Screening for signatures of selection of Tianzhu white yak using genome-wide re-sequencing.
artificial selection
candidate genes
coat color
environmental adaptation
pigmentation
Journal
Animal genetics
ISSN: 1365-2052
Titre abrégé: Anim Genet
Pays: England
ID NLM: 8605704
Informations de publication
Date de publication:
Oct 2019
Oct 2019
Historique:
accepted:
26
03
2019
pubmed:
28
6
2019
medline:
28
10
2019
entrez:
28
6
2019
Statut:
ppublish
Résumé
The Tianzhu white yak, a domestic yak indigenous to the Qilian Mountains, migrated inland from the Qinghai-Tibet Plateau. Specific ecological and long-term artificial selection influenced the evolution of its pure white coat and physiological characteristics. Therefore, it is not only a natural population that represents a genomic selective region of environmental adaptability but is also an animal model for studying the pigmentation of the yak coat. A total of 24 261 829 variants, including 22 445 252 SNPs, were obtained from 29 yaks by genome-wide re-sequencing. According to the results of a selective sweep analysis of Tianzhu white yak in comparison to Tibetan yaks, nine candidate genes under selection in Tianzhu white yak were identified by combining π, Tajima's D, πA/πB and F
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
534-538Subventions
Organisme : Chongqing Research Program of basic research and frontier technology of China
ID : cstc2018jcyjAX0153
Organisme : National Natural Science Foundation of China
ID : 31172195
Organisme : Fundamental Research Funds for the Central Universities
ID : XDJK2018B014
Informations de copyright
© 2019 Stichting International Foundation for Animal Genetics.
Références
Bardawil T., Rebeiz A., Chaabouni M. et al. (2017) Mutations in the ABCG8 gene are associated with sitosterolaemia in the homozygous form and xanthelasmas in the heterozygous form. European Journal of Dermatology 27, 519-23.
Biscarini F., Cozzi P. & Orozco-Ter Wengel P. (2018) Lessons learnt on the analysis of large sequence data in animal genomics. Animal Genetics 49, 147-58.
Byford E.T., Carr M., Ladikou E., Ahearne M.J. & Wagner S.D. (2018) Circulating Tfh1 (cTfh1) cell numbers and PD1 expression are elevated in low-grade B-cell non-Hodgkin's lymphoma and cTfh gene expression is perturbed in marginal zone lymphoma. PLoS ONE 13, e0190468.
Chen S.Y., Huang Y., Zhu Q., Fontanesi L., Yao Y.G. & Liu Y.P. (2009) Sequence characterization of the MC1R gene in yak (Poephagus grunniens) breeds with different goat colors. Journal of Biomedicine and Biotechnology 2009, 861046-51.
China National Commission of Animal Genetic Resources (2011) Animal Genetic Resources in China: Cattle and Yak. Chinese Agricultural Press, Beijing.
Druml T., Grilz-Seger G., Neuditschko M., Horna M., Ricard A., Pausch H. & Brem G. (2018) Novel insights into Sabino1 and splashed white coat color patterns in horses. Animal Genetics 49, 249-53.
Fagerberg L., Hallström B.M., Oksvold P. et al. (2014) Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Molecular and Cellular Proteomics 13, 397-406.
Guo Y., Walsh A.M., Canavan M. et al. (2018) Immune checkpoint inhibitor PD-1 pathway is down-regulated in synovium at various stages of rheumatoid arthritis disease progression. PLoS ONE 13, e0192704.
Hudson R.R., Slatkin M. & Maddison W.P. (1992) Estimation of levels of gene flow from DNA sequence data. Genetics 132, 583-9.
Kluger H.M., Zito C. R., Turcu G. et al. (2017) PD-L1 studies across tumor types, its differential expression and predictive value in patients treated with immune checkpoint inhibitors. Clinical Cancer Research 23, 4270-9.
Li M., Tian S., Yeung C.K. et al. (2014) Whole-genome sequencing of Berkshire (European native pig) provides insights into its origin and domestication. Scientific Reports 4, 4678.
Li X., Wu Z., Ni J., Liu Y., Meng J., Yu W., Nakanishi H. & Zhou Y. (2016) Cathepsin B regulates collagen expression by fibroblasts via prolonging TLR2/NF-κB activation. Oxidative Medicine and Cellular Longevity 2016, 7894247.
Liang S.Y., Zhou Z.K. & Hou S.S. (2017) The research progress of farm animal genomics based on sequencing technologies. Yi Chuan 39, 276-92.
Liu J., Liu R., Wang J. et al. (2018) Exploring genomic variants related to residual feed intake in local and commercial chickens by whole genomic resequencing. Genes (Basel) 9, 57.
Martin P.M., Palhière I., Ricard A., Tosser-Klopp G. & Rupp R. (2017) Correction: genome wide association study identifies new loci associated with undesired coat color phenotypes in Saanen goats. PLoS ONE 12, e0186029.
Nakamura M., Takii Y., Ito M. et al. (2006) Increased expression of nuclear envelope gp210 antigen in small bile ducts in primary biliary cirrhosis. Journal of Autoimmunity 26, 138-45.
Nazari-Ghadikolaei A., Mehrabani-Yeganeh H., Miarei-Aashtiani S.R., Staiger E.A., Rashidi A. & Huson H.J. (2018) Genome-wide association studies identify candidate genes for coat color and mohair traits in the Iranian Markhoz goat. Frontiers in Genetics 9, 105.
Nei M. & Li W.H. (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences of the United States of America 76, 5269-73.
Nicolas A., Fatima S., Lamri A. et al. (2015) ABCG8 polymorphisms and renal disease in type 2 diabetic patients. Metabolism 64, 713-9.
Qin S.Y., Zhang X.X., Zhao G.H., Zhou D.H., Yin M.Y., Zhao Q. & Zhu X.Q. (2014) First report of Cryptosporidium spp. in white yaks in China. Parasites and Vectors 7, 230.
Qiu Q., Zhang G., Ma T. et al. (2012) The yak genome and adaptation to life at high altitude. Nature Genetics 44, 946-9.
Qiu Q., Wang L., Wang K. et al. (2015) Yak whole-genome resequencing reveals domestication signatures and prehistoric population expansions. Nature Communications 6, 10283.
Tajima F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585-95.
Turner A.W., Nikpay M., Silva A., Lau P., Martinuk A., Linseman T.A., Soubeyrand S. & McPherson R. (2015) Functional interaction between COL4A1/COL4A2 and SMAD3 risk loci for coronary artery disease. Atherosclerosis 242, 543-52.
Uchiyama H., Maehara S., Ohta H., Seki T. & Tanaka Y. (2018) Elevenin regulates the body color through a G protein-coupled receptor NlA42 in the brown planthopper Nilaparvata lugens. General and Comparative Endocrinology 258, 33-8.
Wang K., Li M. & Hakonarson H. (2010) annovar: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research 38, e164.
Yokoyama S., Feige E., Poling L.L., Levy C., Widlund H.R., Khaled M., Kung A.L. & Fisher D.E. (2008) Pharmacologic suppression of MITF expression via HDAC inhibitors in the melanocyte lineage. Pigment Cell and Melanoma Research 21, 457-63.
Zeisel S. (2017) Choline, other methyl-donors and epigenetics. Nutrients 9, 445.
Zhang M.Q., Xu X. & Luo S.J. (2014) The genetics of brown coat color and white spotting in domestic yaks (Bos grunniens). Animal Genetics 45, 652-9.