, August 1, 2007; 85(8): 1885 - 1892. [Abstract] [Full Text] [PDF]

				R. M. Sawalha, S. Brotherstone, W. Y. N. Man, J. Conington, L. Bunger, G. Simm, and B. Villanueva Associations of polymorphisms of the ovine prion protein gene with growth, carcass, and computerized tomography traits in Scottish Blackface lambs J Anim Sci, March 1, 2007; 85(3): 632 - 640. [Abstract] [Full Text] [PDF]

This Article Abstract Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Isler, B. J. Articles by Leymaster, K. A. Search for Related Content PubMed PubMed Citation Articles by Isler, B. J. Articles by Leymaster, K. A.