PLANT BIOLOGY
ANIMAL BIOLOGY
SUBSCRIPTION
E-SUBSCRIPTION
 
MAP
MAIN PAGE

 

 

 

 

Selionova M.I., Trukhachev V.I., Zinovieva N.A., Belous A.А., Aybazov A-M.M. Search for genome-wide associations of single nucleotide polymorphisms with milk quality traits in sheep (Ovis aries L.) of lacon breed. Sel'skokhozyaistvennaya Biologiya [Agricultural Biology], 2024, Vol. 59, № 4, p. 735-748.
(how to cite this article)

doi: 10.15389/agrobiology.2024.4.735eng

UDC: 636.32/.38:575.2

Acknowledgements:
Supported financially by Russian Science Foundation, project No. 21-76-20008

 

SEARCH FOR GENOME-WIDE ASSOCIATIONS OF SINGLE NUCLEOTIDE POLYMORPHISMS WITH MILK QUALITY TRAITS IN SHEEP (Ovis aries L.) OF LACON BREED

M.I. Selionova1 ✉, V.I. Trukhachev1, N.A. Zinovieva2, A.А. Belous2,
A-M.M. Aybazov1

1Russian State Agrarian University — Timiryazev Moscow Agricultural Academy, 49, ul. Timiryazevskaya, Moscow, 127550 Russia, e-mail selionova@rgau-msha.ru (✉ corresponding author), rector@rgau-msha.ru, velikii-1@yandex.ru;
2Ernst Federal Research Center for Animal Husbandry, 60, pos. Dubrovitsy, Podolsk District, Moscow Province, 142132 Russia, e-mail n_zinovieva@mail.ru, abelous.vij@ya.ru

ORCID:
Selionova M.I. orcid.org/0000-0002-9501-8080
Aybazov A-M.M. orcid.org/0000-0002-3704-3210
Trukhachev V.I. orcid.org/0000-0002-4650-1893
Belous A.A. orcid.org/0000-0001-7533-4181
Zinovieva N.A. orcid.org/0000-0003-4017-6863

Final revision received June 18, 2024

Accepted July 29, 2024

 

Dairy sheep breeding has demonstrated dynamic development in Russia in recent years due to increasing consumer demand for premium dairy products. In dairy sheep breeding, marker-associated selection (MAS) and genome-wide association study (GWAS) are recognized as the most promising due to the sequencing of the sheep genome within the Sheep HapMap project and the development of DNA chips of different densities. For some dairy breeds of sheep, GWAS allowed to identify loci under selection pressure and affecting productivity traits and technological properties of sheep milk. At the same time, significantly fewer full genomic studies have been performed for dairy sheep than for dairy cattle and dairy goats, which determined the purpose of the present study. For the first time, a full genomic search for associations of single nucleotide substitutions with milk quality indicators in Lacon sheep breed was performed and genomic regions associated with their dairy productivity were determined. SNP profiles were generated using the Ovine HD BeadChip 600K high density chip (Illumina Inc., San Diego, USA) and the Rstudio 2023.03.0. Quality control, data filtering, association detection for each single nucleotide polymorphism with milk components determined on CombiFoss 7 DC automatic analyzer (FOSS, Denmark) were performed by multiple linear regression analysis in plink 1.90 software (http://zzz.bwh.harvard.edu/plink/), data visualisation was performed in qqman package using R programming language (https://github.com/stephenturner/qqman), gene identification by SNP positions set according to the sheep genome assembly OAR version 3.1, using the Ensembl Genes release 103 web resource, structural annotation of genomic regions covering a ±0.20 Mb window of identified SNPs in the DAVID v6.8 (https://david.ncifcrf.gov). 64 full genomic (p < 1,06×10-6) and 270 prospective (p < 2,11×10-5) SNPs were identified, with the largest number of full genomic SNPs (14, 6 and 13) identified on chromosomes 1, 3 and 13, respectively. Twenty-two and 19 full genome SNPs identified on five (OAR 1, 3, 12, 13 and 26) and four (OAR 1, 3, 13 and 26) chromosomes show associations with protein mass fraction and β-casein content, 6 SNPs on three chromosomes (OAR 1, 3, 26) are associated with fat mass fraction indicator, 7, 5 and 4 SNPs respectively on four (OAR 1, 3, 5 and 17) and three chromosomes (OAR 1, 24, 26 and OAR 1, 6, 17) are associated with polyunsaturated, saturated and monounsaturated fatty acids. Two SNPs of high significance, oar3_OAR1_24401030 and oar3_OAR2_241055039 are common to three traits, namely mass protein, β-casein and fat mass fraction. Structural annotation of genomic regions identified 61 genes with described biological functions, of which 11 genes show association with a number of phenotypic traits in sheep identified in other GWAS studies. The genes identified, according to gene ontology terms, were involved in immune formation and regulation system (GPX7, JAK1, CD8B), cellular metabolism and transport of substances (UBE2U, ACO1, FABP1, ACBD5), formation and development of internal organs and skeletal cartilage system (BMPR1B, OXSM), oogenesis, fertilization and early embryo development (ZPBP, ZP2).

Keywords: Ovis aries, ewes, milk components, protein, fat, saturated fatty acids, monounsaturated fatty acids, polyunsaturated, candidate genes, GWAS, SNP, QTL.

 

REFERENCES

  1. Popescu A., Stanciu M., Antonie I. Livestock and milk and meat production in the top five EU countries rearing sheep and goats, 2012-2021. Management. Economic Engineering in Agriculture and rural development, 2022, 22(3): 2284-7995.
  2. Shuvarikov A.S, Kanina K.A., Robkova T.O., Yurova E.A. Ovtsy, kozy, sherstyanoe delo, 2018, 1: 20-22 (in Russ.).
  3. Dettori M.L., Pazzola M., Noce A., Landi V., Vacca G.M. Variations in casein genes are associated with milk protein and fat contents in Sarda goats (Capra hircus), with an important role of CSN1S2 for milk yield. Animals, 2023, 14(1): 56 CrossRef
  4. Kruchinin A.G., Bigaeva A.V., Turovskaya S.N., Illarionova E.E. Pishchevaya promyshlennost’, 2020, 8: 36-40 CrossRef (in Russ.).
  5. Arranz J.J., Gutiérrez-Gil B. Detection of QTL underlying milk traits in sheep: An update. In: Milk production. Advanced genetic traits. Sellular mechanism. Animal management health. InTech, 2012: 97-126 CrossRef 
  6. Wang P., Li X., Zhu Y., Wei J., Zhang C., Kong Q., Nie X., Zhang Q., Wang Z. Genome-wide association analysis of milk production, somatic cell score, and body conformation traits in Holstein cows. Frontiers in Veterinary Science, 2022, 9: 932034 CrossRef
  7. Getaneh M., Wondimagegn K. Candidate genes associated with economically important traits in dairy goats. Cogent Food & Agriculture, 2022, 8(1): 2149131 CrossRef
  8. Zhang T.Y., Zhu C.Y., Du L.X., Zhao F.P. Advances in genome-wide association studies for important traits in sheep and goats. Yi Chuan, 2017, 39(6): 491-500 CrossRef
  9. Marina H., Gutiérrez-Gil B., Esteban-Blanco C., Suárez-Vega A., Pelayo R., Arranz J.J. Analysis of whole genome resequencing datasets from a worldwide sample of sheep breeds to identify potential causal mutations influencing milk composition traits. Animals, 2020, 10(9): 1542 CrossRef
  10. Pulina G., Milan M.J., Lavin M.P., Theodoridis A., Morin E., Capote J. Thomas D.L., Francesconi A.H.D., Caja G. Invited review: Current production trends, farm structures, and economics of the dairy sheep and goat sectors. Journal Dairy Science, 2018, 101: 6715-6729 CrossRef
  11. Mucha S., Tortereau F., Doeschl-Wilson A., Rupp R., Conington J. Animal Board invited review: meta-analysis of genetic parameters for resilience and efficiency traits in goats and sheep. Animal, 2022, 16(3): 100456 CrossRef
  12. Li H., Wu X.-L., Tait R.G., Jr, Bauck S., Thomas D.L., Murphy T.W., Rosa G.J.M. Genome-wide association study of milk production traits in a crossbred dairy sheep population using three statistical models. Animal Genetics, 2020, 51: 624-628 CrossRef
  13. Jawasreh K., Haddad N., Abulubbad A., Al-Amareen A. Genome-wide association study for milk production of Awassi sheep in Jordan. Journal of the Saudi Society of Agricultural Sciences, 2022, 21(5): 302-309 CrossRef
  14. Sutera A.M., Tolone M., Mastrangelo S., Di Gerlando R., Sardina M. T., Portolano B., Pong-Wong R., Riggio V. Detection of genomic regions underlying milk production traits in Valle del Belice dairy sheep using regional heritability mapping. Journal of Animal Breeding and Genetics, 2021, 138(5): 552-561 CrossRef
  15. Marina H., Pelayo R., Suárez-Vega A., Gutiérrez-Gil B., Esteban-Blanco C., Arranz J.J. Genome-wide association studies (GWAS) and post-GWAS analyses for technological traits in Assaf and Churra dairy breeds. Journal of Dairy Science, 2021, 104(11): 11850-11866 CrossRef
  16. Argyriadou A., Michailidou S., Vouraki S., Tsartsianidou V., Triantafyllidis A., Gelasakis A., Banos G., Arsenos G. A genome-wide association study reveals novel SNP markers associated with resilience traits in two Mediterranean dairy sheep breeds. Frontiers in Genetics, 2023, 14: 1294573 CrossRef
  17. Li R., Ma Y., Jiang L. Review: Research progress of dairy sheep milk genes. Agriculture, 2022, 12: 169 CrossRef
  18. Duggal P., Gillanders E.M., Holmes T.N., Bailey-Wilson J.E. Establishing an adjusted P-value threshold to control the family-wide type 1 error in genome wide association studies. BMC Genomics, 2008, 9(1): 516 CrossRef
  19. Zhou X., Stephens M. Genome-wide efficient mixed-model analysis for association studies. Nature Genetics,2012, 44(7): 821-824 CrossRef
  20. Turner S. qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. Journal of Open Source Software, 2018, 3: 731 CrossRef
  21. Lin C., Li F., Zhang X., Zhang D., Li X., Zhang Y., Zhao Y., Song Q., Wang J., Zhou B., Cheng J., Xu D., Li W., Zhao L., Wang W. Expression and polymorphisms of CD8B gene and its associations with body weight and size traits in sheep. Animal Biotechnology, 2023, 34(4): 1214-1222 CrossRef
  22. Akhatayeva Z., Bi Y., He Y., Khan R., Li J., Li H., Pan C., Lan X. Survey of the relationship between polymorphisms within the BMPR1B gene and sheep reproductive traits. Animal Biotechnology, 2023, 34(3): 718-727 CrossRef
  23. Saranjam N., Farhoodi M., Ghasem A., Mohammadsadegh M., Farzaneh N. Associations between milk fat, protein and fat-to-protein ratio with some reproductive indices in dairy cows. The Indian Journal of Animal Sciences, 2020, 90: 764-767 CrossRef
  24. Guliński P., Socha S. The relationship between milk fat to protein ratio and selected production traits of Polish Holstein-Friesian cows. Animal Science Papers and Reports, 2021, 39: 213-223.
  25. Khanduri A., Sahu A.R., Wani S.A., Khan R.I.N., Pandey A., Saxena S., Malla W.A., Mondal P., Rajak K.K., Muthuchelvan D., Mishra B., Sahoo A.P., Singh Y.P., Singh R.K., Gandham R.K., Mishra B.P. Dysregulated miRNAome and proteome of PPRV infected goat PBMCs reveal a coordinated immune response. Frontiers in Immunology, 2018, 9: 2631 CrossRef
  26. Yang J., Li W.R., Lv F.H., He S.G., Tian S.L., Peng W.F., Sun Y.W., Zhao Y.X., Tu X.L., Zhang M., Xie X.L., Wang Y.T., Li J.Q., Liu Y.G., Shen Z.Q., Wang F., Liu G.J., Lu H.F., Kantanen J., Han J.L., Liu M.J. Whole-genome sequencing of native sheep provides insights into rapid adaptations to extreme environments. Molecular Biology and Evolution, 2016, 33(10): 2576-2592 CrossRef
  27. Yang M., Zhao W., Wang Z., Liu J., Sun X., Wang S. Detection of key gene InDels in JAK/STAT pathway and their associations with growth traits in four Chinese sheep breeds. Gene, 2023, 888: 147750 CrossRef
  28. Chaimowitz N.S., Forbes L.R. Human diseases caused by impaired signal transducer and activator of transcription and Janus kinase signaling. Current Opinion Pediatrics, 2019, 31(6): 843-850 CrossRef
  29. Easa A., Selionova M., Aibazov M., Mamontova T., Sermyagin A., Belous A., Abdelmanova A., Deniskova T., Zinovieva N. Identification of genomic regions and candidate genes associated with body weight and body conformation traits in Karachai goats. Genes, 2022, 13(10): 1773 CrossRef
  30. Wang J., Suo J., Yang R., Zhang C.L., Li X., Han Z., Zhou W., Liu S., Gao Q. Genetic diversity, population structure, and selective signature of sheep in the northeastern Tarim Basin. Frontiers in Genetics, 2023, 14: 1281601 CrossRef
  31. Smathers R.L., Petersen D.R. The human fatty acid-binding protein family: evolutionary divergences and functions. Human Genomics, 2011, 5(3): 170-191 CrossRef
  32. Yang R., Zhou D., Yan Z., Zhao Z., Wang Y., Li J., Ren L., Xie L., Wang X. Fatty acid binding protein 1 and fatty acid synthetase over-expression have differential effects on collagen III synthesis and cross-linking in Zongdihua pig primary adipocytes. PLoS ONE, 2023, 8(5): e0270614 CrossRef
  33. Listyarini K., Sumantri C., Rahayu S., Islam M.A., Akter S.H., Uddin M.J., Gunawan A. Hepatic transcriptome analysis reveals genes, polymorphisms, and molecules related to lamb tenderness. Animals, 2023, 13(4): 674 CrossRef
  34. Gunawan A., Listyarini K., Harahap R.S., Jakaria Roosita K., Sumantri C., Inounu I., Akter S.H., Islam M.A., Uddin, M.J. Hepatic transcriptome analysis identifies genes, polymorphisms and pathways involved in the fatty acids metabolism in sheep. PLoS ONE, 2021, 16(12): e0260514 CrossRef
  35. Ishimura S., Furuhashi M., Watanabe Y., Hoshina K., Fuseya T., Mita T., Okazaki Y., Koyama M., Tanaka M., Akasaka H., Ohnishi H., Yoshida H., Saitoh S., Miura T. Circulating levels of fatty acid-binding protein family and metabolic phenotype in the general population. PLoS ONE, 2013, 8(11): e81318 CrossRef
  36. Zhang L., Liu J., Zhao F., Ren H., Xu L., Lu J., Zhang S., Zhang X., Wei C., Lu G., Zheng Y., Du L. Genome-wide association studies for growth and meat production traits in sheep. PLoS ONE, 2013, 8(6): e66569 CrossRef
  37. Wassarman P.M., Litscher E.S. Mammalian fertilization: the egg’s multifunctional zona pellucida. The International Journal of Developmental Biology, 2008, 52(5-6): 665-676 CrossRef
  38. Bleil J.D., Greve J.M., Wassarman P.M. Identification of a secondary sperm receptor in the mouse egg zona pellucida: role in maintenance of binding of acrosome-reacted sperm to eggs. Developmental Biology, 1988, 128(2): 376-385 CrossRef
  39. Chen S., Costa V., Beja-Pereira A. Evolutionary patterns of two major reproduction candidate genes (Zp2 and Zp3) reveal no contribution to reproductive isolation between bovine species. BMC Evolutionary Biology, 2011, 11: 24 CrossRef

 

back

 


CONTENTS

 

 

Full article PDF (Rus)