Whole genome resequencing-based analysis of plateau adaptation in Meiren yak (Bos grunniens)

References

• Qi X, Zhang Q, He Y, et al. The transcriptomic landscape of yaks reveals molecular pathways for high altitude adaptation. Genome Biol Evol. 2019:11(1):72–85.
   PubMed Web of Science ®Google Scholar
• Bao Q, Zhang X, Bao P, et al. Using weighted gene co-expression network analysis (WGCNA) to identify the hub genes related to hypoxic adaptation in yak (Bos grunniens). Genes Genom. 2021;43(10):1231–1246.
   PubMed Web of Science ®Google Scholar
• Ma SL, Li XW, Li X, et al. Assessment of genetic structure of 3 Maiwa yak preserved populations based ongenotyping-by-sequencing technology. Acta Pratacult Sin. 2022;31(09):183–194.
   Google Scholar
• Wang H, Chai Z, Hu D, et al. A global analysis of CNVs in diverse yak populations using whole-genome resequencing. BMC Genom. 2019;20(1):61.
   PubMedGoogle Scholar
• Jie Z, Zhen ZX, Ai LC, et al. Identification of meat from yak and cattle using SNP markers with integrated allele-specific polymerase chain reaction-capillary electrophoresis method. Meat Sci. 2019;148:120–126.
   PubMed Web of Science ®Google Scholar
• Yan XJ, Lei YH, Xie P, et al. Recent progress in processing technologies for yak jerky meat. Meat Research/Roulei Yanjiu. 2019;33(3):67–71.
   Google Scholar
• Wang K, Hu QJ, Ma H, et al. Genome-wide variation within and between wild and domestic yak. Mol Ecol Resour. 2014;14(4):794–801.
   PubMed Web of Science ®Google Scholar
• Radzik-Rant A, Wojtunik K, Gutowski A. Characteristics and distribution of yak in the world. Wiadomości Zootech. 2014;52(2):130–141.
   Google Scholar
• Wu J. The distributions of Chinese yak breeds in response to climate change over the past 50 years. Anim Sci J. 2016;87(7):947–958.
   PubMed Web of Science ®Google Scholar
• Das PP, Krishnan G, Doley J, et al. Establishing gene Amelogenin as sex-specific marker in yak by genomic approach. J Genet. 2019;98:7–12.
   PubMed Web of Science ®Google Scholar
• Wang XD, Pei J, Bao PJ, et al. Mitogenomic diversity and phylogeny analysis of yak (Bos grunniens). BMC Genomics. 2021;22(1):325.
   PubMed Web of Science ®Google Scholar
• Lan DL, Ji WH, Xiong XR, et al. Population genome of the newly discovered Jinchuan yak to understand its adaptive evolution in extreme environments and generation mechanism of the multirib trait. Integr Zool. 2020;16(5):685–695.
   PubMed Web of Science ®Google Scholar
• Tang YQ. Development of highland special ecological yak problems and countermeasures. China Livest Poult Seed Ind. 2020;16(11):30.
   Google Scholar
• Wang Q, Li D, Guo A, et al. Whole-genome resequencing of Dulong Chicken reveal signatures of selection. Br Poult Sci. 2020;61(6):624–631.
   PubMed Web of Science ®Google Scholar
• Chen QM, Huang YF, Wang ZH, et al. Whole-genome resequencing reveals diversity and selective signals in Longlin goat. Gene. 2021;771:145371–145385.
   PubMed Web of Science ®Google Scholar
• Gulcher J, Stefansson K. Population genomics: laying the groundwork for genetic disease modeling and targeting. Clin Chem Lab Med. 1998;36(8):523–527.
   PubMed Web of Science ®Google Scholar
• Ellegren H. Genome sequencing and population genomics in non-model organisms. Trends Ecol Evol. 2014;29(1):51–63.
   PubMed Web of Science ®Google Scholar
• Begun DJ, Holloway AK, Stevens K, et al. Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol. 2007;5(11):e310.
   PubMed Web of Science ®Google Scholar
• Xu XY, Bai GH. Whole-genome resequencing: changing the paradigms of SNP detection molecular mapping and gene discovery. Mol Breed. 2015;35(1):11.
   Web of Science ®Google Scholar
• Liu YC, Sun X, Driscoll C, et al. Genome-wide evolutionary analysis of natural history and adaptation in the world’s tigers. Curr Biol. 2018;28(23):3840–3849.e6.
   PubMed Web of Science ®Google Scholar
• Kim J, Hanotte O, Mwai OA, et al. The genome landscape of indigenous African cattle. Genome Biol. 2017;18(1):34.
   PubMedGoogle Scholar
• Wu DD, Ding XD, Wang S, et al. Pervasive introgression facilitated domestication and adaptation in the Bos species complex. Nat Ecol Evol. 2018;2(7):1139–1145.
   PubMed Web of Science ®Google Scholar
• Guo JZ, Tao HX, Li PF, et al. Whole-genome sequencing reveals selection signatures associated with important traits in six goat breeds. Sci Rep. 2018;8(1):10405–10415.
   PubMedGoogle Scholar
• Chen NB, Cai YD, Chen QM, et al. Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia. Nat Commun. 2018;9(1):1–13.
   PubMedGoogle Scholar
• Fan HH, Wang TJ, Li Y, et al. Development and validation of a 1 K sika deer (Cervus nippon) SNP Chip. BMC Genom Data. 2021;22(1):35.
   PubMedGoogle Scholar
• Li XK, Su R, Wan WT, et al. Identification of selection signals by large-scale whole-genome resequencing of cashmere goats. Sci Rep. 2017;7(1):15142.
   PubMedGoogle Scholar
• Li QF, Zhao XB, Liu HL, Li N, Xie Z. A review of the research on taxonomic status in yak (Poephagus). Acta Zootaxonom Sin. 2006;31(3):520–524.
   Google Scholar
• Xu SY, Zhao LL, Xiao SJ, Gao TX. Whole genome resequencing data for three rockfish species of Sebastes. Sci Data. 2019;6(1):97.
   PubMedGoogle Scholar
• Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014;30(15):2114–2120.
   PubMed Web of Science ®Google Scholar
• Mckenna A, Hanna M, Banks E, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297–1303.
   PubMed Web of Science ®Google Scholar
• Purcell S, Neale B, Todd-Brown K, et al. PLINK: A tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81(3):559–575.
   PubMed Web of Science ®Google Scholar
• Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14(6):587–589.
   PubMed Web of Science ®Google Scholar
• Manichaikul A, Mychaleckyj JC, Rich SS, Daly K, Sale M, Chen WM. Robust relationship inference in genome-wide association studies. Bioinformatics 2010;26(22):2867–2873.
   PubMed Web of Science ®Google Scholar
• Haubold B, Pfaffelhuber P, Lynch M. mlRho–a program for estimating the population mutation and recombination rates from shotgun‐sequenced diploid genomes. Mol Ecol. 2010;19(1):277–284.
   PubMedGoogle Scholar
• Zhang C, Dong SS, Xu JY, He WM, Yang TL. PopLDdecay: A fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics 2019;35(10):1786–1788.
   PubMed Web of Science ®Google Scholar
• Danecek P, Auton A, Abecasis G, et al. The variant call format and VCFtools. Bioinformatics 2011;27(15):2156–2158.
   PubMed Web of Science ®Google Scholar
• Shi HB, Li TT, Su MC, et al. Whole genome sequencing revealed genetic diversity, population structure, and selective signature of Panou Tibetan sheep. BMC Genom. 2023;24(1):50.
   PubMed Web of Science ®Google Scholar
• Chen H, Patterson N, Reich D. Population differentiation as a test for selective sweeps. Genome Res. 2010;20(3):393–402.
   PubMed Web of Science ®Google Scholar
• Kang YD, Guo SK, Wang XD, et al. Whole-genome resequencing highlights the unique characteristics of Kecai Yaks. Animals (Basel). 2022;12(19):2682–2692.
   PubMedGoogle Scholar
• Chen B, Hua ZY, Qin XN, Li ZJ. Integrated microarray to identify the Hub miRNAs and constructed miRNA–mRNA network in neuroblastoma via bioinformatics analysis. Neurochem Res. 2021;46(2):197–212.
   PubMed Web of Science ®Google Scholar
• Qiu Q, Zhang GJ, Ma T, et al. The yak genome and adaptation to life at high altitude. Nat Genet. 2012;44(8):946–949.
   PubMed Web of Science ®Google Scholar
• Liu Y, Yan CY, Matthew C, Wood B, Hou FJ. Key sources and seasonal dynamics of greenhouse gas fluxes from yak grazing systems on the Qinghai-Tibetan Plateau. Sci Rep. 2017;7(1):40857–40867.
   PubMedGoogle Scholar
• Wang MS, Li Y, Peng MS, et al. Genomic analyses reveal potential independent adaptation to high altitude in Tibetan chickens. Mol Biol Evol. 2015;32(7):1880–1889.
   PubMed Web of Science ®Google Scholar
• Wang GD, Zhai WW, Yang HC, et al. Out of southern East Asia: the natural history of domestic dogs across the world. Cell Res. 2016;26(1):21–33.
   PubMed Web of Science ®Google Scholar
• Leocard S. Selective sweep and the size of the hitchhiking set. Adv Appl Probab. 2009;41(3):731–764.
   Web of Science ®Google Scholar
• Zhou T, Wang N, Wang Y, et al. Nucleotide evolution, domestication selection, and genetic relationships of chloroplast genomes in the economically important crop genus gossypium. Front Plant Sci. 2022;13:873788–873803.
   PubMed Web of Science ®Google Scholar
• Xiang H, Li X, Dai FY, et al. Comparative methylomics between domesticated and wild silkworms implies possible epigenetic influences on silkworm domestication. BMC Genom. 2013;14(1):646.
   PubMedGoogle Scholar
• Friedrich J, Talenti A, Arvelius P, Strandberg E, Haskell MJ, Wiener P. Unravelling selection signatures in a single dog breed suggests recent selection for morphological and behavioral traits. Adv Genet (Hoboken). 2020;1(1):e10024.
   PubMedGoogle Scholar
• Rezvannejad E, Asadollahpour NH, Esmailizadeh A. Detection of candidate genes affecting milk production traits in sheep using whole-genome sequencing analysis. Vet Med Sci. 2022;8(3):1197–1204.
   PubMed Web of Science ®Google Scholar
• Wanders RJA, Vreken P, Ferdinandusse S, et al. Peroxisomal fatty acid α-and β-oxidation in humans: enzymology, peroxisomal metabolite transporters and peroxisomal diseases. Biochem Soc Trans. 2001;29(2):250–267.
   PubMedGoogle Scholar
• Wang YL, Li X, Cao Y, et al. Effect of the ACAA1 gene on preadipocyte differentiation in sheep. Front Genet. 2021;12:649140–649149.
   PubMed Web of Science ®Google Scholar
• Lisowski P, Kościuczuk EM, Gościk J, Pierzchała M, Rowińska B, Zwierzchowski L. Hepatic transcriptome profiling identifies differences in expression of genes associated with changes in metabolism and postnatal growth between Hereford and Holstein‐Friesian bulls. Anim Genet. 2014;45(2):288–292.
   PubMed Web of Science ®Google Scholar
• Li GX, Fu SY, Chen Y, et al. MicroRNA-15a regulates the differentiation of intramuscular preadipocytes by targeting ACAA1, ACOX1 and SCP2 in chickens. Int J Mol Sci. 2019;20(16):4063–4075.
   PubMed Web of Science ®Google Scholar
• Wiley DM, Jin SW. Bone Morphogenetic Protein functions as a context-dependent angiogenic cue in vertebrates. Semin Cell Dev Biol. 2011;22(9):1012–1018.
   PubMed Web of Science ®Google Scholar
• Maguer-Satta V, Rimokh R. FLRG, member of the follistatin family, a new player in hematopoiesis. Mol Cell Endocrinol. 2004;225(1–2):109–118.
   PubMed Web of Science ®Google Scholar
• Nemeth E. Iron regulation and erythropoiesis. Curr Opin Hematol. 2008;15(3):169–175.
   PubMed Web of Science ®Google Scholar
• Yang M, Guo MY, Hu YH, Jiang Y. Scube regulates synovial angiogenesis-related signaling. Med Hypotheses. 2013;81(5):948–953.
   PubMed Web of Science ®Google Scholar
• Ding A, Li CH, Yu CY, Zhou HT, Zhang ZH. Long non-coding RNA MALAT1 enhances angiogenesis during bone regeneration by regulating the miR-494/SP1 axis. Lab Invest. 2021;101(11):1458–1466.
   PubMed Web of Science ®Google Scholar
• Detmer K, Walker AN. Bone morphogenetic proteins act synergistically with haematopoietic cytokines in the differentiation of haematopoietic progenitors. Cytokine. 2002;17(1):36–42.
   PubMed Web of Science ®Google Scholar
• Chen DF, Tian W, Li Y, Tang WJ, Zhang C. Osteoblast-specific transcription factor Osterix (Osx) and HIF-1α cooperatively regulate gene expression of vascular endothelial growth factor (VEGF). Biochem Biophys Res Commun. 2012;424(1):176–181.
   PubMed Web of Science ®Google Scholar
• Chen DI, Zhao M, Mundy GR. Bone morphogenetic proteins. Growth Fact. 2004;22(4):233–241.
   PubMed Web of Science ®Google Scholar
• Magga J, Vainio L, Kilpiö T, et al. Systemic blockade of ACVR2B ligands protects myocardium from acute ischemia-reperfusion injury. Mol Ther. 2019;27(3):600–610.
   PubMed Web of Science ®Google Scholar
• Bai L, Liu BN, Ji CM, et al. Hypoxic and cold adaptation insights from the Himalayan marmot genome. Iscience 201911:519–530.
   PubMed Web of Science ®Google Scholar