نوع مقاله : مقاله پژوهشی

نویسندگان

1 دانشجوی دکتری تخصصی، گروه علوم دامی، پردیس کشاورزی و منابع طبیعی، دانشگاه ‏تهران، کرج، ایران

2 دانشیار، گروه علوم دامی، پردیس کشاورزی و منابع طبیعی، دانشگاه تهران، کرج، ایران

3 دانش‌آموخته دکتری، گروه علوم دامی، پردیس کشاورزی و منابع طبیعی، دانشگاه تهران، کرج، ایران

4 محقق، گروه علوم دامی، دانشکده کشاورزی و علوم محیط زیست، دانشگاه جورجیا، جورجیا، ایالات متحده آمریکا

5 استادیار، گروه علوم دامی، دانشکده کشاورزی، دانشگاه تبریز، تبریز، ایران

6 استاد، گروه علوم دامی، پردیس کشاورزی و منابع طبیعی، دانشگاه تهران، کرج، ایران

چکیده

انتخاب ژنتیکی برای افزایش تولید شیر و سودآوری اقتصادی در صنعت گاوهای شیری با کاهش عملکرد تولیدمثلی از جمله کاهش زنده‌مانی رویان و افزایش از دست رفتن آبستنی همراه بوده است. در پژوهش حاضر، هدف اصلی، استفاده از پروفایل ترانسکریپتوم بافت آندومتریوم و جسم زرد دو دسته از گاوهای شیری هلشتاین با باروری بالا و پایین، به منظور شناسایی ژن‌های مؤثر در حفظ باروری به‌ویژه اوایل دوره آبستنی است. در تجزیه داده‌های RNA-Seq برای مقایسه بیان ژنی، 4538 ژن استخراج شد که در مجموع 1466 ژن تفاوت بیانی معنی‌داری نشان دادند (P<0.000001, Fold change<0.5). سپس با مقایسه ژن‌های مربوطه در میان پروفایل‌های ترانسکریپتوم، ژن‌های مشترک بین بافت آندومتریوم (روزهای هفت و 13 چرخه فحلی) و جسم زرد (در روز 13 چرخه فحلی) شامل ژن­های SYNM، PARM1، NXPE2، NT5DC3، COL4A3، COL12A1، ALPK3، ADAMDEC1، SERPINA14، S100A9، PI16، OAS1X، MSTN، MASP1، CD83، CA2، C2، C5، JSP.1 و SAA3 مشخص شدند. بررسی نتایج حاشیه‌نویسی این ژن‌ها ثابت کرد که در فرآیند اصلی مسیرهای متابولیک و سیگنالینگ مرتبط با سیستم حمل‌و‌نقل یونی، التهاب، عملکرد سیستم ایمنی بدن و ساختار ماتریس سلولی دارای نقش می‌باشند. پژوهش حاضر می‌‌تواند بینش جدیدی از شواهد مولکولی در راستای سازوکارهای زیستی پروفایل ترانسکریپتوم در محیط رحم و بیومارکرهای مرتبط با باروری در گاوهای شیری ارائه دهد.

کلیدواژه‌ها

عنوان مقاله [English]

Comparison of differential expression profiles of candidate genes related to fertility ‎traits using transcriptome perspective based on RNA-Seq in Holstein dairy cows

نویسندگان [English]

  • Farzad Ghafouri 1
  • Mostafa Sadeghi 2
  • Abolfazl Bahrami 3
  • Rostam Abdollahi-Arpanahi 4
  • Arash Javanmard 5
  • Seyed Reza Miraei-Ashtiani 6

1 Ph.D. Candidate, Department of Animal Science, College of Agriculture and ‎Natural Resources, University of Tehran, Karaj, Iran

2 Associate Professor, Department of Animal Science, College of Agriculture and Natural Resources, ‎University of Tehran, Karaj, Iran

3 Ph.D. Graduate, Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, ‎Karaj, Iran

4 Researcher, Department of Animal and Dairy Sciences, University of Georgia, Georgia, USA

5 Assistant Professor, Department of Animal Sciences, Faculty of Agriculture, University of Tabriz, Tabriz, Iran

6 Professor, Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran

چکیده [English]

Genetic selection for increasing milk production and economic profitability in the dairy industry has been associated with reduction in reproductive performance, including lower embryo survival and pregnancy loss. The main purpose of this study was to use the transcriptome profiles of endometrial tissue and Corpus luteum of two groups of high and low fertility Holstein dairy cows to identify genes that are effective in reproductive rate, especially in early pregnancy. By the analysis of RNA-Seq data to express the gene differences, 4538 genes were extracted, which a total of 1466 genes showed significant expression differences (P<0.000001, Fold change<0.5). Then, by comparing the relevant genes among transcriptome profiles, common genes between endometrial tissue (on days 7 and 13 of the estrous cycle) and Corpus luteum (on day 13 of the estrous cycle) including SYNM, PARM1, NXPE2, NT5DC3, COL4A3, COL12A1, ALPK3, ADAMDEC1, SERPINA14, S100A9, PI16, OAS1X, MSTN, MASP1, CD83, CA2, C2, C5, JSP.1 and SAA3 were identified. Annotation results of these genes indicated that they have a role in the main process of metabolic and signaling pathways related to the ion transport system, inflammation, immune system function, and cell-matrix structure. Overall, the present study can provide new insights into the molecular evidence for the biological mechanisms of transcriptome profiling in the uterine environment and biomarkers related to fertility in dairy cows.

کلیدواژه‌ها [English]

  • corpus luteum
  • Endometrium
  • fertility
  • Holstein cows
  • Transcriptome‎
  1. Andrews, S. (2010). FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc
  2. Bahrami, A., Miraie-Ashtiani, S.R., Sadeghi, M. & Najafi, A. (2017). Transcriptome profiling of granulosa cells of bovine ovarian follicles during different stages of folliculogenesis. Iranian Journal of Animal Science, 48(3), 463-471. (In Farsi)
  3. Berisha, B., Schams, D., Kosmann, M., Amselgruber, W. & Einspanier, R. (2000). Expression and localisation of vascular endothelial growth factor and basic fibroblast growth factor during the final growth of bovine ovarian follicles. Journal of Endocrinology, 167(3), 371-382.
  4. Berry, D.P., Wall, E. & Pryce, J.E. (2014). Genetics and genomics of reproductive performance in dairy and beef cattle. Animal, 8(s1), 105-121.
  5. Bisinotto, R.S., Ribeiro, E.S. & Santos, J.E.P. (2014). Synchronisation of ovulation for management of reproduction in dairy cows. Animal, 8(s1), 151-159.
  6. Blankenberg, D., Gordon, A., Von Kuster, G., Coraor, N., Taylor, J., Nekrutenko, A. & Galaxy Team. (2010). Manipulation of FASTQ data with Galaxy. Bioinformatics, 26(14), 1783-1785.
  7. Bolger, A.M., Lohse, M. & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114-2120.
  8. Butler, S.T. (2014). Nutritional management to optimize fertility of dairy cows in pasture-based systems. Animal, 8(s1), 15-26.
  9. Butler, W.R. (2003). Energy balance relationships with follicular development, ovulation and fertility in postpartum dairy cows. Livestock Production Science, 83(2-3), 211-218.
  10. Carroll, M.C. (2008). Complement and humoral immunity. Vaccine, 26, I28-I33.
  11. Cerri, R.L.A., Thompson, I.M., Kim, I.H., Ealy, A.D., Hansen, P.J., Staples, C.R., Li, J.L., Santos, J.E.P. & Thatcher, W.W. (2012). Effects of lactation and pregnancy on gene expression of endometrium of Holstein cows at day 17 of the estrous cycle or pregnancy. Journal of Dairy Science, 95(10), 5657-5675.
  12. Cochran, S.D., Cole, J.B., Null, D.J. & Hansen, P.J. (2013). Discovery of single nucleotide polymorphisms in candidate genes associated with fertility and production traits in Holstein cattle. BMC Genetics, 14(1), 1-23.
  13. Connor, E.E., Siferd, S., Elsasser, T.H., Evock-Clover, C.M., Van Tassell, C.P., Sonstegard, T.S., Fernandes, V.M. & Capuco, A.V. (2008). Effects of increased milking frequency on gene expression in the bovine mammary gland. BMC Genomics, 9(1), 1-14.
  14. Davis, J.S., Rueda, B.R. & Spanel-Borowski, K. (2003). Microvascular endothelial cells of the Corpus luteum. Reproductive Biology and Endocrinology, 1(1), 1-15.
  15. De Vries, A. (2006). Economic value of pregnancy in dairy cattle. Journal of Dairy Science, 89(10), 3876-3885.
  16. Fiems, L.O. (2012). Double muscling in cattle: genes, husbandry, carcasses and meat. Animals, 2(3), 472-506.
  17. Fonseca, L.F.S., dos Santos Silva, D.B., Gimenez, D.F.J., Baldi, F., Ferro, J.A., Chardulo, L.A.L. & de Albuquerque, L.G. (2020). Gene expression profiling and identification of hub genes in Nellore cattle with different marbling score levels. Genomics, 112(1), 873-879.
  18. Forde, N., Simintiras, C.A., Sturmey, R., Mamo, S., Kelly, A.K., Spencer, T.E., Bazer, F.W. & Lonergan, P. (2014). Amino acids in the uterine luminal fluid reflects the temporal changes in transporter expression in the endometrium and conceptus during early pregnancy in cattle. PLoS One, 9(6), e100010.
  19. Funeshima, N., Tanikawa, N., Yaginuma, H., Watanabe, H., Iwata, H., Kuwayama, T., Hamano, S. & Shirasuna, K. (2020). Adverse reproductive effects of S100A9 on bovine sperm and early embryonic development in vitro. Plos One, 15(1), e0227885.
  20. García-Pelagio, K.P., Muriel, J., O'Neill, A., Desmond, P.F., Lovering, R.M., Lund, L., Bond, M. & Bloch, R.J. (2015). Myopathic changes in murine skeletal muscle lacking synemin. American Journal of Physiology-Cell Physiology, 308(6), C448-C462.
  21. Gecaj, R.M., Schanzenbach, C.I., Kirchner, B., Pfaffl, M.W., Riedmaier, I., Tweedie-Cullen, R.Y. & Berisha, B. (2017). The dynamics of microRNA transcriptome in bovine corpus luteum during its formation, function, and regression. Frontiers in Genetics, 8, 213.
  22. Ghafouri, F., Sadeghi, M., Bahrami, A. & Miraei Ashtiani, S.R. (2020). Identification of genes affecting the amount of abdominal fat in broiler chickens‎ using microarray and RNA sequencing data. Iranian Journal of Animal Science, 50(4), 259-269. (In Farsi)
  23. Gibbs, G.M., Roelants, K. & O'bryan, M.K. (2008). The CAP superfamily: cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins—roles in reproduction, cancer, and immune defense. Endocrine Reviews, 29(7), 865-897.
  24. Granger, B.L. & Lazarides, E. (1980). Synemin: a new high molecular weight protein associated with desmin and vimentin filaments in muscle. Cell, 22(3), 727-738.
  25. Hernández-Montiel, W., Martínez-Núñez, M.A., Ramón-Ugalde, J.P., Román-Ponce, S.I., Calderón-Chagoya, R. & Zamora-Bustillos, R. (2020). Genome-wide association study reveals candidate genes for litter size traits in Pelibuey sheep. Animals, 10(3), 434.
  26. Höglund, J.K., Sahana, G., Guldbrandtsen, B. & Lund, M.S. (2014). Validation of associations for female fertility traits in Nordic Holstein, Nordic Red and Jersey dairy cattle. BMC Genetics, 15(1), 1-7.
  27. Kadri, N.K., Sahana, G., Charlier, C., Iso-Touru, T., Guldbrandtsen, B., Karim, L., Nielsen, U.S., Panitz, F., Aamand, G.P., Schulman, N. & Georges, M. (2014). A 660-Kb deletion with antagonistic effects on fertility and milk production segregates at high frequency in Nordic Red cattle: additional evidence for the common occurrence of balancing selection in livestock. PLoS Genet, 10(1), e1004049.
  28. Khatkar, M.S., Randhawa, I.A.S. & Raadsma, H.W. (2014). Meta-assembly of genomic regions and variants associated with female reproductive efficiency in cattle. Livestock Science, 166, 144-157.
  29. Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R. & Salzberg, S.L. (2013). TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology, 14(4), 1-13.
  30. Locatelli, Y., Forde, N., Blum, H., Graf, A., Piégu, B., Mermillod, P., Wolf, E., Lonergan, P. & Saint-Dizier, M. (2019). Relative effects of location relative to the corpus luteum and lactation on the transcriptome of the bovine oviduct epithelium. BMC Genomics, 20(1), 1-13.
  31. Lucy, M.C. (2001). Reproductive loss in high-producing dairy cattle: where will it end?. Journal of Dairy Science, 84(6), 1277-1293.
  32. Lutwak-Mann, CE. (1955). Carbonic anhydrase in the female reproductive tract. Occurrence, distribution and hormonal dependence. Journal of Endocrinology, 13(1), 26-38.
  33. Mansouri-Attia, N., Aubert, J., Reinaud, P., Giraud-Delville, C., Taghouti, G., Galio, L., Everts, R.E., Degrelle, S., Richard, C., Hue, I. & Yang, X. (2009). Gene expression profiles of bovine caruncular and intercaruncular endometrium at implantation. Physiological Genomics, 39(1), 14-27.
  34. Min, L., Cheng, J., Zhao, S., Tian, H., Zhang, Y., Li, S., Yang, H., Zheng, N. & Wang, J. (2016). Plasma-based proteomics reveals immune response, complement and coagulation cascades pathway shifts in heat-stressed lactating dairy cows. Journal of Proteomics, 146, 99-108.
  35. Mondal, S. & Prakash, B.S. (2002). Comparison of luteal function between cows and buffaloes during estrous cycle. Indian Journal of Dairy Science, 55(3), 142-144.
  36. Moore, S.G., Pryce, J.E., Hayes, B.J., Chamberlain, A.J., Kemper, K.E., Berry, D.P., McCabe, M., Cormican, P., Lonergan, P., Fair, T. & Butler, S.T. (2016). Differentially expressed genes in endometrium and corpus luteum of Holstein cows selected for high and low fertility are enriched for sequence variants associated with fertility. Biology of Reproduction, 94(1), 19-1.
  37. Moran, B., Butler, S.T., Moore, S.G., MacHugh, D.E. & Creevey, C.J. (2017). Differential gene expression in the endometrium reveals cytoskeletal and immunological genes in lactating dairy cows genetically divergent for fertility traits. Reproduction, Fertility and Development, 29(2), 274-282.
  38. Murata, E., Kozaki, S., Murakami, T., Shimizu, K., Okada, A., Ishiguro, N. & Inoshima, Y. (2020). Differential expression of serum amyloid A1 and A3 in bovine epithelia. Journal of Veterinary Medical Science, 19-0473.
  39. Neuvians, T.P., Berisha, B. & Schams, D. (2004). Vascular endothelial growth factor (VEGF) and fibroblast growth factor (FGF) expression during induced luteolysis in the bovine corpus luteum. Molecular Reproduction and Development: Incorporating Gamete Research, 67(4), 389-395.
  40. Otto, P.I., Guimarães, S.E., Verardo, L.L., Azevedo, A.L.S., Vandenplas, J., Soares, A.C., Sevillano, C.A., Veroneze, R., Maria de Fatima, A.P., de Freitas, C. & Prata, M.C.A. (2018). Genome-wide association studies for tick resistance in Bos taurus× Bos indicus crossbred cattle: A deeper look into this intricate mechanism. Journal of Dairy Science, 101(12), 11020-11032.
  41. Padua, M.B. & Hansen, P.J. (2010). Evolution and function of the uterine serpins (SERPINA14). American Journal of Reproductive Immunology, 64(4), 265-274.
  42. Pescucci, C., Mari, F., Longo, I., Vogiatzi, P., Caselli, R., Scala, E., Abaterusso, C., Gusmano, R., Seri, M., Miglietti, N. & Bresin, E. (2004). Autosomal-dominant Alport syndrome: natural history of a disease due to COL4A3 or COL4A4 gene. Kidney International, 65(5), 1598-1603.
  43. Pritchard, T., Coffey, M., Mrode, R. & Wall, E. (2013). Genetic parameters for production, health, fertility and longevity traits in dairy cows. Animal, 7(1), 34-46.
  44. Raven, L.A., Cocks, B.G., Goddard, M.E., Pryce, J.E. & Hayes, B.J. (2014). Genetic variants in mammary development, prolactin signalling and involution pathways explain considerable variation in bovine milk production and milk composition. Genetics Selection Evolution, 46(1), 1-13.
  45. Robinson, M.D., McCarthy, D.J. & Smyth, G.K. (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26(1), 139-140.
  46. Robinson, R.S., Hammond, A.J., Wathes, D.C., Hunter, M.G. & Mann, G.E. (2008). Corpus luteum–endometrium–embryo interactions in the dairy cow: underlying mechanisms and clinical relevance. Reproduction in Domestic Animals, 43, 104-112.
  47. Rodriguez-Martinez, H., Hultgren, J., Båge, R., Bergqvist, A.S., Svenssson, C., Bergsten, C., Lidfors, L., Gunnarsson, S., Algers, B., Emanuelson, U. & Berglund, B. (2008). Reproductive Performance in High-Producing Dairy Cows. R01:R0108. 1-23
  48. Royal, M., Mann, G.E. & Flint, A.P.F. (2000). Strategies for reversing the trend towards subfertility in dairy cattle. The Veterinary Journal, 160(1), 53-60.
  49. Sahana, G., Guldbrandtsen, B., Bendixen, C. & Lund, M.S. (2010). Genome‐wide association mapping for female fertility traits in Danish and Swedish Holstein cattle. Animal Genetics, 41(6), 579-588.
  50. Sarkar, M., Schilffarth, S., Schams, D., Meyer, H.H.D. & Berisha, B. (2011). The expression of thrombopoietin and its receptor during different physiological stages in the bovine ovary. Reproduction in Domestic Animals, 46(5), 757-762.
  51. Sherman, B.T. & Lempicki, R.A. (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols, 4(1), 44.
  52. Spencer, T.E., Sandra, O. & Wolf, E. (2008). Genes involved in conceptus-endometrial interactions in ruminants: insights from reductionism and thoughts on holistic approaches. Reproduction (Cambridge, England), 135(2), 165-179.
  53. Sugino, N. & Okuda, K. (2007). Species-related differences in the mechanism of apoptosis during structural luteolysis. Journal of Reproduction and Development, 53(5), 977-986.
  54. Thatcher, W.W., Santos, J.E.P., Silvestre, F.T., Kim, I.H. & Staples, C.R. (2010). Perspective on physiological/endocrine and nutritional factors influencing fertility in post‐partum dairy cows. Reproduction in Domestic Animals, 45, 2-14.
  55. VanRaden, P.M., Sanders, A.H., Tooker, M.E., Miller, R.H., Norman, H.D., Kuhn, M.T. & Wiggans, G.R. (2004). Development of a national genetic evaluation for cow fertility. Journal of Dairy Science, 87(7), 2285-2292.
  56. Walsh, S.W., Williams, E.J. & Evans, A.C.O. (2011). A review of the causes of poor fertility in high milk producing dairy cows. Animal Reproduction Science, 123(3-4), 127-138.
  57. Wang, Y., Han, X., Zhang, L., Cao, N., Cao, L. & Yang, L. (2019). Early pregnancy induces expression of STAT1, OAS1 and CXCL10 in ovine spleen. Animals, 9(11), 882.
  58. Yassin, M., Kissow, H., Vainer, B., Joseph, P.D., Hay-Schmidt, A., Olsen, J. & Pedersen, A.E. (2018). Cytoglobin affects tumorigenesis and the expression of ulcerative colitis-associated genes under chemically induced colitis in mice. Scientific Reports, 8(1), 1-16.
  59. Yoshioka, S., Abe, H., Sakumoto, R. & Okuda, K. (2013). Proliferation of luteal steroidogenic cells in cattle. PLoS One, 8(12), e84186.
  60. Zhang, H., Wei, Y., Zhang, F., Liu, Y., Wang, H., Li, Y. & Li, G. (2019). Polymorphisms of mannose-binding lectin-associated serine protease 1 (MASP1) and its relationship with milk performance traits and complement activity in Chinese Holstein cattle. Research in Veterinary Science, 124, 346-351.
  61. Zolini, A.M., Negrón-Pérez, V.M. & Hansen, P.J. (2019). Importance of prostate androgen-regulated mucin-like protein 1 in development of the bovine blastocyst. BMC Developmental Biology, 19(1), 1-12.
  62. Zonuzagh, J.J., Shahrbabak, M.M. & Nejati-Javaremi, A. (2020). Transcriptome profile of endometrium for growth and elongation of dairy cattle embryo. Animal Production Research, 9(2), 1-13. (In Farsi)
  63. Zou, Y., Zwolanek, D., Izu, Y., Gandhy, S., Schreiber, G., Brockmann, K., Devoto, M., Tian, Z., Hu, Y., Veit, G. & Meier, M. (2014). Recessive and dominant mutations in COL12A1 cause a novel EDS/myopathy overlap syndrome in humans and mice. Human Molecular Genetics, 23(9), 2339-2352.