Performance Measurement and Comparative Transcriptome Analysis Revealed the Efforts on Hybrid Improvement of Qinchuan Cattle

References

• Ball PJH, Peters AR. Reproduction in cattle. Reprod Cattle 2004;4(1972):71–8. doi:10.1136/inpract.5.5.153.
   Google Scholar
• Qiu H, Ju ZY, Chang ZJ. A survey of cattle production in China. World Anim Rev 1993;3:75.
   Google Scholar
• Mei CG, Gui LS, Fu CZ, Wang HC, Wang JL, Cheng G, Zan LS. Polymorphisms in the bovine CIDEC gene are associated with body measurement traits and meat quality traits in Qinchuan cattle. Genet Mol Res 2015;14(3):9013–23. doi:10.4238/2015.august.7.10.
   PubMed Web of Science ®Google Scholar
• Genomes PC. An integrated map of genetic variation from 1,092 human genomes. Nature 2012;491(7422):56–65. doi:10.1038/nature11632.
   PubMed Web of Science ®Google Scholar
• Mei C, Wang H, Zhu W, Wang H, Cheng G, Qu K, Guang X, Li A, Zhao C, Yang W, et al. Whole-genome sequencing of the endangered bovine species Gayal (Bos frontalis) provides new insights into its genetic features. Sci Rep UK 2016;6:19787. doi:10.1038/srep19787.
   PubMed Web of Science ®Google Scholar
• Mei CG, Wang HC, Liao QJ, Wang LZ, Cheng G, Wang HB, Zhao CP, Zhao SC, Song JZ, Guang XM, et al. Genetic architecture and selection of Chinese cattle revealed by whole genome resequencing. Mol Biol Evol 2017; msx322. doi:10.1093/molbev/msx322.
   Web of Science ®Google Scholar
• Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008;5(7):621–8. doi:10.1038/nmeth.1226.
   PubMed Web of Science ®Google Scholar
• Costa V, Angelini C, De Feis I, Ciccodicola A. Uncovering the complexity of transcriptomes with RNA-Seq. J Biomed Biotechnol. 2010;2010:853916. doi:10.1155/2010/853916.
   PubMed Web of Science ®Google Scholar
• Wang Z, Gerstein M, Snyder M. RNA-Seq: A revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10(1):57–63. doi:10.1038/nrg2484.
   PubMed Web of Science ®Google Scholar
• Wang Z, Fang B, Chen J, Zhang X, Luo Z, Huang L, Chen X, Li Y. De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas). BMC Genomics 2010;11(726). doi:10.1186/1471-2164-11-726.
   Google Scholar
• Zenoni S, Ferrarini A, Giacomelli E, Xumerle L, Fasoli M, Malerba G, Bellin D, Pezzotti M, Delledonne M. Characterization of transcriptional complexity during berry development in Vitis vinifera using RNA-Seq. Plant Physiol. 2010;152(4):1787–95. doi:10.1104/pp.109.149716.
   PubMed Web of Science ®Google Scholar
• Tang Q, Ma X, Mo C, Wilson IW, Song C, Zhao H, Yang Y, Fu W, Qiu D. An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis. BMC Genomics 2011;12(1):343. doi:10.1186/1471-2164-12-343
   PubMed Web of Science ®Google Scholar
• Yang SS, Tu ZJ, Cheung F, Xu WW, Lamb JF, Jung HJ, Vance CP, Gronwald JW. Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems. BMC Genomics 2011;12(1):199. doi:10.1186/1471-2164-12-199.
   PubMedGoogle Scholar
• Jäger M, Ott CE, Grünhagen J, Hecht J, Schell H, Mundlos S, Duda GN, Robinson PN, Lienau J. Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing. BMC Genomics 2011;12(1):158. doi:10.1186/1471-2164-12-158.
   PubMedGoogle Scholar
• Jun H, Daiwen C, Bing Y. Metabolic and transcriptomic responses of weaned pigs induced by different dietary amylose and amylopectin ratio. PLoS One. 2010;5(11):e15110. doi:10.1371/journal.pone.0015110.
   PubMed Web of Science ®Google Scholar
• Gu Z, Eleswarapu S, Jiang H. Identification and characterization of microRNAs from the bovine adipose tissue and mammary gland. FEBS Lett. 2007;581(5):981–8. doi:10.1016/j.febslet.2007.01.081.
   PubMed Web of Science ®Google Scholar
• Wickramasinghe S, Rincon G, Islas-Trejo A, Medrano JF. Transcriptional profiling of bovine milk using RNA sequencing. BMC Genomics 2012;13(1):45. doi:10.1186/1471-2164-13-45.
   PubMedGoogle Scholar
• Miar Y, Plastow GS, Bruce HL, Moore SS, Durunna ON, Nkrumah JD, Wang Z. Estimation of genetic and phenotypic parameters for ultrasound and carcass merit traits in crossbred beef cattle. Can J Anim Sci. 2014;94(2):273–80.
   Web of Science ®Google Scholar
• Luis Nunes J, Fernandez A, Lecumberry F. Intramuscular fat percentage estimation through ultrasound images. Asian-Australas J Anim Sci 2014;8626:116–22.
   Google Scholar
• Bioinformatics B. FastQC a quality control tool for high throughput sequence data. Cambridge, UK: Babraham Institute; 2011.
   Google Scholar
• Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14(4):R36. doi:10.1186/gb-2013-14-4-r36.
   PubMed Web of Science ®Google Scholar
• Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):354–57. doi:10.1038/nmeth.1923.
   Web of Science ®Google Scholar
• Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, Van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28(5):511–5. doi:10.1038/nbt.1621.
   PubMed Web of Science ®Google Scholar
• Tarazona S, García-Alcalde F, Dopazo J, Ferrer A, Conesa A. Differential expression in RNA-seq: A matter of depth. Genome Res. 2011;21(12):2213–23. doi:10.1101/gr.124321.111.
   PubMed Web of Science ®Google Scholar
• Tarazona S, Furió-Tarí P, Turrà D, Pietro AD, Nueda MJ, Ferrer A, Conesa A. Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package. Nucleic Acids Res. 2015;43(21):e140. doi:10.1093/nar/gkv711.
   PubMed Web of Science ®Google Scholar
• Huang DW, Sherman BT, Tan Q, Kir J, Liu D, Bryant D, Guo Y, Stephens R, Baseler MW, Lane HC, et al. DAVID bioinformatics resources: Expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 2007;35S:W169–75. doi:10.1093/nar/gkm415.
   Google Scholar
• Trapnell C, Pachter L, Salzberg S L. TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics 2009; 25(9):1105–11. doi:10.1093/bioinformatics/btp120.
   PubMed Web of Science ®Google Scholar
• Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001;25(4):402–8. doi:10.1006/meth.2001.1262.
   PubMed Web of Science ®Google Scholar
• Morozova O, Hirst M, Marra MA. Applications of new sequencing technologies for transcriptome analysis. Annu Rev Genomics Hum Genet. 2009;10:135–51. doi:10.1146/annurev-genom-082908-145957.
   PubMed Web of Science ®Google Scholar
• Huang W, Khatib H. Comparison of transcriptomic landscapes of bovine embryos using RNA-Seq. BMC Genomics 2010;11(1):711. doi:10.1186/1471-2164-11-711.
   PubMedGoogle Scholar
• Cánovas A, Rincón G, Bevilacqua C, Islas-Trejo A, Brenaut P, Hovey RC, Boutinaud M, Morgenthaler C, VanKlompenberg MK, Martin P, et al. Comparison of five different RNA sources to examine the lactating bovine mammary gland transcriptome using RNA-Sequencing. Sci Rep UK 2013;4(4);5297–5297. doi:10.1038/srep05297.
   Google Scholar
• Li Y, Carrillo JA, Ding Y, He Y, Zhao C, Zan L, Song J. Ruminal transcriptomic analysis of grass-fed and grain-fed angus beef cattle. Plos One 2015;10(6):e0116437. doi:10.1371/journal.pone.0116437.
   PubMed Web of Science ®Google Scholar
• Huang W, Nadeem A, Zhang B, Babar M, Soller M, Khatib H. Characterization and comparison of the leukocyte transcriptomes of three cattle breeds. Plos One 2012;7(1):e30244. doi:10.1371/journal.pone.0030244.
   PubMed Web of Science ®Google Scholar
• Schutte AE, Van Vuuren D, Van Rooyen JM, Huisman HW, Schutte R, Malan L, Malan NT. Inflammation, obesity and cardiovascular function in African and Caucasian women from South Africa: The POWIRS study. J Hum Hypertens. 2006;20(11):850–9.
   PubMed Web of Science ®Google Scholar
• Kim B, Jang Y, Paik JK, Kim OY, Lee SH, Ordovas JM, Lee JH. Adiponectin gene polymorphisms are associated with long-chain omega 3-Polyunsaturated fatty acids in serum phospholipids in nondiabetic Koreans. J Clin Endocrinol Metab. 2010;95(11):E347–E351. doi:10.1210/jc.2010-0391.
   PubMed Web of Science ®Google Scholar
• Grahn TH, Zhang Y, Lee MJ, Sommer AG, Mostoslavsky G, Fried SK, Greenberg AS, Puri V. FSP27 and PLIN1 interaction promotes the formation of large lipid droplets in human adipocytes. Biochem Biophys Res Commun. 2013;432(2):296–301. doi:10.1016/j.bbrc.2013.01.113.
   PubMed Web of Science ®Google Scholar
• Janssen MCH, et al. Symptomatic lipid storage in carriers for the PNPLA2 gene. Eur J Hum Genet. 2013;21(8):892. doi:10.1038/ejhg.2012.256.
   Web of Science ®Google Scholar
• Magré J, Delépine M, Van Maldergem L, Robert JJ, Maassen JA, Meier M, Panz VR, Kim CA, Tubiana-Rufi N, Czernichow P, et al. Prevalence of mutations in AGPAT2 among human lipodystrophies. Diabetes 2003;52(6):1573–8. doi:10.2337/diabetes.52.6.1573.
   PubMed Web of Science ®Google Scholar
• Licht AH, Nübel T, Feldner A, Jurisch-Yaksi N, Marcello M, Demicheva E, Hu JH, Hartenstein B, Augustin HG, Hecker M, et al. Junb regulates arterial contraction capacity, cellular contractility, and motility via its target Myl9 in mice. J Clin Invest. 2010;120(7):2307–18. doi:10.1172/JCI41749.
   PubMed Web of Science ®Google Scholar
• Chang CC, Campoli M, Restifo NP, Wang X, Ferrone S. Immune selection of Hot-Spot β2-Microglobulin gene mutations, HLA-A2 allospecificity loss, and antigen-processing machinery component down-regulation in melanoma cells derived from recurrent metastases following immunotherapy. J Immunol. 2005;174(3):1462–71.
   PubMed Web of Science ®Google Scholar
• Charoensook R, Gatphayak K, Sharifi AR, Chaisongkram C, Brenig B, Knorr C. Polymorphisms in the bovine HSP90AB1 gene are associated with heat tolerance in Thai indigenous cattle. Trop Anim Health Pro. 2012;44(4):921–8. doi:10.1007/s11250-011-9989-8.
   PubMed Web of Science ®Google Scholar
• Pagan M, Davis ME, Stick DA, Simmen RC, Raney NE, Tempelman RJ, Ernst CW. Evaluation of serum insulin-like growth factor binding proteins (IGFBP) in Angus cattle divergently selected for serum IGF-I concentration. Domest Anim Endocrin. 2003;25(4):345–58.
   PubMed Web of Science ®Google Scholar
• Rivera GM, Fortune JE. Development of codominant follicles in cattle is associated with a follicle-stimulating hormone-dependent insulin-like growth factor binding protein-4 protease. Biol Reprod. 2001;65(1):112–8.
   PubMed Web of Science ®Google Scholar
• Ovsyannikova IG, Haralambieva IH, Kennedy RB, O’byrne MM, Pankratz VS, Poland GA. Genetic variation in IL18R1 and IL18 genes and inteferon γ ELISPOT response to smallpox vaccination: An unexpected relationship. J Infect Dis. 2013;208(9):1422–30. doi:10.1093/infdis/jit341.
   PubMed Web of Science ®Google Scholar
• Vandre RK, Sharma AK, Gowane GR, Sankar M, Sanyal A, Bisht P, Pattnaik B. Trend of association of BoLA-DQA1 alleles with FMDV vaccine elicited immune response in crossbred cattle. Indian J Animal Sci. 2014;84(6):619–23.
   Web of Science ®Google Scholar
• Modrek B, Lee C. A genomic view of alternative splicing. Nat Genet. 2002;30(1):13–9.
   PubMed Web of Science ®Google Scholar
• Nie L, Wu HJ, Hsu JM, Chang SS, LaBaff AM, Li CW, Wang Y, Hsu JL, Hung MC. Long non-coding RNAs: Versatile master regulators of gene expression and crucial players in cancer. Am J Transl Res. 2012;4(2):127–50.
   PubMed Web of Science ®Google Scholar
• Lee JT. Lessons from X-chromosome inactivation: Long ncRNA as guides and tethers to the epigenome. Gene Dev. 2009;23(16):1831–42. doi:10.1101/gad.1811209.
   PubMed Web of Science ®Google Scholar
• Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D, Khalil AM, Zuk O, Amit I, Rabani M, et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 2010;142(3):409–19. doi:10.1016/j.cell.2010.06.040.
   PubMed Web of Science ®Google Scholar
• Huarte M, Rinn JL. Large non-coding RNAs: Missing links in cancer? Hum Mol Genet. 2010;19(2):R152–61. doi:10.1093/hmg/ddq353.
   PubMedGoogle Scholar
• Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010;464(7291):1071–6. doi:10.1038/nature08975.
   PubMed Web of Science ®Google Scholar
• Broadbent KM, Park D, Wolf AR, Van Tyne D, Sims JS, Ribacke U, Volkman S, Duraisingh M, Wirth D, Sabeti PC, et al. A global transcriptional analysis of Plasmodium falciparum malaria reveals a novel family of telomere-associated lncRNAs. Genome Biol. 2011;12(6):R56. doi:10.1186/gb-2011-12-6-r56.
   PubMed Web of Science ®Google Scholar