Поиск геномных вариантов, ассоциированных с живой массой у овец, на основе анализа высокоплотных SNP генотипов
Автор: Денискова Т.Е., Петров С.Н., Сермягин А.А., Доцев А.В., Форнара М.С., Reyer H., Wimmers K., Багиров В.А., Brem G., Зиновьева Н.А.
Журнал: Сельскохозяйственная биология @agrobiology
Рубрика: Молекулярная структура генома
Статья в выпуске: 2 т.56, 2021 года.
Бесплатный доступ
Живая масса - один из важнейших экономически полезных признаков, характеризующийся сложным наследованием, поэтому поиск генетических механизмов, влияющих на ее формирование, вызывает повышенный научный интерес. В настоящей работе впервые представлены результаты анализа полногеномных ассоциаций в ресурсной популяции овец ( Ovis aries ) возвратных кроссов (романовская × катадин) × романовская, живая масса которых фиксировалась в возрастной динамике, а SNP-профили были получены с помощью высокоплотного ДНК-чипа. В результате были идентифицированы 38 SNP, достоверно ассоциированных с живой массой (p
Домашние овцы, ресурсная популяция, snp-маркеры, днк-чипы, gwas, живая масса, гены-кандидаты
Короткий адрес: https://sciup.org/142229475
IDR: 142229475 | DOI: 10.15389/agrobiology.2021.2.279rus
Список литературы Поиск геномных вариантов, ассоциированных с живой массой у овец, на основе анализа высокоплотных SNP генотипов
- Jaquiery A.L., Oliver M.H., Bloomfield F.H., Harding J.E. Periconceptional events perturb postnatal growth regulation in sheep. Pediatric Research, 2011, 70(3): 261-266 (doi: 10.1203/PDR.0b013e3182242deb).
- Хайитов А.Х., Джураева У.Ш. Морфофизиологические закономерности роста костной и мышечной тканей у овец. Известия Санкт-Петербургского государственного аграрного университета, 2017, 3(48): 72-80.
- Сомова М.М., Мельникова Е.Е., Абрамова М.В., Коновалов А.В., Никитин С.А., Сермягин А.А. Зависимость показателей живой массы и скорости роста у ягнят романовской породы от различных паратипических факторов. Зоотехния, 2020, 8: 12-16.
- Трухачев В.И., Селионова М.И., Криворучко А.Ю., Айбазов А.М.М. Генетические маркеры мясной продуктивности овец (Ovis aries L.). Сообщение I. миостатин, кальпаин, кальпастатин (обзор). Сельскохозяйственная биология, 2018, 53(6): 1107-1119 (doi: 10.15389/agrobiology.2018.6.1107rus).
- Сермягин А.А., Белоус А.А., Требунских Е.А., Зиновьева Н.А. Показатели кормового поведения как новые селекционные признаки в разведении свиней. Сельскохозяйственная биология, 2020, 55(6): 1126-1138 (doi: 10.15389/agrobiology.2020.6.1126rus).
- 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 (doi: 10.1371/journal.pone.0066569).
- Al-Mamun H.A., Kwan P., Clark S.A., Ferdosi M.H., Tellam R., Gondro C. Genome-wide association study of body weight in Australian Merino sheep reveals an orthologous region on OAR6 to human and bovine genomic regions affecting height and weight. Genetics Selection Evolution, 2015, 47(1): 66 (doi: 10.1186/s12711-015-0142-4).
- Matika O., Riggio V., Anselme-Moizan M., Law A.S., Pong-Wong R., Archibald A.L., Bishop S.C. Genome-wide association reveals QTL for growth, bone and in vivo carcass traits as assessed by computed tomography in Scottish Blackface lambs. Genetics Selection Evolution, 2016, 48: 11 (doi: 10.1186/s12711-016-0191-3).
- Ghasemi M., Zamani P., Vatankhah M., Abdoli R. Genome-wide association study of birth weight in sheep. Animal, 2019, 13(9): 1797-1803 (doi: 10.1017/S1751731118003610).
- Lu Z., Yue Y., Yuan C., Liu J., Chen Z., Niu C., Sun X., Zhu S., Zhao H., Guo T., Yang B. Genome-wide association study of body weight traits in Chinese fine-wool sheep. Animals, 2020, 10(1): 170 (doi: 10.3390/ani10010170).
- Pasandideh M., Gholizadeh M., Rahimi-Mianji G. A genome-wide association study revealed five SNP affecting 8-month weight in sheep. Animal Genetics, 2020, 51(6): 973-976 (doi: 10.1111/age.12996).
- Cao Y., Song X., Shan H., Jiang J., Xiong P., Wu J., Shi F., Jiang Y. Genome-wide association study of body weights in Hu sheep and population verification of related single-nucleotide polymorphisms. Frontiers in Genetics, 2020, 11: 588 (doi: 10.3389/fgene.2020.00588).
- Zlobin A.S., Nikulin P.S., Volkova N.A., Zinovieva N.A., Iolchiev B.S., Bagirov V.A., Borodin P.M., Aksenovich T.I., Tsepilov Y.A. Multivariate analysis identifies eight novel loci associated with meat productivity traits in sheep. Genes, 2021, 12(3): 367 (doi: 10.3390/genes12030367).
- Ledur M.C., Navarro N., Perez-Enciso M. Large-scale SNP genotyping in crosses between out-bred lines: how useful is it? Heredity, 2009, 105: 173-182 (doi: 10.1038/hdy.2009.149).
- Денискова Т.Е., Доцев А.В., Петров С.Н., Форнара М.С., Рейер Х., Виммерс К., Баги-ров В.А., Брем Г., Зиновьева Н.А. Геномная оценка и фенотипическая характеристика F2 ресурсной популяции овец. Аграрная наука Евро-Северо-Востока, 2019, 20(5): 498-507 (doi: 10.30766/2072-9081.2019.20.5.498-507).
- Chang C.C., Chow C.C., Tellier L.C., Vattikuti S., Purcell S.M., Lee J.J. Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience, 2015, 4(7): 1-16 (doi: 10.1186/s13742-015-0047-8).
- Turner S.D. qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. biorXiv (doi: 10.1101/005165).
- R Core Team (2018). R: a language and environment for statistical computing. R foundation for statistical computing, Vienna, Austria. Режим доступа: https://www.R-project.org/. Без даты.
- McLaren W., Gil L., Hunt S.E., Riat H.S., Ritchie G.R., Thormann A., Flicek P., Cunningham F. The Ensembl Variant Effect Predictor. Genome Biology, 2016, 17(1): 122 (doi: 10.1186/s13059-016-0974-4).
- Da Wei H., Sherman B.T., Lempicki R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols, 2009, 4(1): 44-57 (doi: 10.1038/nprot.2008.211).
- Hu Z.L., Park C.A., Reecy J.M. Building a livestock genetic and genomic information knowledgebase through integrative developments of Animal QTLdb and CorrDB. Nucleic Acids Research, 2019, 47(D1): D701-D710 (doi: 10.1093/nar/gky1084).
- Du Y., Liu B., Guo F., Xu G., Ding Y., Liu Y., Sun X., Xu G. The essential role of Mbd5 in the regulation of somatic growth and glucose homeostasis in mice. PLoS ONE, 2012, 7(10): e47358 (doi: 10.1371/journal.pone.0047358).
- Chung B.H., Stavropoulos J., Marshall C.R., Weksberg R., Scherer, S.W., Yoon G. 2q23 de novo microdeletion involving the MBD5 gene in a patient with developmental delay, postnatal microcephaly and distinct facial features. American Journal of Medical Genetics. Part A, 2011, 155(2): 424-429 (doi: 10.1002/ajmg.a.33821).
- Bravo-Oro A., Lurie I.W., Elizondo-Cardenas G., Pena-Zepeda C., Salazar-Martinez A., Correa-Gonzalez C., Castrillo J.L., Avila S., Esmer C. A novel interstitial deletion of 2q22.3 q23.3 in a patient with dysmorphic features, epilepsy, aganglionosis, pure red cell aplasia, and skeletal malformations. American Journal of Medical Genetics. Part A, 2015, 167(8): 1865-1871 (doi: 10.1002/ajmg.a.36806).
- Klingseisen A., Jackson A.P. Mechanisms and pathways of growth failure in primordial dwarfism. Genes & Development, 2011, 25(19): 2011-2024 (doi: 10.1101/gad.169037).
- de Munnik S.A., Hoefsloot E.H., Roukema J., Schoots J., Knoers N.V., Brunner H.G., Jackson A.P., Bongers E.M. Meier-Gorlin syndrome. Orphanet Journal of Rare Diseases, 2015, 10: 114 (doi: 10.1186/s13023-015-0322-x).
- Goh B.C., Singhal V., Herrera A.J., Tomlinson R.E., Kim S., Faugere M.C., Germain-Lee E.L., Clemens T.L., Lee S.J., DiGirolamo D.J. Activin receptor type 2A (ACVR2A) functions directly in osteoblasts as a negative regulator of bone mass. The Journal of Biological Chemistry, 2017, 292(33): 13809-13822 (doi: 10.1074/jbc.M117.782128).
- Rovadoscki G.A., Pertile S.F.N., Alvarenga A.B., Cesar A.S.M., Pertille F., Petrini J., Franzo V., Soares W.V.B., Morota G., Spangler M.L., Pinto L.F.B., Carvalho G.G.P., Lanna D.P.D., Coutinho L.L., Mourao G.B. Estimates of genomic heritability and genome-wide association study for fatty acids profile in Santa Ines sheep. BMC Genomics, 2018, 19(1): 375 (doi: 10.1186/s12864-018-4777-8).
- Arora R., Kumar N.S., Sudarshan S., Fairoze M.N., Kaur M., Sharma A., Girdhar Y., Sreesujatha R.M., Devatkal S.K., Ahlawat S., Vijh R.K., Manjunatha S.S. Transcriptome profiling of longissimus thoracis muscles identifies highly connected differentially expressed genes in meat type sheep of India. PLoS ONE, 2019, 14(6): e0217461 (doi: 10.1371/journal.pone.0217461).
- Randhawa I.A.S., Khatkar M.S., Thomson P.C., Raadsma H.W. Composite selection signals for complex traits exemplified through bovine stature using multibreed cohorts of European and African Bos taurus. G3 Genes\Genomes\Genetics, 2015, 5(7): 1391-1401 (doi: 10.1534/g3.115.017772).
- Widmann P., Reverter A., Fortes M.R.S., Weikard R., Suhre K., Hammon H., Albrecht E., Kuehn C. A systems biology approach using metabolomic data reveals genes and pathways interacting to modulate divergent growth in cattle. BMC Genomics, 2013, 14: 798 (doi: 10.1186/14712164-14-798).
- Doyle J.L., Berry D.P., Veerkamp R.F., Carthy T.R., Evans R.D., Walsh S.W., Purfield D.C. Genomic regions associated with muscularity in beef cattle differ in five contrasting cattle breeds. Genetics Selection Evolution, 2020, 52(1): 2 (doi: 10.1186/s12711-020-0523-1).
- Grigoletto L., Ferraz J., Oliveira H.R., Eler J.P., Bussiman F.O., Abreu Silva B.C., Baldi F., Brito L.F. Genetic architecture of carcass and meat quality traits in Montana Tropical® composite beef cattle. Frontiers in Genetics, 2020, 11: 123 (doi: 10.3389/fgene.2020.00123).
- Liu X., Guo X.Y., Xu X.Z., Wu M., Zhang X., Li Q., Ma P.P., Zhang Y., Wang C.Y., Geng F.J., Qin C.H., Liu L., Shi W.H., Wang Y.C., Yu Y. Novel single nucleotide polymorphisms of the bovine methyltransferase 3b gene and their association with meat quality traits in beef cattle. Genetics and Molecular Research, 2012, 11(3): 2569-2577 (doi: 10.4238/2012.June.29.1).
- Gan Q., Li Y., Liu Q., Lund M., Su G., Liang X. Genome-wide association studies for the concentrations of insulin, triiodothyronine, and thyroxine in Chinese Holstein cattle. Tropical Animal Health and Production, 2020, 52(4): 1655-1660 (doi: 10.1007/s11250-019-02170-z).
- Hu Z., Wu J., Qin L., Jin H., Lv Y., Zhang R., Xiao C., Cao Y., Zhao Y. ALDH1A1 effect on Yan Yellow Cattle preadipocyte differentiation. Animal Biotechnology, 2019: 1-10 (doi: 10.1080/10495398.2019.1679824).
- Clark D.L., Boler D.D., Kutzler L.W., Jones K.A., McKeith F.K., Killefer J., Carr T.R., Dilger A.C. Muscle gene expression associated with increased marbling in beef cattle. Animal Biotechnology, 2011, 22(2): 51-63 (doi: 10.1080/10495398.2011.552031).
- Zhang X., Hirschfeld M., Beck J., Kupke A., Köhler K., Schütz E., Brenig B. Osteogenesis imperfecta in a male holstein calf associated with a possible oligogenic origin. The Veterinary Quarterly, 2020, 40(1): 58-67 (doi: 10.1080/01652176.2020.1721611).
- An B., Xia J., Chang T., Wang X., Miao J., Xu L., Zhang L., Gao X., Chen Y., Li J., Gao H. Genome-wide association study identifies loci and candidate genes for internal organ weights in Simmental beef cattle. Physiological Genomics, 2018, 50(7): 523-531 (doi: 10.1152/physiol-genomics.00022.2018).
- Milner J.M., Rowan A.D., Cawston T.E., Young D.A. Metalloproteinase and inhibitor expression profiling of resorbing cartilage reveals pro-collagenase activation as a critical step for collagenol-ysis. Arthritis Research & Therapy, 2006, 8(5): R142 (doi: 10.1186/ar2034).
- Zhang H., Takeda H., Tsuji T., Kamiya N., Rajderkar S., Louie K., Collier C., Scott G., Ray M., Mochida Y., Kaartinen V., Kunieda T., Mishina Y. Generation of Evc2/Limbin global and conditional KO mice and its roles during mineralized tissue formation. Genesis, 2015, 53(9): 612-626 (doi: 10.1002/dvg.22879).
- Correa-Rodríguez M., Schmidt Rio-Valle J., Rueda-Medina B. AKAP11 gene polymorphism is associated with bone mass measured by quantitative ultrasound in young adults. International Journal of Medical Sciences, 2018, 15(10): 999-1004 (doi: 10.7150/ijms.25369).
- Oh J.H., Lee J.Y., Joung S.H., Oh Y.T., Kim H.S., Lee N.K. Insulin enhances RANKL-induced osteoclastogenesis via ERK1/2 activation and induction of NFATc1 and Atp6v0d2. Cellular Signalling, 2015, 27(12): 2325-2331 (doi: 10.1016/j.cellsig.2015.09.002).
- Chen J., Tu X., Esen E., Joeng K.S., Lin C., Arbeit J.M., Rüegg M.A., Hall M.N., Ma L., Long F. WNT7B promotes bone formation in part through mTORC1. PLoS Genetics, 2014, 10(1): e1004145 (doi: 10.1371/journal.pgen.1004145).
- Sawai M., Uchida Y., Ohno Y., Miyamoto M., Nishioka C., Itohara S., Sassa T., Kihara A. The 3-hydroxyacyl-CoA dehydratases HACD1 and HACD2 exhibit functional redundancy and are active in a wide range of fatty acid elongation pathways. The Journal of Biological Chemistry, 2017, 292(37): 15538-15551 (doi: 10.1074/jbc.M117.803171).
- Knigge A., Klöting N., Schön M.R., Dietrich A., Fasshauer M., Gärtner D., Lohmann T., Dreßler M., Stumvoll M., Kovacs P., Blüher M. ADCY5 gene expression in adipose tissue is related to obesity in men and mice. PLoS ONE, 2015, 10(3): e0120742 (doi: 10.1371/jour-nal.pone.0120742).
- Bagchi D.P., Li Z., Corsa C.A., Hardij J., Mori H., Learman B S., Lewis K.T., Schill R.L., Romanelli S.M., MacDougald O.A. Wntless regulates lipogenic gene expression in adipocytes and protects against diet-induced metabolic dysfunction. Molecular Metabolism, 2020, 39: 100992 (doi: 10.1016/j.molmet.2020.100992).
- McDaneld T.G., Hannon K., Moody D.E. Ankyrin repeat and SOCS box protein 15 regulates protein synthesis in skeletal muscle. American Journal of Physiology. Regulatory, Integrative and Comparative Physiology, 2006, 290(6): R1672-R1682 (doi: 10.1152/ajpregu.00239.2005).
- Smith J.A., Curry E.G., Blue R.E., Roden C., Dundon S., Rodríguez-Vargas A., Jordan D.C., Chen X., Lyons S.M., Crutchley J., Anderson P., Horb M.E., Gladfelter A.S., Giudice J. FXR1 splicing is important for muscle development and biomolecular condensates in muscle cells. The Journal of Cell Biology, 2020, 219(4): e201911129 (doi: 10.1083/jcb.201911129).
- Fukuda S., Kaneshige A., Kaji T., Noguchi Y.T., Takemoto Y., Zhang L., Tsujikawa K., Ko-kubo H., Uezumi A., Maehara K., Harada A., Ohkawa Y., Fukada S.I. Sustained expression of HeyL is critical for the proliferation of muscle stem cells in overloaded muscle. eLife, 2019, 8: e48284 (doi: 10.7554/eLife.48284).
- Wadhwa R., Yaguchi T., Kaur K., Suyama E., Kawasaki H., Taira K., Kaul S.C. Use of a randomized hybrid ribozyme library for identification of genes involved in muscle differentiation. The Journal of Biological Chemistry, 2004, 279(49): 51622-51629 (doi: 10.1074/jbc.M407428200).
- Picard B., Lefaucheur L., Berri C., Duclos M.J. Muscle fibre ontogenesis in farm animal species. Reproduction Nutrition Development, 2002, 42(5): 415-431 (doi: 10.1051/rnd:2002035).
- Bonnet M., Cassar-Malek I., Chilliard Y., Picard B. Ontogenesis of muscle and adipose tissues and their interactions in ruminants and other species. Animal, 2010, 4(7), 1093-1109 (doi: 10.1017/S1751731110000601).
- Roldan D.L., Dodero A.M., Bidinost F., Taddeo H.R., Allain D., Poli M.A., Elsen J.M. Merino sheep: a further look at quantitative trait loci for wool production. Animal, 2010, 4(8):1330-1340 (doi: 10.1017/S1751731110000315).
- Matika O., Sechi S., Pong-Wong R., Houston R.D., Clop A., Woolliams J.A., Bishop S.C. Characterization of OAR1 and OAR18 QTL associated with muscle depth in British commercial terminal sire sheep. Animal Genetics, 2011, 42(2): 172-180 (doi: 10.1111/j.l365-2052.2010.02121.x).
- Cavanagh C.R., Jonas E., Hobbs M., Thomson P.C., Tammen I., Raadsma H.W. Mapping Quantitative Trait Loci (QTL) in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL. Genetics Selection Evolution, 2010, 42(1): 36 (doi: 10.1186/1297-9686-42-36).