Skip to main content
SpringerLink
Log in

Genetic Variability and Linkage Disequilibrium Patterns in the Bovine DNAJA1 Gene

  • Research
  • Published:
Molecular Biotechnology Aims and scope Submit manuscript

Abstract

Correlation between expression level of the bovine DNAJA1 gene and meat tenderness was recently found in Charolais longissimus thoracis muscle samples, suggesting that this gene could play an important role in meat tenderness. Here, we report the validation of polymorphisms within the bovine DNAJA1 gene, and the haplotype variability and extent of linkage disequilibrium in the three main French beef breeds (Blonde d’Aquitaine, Charolais, Limousin). Genotyping 18 putative SNPs revealed that 16 SNPs were polymorphic within the breeds tested. Two SNPs were removed from further analyses as one SNP had a low genotyping call rate, while the other SNP was not in Hardy–Weinberg equilibrium. The degree of heterozygosity observed for the remaining 14 SNPs varied between breeds, with Charolais being the breed with the highest genetic variation and Blonde d’Aquitaine the lowest. Linkage disequilibrium and haplotype structure of DNAJA1 were different between breeds. Eighteen different haplotypes, including three shared by all breeds, were discovered, and two to three tag SNPs (depending on the breed) are sufficient to capture all the genetic variability seen in these haplotypes. The results of this study will facilitate the design of optimal future association studies evaluating the role of the DNAJA1 gene in meat tenderness.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  1. Casas, E., Keele, J. W., Shackelford, S. D., Koohmaraie, M., Sonstegard, T. S., Smith, T. P. L., et al. (1998). Association of the muscle hypertrophy locus with carcass traits in beef cattle. Journal of Animal Science, 76, 468–473.

    CAS  Google Scholar 

  2. Keele, J. W., Shackelford, S. D., Kappes, S. M., Koohmaraie, M., & Stone, R. T. (1999). A region on bovine chromosome 15 influences beef longissimus tenderness in steers. Journal of Animal Science, 77, 1364–1371.

    CAS  Google Scholar 

  3. Casas, E., Shackelford, S. D., Keele, J. W., Stone, R. T., Kappes, S. M., & Koohmaraie, M. (2000). Quantitative trait loci affecting growth and carcass composition of cattle segregating alternate forms of myostatin. Journal of Animal Science, 78, 560–569.

    CAS  Google Scholar 

  4. Casas, E., Stone, R. T., Keele, J. W., Shackelford, S. D., Kappes, S. M., & Koohmaraie, M. (2001). A comprehensive search for quantitative trait loci affecting growth and carcass composition of cattle segregating alternative forms of the myostatin gene. Journal of Animal Science, 79, 854–860.

    CAS  Google Scholar 

  5. Casas, E., Shackelford, S. D., Keele, J. W., Koohmaraie, M., Smith, T. P. L., & Stone, R. T. (2003). Detection of quantitative trait loci for growth and carcass composition in cattle. Journal of Animal Science, 81, 2976–2983.

    CAS  Google Scholar 

  6. Drinkwater, R. D., Li, Y., Lenane, I., Davis, G. P., Shorthose, R., Harrison, B. E., et al. (2006). Detecting quantitative trait loci affecting beef tenderness on bovine chromosome 7 near calpastatin and lysil oxidase. Australian Journal of Experimental Agriculture, 46, 159–164.

    Article  CAS  Google Scholar 

  7. Alexander, L. J., MacNeil, M. D., Geary, T. W., Snelling, W. M., Rule, D. C., & Scanga, J. A. (2007). Quantitative trait loci with additive effects on palatability and fatty acid composition of meat in a Wagyu-Limousin F2 population. Animal Genetics, 38, 506–513.

    Article  CAS  Google Scholar 

  8. Davis, G. P., Moore, S. S., Drinkwater, R. D., Shorthose, W. R., Loxton, I. D., Barendse, W., et al. (2007). QTL for meat tenderness in the M. Longissimus lumborum of cattle. Animal Genetics, 39, 40–45.

    Article  CAS  Google Scholar 

  9. Gutiérrez-Gil, B., Wiener, P., Nute, G. R., Burton, D., Gill, J. L., Wood, J. D., et al. (2008). Detection of quantitative trait loci for meat quality traits in cattle. Animal Genetics, 39, 51–61.

    Article  Google Scholar 

  10. Barendse, W. J. (2002). DNA markers for meat tenderness. International patent application PCT/AU02/00122; International patent publication WO 02/064820 A1.

  11. Schenkel, F. S., Miller, S. P., Jiang, Z., Mandell, I. B., Ye, X., Li, H., et al. (2006). Association of a single nucleotide polymorphism in the calpastatin gene with carcass and meat quality traits of beef cattle. Journal of Animal Science, 84, 291–299.

    CAS  Google Scholar 

  12. Page, B. T., Casas, E., Heaton, M. P., Cullen, N. G., Hyndman, D. L., Morris, C. A., et al. (2002). Evaluation of single-nucleotide polymorphism in CAPN1 for association with meat tenderness in cattle. Journal of Animal Science, 80, 3077–3085.

    CAS  Google Scholar 

  13. White, S. N., Casas, E., Wheeler, T. L., Shackelford, S. D., Koohmaraie, M., Riley, D. G., et al. (2005). A new single nucleotide polymorphism in CAPN1 extends the current tenderness marker test to include cattle of Bos indicus, Bos Taurus, and crossbred descent. Journal of Animal Science, 83, 2001–2008.

    CAS  Google Scholar 

  14. Page, B. T., Casas, E., Quaas, R. L., Thallman, R. M., Wheeler, T. L., Shackelford, S. D., et al. (2004). Association of markers in the bovine CAPN1 gene with meat tenderness in large crossbred populations that sample influential industry sires. Journal of Animal Science, 82, 3474–3481.

    CAS  Google Scholar 

  15. Casas, E., White, S. N., Wheeler, T. L., Shackelford, S. D., Koohmaraie, M., Riley, D. G., et al. (2006). Effects of calpastatin and μ-calpain markers in beef cattle on tenderness traits. Journal of Animal Science, 84, 520–525.

    Article  CAS  Google Scholar 

  16. Morris, C. A., Cullen, N. G., Hickey, S. M., Dobbie, P. M., Veenvliet, B. A., Manley, T. R., et al. (2006). Genotypic effects of calpain 1 and calpastatin on the tenderness of cooked M. longissimu dorsi steaks from Jersey x Limousin, Angus and Hereford-cross cattle. Animal Genetics, 37, 411–414.

    Article  CAS  Google Scholar 

  17. Costello, S., O’Doherty, E., Troy, D. J., Ernst, C. W., Kim, K.-S., Stapelton, P., et al. (2007). Association of polymorphisms in the calpain I, calpain II and growth hormone genes with tenderness in bovine M. longissimus dorsi. Meat Science, 75, 551–557.

    Article  CAS  Google Scholar 

  18. Van Eenennaam, A. L., Li, J., Thallman, R. M., Quaas, R. L., Dikeman, M. E., Gill, C. A., et al. (2007). Validation of commercial DNA tests for quantitative beef quality traits. Journal of Animal Science, 85, 891–900.

    Article  CAS  Google Scholar 

  19. Wheeler, T. L., Shackelford, S. D., Casas, E., Cundiff, L. V., & Koohmaraie, M. (2001). The effects of Piedmontese inheritance and myostatin genotype on the palatability of longissimus thoracis, gluteus medius, semimembranosus, and biceps femoris. Journal of Animal Science, 79, 3069–3074.

    CAS  Google Scholar 

  20. Lines, S. S., Pitchford, W. S., Kruk, Z. A., & Bottema, C. D. K. (2009). Limousin myostatin F94L variants affects semitendinosus tenderness. Meat Science, 81, 126–131.

    Article  CAS  Google Scholar 

  21. Di Stasio, L., Brugiapaglia, A., Destefanis, G., Albera, A., & Sartore, S. (2003). GH1 as candidate gene for variability of meat production traits in Piemontese cattle. Journal of Animal Breeding and Genetics, 120, 358–361.

    Article  CAS  Google Scholar 

  22. Schenkel, F. S., Miller, S. P., Ye, X., Moore, S. S., Nkrumah, J. D., Li, C., et al. (2005). Association of single nucleotide polymorphisms in the leptin gene with carcass and meat quality traits of beef cattle. Journal of Animal Science, 83, 2009–2020.

    CAS  Google Scholar 

  23. Barendse, W., Harrison, B. E., Bunch, R. J., & Thomas, M. B. (2008). Variation at the Calpain 3 gene is associated with meat tenderness in zebu and composite breeds of cattle. BMC Genetics, 9, 41.

    Article  CAS  Google Scholar 

  24. Bernard, C., Cassar-Malek, I., Le Cunff, M., Dubroeucq, H., Renand, G., & Hocquette, J.-F. (2007). New indicators of beef sensory quality revealed by expression of specific genes. Journal of Agricultural and Food Chemistry, 55, 5229–5237.

    Article  CAS  Google Scholar 

  25. Gotoh, T., Terada, K., Oyadomari, S., & Mori, M. (2004). Hsp70-DnaJ chaperone pair prevents nitric oxide- and CHOP-induced apoptosis by inhibiting translocation of Bax to mitochondria. Cell Death and Differentiation, 11, 390–402.

    Article  CAS  Google Scholar 

  26. Lin, C. H., Yeakley, J. M., McDaniel, T. K., & Shen, R. (2009). Medium- to high-throughput SNP genotyping using VeraCode microbeads. Methods in Molecular Biology, 496, 129–142.

    Article  CAS  Google Scholar 

  27. Barrett, J. C., Fry, B., Maller, J., & Daly, M. J. (2005). Haploview: Analysis and visualization of LD and haplotype maps. Bioinformatics, 21, 263–265.

    Article  CAS  Google Scholar 

  28. Wang, N., Akey, J. M., Zhang, K., Chakraborty, R., & Jin, L. (2002). Distribution of recombination crossovers and the origin of haplotype blocks: The interplay of population history, recombination, and mutation. American Journal of Human Genetics, 71, 1227–1234.

    Article  CAS  Google Scholar 

  29. Stephens, M., Smith, N. J., & Donnelly, P. (2001). A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics, 68, 978–989.

    Article  CAS  Google Scholar 

  30. De Bakker, P. I., Yelensly, R., Pe’er, I., Gabriel, S. B., Daly, M. J., & Altshuler, D. (2005). Efficiency and power in genetic association studies. Nature Genetics, 37, 1217–1223.

    Article  CAS  Google Scholar 

  31. The Bovine HapMap Consortium. (2009). Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science, 324, 528–532.

    Article  CAS  Google Scholar 

  32. Moazami-Goudarzi, K., Laloe, D., Furet, J. P., & Grosclaude, F. (1997). Analysis of genetic relationships between 10 cattle breeds with 17 microsatellites. Animal Genetics, 28, 338–345.

    Article  CAS  Google Scholar 

  33. Loftus, R. T., Ertugrul, O., Harba, A. H., El-Barody, A., MacHugh, D. E., Park, S. D. E., et al. (1999). A microsatellite survey of cattle from a centre of origin: The Near East. Molecular Ecology, 8, 2015–2022.

    Article  CAS  Google Scholar 

  34. Maudet, C., Luikart, G., & Taberlet, P. (2002). Genetic diversity and assignment tests among seven French cattle breeds based on microsatellite DNA analysis. Journal of Animal Science, 80, 942–950.

    CAS  Google Scholar 

  35. Mateus, J. C., Penedo, M. C. D., Alves, V. C., Ramos, M., & Rangel-Figueiredo, T. (2004). Genetic diversity and differentiation in Portuguese cattle breeds using microsatellites. Animal Genetics, 35, 106–113.

    Article  CAS  Google Scholar 

  36. European Cattle Genetic Diversity Consortium. (2006). Marker-assisted conservation of European cattle breeds: An evaluation. Animal Genetics, 37, 475–481.

    Article  Google Scholar 

  37. MacNeil, M. D., Cronin, M. A., Blackburn, H. D., Richards, C. M., Lockwood, D. R., & Alexander, L. J. (2007). Genetic relationships between feral cattle from Chirikof Island, Alaska and other breeds. Animal Genetics, 38, 193–197.

    Article  CAS  Google Scholar 

  38. Zhang, G. X., Wang, Z. G., Chen, W. S., Wu, C. X., Han, X., Chang, H., et al. (2007). Genetic diversity and population structure of indigenous yellow cattle breeds of China using 30 microsatellite markers. Animal Genetics, 38, 550–559.

    Article  CAS  Google Scholar 

  39. Lewontin, R. C. (1964). The interaction of selection and linkage. I. General considerations; heterotic models. Genetics, 40, 250–256.

    Google Scholar 

  40. Hill, W. G., & Robertson, A. (1968). Linkage disequilibrium in finite populations. Theoretical and Applied Genetics, 38, 226–231.

    Article  Google Scholar 

  41. Ardlie, K. G., Kruglyak, L., & Seielstad, M. (2002). Patterns of linkage disequilibrium in the human genome. Nature Review Genetics, 3, 299–309.

    Article  CAS  Google Scholar 

  42. Du, F.-X., Clutter, A., & Lohuis, M. M. (2007). Characterizing linkage disequilibrium in pig populations. International Journal of Biological Sciences, 3, 166–178.

    CAS  Google Scholar 

  43. Zhao, H., Nettleton, D., & Dekkers, J. C. M. (2007). Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between single nucleotide polymorphisms. Genetics Research, 89, 1–6.

    Article  CAS  Google Scholar 

  44. Sargolzaei, M., Schenkel, F. S., Jansen, G. B., & Schaeffer, L. R. (2008). Extent of linkage disequilibrium in Holstein cattle in North America. Journal of Dairy Science, 91, 2106–2117.

    Article  CAS  Google Scholar 

  45. McKay, S. D., Schnabel, R. D., Murdoch, B. M., Matukumalli, L. K., Aerts, J., Coppieters, W., et al. (2007). Whole genome linkage disequilibrium maps in cattle. BMC Genetics, 8, 74.

    Article  CAS  Google Scholar 

  46. Khatkar, M. S., Nicholas, F. W., Collins, A. R., Zenger, K. R., Cavanagh, J. A. L., Barris, W., et al. (2008). Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel. BMC Genomics, 9, 197.

    Article  CAS  Google Scholar 

  47. Kim, E.-S., & Kirkpatrick, B. W. (2009). Linkage disequilibrium in the North American Holstein population. Animal Genetics, 40, 279–288.

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors are grateful to the International Bovine Genome Sequencing Consortium for the identification and submission into the public domain of the bovine SNPs used during this work. The authors also would like to thank the following breeding companies for providing blood samples for the animals tested in this study: Midatest, UALC, UCATRC and UCEF. This work was funded by INRA, the Université de Limoges, Agence Nationale de la Recherche (contracts ANR-05-GANI-005 and ANR-05-GANI-017-01) and APIS GENE (contract 01-2005-QualviGenA-02).

Author information

Author notes

  1. Amandine Marty

    Present address: Euralis, 31700, Mondonville, France

Authors and Affiliations

  1. Plateforme Génomique, Génopole Toulouse Midi-Pyrénées, 31320, Auzeville, France

    Amandine Marty

  2. LABOGENA, Domaine de Vilbert, 78352, Jouy-en-Josas, France

    Yves Amigues

  3. Laboratoire de Génétique Cellulaire, INRA/ENVT, UMR444, 31326, Castanet Tolosan, France

    Bertrand Servin

  4. Unité Génétique Animale et Biologie Intégrative, INRA/AgroParisTech, UMR1313, Domaine de Vilbert, 78352, Jouy-en-Josas, France

    Gilles Renand

  5. Unité de Génétique Moléculaire Animale, Faculté des Sciences, INRA/Université de Limoges, UMR1061, 123 Avenue Albert Thomas, 87060, Limoges, France

    Hubert Levéziel & Dominique Rocha

Authors
  1. Amandine Marty
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yves Amigues
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Bertrand Servin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Gilles Renand
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hubert Levéziel
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Dominique Rocha
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Dominique Rocha.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Marty, A., Amigues, Y., Servin, B. et al. Genetic Variability and Linkage Disequilibrium Patterns in the Bovine DNAJA1 Gene. Mol Biotechnol 44, 190–197 (2010). https://doi.org/10.1007/s12033-009-9228-y

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12033-009-9228-y

Keywords

Search

Navigation