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Genetics

Whole-genome resequencing of Dulong Chicken reveal signatures of selection

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Pages 624-631 | Received 06 Dec 2019, Accepted 14 May 2020, Published online: 04 Sep 2020

References

  • An, B., J. Xia, T. Chang, X. Wang, L. Xu, L. Zhang, X. Gao, Y. Chen, J. Li, and H. Gao. 2019. “Genome-wide Association Study Reveals Candidate Genes Associated with Body Measurement Traits in Chinese Wagyu Beef Cattle.” Animal Genetics 50 (4): 386–390.
  • Axelsson, E., A. Ratnakumar, M. L. Arendt, K. Maqbool, M. T. Webster, M. Perloski, O. Liberg, J. M. Arnemo, A. Hedhammar, and K. Lindblad-Toh. 2013. “The Genomic Signature of Dog Domestication Reveals Adaptation to a Starch-rich Diet.” Nature 495 (7441): 360–364.
  • Ben-Bassat, H., and B. Y. Klein. 2000. “Inhibitors of Tyrosine Kinases in the Treatment of Psoriasis.” Current Pharmaceutical Design 6 (9): 933–942.
  • Benini, A., F. Cignarella, L. Calvarini, S. Mantovanelli, E. Giacopuzzi, D. Zizioli, and G. Borsani. 2015. “Slc7a6os Gene Plays a Critical Role in Defined Areas of the Developing CNS in Zebrafish.” PLoS One 10 (3): e0119696.
  • Bernard, M., C. Dejos, T. Berges, M. Regnacq, and P. Voisin. 2014. “Activation of Rhodopsin Gene Transcription in Cultured Retinal Precursors of Chicken Embryo: Role of Ca(2+) Signalling and Hyperpolarization-activated Cation Channels.” Journal of Neurochemistry 129 (1): 85–98.
  • Bian, C., Y. Huang, J. Li, X. You, Y. Yi, W. Ge, and Q. Shi. 2019. “Divergence, Evolution and Adaptation in Ray-finned Fish Genomes.” Science China. Life Sciences 62 (8): 1003–1018.
  • Blanc, R. S., G. Vogel, T. Chen, C. Crist, and S. Richard. 2016. “PRMT7 Preserves Satellite Cell Regenerative Capacity.” Cell Reports 14 (6): 1528–1539.
  • Carre, G. A., I. Couty, C. Hennequet-Antier, and M. S. Govoroun. 2011. “Gene Expression Profiling Reveals New Potential Players of Gonad Differentiation in the Chicken Embryo.” PLoS One 6 (9): e23959.
  • Cedraz de Oliveira, H., A. A. J. Pinto Garcia, J. G. Gonzaga Gromboni, R. Vasconcelos Farias Filho, C. Souza Do Nascimento, and A. Arias Wenceslau. 2017. “Influence of Heat Stress, Sex and Genetic Groups on Reference Genes Stability in Muscle Tissue of Chicken.” PLoS One 12 (5): e0176402.
  • Committee, E. 2014. Notes on Genetic Resources of Livestock and Poultry in Yunnan Province. Kunming: Yunnan Science and Technology Press.
  • Corbley, M. J., V. Cherington, P. M. Traxler, N. B. Lydon, and T. M. Roberts. 1996. “A Strategy for Screening Anti-tumor Drugs Utilizing Oncogenes Encoded in Retroviral Vectors.” International Journal of Cancer 66 (6): 753–759.
  • Czechanski, A., H. Kim, C. Byers, I. Greenstein, J. Stumpff, and L. G. Reinholdt. 2015. “Kif18a Is Specifically Required for Mitotic Progression during Germ Line Development.” Developmental Biology 402 (2): 253–262.
  • Denny, S. K., D. Yang, C. H. Chuang, J. J. Brady, J. S. Lim, B. M. Gruner, S. H. Chiou, et al.. 2016. “Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility.” Cell 166 (2): 328–342.
  • Felsenstein, J. 1985. “Confidence Limits on Phylogenies: An Approach Using the Bootstrap.” Evolution; International Journal of Organic Evolution 39 (4): 783–791.
  • Gou, X., Z. Wang, N. Li, F. Qiu, Z. Xu, D. Yan, S. Yang, et al.. 2014. “Whole-genome Sequencing of Six Dog Breeds from Continuous Altitudes Reveals Adaptation to High-altitude Hypoxia.” Genome Research 24 (8): 1308–1315.
  • Guan, H., N. Li, X. Wang, X. Shan, Z. Li, and Z. Lin. 2019. “Role of Paip1 on Angiogenesis and Invasion in Pancreatic Cancer.” Experimental Cell Research 376 (2): 198–209.
  • Guo, X., Q. Fang, C. Ma, B. Zhou, Y. Wan, and R. Jiang. 2016. “Whole-genome Resequencing of Xishuangbanna Fighting Chicken to Identify Signatures of Selection.” Genetics, Selection, Evolution: GSE 48 (1): 62.
  • Hopkins, P. N. 2013. “Molecular Biology of Atherosclerosis.” Physiological Reviews 93 (3): 1317–1542.
  • Hu, X. J., J. Yang, X. L. Xie, F. H. Lv, Y. H. Cao, W. R. Li, M. J. Liu, et al.. 2019. “The Genome Landscape of Tibetan Sheep Reveals Adaptive Introgression from Argali and the History of Early Human Settlements on the Qinghai-Tibetan Plateau.” Molecular Biology and Evolution 36 (2): 283–303.
  • Ito, W., M. Chehab, S. Thakur, J. Li, and A. Morozov. 2011. “BDNF-restricted Knockout Mice as an Animal Model for Aggression.” Genes, Brain, and Behavior 10 (3): 365–374.
  • Karlsson, E. K., I. Baranowska, C. M. Wade, N. H. Salmon Hillbertz, M. C. Zody, N. Anderson, T. M. Biagi, et al.. 2007. “Efficient Mapping of Mendelian Traits in Dogs through Genome-wide Association.” Nature Genetics 39 (11): 1321–1328.
  • Kozma, R., P. Rodin-Morch, and J. Hoglund. 2019. “Genomic Regions of Speciation and Adaptation among Three Species of Grouse.” Scientific Reports 9 (1): 812.
  • Kumar, A., J. C. Lawrence Jr., D. Y. Jung, H. J. Ko, S. R. Keller, J. K. Kim, M. A. Magnuson, and T. E. Harris. 2010. “Fat Cell-specific Ablation of Rictor in Mice Impairs Insulin-regulated Fat Cell and Whole-body Glucose and Lipid Metabolism.” Diabetes 59 (6): 1397–1406.
  • Kumar, V. H. S., J. Chaker El Khoury, R. Gronostajski, H. Wang, L. Nielsen, and R. M. Ryan. 2017. “Nfib Hemizygous Mice are Protected from Hyperoxic Lung Injury and Death.” Physiological Reports 5 (16): e13398.
  • Lanikova, L., N. S. Reading, H. Hu, T. Tashi, T. Burjanivova, A. Shestakova, B. Siwakoti, et al.. 2017. “Evolutionary Selected Tibetan Variants of HIF Pathway and Risk of Lung Cancer.” Oncotarget 8 (7): 11739–11747.
  • Law, C., M. Paquet, and A. Kania. 2014. “Emergence of Motor Circuit Activity.” PLoS One 9 (4): e93836.
  • Lawal, R. A., R. M. Al-Atiyat, R. S. Aljumaah, P. Silva, J. M. Mwacharo, and O. Hanotte. 2018. “Whole-Genome Resequencing of Red Jungle fowl and Indigenous Village Chicken Reveal New Insights on the Genome Dynamics of the Species.” Frontiers in Genetics 9: 264. doi:10.3389/fgene.2018.00264.
  • Li, D., T. Che, B. Chen, S. Tian, X. Zhou, G. Zhang, M. Li, et al.. 2017. “Genomic Data for 78 Chickens from 14 Populations.” GigaScience 6 (6): 1–5.
  • Li, D., Y. Li, M. Li, T. Che, S. Tian, B. Chen, X. Zhou, et al.. 2019a. “Population Genomics Identifies Patterns of Genetic Diversity and Selection in Chicken.” BMC Genomics 20 (1): 263.
  • Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, and R. Durbin. 2009. “The Sequence Alignment/Map Format and SAMtools.” Bioinformatics (Oxford, England) 25 (16): 2078–2079.
  • Li, H., and R. Durbin. 2010. “Fast and Accurate Long-read Alignment with Burrows-Wheeler Transform.” Bioinformatics (Oxford, England) 26 (5): 589–595.
  • Li, N., J. Piao, X. Wang, K. Y. Kim, J. Y. Bae, X. Ren, and Z. Lin. 2019b. “Paip1 Indicated Poor Prognosis in Cervical Cancer and Promoted Cervical Carcinogenesis.” Cancer Research and Treatment: Official Journal of Korean Cancer Association 51 (4): 1653–1665.
  • Li, Q. Q., P. Zhang, M. M. Li, L. Li, Y. D. Hu, S. K. Mishra, A. W. Guo, G. Y. Li, D. Y. Li, and Y. Q. Duan. 2020. “Genetic Diversity and Relationship of Dulong Chickens Using Mitochondrial DNA Control Region.” Mitochondrial DNA Part B 5 (1): 275–280.
  • Librado, P., and C. Gamba. 2017. “Ancient Genomic Changes Associated with Domestication of the Horse.” Science 356 (6336): 442–445.
  • Matsubara, Y., M. Aoki, T. Endo, and K. Sato. 2013. “Characterization of the Expression Profiles of Adipogenesis-related Factors, ZNF423, KLFs and FGF10, during Preadipocyte Differentiation and Abdominal Adipose Tissue Development in Chickens.” Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology 165 (3): 189–195.
  • Meimaridou, E., M. Goldsworthy, V. Chortis, E. Fragouli, P. A. Foster, W. Arlt, R. Cox, and L. A. Metherell. 2018. “NNT Is a Key Regulator of Adrenal Redox Homeostasis and Steroidogenesis in Male Mice.” The Journal of Endocrinology 236 (1): 13–28.
  • Meuwissen, T., and M. Goddard. 2010. “Accurate Prediction of Genetic Values for Complex Traits by Whole-genome Resequencing.” Genetics 185 (2): 623–631.
  • Miao, B., Z. Wang, and Y. Li. 2017. “Genomic Analysis Reveals Hypoxia Adaptation in the Tibetan Mastiff by Introgression of the Gray Wolf from the Tibetan Plateau.” Molecular Biology and Evolution 34 (3): 734–743.
  • Nagata, T., N. Kobayashi, S. Shinagawa, H. Yamada, K. Kondo, and K. Nakayama. 2014. “Plasma BDNF Levels are Correlated with Aggressiveness in Patients with Amnestic Mild Cognitive Impairment or Alzheimer Disease.” Journal of Neural Transmission (Vienna, Austria: 1996) 121 (4): 433–441.
  • Piao, J., L. Chen, T. Jin, M. Xu, C. Quan, and Z. Lin. 2018. “Paip1 Affects Breast Cancer Cell Growth and Represents a Novel Prognostic Biomarker.” Human Pathology 73: 33–40. doi:10.1016/j.humpath.2017.10.037.
  • Previti, A., B. Guercio, and A. Passantino. 2016. “Protection of Farmed Camels (Camelus Dromedarius): Welfare Problems and Legislative Perspective.” Animal Science Journal = Nihon Chikusan Gakkaiho 87 (2): 183–189.
  • Qiu, Q., L. Wang, K. Wang, Y. Yang, T. Ma, Z. Wang, X. Zhang, et al.. 2015. “Yak Whole-genome Resequencing Reveals Domestication Signatures and Prehistoric Population Expansions.” Nature Communications 6: 10283. doi:10.1038/ncomms10283.
  • Roth, L. S., and O. Lind. 2013. “The Impact of Domestication on the Chicken Optical Apparatus.” PLoS One 8 (6): e65509.
  • Rubin, C. J., M. C. Zody, J. Eriksson, J. R. Meadows, E. Sherwood, M. T. Webster, L. Jiang, et al.. 2010. “Whole-genome Resequencing Reveals Loci under Selection during Chicken Domestication.” Nature 464 (7288): 587.
  • Saitou, N., and M. Nei. 1987. “The Neighbor-joining Method: A New Method for Reconstructing Phylogenetic Trees.” Molecular Biology and Evolution 4 (4): 406–425.
  • Sekine, K., H. Ohuchi, M. Fujiwara, M. Yamasaki, T. Yoshizawa, T. Sato, N. Yagishita, et al.. 1999. “Fgf10 Is Essential for Limb and Lung Formation.” Nature Genetics 21 (1): 138–141.
  • Sekine, K., H. Ohuchi, M. Fujiwara, M. Yamasaki, T. Yoshizawa, T. Sato, N. Yagishita, et al.. 2019. “Publisher Correction: Fgf10 Is Essential for Limb and Lung Formation.” Nature Genetics 51 (5): 921.
  • Selleck, S. B. 2000. “Proteoglycans and Pattern Formation: Sugar Biochemistry Meets Developmental Genetics.” Trends in Genetics: TIG 16 (5): 206–212.
  • Shaffer, J. R., and E. Orlova. 2016. “Genome-Wide Association Study Reveals Multiple Loci Influencing Normal Human Facial Morphology.” PLoS Genetics 12 (8): e1006149.
  • Shahjahan, M., R. R. Liu, G. P. Zhao, J. J. Zhang, M. Q. Zheng, Q. H. Li, and J. Wen. 2015. “Polymorphisms in GJA1 and Their Association with Growth Traits in Chicken.” Genetics and Molecular Research: GMR 14 (4): 18839–18850.
  • Shin, M., S. Noji, A. Neubuser, and S. Yasugi. 2006. “FGF10 Is Required for Cell Proliferation and Gland Formation in the Stomach Epithelium of the Chicken Embryo.” Developmental Biology 294 (1): 11–23.
  • Spalletta, G., D. W. Morris, F. Angelucci, I. A. Rubino, I. Spoletini, P. Bria, G. Martinotti, et al.. 2010. “BDNF Val66Met Polymorphism Is Associated with Aggressive Behavior in Schizophrenia.” European Psychiatry: The Journal of the Association of European Psychiatrists 25 (6): 311–313.
  • Stapley, J., J. Reger, P. G. Feulner, C. Smadja, J. Galindo, R. Ekblom, C. Bennison, A. D. Ball, A. P. Beckerman, and J. Slate. 2010. “Adaptation Genomics: The Next Generation.” Trends in Ecology & Evolution 25 (12): 705–712. Review.
  • Talwelkar, S. S., A. SN, J. R. Devlin, A. Hemmes, and S. Potdar. 2019. “Receptor Tyrosine Kinase Signaling Networks Define Sensitivity to ERBB Inhibition and Stratify Kras Mutant Lung Cancers.” Molecular Cancer Therapeutics 18 (10): 1863–1874.
  • Tiunova, A. A., N. V. Komissarova, and K. V. Anokhin. 2018. “Prenatal Sensory Stimulation Induces BDNF Gene Expression in the Brain and Potentiates the Development of Species-Specific Predisposition in Newborn Chicks.” Bulletin of Experimental Biology and Medicine 166 (2): 229–232.
  • Tolosa, A., X. Zhou, B. Spittau, and K. Krieglstein. 2013. “Establishment of a Survival and Toxic Cellular Model for Parkinson’s Disease from Chicken Mesencephalon.” Neurotoxicity Research 24 (2): 119–129.
  • Umair, M., F. Ahmad, M. Bilal, W. Ahmad, and M. Alfadhel. 2018. “Clinical Genetics of Polydactyly: An Updated Review.” Frontiers in Genetics 9: 447. doi:10.3389/fgene.2018.00447.
  • Wang, K., M. Li, and H. Hakonarson. 2010. “ANNOVAR: Functional Annotation of Genetic Variants from High-throughput Sequencing Data.” Nucleic Acids Research 38 (16): e164.
  • Wang, K., Y. Yang, L. Wang, T. Ma, H. Shang, L. Ding, J. Han, and Q. Qiu. 2016a. “Different Gene Expressions between Cattle and Yak Provide Insights into High-altitude Adaptation.” Animal Genetics 47 (1): 28–35.
  • Wang, M. S., R. W. Zhang, L. Y. Su, Y. Li, M. S. Peng, H. Q. Liu, L. Zeng, et al.. 2016b. “Positive Selection Rather than Relaxation of Functional Constraint Drives the Evolution of Vision during Chicken Domestication.” Cell Research 26 (5): 556–573.
  • Wang, M. S., Y. Li, M. S. Peng, L. Zhong, Z. J. Wang, Q. Y. Li, X. L. Tu, et al.. 2015. “Genomic Analyses Reveal Potential Independent Adaptation to High Altitude in Tibetan Chickens.” Molecular Biology and Evolution 32 (7): 1880–1889.
  • Wu, N., D. Jia, A. H. Ibrahim, C. J. Bachurski, R. M. Gronostajski, and D. MacPherson. 2016. “NFIB Overexpression Cooperates with Rb/p53 Deletion to Promote Small Cell Lung Cancer.” Oncotarget 7 (36): 57514–57524.
  • Xiang, H., J. Gao, B. Yu, H. Zhou, D. Cai, Y. Zhang, X. Chen, X. Wang, M. Hofreiter, and X. Zhao. 2014. “Early Holocene Chicken Domestication in Northern China.” Proceedings of the National Academy of Sciences 111 (49): 17564–17569.
  • Yokoyama, S. 2002. “Molecular Evolution of Color Vision in Vertebrates.” Gene 300 (1–2): 69–78.
  • Yuan, D., X. Yang, Z. Yuan, Y. Zhao, and J. Guo. 2017. “TLE1 Function and Therapeutic Potential in Cancer.” Oncotarget 8 (9): 15971–15976.
  • Zampiga, M., J. Flees, A. Meluzzi, S. Dridi, and F. Sirri. 2018. “Application of Omics Technologies for A Deeper Insight into Quali-quantitative Production Traits in Broiler Chickens: A Review.” Journal of Animal Science and Biotechnology 9: 61. doi:10.1186/s40104-018-0278-5.
  • Zappaterra, M., M. Mazzoni, P. Zambonelli, and R. Davoli. 2018. “Investigation of the Perilipin 5 Gene Expression and Association Study of Its Sequence Polymorphism with Meat and Carcass Quality Traits in Different Pig Breeds.” Animal: An International Journal of Animal Bioscience 12 (6): 1135–1143.
  • Zhang, B., D. Ban, X. Gou, Y. Zhang, L. Yang, Y. Chamba, and H. Zhang. 2019. “Genome-wide DNA Methylation Profiles in Tibetan and Yorkshire Pigs under High-altitude Hypoxia.” Journal of Animal Science and Biotechnology 10: 25. doi:10.1186/s40104-019-0316-y.
  • Zhang, H., J. Q. Yu, L. L. Yang, L. M. Kramer, X. Y. Zhang, W. Na, J. M. Reecy, and H. Li. 2017. “Identification of Genome-wide SNP-SNP Interactions Associated with Important Traits in Chicken.” BMC Genomics 18 (1): 892.
  • Zhang, R., R. Li, Q. Feng, L. Zhi, Z. Li, Y. O. Xu, and Y. Lin. 2018. “Expression Profiles and Associations of FGF1 and FGF10 with Intramuscular Fat in Tibetan Chicken.” British Poultry Science 59 (6): 613–617. doi:10.1080/00071668.2018.1507018
  • Zhou, Y., B. Zhou, L. Pache, and M. Chang. 2019. “Metascape Provides a Biologist-oriented Resource for the Analysis of Systems-level Datasets.” Nature Communications 10 (1): 1523.

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