Preview

Аграрная наука

Расширенный поиск

Генетическая архитектура признаков воспроизводства свиней породы ландрас российской репродукции

https://doi.org/10.32634/0869-8155-2023-372-7-31-39

Полный текст:

Аннотация

Актуальность. В настоящее время развитие молекулярной и популяционной генетики является актуальной задачей. Необходимость выявления достоверных генов-кандидатов связано с увеличением поголовья свиней и увеличением качества выходной продукции — как племенной, так и мясной. В связи с этим метод полногеномного анализа решает вопросы генетической обусловленности количественных и хозяйственно полезных признаков.

Методы. В исследовании метод GWAS применялся по воспроизводительным показателям свиноматок породы ландрас.

Результаты. Были выявлены и описаны 35 достоверных и имеющих биологический функционал генов-кандидатов, расположенных вблизи или внутри идентифицированных значимых SNP, и отвечающих за различные воспроизводительные показатели организма свиноматок. Гены были отнесены к двум кластерам, из них 20 генов относились к 1-му кластеру, отвечавшему за митохондриальный и сопряженный транспорт электронов, синтез АТФ, а также связывание жирных кислот и триптофана (AFF4, IL13, IL4, IRF1, SHROOM1, IL-5, UQCRQ, MRPL13, TTR, ENPEP, NOL4, PCDH7, DSG3, RASSF6, ALB, AFP, ANKRD17, SOX9), и 15 — ко 2-му, связанному с ответом на бактериальную и вирусную инфекцию (YTHDC2, KIF3A, EYA1, DSG2, DSG4, PPIH, RNF125, TRAPPC8, PITX2, KIAA1462, MTPAP, JMJD6, METTL23, SRSF2 и U2AF1).

Об авторах

А. А. Белоус
Федеральный исследовательский центр животноводства — ВИЖ им. академика Л.К. Эрнста
Россия

Анна Александровна Белоус, кандидат биологических наук, лаборатория генетических технологий в агро- и аквахозяйстве,

Дубровицы, 60, Подольск, Московская обл., 142132



В. В. Волкова
Федеральный исследовательский центр животноводства — ВИЖ им. академика Л.К. Эрнста
Россия

Валерия Владимировна Волкова, кандидат биологических наук, лаборатория функциональной и эволюционной геномики животных,

Дубровицы, 60, Подольск, Московская обл., 142132



А. А. Решетникова
Федеральный исследовательский центр животноводства — ВИЖ им. академика Л.К. Эрнста
Россия

Анастасия Александровна Решетникова, младший научный сотрудник, лаборатория генетических технологий в агро- и аквахозяйстве,

Дубровицы, 60, Подольск, Московская обл., 142132



П. И. Отраднов
Федеральный исследовательский центр животноводства — ВИЖ им. академика Л.К. Эрнста
Россия

Петр Ильич Отраднов, младший научный сотрудник, лаборатория генетических технологий в агро- и аквахозяйстве, отдел популяционной генетики и генетических основ разведения животных,

Дубровицы, 60, Подольск, Московская обл., 142132



Н. А. Зиновьева
Федеральный исследовательский центр животноводства — ВИЖ им. академика Л.К. Эрнста
Россия

Наталия Анатольевна Зиновьева, доктор биологических наук, академик РАН, профессор, директор,

Дубровицы, 60, Подольск, Московская обл., 142132



Список литературы

1. Teng G., Yu Q. Pig behavior research and its application in breeding-landrace pigs as an example. Biomedical Research. 2017; 28 (Spec. Iss.): 111–117.

2. Alam M., Chang H.-K., Lee S.-S., Choi T.-J. Genetic analysis of major production and reproduction traits of Korean Duroc, Landrace and Yorkshire pigs. Animals. 2021; 11(5): 1321. https://doi.org/10.3390/ani11051321

3. Sato S. et al. SNP- and haplotype-based genome-wide association studies for growth, carcass, and meat quality traits in a Duroc multigenerational population. BMC Genetics. 2016; 17: 60. https://doi.org/10.1186/s12863-016-0368-3

4. Sevón-Aimonen M.-L., Uimari P. Heritability of sow longevity and lifetime prolificacy in Finnish Yorkshire and Landrace pigs. Agricultural and Food Science. 2013; 22(3): 325–330. https://doi.org/10.23986/afsci.7991

5. Ogawa S., Kimata M., Ishii K., Uemoto Y., Satoh M. Genetic analysis for sow stayability at different parities in purebred Landrace and Large White pigs. Animal Science Journal. 2021; 92(1): e13599. https://doi.org/10.1111/asj.13599

6. Wu P. et al. Single step genome-wide association studies based on genotyping by sequence data reveals novel loci for the litter traits of domestic pigs. Genomics. 2018; 110(3): 171–179. https://doi.org/10.1016/j.ygeno.2017.09.009

7. Sell-Kubiak E., Dobrzanski J., Derks M.F.L., Lopes M.S., Szwaczkowski T. Meta-analysis of SNPs determining litter traits in pigs. Genes. 2022; 13(10): 1730. https://doi.org/10.3390/genes13101730

8. Guo X., Su G., Christensen O.F., Janss L., Lund M.S. Genome-wide association analyses using a Bayesian approach for litter size and piglet mortality in Danish Landrace and Yorkshire pigs. BMC Genomics. 2016; 17: 468.https://doi.org/10.1186/s12864-016-2806-z

9. An S.M. et al. Effect of single nucleotide polymorphisms in IGFBP2 and IGFBP3 genes on litter size traits in Berkshire pigs. Animal Biotechnology. 2018; 29(4): 301–308. https://doi.org/10.1080/10495398.2017.1395345

10. Fabbri M.C. et al. Identification of candidate genes associated with bacterial and viral infections in wild boars hunted in Tuscany (Italy). Scientific Reports. 2022; 12: 8145. https://doi.org/10.1038/s41598-022-12353-8

11. Lin C. et al. AFF4, a component of the ELL/P-TEFb elongation complex and a shared subunit of MLL chimeras, can link transcription elongation to leukemia. Molecular Cell. 2010; 37(3): 429–437. https://doi.org/10.1016/j.molcel.2010.01.026

12. Wang M. et al. Associations of IL-4, IL-4R, and IL-13 gene polymorphisms in coal workersʼ pneumoconiosis in China: a case-control study. PLoS ONE. 2011; 6(8): e22624. https://doi.org/10.1371/journal.pone.0022624

13. Dawson H.D. et al. Molecular and metabolomic changes in the proximal colon of pigs infected with Trichuris suis. Scientific Reports. 2020; 10: 12853. https://doi.org/10.1038/s41598-020-69462-5

14. Liu Y. et al. Effect of single nucleotide polymorphism of IRF1 gene on cytokine traits in three pig breeds. Journal of Animal and Veterinary Advances. 2010; 9(18): 2346–2350. https://doi.org/10.3923/javaa.2010.2346.2350

15. Zhao Z. et al. Suppression of SHROOM1 improves in vitro and in vivo gene integration by promoting homology-directed repair. International Journal of Molecular Sciences. 2020; 21(16): 5821. https://doi.org/10.3390/ijms21165821

16. Xing K. et al. Identification of genes for controlling swine adipose deposition by integrating transcriptome, whole-genome resequencing, and quantitative trait loci data. Scientific Reports. 2016; 6: 23219. https://doi.org/10.1038/srep23219

17. Keel B.N. et al. RNA-Seq Meta-analysis identifies genes in skeletal muscle associated with gain and intake across a multi-season study of crossbred beef steers. BMC Genomics. 2018; 19: 430. https://doi.org/10.1186/s12864-018-4769-8

18. Kong R.S.G., Liang G., Chen Y., Stothard P., Guan L.L. Transcriptome profiling of the rumen epithelium of beef cattle differing in residual feed intake. BMC Genomics. 2016; 17: 592. https://doi.org/10.1186/s12864-016-2935-4

19. Cai M., Li H., Chen R., Zhou X. MRPL13 promotes tumor cell proliferation, migration and EMT process in breast cancer through the PI3K-AKT-mTOR pathway. Cancer Management and Research. 2021; 13: 2009–2024. https://doi.org/10.2147/CMAR.S296038

20. Drag M.H., Kogelman L.J.A., Maribo H., Meinert L., Thomsen P.D., Kadarmideen H.N. Characterization of eQTLs associated with androstenone by RNA sequencing in porcine testis. Physiological Genomics. 2019; 51(10): 488–499. https://doi.org/10.1152/physiolgenomics.00125.2018

21. Gaudet P., Livstone M.S., Lewis S.E., Thomas P.D. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in Bioinformatics. 2011; 12(5): 449–462. https://doi.org/10.1093/bib/bbr042

22. Tang Z. et al. Genome-wide association study reveals candidate genes for growth relevant traits in pigs. Frontiers in Genetics 2019; 10: 302. https://doi.org/10.3389/fgene.2019.00302

23. Holmes R.S., Spradling-Reeves K.D., Cox L.A. Mammalian glutamyl aminopeptidase genes (ENPEP) and proteins: Comparative studies of a major contributor to arterial hypertension. Journal of data mining in genomics & proteomics. 2017; 8(2): 2. https://doi.org/10.4172/2153-0602.1000211

24. Li X. et al. Analyses of porcine public SNPs in coding-gene regions by resequencing and phenotypic association studies. Molecular Biology Reports. 2011; 38(7): 3805–3820. https://doi.org/10.1007/s11033-010-0496-1

25. Reverter A. et al. A gene co-association network regulating gut microbial communities in a Duroc pig population. Microbiome. 2021; 9: 52. https://doi.org/10.1186/s40168-020-00994-8

26. Fang Z.-H., Pausch H. Multi-trait meta-analyses reveal 25 quantitative trait loci for economically important traits in Brown Swiss cattle. BMC Genomics. 2019; 20: 695. https://doi.org/10.1186/s12864-019-6066-6

27. Johansson M. et al. The gene for dominant white color in the pig is closely linked to ALB and PDGFRA on chromosome 8. Genomics. 1992; 14(4): 965–969. https://doi.org/10.1016/s0888-7543(05)80118-1

28. Whyte J.J., Prather R.S. Genetic modifications of pigs for medicine and agriculture. Molecular Reproduction and Development. 2011; 78(10–11): 879–891. https://doi.org/10.1002/mrd.21333

29. Sidor C., Borreguero-Munoz N., Fletcher G.C., Elbediwy A., Guillermin O., Thompson B.J. Mask family proteins ANKHD1 and ANKRD17 regulate YAP nuclear import and stability. Elife. 2019; 8: e48601. https://doi.org/10.7554/eLife.48601

30. Brenig B., Duan Y., Xing Y., Ding N., Huang L., Schütz E. Porcine SOX9 gene expression is influenced by an 18bp indel in the 5’-untranslated region. PLoS ONE. 2015; 10(10): e0139583. https://doi.org/10.1371/journal.pone.0139583

31. Stachowiak M. et al. Polymorphisms in the SOX9 region and testicular disorder of sex development (38, XX; SRY-negative) in pigs. Livestock Science. 2017; 203: 48–53. https://doi.org/10.1016/j.livsci.2017.07.002

32. Hsu P.J. et al. Ythdc2 is an N6-methyladenosine binding protein that regulates mammalian spermatogenesis. Cell Research. 2017; 27(9): 1115–1127. https://doi.org/10.1038/cr.2017.99

33. Stevens M.L. et al. Disease-associated KIF3A variants alter gene methylation and expression impacting skin barrier and atopic dermatitis risk. Nature Communications. 2020; 11: 4092. https://doi.org/10.1038/s41467-020-17895-x

34. Qin M., Li C., Li Z., Chen W., Zeng Y. Genetic diversities and differentially selected regions between Shandong indigenous pig breeds and western pig breeds. Frontiers in Genetics. 2020; 10: 1351. https://doi.org/10.3389/fgene.2019.01351

35. Almasoudi S.H., Schlosser G. Eya1 protein distribution during embryonic development of Xenopus laevis. Gene Expression Patterns. 2021; 42: 119213. https://doi.org/10.1016/j.gep.2021.119213

36. Berghöfer J., Khaveh N., Mundlos S., Metzger J. Simultaneous testing of ruleand model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs. BMC Genomics. 2022; 23: 564. https://doi.org/10.1186/s12864-022-08801-4

37. Souza M.R. et al. Transcriptome analysis identifies genes involved with the development of umbilical hernias in pigs. PLoS ONE. 2020; 15(5): e0232542. https://doi.org/10.1371/journal.pone.0232542

38. Tian M. et al. Transcriptome analysis reveals genes contributed to Min pig villi hair follicle in different seasons. Veterinary Sciences. 2022; 9(11): 639. https://doi.org/10.3390/vetsci9110639

39. Diao S.-q. et al. Exploring the genetic features and signatures of selection in South China indigenous pigs. Journal of Integrative Agriculture. 2021; 20(5): 1359–1371. https://doi.org/10.1016/S2095-3119(20)63260-9

40. Dunkelberger J.R. et al. Genomic regions associated with host response to porcine reproductive and respiratory syndrome vaccination and co-infection in nursery pigs. BMC Genomics. 2017; 18: 865. https://doi.org/10.1186/s12864-017-4182-8

41. Cruz C.D., Torre A., Troncos G., Lambrechts L., Leguia M. Targeted full-genome amplification and sequencing of dengue virus types 1–4 from South America. Journal of Virological Methods. 2016; 235: 158–167. https://doi.org/10.1016/j.jviromet.2016.06.001

42. Wu W.J. et al. Identification of four SNPs and association analysis with meat quality traits in the porcine Pitx2c gene. Science China Life Sciences. 2011; 54(5): 426–433. https://doi.org/10.1007/s11427-011-4167-9

43. Wu W., Ren Z., Wang Y., Chao Z., Xu D., Xiong Y. Molecular characterization, expression patterns and polymorphism analysis of porcine Six1 gene. Molecular Biology Reports. 2011; 38(4): 2619–2632. https://doi.org/10.1007/s11033-010-0403-9

44. Pérez-Montarelo D. et al. Identification of genes regulating growth and fatness traits in pig through hypothalamic transcriptome analysis. Physiological Genomics. 2014; 46(6): 195–206. https://doi.org/10.1152/physiolgenomics.00151.2013

45. Han X., Jiang T., Yu L., Zeng C., Fan B., Liu B. Molecular characterization of the porcine MTPAP gene associated with meat quality traits: chromosome localization, expression distribution, and transcriptional regulation. Molecular and Cellular Biochemistry. 2012; 364(1–2): 173–180. https://doi.org/10.1007/s11010-011-1216-4

46. Vangimalla S.S., Ganesan M., Kharbanda K.K., Osna N.A. Bifunctional enzyme JMJD6 contributes to multiple disease pathogenesis: new twist on the old story. Biomolecules. 2017; 7(2): 41. https://doi.org/10.3390/biom7020041

47. Pan Y. et al. METTL23 mutation alters histone H3R17 methylation in normaltension glaucoma. The Journal of Clinical Investigation. 2022; 132(21): e153589. https://doi.org/10.1172/JCI153589

48. Zhang Y. et al. Effective quality breeding directions: comparison and conservative analysis of hepatic super-enhancers between Chinese and Western pig breeds. Biology. 2022; 11(11): 1631. https://doi.org/10.3390/biology11111631

49. Okeyo-Owuor T. et al. U2AF1 mutations alter sequence specificity of pre-mRNA binding and splicing. Leukemia. 2015; 29(4): 909–917. https://doi.org/10.1038/leu.2014.303


Рецензия

Для цитирования:


Белоус А.А., Волкова В.В., Решетникова А.А., Отраднов П.И., Зиновьева Н.А. Генетическая архитектура признаков воспроизводства свиней породы ландрас российской репродукции. Аграрная наука. 2023;(7):31-39. https://doi.org/10.32634/0869-8155-2023-372-7-31-39

For citation:


Belous A.A., Volkova V.V., Reshetnikova A.A., Otradnov P.I., Zinovyeva N.A. Genetic architecture of reproductive traits in Russian Landrace pigs. Agrarian science. 2023;(7):31-39. (In Russ.) https://doi.org/10.32634/0869-8155-2023-372-7-31-39

Просмотров: 52


Creative Commons License
Контент доступен под лицензией Creative Commons Attribution 4.0 License.


ISSN 0869-8155 (Print)
ISSN 2686-701X (Online)