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Comprehensive analysis of runs of homozygosity and heterozygosity in Holstein cattle on the basis of medium and high density SNP panels and large population sample Cover

Comprehensive analysis of runs of homozygosity and heterozygosity in Holstein cattle on the basis of medium and high density SNP panels and large population sample

Open Access
|Apr 2024

References

  1. Barbato O., Menchetti L., Brecchia G., Barile V.L. (2022). Using pregnancy-associated glycoproteins (PAGs) to improve reproductive management: From dairy cows to other dairy livestock. Animals, 12: 2033.
  2. Biscarini F., Cozzi P., Gaspa G., Marras G. (2019). detectRUNS: Detect runs of homozygosity and runs of heterozygosity in diploid genomes. Retrieved from https://cran.rproject.org/web/packages/detectRUNS/index.html
  3. Biscarini F., Mastrangelo S., Catillo G., Senczuk G., Ciampolini R. (2020). Insights into genetic diversity, runs of homozygosity and heterozygosity-rich regions in Maremmana semi-feral cattle using pedigree and genomic data. Animals, 10: 2285.
  4. Blott S., Kim J.J., Moisio S., Schmidt-Kuntzel A., Cornet A., Berzi P., Cambisano N., Ford C., Grisart B., Johnson D., Karim L., Simon P., Snell R., Spelman R., Wong J., Vilkki J., Georges M., Farnir F., Coppieters W. (2003). Molecular dissection of a quantitative trait locus: a phenylalanine-to-tyrosine substitution in the transmembrane domain of the bovine growth hormone receptor is associated with a major effect on milk yield and composition. Genetics, 163: 253–266.
  5. Buaban S., Lengnudum K., Boonkum W., Phakdeedindan P. (2022). Genome-wide association study on milk production and somatic cell score for Thai dairy cattle using weighted single-step approach with random regression test-day model. J. Dairy Sci., 105: 468–494.
  6. Ceballos F.C., Joshi P.K., Clark D.W., Ramsay M., Wilson J.F. (2018). Runs of homozygosity: windows into population history and trait architecture. Nat. Rev. Genet., 19: 220–234.
  7. Curik I., Ferencakovic M., Sölkner J. (2014). Inbreeding and runs of homozygosity: A possible solution to an old problem. Livest. Sci., 166: 26–34.
  8. Dai W., Zou Y., White R.R., Liu J., Liu H. (2018). Transcriptomic profiles of the bovine mammary gland during lactation and the dry period. Funct. Integr. Genom., 18: 125–140.
  9. Dash S., Singh A., Dixit S.P., Kumar A. (2022). Identification of selection signatures for milk performance traits among indigenous dairy cattle breeds using high density genomic information. Ind. J. Anim. Res., 10.18805/IJAR.B-4908.
  10. Davila K.M.S., Howell A., Nunez A., Orelien A., Roe V., Rodriguez E., Dikmen S., Mateescu R.G. (2020). Genome-wide association study identifies variants associated with hair length in Brangus cattle. Anim Genet., 51: 811–814.
  11. de Camargo G.M., Costa R.B., de Albuquerque L.G., Regitano L.C., Baldi F., Tonhati H. (2015). Polymorphisms in TOX and NCOA2 genes and their associations with reproductive traits in cattle. Reprod. Fert. Develop., 27: 523–528.
  12. Djari A., Esquerré D., Weiss B., Martins F., Meersseman C., Boussaha M., Klopp C., Rocha D. (2013). Gene-based single nucleotide polymorphism discovery in bovine muscle using next-generation transcriptomic sequencing. BMC Genom., 14: 307.
  13. Eisen D.P., Osthoff M. (2014). If there is an evolutionary selection pressure for the high frequency of MBL2 polymorphisms, what is it? Clin. Exp. Immunol., 176: 165–171.
  14. El-Komy S.M., Saleh A.A., Abdel-Hamid T.M., El-Magd M.A. (2020) Association of GHR polymorphisms with milk production in buffaloes. Animals, 10: 1203.
  15. Falaleeva M., Surface J., Shen M., de la Grange P., Stamm S. (2015). SNORD116 and SNORD115 change expression of multiple genes and modify each other’s activity. Gene, 572: 266–273.
  16. Ferencakovic M., Hamzic E., Gredler B., Curik I., Sölkner J. (2011). Runs of homozygosity reveal genome-wide autozygosity in the Austrian Fleckvieh cattle. Agric. Conspec. Sci., 76: 325–328.
  17. Ferenčaković M., Sölkner J., Curik I. (2013). Estimating autozygosity from high-throughput information: Effects of SNP density and genotyping errors. Genet. Sel. Evol., 45: 42.
  18. Fijarczyk A., Babik W. (2015). Detecting balancing selection in genomes: Limits and prospects. Mol. Ecol., 24: 3529–3545.
  19. Fontanesi L., Scotti E., Dall’Olio S., Oulmouden A., Russo V. (2012). Identification and analysis of single nucleotide polymorphisms in the myosin VA (MYO5A) gene and its exclusion as the causative gene of the dilute coat colour locus in rabbit. World Rabbit Sci., 20: 35–41.
  20. Forutan M., Ansari Mahyari S., Baes C., Melzer N., Schenkel F.S., Sargolzaei M. (2018). Inbreeding and runs of homozygosity before and after genomic selection in North American Holstein cattle. BMC Genom., 19: 98.
  21. Gibson J., Morton N.E. Collins A. (2006). Extended tracts of homozygosity in outbred human populations. Hum. Mol. Genet., 15: 789–795.
  22. Graber M., Kohler S., Kaufmann T., Doherr M.G., Bruckmaier R.M., van Dorland H.A. (2010). A field study on characteristics and diversity of gene expression in the liver of dairy cows during the transition period. J. Dairy. Sci., 93: 5200–5215.
  23. Hadi Z., Atashi H., Dadpasand M., Derakhshandeh A., Ghahramani Seno M.M. (2015). The relationship between growth hormone polymorphism and growth hormone receptor genes with milk yield and reproductive performance in Holstein dairy cows. Iran J. Vet. Res., 16: 244–248.
  24. Howrigan D.P., Simonson M.A., Keller M.C. (2011). Detecting autozygosity through runs of homozygosity: A comparison of three autozygosity detection algorithms. BMC Genom., 12: 460.
  25. Jiang J., Ma L., Prakapenka D., Vanraden P.M., Cole J.B., Cole J.B. (2019). A large-scale genome-wide association study in US Holstein cattle. Front. Genet., 10: 412.
  26. Kadri N.K., Guldbrandtsen B., Lund M.S., Sahana G. (2015). Genetic dissection of milk yield traits and mastitis resistance QTL on chromosome 20 in dairy cattle. J. Dairy. Sci., 98: 9015–9025.
  27. Karim S., Saharti S., Alganmi N., Mirza Z., Alfares A., Turkistany S., Al-Attas M., Noureldin H., Al Sakkaf K., Abusamra H., Al-Qahtani M., Abuzenadah A. (2021). Two novel homozygous HPS6 mutations (double mutant) identified by whole-exome sequencing in a Saudi consanguineous family suspected for oculocutaneous albinism. Life (Basel), 12: 14.
  28. Keller M.C., Visscher P.M., Goddard M.E. (2011). Quantification of inbreeding due to distant ancestors and its detection using dense single nucleotide polymorphism data. Genetics, 189: 237–249.
  29. Kennedy K.M., Donkin S.S., Allen M.S. (2020). Effects of propionate concentration on short-term metabolism in liver explants from dairy cows in the postpartum period. J. Dairy. Sci., 103: 11449–11460.
  30. Kim E.S., Sonstegard T.S., Van Tassell C.P., Wiggans G., Rothschild M.F. (2015). The relationship between runs of homozygosity and inbreeding in Jersey cattle under selection. PLoS One, 10(7):e0129967.
  31. Kudo Y., Guardavaccaro D., Santamaria P.G., Koyama-Nasu R., Latres E., Bronson R., Yamasaki L., Pagano M. (2004). Role of Fbox protein βTrcp1 in mammary gland development and tumorigenesis. Mol. Cell. Biol., 24: 8184–8194.
  32. Li G., Tang J., Huang J., Jiang Y., Fan Y., Wang X., Ren J. (2022). Genome-wide estimates of runs of homozygosity, heterozygosity, and genetic load in two Chinese indigenous goat breeds. Front. Genet., 13: 774196.
  33. Li Y., Zhou H., Cheng L., Zhao J., Hickford J. (2020). Variation in the stearoyl-CoA desaturase gene (SCD) and its influence on milk fatty acid composition in late-lactation dairy cattle grazed on pasture. Arch. Anim. Breed., 63: 355–366.
  34. Ma L., Luo H., Brito L.F., Chang Y., Chen Z., Lou W., Zhang F., Wang L., Guo G., Wang Y. (2023). Estimation of genetic parameters and single-step genome-wide association studies for milk urea nitrogen in Holstein cattle. J. Dairy. Sci., 106: 352–363.
  35. Mackiewicz D., Oliveira P.M.C., Oliveira S.M., Cebrat S. (2013). Distribution of recombination hotspots in the human genome – a comparison of computer simulations with real data. PLoS ONE., 8:e65272.
  36. Makino T., Rubin C.J., Carneiro M., Axelsson E., Andersson L., Webster, M.T. (2018). Elevated proportions of deleterious genetic variation in domestic animals and plants. Genome Biol. Evol., 10: 276–290.
  37. Marete A., Lund M.S., Boichard D., Ramayo-Caldas Y. (2018) A system- based analysis of the genetic determinism of udder conformation and health phenotypes across three French dairy cattle breeds. PLoS ONE 13(7): e0199931.
  38. Marras G., Gaspa G., Sorbolini S., Dimauro C., Ajmone-Marsan P., Valentini A., Williams J.L., Macciotta N.P.P. (2015). Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmed in Italy. Anim. Genet., 46: 110–121.
  39. Marras G., Wood B.J., Makanjuola B., Malchiodi F., Peeters K., van As P., Baes C.F., Biscarini F. (2018). Characterization of runs of homozygosity and heterozygosity-rich regions in a commercial turkey (Meleagris gallopavo) population. Proc. 11th World Congress of Genetics Applied to Livestock Production, Auckland, New Zealand.
  40. Mastrangelo S., Tolone M., Gerlando R.D., Fontanesi L., Sardina M.T., Portolano B. (2016). Genomic inbreeding estimation in small populations: Evaluation of runs of homozygosity in three local dairy cattle breeds. Animal, 10: 746–754.
  41. McQuillan R., Leutenegger A.L., Abdel-Rahman R., Franklin C.S., Pericic M., Barac-Lauc L., Smolej-Narancic N., Janicijevic B., Polasek O., Tenesa A., MacLeod A.K., Farrington S.M., Rudan P., Hayward C., Vitart V., Rudan I., Wild S.H., Dunlop M.G., Wright A.F., Campbell H., Wilson J.F. (2008). Runs of homozygosity in European populations. Am. J. Hum. Genet., 83: 359–372.
  42. Melo-Baez B., Wong Y.S., Aguilera C.J., Cabezas J., Mançanares A.C.F., Riadi G., Castro F.O., Rodriguez-Alvarez L. (2020). MicroRNAs from extracellular vesicles secreted by bovine embryos as early biomarkers of developmental competence. Int. J. Mol. Sci., 21: 8888.
  43. Mohammadi A., Alijani S., Rafat S.A., Abdollahi-Arpanashi R. (2020). Genome-wide association study and pathway analysis for female fertility traits in Iranian Holstein cattle. Ann. Anim. Sci., 20: 825–851.
  44. Mulim H.A., Brito L.F., Pinto L.F.B., Ferraz J.B.S., Grigoletto L., Silva M.R., Pedrosa V.B. (2022). Characterization of runs of homozygosity, heterozygosity-enriched regions, and population structure in cattle populations selected for different breeding goals. BMC Genom., 23: 209.
  45. Nayeri S., Stothard P. (2016). Tissues, metabolic pathways and genes of key importance in lactating dairy cattle. Springer Sci. Rev., 4: 49–77.
  46. Nothnagel M., Lu T.T., Kayser M., Krawczak M. (2010). Genomic and geographic distribution of SNP-defined runs of homozygosity in Europeans. Hum. Mol. Genet., 19: 2927–2935.
  47. Pedrosa V.B., Schenkel F.S., Chen S.Y., Oliveira H.R., Casey T.M., Melka M.G., Brito L.F. (2021). Genomewide association analyses of lactation persistency and milk production traits in Holstein cattle based on imputed whole-genome sequence data. Genes (Basel), 12: 1830.
  48. Pemberton T.J., Absher D., Feldmand M.W., Myers R.M., Rosenberg N.A., Li J.Z. (2012). Genomic patterns of homozygosity in worldwide human populations. Am. J. Hum. Genet., 10: 275–292.
  49. Peripolli E., Munari D.P., Silva M.V.G.B., Lima A.L.F., Irgang R., Baldi F. (2017). Runs of homozygosity: current knowledge and applications in livestock. Anim. Genet., 48: 255–271.
  50. Purfield D.C., Berry D.P., McParland S., Bradley D.G. (2012). Runs of homozygosity and population history in cattle. BMC Genet., 13: 70.
  51. Qi Y., Purtell L., Fu M., Lee N.J., Aepler J., Zhang L., Loh K., Enriquez R.F., Baldock P.A., Zolotukhin S., Campbell L.V., Herzog H. (2016). Snord116 is critical in the regulation of food intake and body weight. Sci. Rep., 6: 18614.
  52. Reese S.T., Geary T.W., Franco G.A., Moraes J.G.N., Spencer T.E., Pohler K.G. (2019). Pregnancy associated glycoproteins (PAGs) and pregnancy loss in high vs sub fertility heifers. Theriogenology, 135: 7–12.
  53. Santos W., Schettini G., Fonseca M.G., Pereira G.L., Chardulo L.A., Neto O., Baldassini W.A., de Oliveira H.N., Curi R.A. (2021). Fine-scale estimation of inbreeding rates, runs of homozygosity and genome-wide heterozygosity levels in the Mangalarga Marchador horse breed. J. Anim. Breed. Genet., 138: 161–173.
  54. Senczuk G., Guerra L., Mastrangelo S., Campobasso C., Zoubeyda K., Imane M., Marletta D., Kusza S., Karsli T., Gaouar S.B.S., Pilla F., Ciani E., The Bovita Consortium (2020). Fifteen shades of grey: combined analysis of genome-wide SNP data in steppe and Mediterranean grey cattle sheds new light on the molecular basis of coat color. Genes, 11: 932.
  55. Sonzogni M., Zhai P., Mientjes E.J., van Woerden G.M., Elgersma Y. (2020). Assessing the requirements of prenatal UBE3A expression for rescue of behavioral phenotypes in a mouse model for Angelman syndrome. Mol. Autism., 11: 70.
  56. Strucken E.M., Laurenson Y.C., Brockmann G.A. (2015). Go with the flow-biology and genetics of the lactation cycle. Front. Genet., 6: 118.
  57. Suzuki J. Jr., Therrien J., Filion F., Lefebvre R., Goff A.K., Smith L.C. (2009). In vitro culture and somatic cell nuclear transfer affect imprinting of SNRPN gene in pre- and post-implantation stages of development in cattle. BMC Dev. Biol., 9: 9.
  58. Szmatoła T., Gurgul A., Ropka-Molik K., Jasielczuk I., Zabek T., Bugno-Poniewierska M. (2016). Characteristics of runs of homozygosity in selected cattle breeds maintained in Poland. Livest. Sci., 188: 72–80.
  59. Szmatoła T., Gurgul A., Jasielczuk I., Ząbek T., Ropka-Molik K., Litwińczuk Z., Bugno-Poniewierska M. (2019). A comprehensive analysis of runs of homozygosity of eleven cattle breeds representing different production types. Animals (Basel), 9: 1024.
  60. Szmatoła T., Gurgul A., Jasielczuk I., Oclon E., Ropka-Molik K., Stefaniuk-Szmukier M., Polak G., Tomczyk-Wrona I., Bugno-Poniewierska M. (2022). Assessment and distribution of runs of homozygosity in horse breeds representing different utility types. Animals (Basel), 12: 3293.
  61. Tian Z., Zhang Y., Zhang H., Sun Y., Mao Y., Yang Z., Li M. (2022). Transcriptional regulation of milk fat synthesis in dairy cattle. J. Funct. Foods, 96: 105208.
  62. Topolski P., Jagusiak W. (2019). Inbreeding in a population of Polish Holstein-Friesian young bulls before and after genomic selection. Ann. Anim. Sci., 20: 71–83.
  63. Tsartsianidou V., Sánchez-Molano E., Kapsona V.V., Basdagianni Z., Chatziplis D., Arsenos G., Triantafyllidis A., Banos G. (2021). A comprehensive genome-wide scan detects genomic regions related to local adaptation and climate resilience in Mediterranean domestic sheep. Genet. Sel. Evol., 53: 90.
  64. van den Berg I., Fritz S., Rodriguez S., Rocha D., Boussaha M., Lund M.S., Boichard D. (2014). Concordance analysis for QTL detection in dairy cattle: a case study of leg morphology. Genet. Sel. Evol., 46: 31.
  65. van den Berg I., Hayes B.J., Chamberlain A.J., Goddard M.E. (2019). Overlap between eQTL and QTL associated with production traits and fertility in dairy cattle. BMC Genom., 20: 291.
  66. Viitala S., Szyda J., Blott S., Schulman N., Lidauer M., Mäki-Tanila A., Georges M., Vilkki J. (2006). The role of the bovine growth hormone receptor and prolactin receptor genes in milk, fat and protein production in Finnish Ayrshire dairy cattle. Genetics, 173: 2151–2164.
  67. Vries L.D., Casey T., Dover H., VandeHaar M.J., Plaut K. (2011). Effects of transforming growth factor-β on mammary remodeling during the dry period of dairy cows. J. Dairy Sci., 94: 6036–6046.
  68. Wang J., Lou S.S., Wang T., Wu R.J., Li G., Zhao M., Lu B., Li Y.Y., Zhang J., Cheng X., Shen Y., Wang X., Zhu Z.C., Li M.J., Takumi T., Yang H., Yu X., Liao L., Xiong Z.Q. (2019). UBE3A-mediated PTPA ubiquitination and degradation regulate PP2A activity and dendritic spine morphology. Proc. Natl. Acad. Sci. USA, 116: 12500–12505.
  69. Wang X., Li G., Ruan D., Zhuang Z., Ding R., Quan J., Wang S., Jiang Y., Huang J., Gu T., Hong L., Zheng E., Li Z., Cai G., Wu Z., Yang J. (2022). Runs of homozygosity uncover potential functionalaltering mutation associated with body weight and length in two Duroc pig lines. Front. Vet. Sci., 9: 832633.
  70. Weber C., Hametner C., Tuchscherer A., Losand B., Kanitz E., Otten W., Sauerwein H., Bruckmaier R.M., Becker F., Kanitz W., Hammon H.M. (2013). Hepatic gene expression involved in glucose and lipid metabolism in transition cows: effects of fat mobilization during early lactation in relation to milk performance and metabolic changes. J. Dairy Sci., 96: 5670–5681.
  71. Williams J.L., Hall S.J.G., Del Corvo M., Ballingall K.T., Colli L., Ajmone Marsan P., Biscarini F. (2016). Inbreeding and purging at the genomic level: the Chillingham cattle reveal extensive, nonrandom SNP heterozygosity. Anim. Genet., 47: 19–27.
  72. Ye T., Shaukat A., Yang L., Chen C., Zhou Y., Yang L. (2022). Evolutionary and association analysis of buffalo FABP family genes reveal their potential role in milk performance. Genes (Basel), 13: 600.
  73. Zhang H., Wu Z., Yang L., Zhang Z., Chen H., Ren J. (2021). Novel mutations in the Myo5a gene cause a dilute coat color phenotype in mice. FASEB J., 35: e21261.
  74. Zhao G.F., Chen H., Lei C.Z., Zhang C.L., Zhang L., Lan X.Y., Fang X.T., Kang X.T. (2007). Study on SNPs of GHR gene and its associations with growth traits in Qinchuan cattle. Yi Chuan., 29: 319–323.
  75. Zhou H., Cheng L., Azimu W., Hodge S., Edwards G.R., Hickford J.G.H. (2015). Variation in the bovine FABP4 gene affects milk yield and milk protein content in dairy cows. Sci. Rep., 5: 10023.
  76. Zinovieva N.A., Dotsev A.V., Sermyagin A.A., Deniskova T.E., Abdelmanova A.S., Kharzinova V.R., Sölkner J., Reyer H., Wimmers K., Brem G. (2020). Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis. PLoS One., 15(11):e0242200.
DOI: https://doi.org/10.2478/aoas-2023-0100 | Journal eISSN: 2300-8733 | Journal ISSN: 1642-3402
Language: English
Page range: 431 - 444
Submitted on: Aug 1, 2023
Accepted on: Oct 4, 2023
Published on: Apr 23, 2024
Published by: National Research Institute of Animal Production
In partnership with: Paradigm Publishing Services
Publication frequency: 4 issues per year

© 2024 Tomasz Szmatoła, Artur Gurgul, Igor Jasielczuk, Katarzyna Ropka-Molik, published by National Research Institute of Animal Production
This work is licensed under the Creative Commons Attribution 4.0 License.