Revelation of genes associated with energy generating metabolic pathways in the fighter type Aseel chicken of India through skeletal muscle transcriptome sequencing

References

• Kanginakudru S, Metta M, Jakati R, Nagaraju J. Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken. BMC Evol Biol. 2008;8:174.
   PubMed Web of Science ®Google Scholar
• Kanakachari M, Rahman H, Chatterjee RN, Bhattacharya TK. Signature of Indian native chicken breeds: a perspective. World Poult Sci J. 2022;78(2):421–445.
   Web of Science ®Google Scholar
• Haunshi S, Rajkumar U. Native chicken production in India: present status and challenges. Livestock Res Rural Develop. 2020;32(11).
   Google Scholar
• Sehrawat R, Sharma R, Ahlawat S, et al. First report on better functional property of black chicken meat from India. IJAR. 2021;55(Of):727–733.
   Google Scholar
• Sharma R, Sehrawat R, Ahlawat S, et al. An attempt to valorize the only black meat chicken breed of India by delineating superior functional attributes of its meat. Sci Rep. 2022;12(1):3555.
   PubMed Web of Science ®Google Scholar
• Pandey AK, Sharma R, Ahlawat SPS. Poultry Genetic Resources of India. Aseel. Published by National Bureau of Animal genetic Resources (NBAGR), Karnal, Haryana, India. Monograph 15. 2005. https://nbagr.icar.gov.in/wp-content/uploads/2020/02/. ASEEL-POULTRY.pdf.
   Google Scholar
• Ahlawat S, Arora R, Sharma U, et al. Comparative gene expression profiling of milk somatic cells of Sahiwal cattle and Murrah buffaloes. Gene. 2021;764:145101.
   PubMed Web of Science ®Google Scholar
• Kumar A, Kaur M, Ahlawat S, et al. Transcriptomic diversity in longissimus thoracis muscles of Barbari and Changthangi goat breeds of India. Genomics. 2021;113(4):1639–1646.
   PubMed Web of Science ®Google Scholar
• Arora R, Siddaraju NK, Manjunatha SS, et al. Muscle transcriptome provides the first insight into the dynamics of gene expression with progression of age in sheep. Sci Rep. 2021;11(1):22360.
   PubMed Web of Science ®Google Scholar
• Wu P, Zhang X, Zhang G, et al. Transcriptome for the breast muscle of Jinghai yellow chicken at early growth stages. PeerJ. 2020;8:e8950.
   PubMed Web of Science ®Google Scholar
• Kumar H, Choo H, Iskender AU, et al. RNA seq analyses of chicken reveals biological pathways involved in acclimation into different geographical locations. Sci Rep. 2020;10(1):19288.
   PubMed Web of Science ®Google Scholar
• Deist MS, Gallardo RA, Dekkers JCM, Zhou HJ, Lamont SJ. Novel combined tissue transcriptome analysis after lentogenic Newcastle disease virus challenge in inbred chicken lines of differential resistance. Front Genet. 2020;11:11.
   PubMed Web of Science ®Google Scholar
• Liu J, Lei Q, Li F, et al. Dynamic transcriptomic analysis of breast muscle development from the embryonic to post-hatching periods in chickens. Front Genet. 2019;10:1308.
   PubMed Web of Science ®Google Scholar
• Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44–57.
   PubMed Web of Science ®Google Scholar
• Kamburov A, Wierling C, Lehrach H, Herwig R. ConsensusPathDB-a database for integrating human functional interaction networks. Nucleic Acids Res. 2009;37(Database issue):D623–D628.
   PubMedGoogle Scholar
• Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504.
   PubMed Web of Science ®Google Scholar
• Chin CH, Chen SH, Wu HH, Ho CW, Ko MT, Lin CY. cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst Biol. 2014;8(S4):S11.
   PubMedGoogle Scholar
• Szklarczyk D, Morris JH, Cook H, et al. The STRING database in 2017: Quality controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res. 2017;45(D1):D362–D368.
   PubMed Web of Science ®Google Scholar
• Chiang Hsin I, Berghman LR, Huaijun Z. Inhibition of NF-kB 1 (NF-kBp50) by RNA interference in chicken macrophage HD11 cell line challenged with Salmonella enteritidis. Genet Mol Biol. 2009;32(3):507–515.
   PubMed Web of Science ®Google Scholar
• Wan Y, Sihua J, Chendong M, Zhicheng W, Qi F, Runshen J. RNA-Seq reveals seven promising candidate genes affecting the proportion of thick egg albumen in layer-type chickens. Sci Rep. 2017;7(1):1–9.
   PubMedGoogle Scholar
• Cogburn LA, Nares T, Chuming C, et al. Transcriptional profiling of liver during the critical embryo-to-hatchling transition period in the chicken (Gallus gallus). BMC Genomics. 2018;19(1):1–37.
   PubMedGoogle Scholar
• Ren L, Liu A, Wang Q, Wang H, Dong D, Liu L. Transcriptome analysis of embryonic muscle development in Chengkou Mountain Chicken. BMC Genomics. 2021;22(1):1–12.
   PubMed Web of Science ®Google Scholar
• Sharma R, Arora R, Ahlawat S, et al. Study on the muscle transcriptome of two diverse Indian backyard poultry breeds acclimatized to diferent agro-ecological conditions. Mol Biol Rep. 2023;50(3):2453–2461.
   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 DeltaC(T)) method. Methods. 2001;25(4):402–408.
   PubMed Web of Science ®Google Scholar
• Granzier HL, Hutchinson KR, Tonino P, et al. Deleting titin’s I-band/A-band junction reveals critical roles for titin in biomechanical sensing and cardiac function. Proc Natl Acad Sci USA. 2014;111(40):14589–14594.
   PubMed Web of Science ®Google Scholar
• Wei B, Jin JP. TNNT1, TNNT2, and TNNT3: Isoform genes, regulation, and structure-function relationships. Gene. 2016;582(1):1–13.
   PubMed Web of Science ®Google Scholar
• Zhai W, Araujo LF, Burgess SC, et al. Protein expression in pectoral skeletal muscle of chickens as influenced by dietary methionine. Poult Sci. 2012;91(10):2548–2555.
   PubMed Web of Science ®Google Scholar
• Xue Q, Zhang G, Li T, Ling J, Zhang X, Wang J. Transcriptomic profile of leg muscle during early growth in chicken. PLOS One. 2017;12(3):e0173824.
   PubMed Web of Science ®Google Scholar
• Ren P, Liu J, Zhang D, et al. Transcriptome analysis of breast muscle and liver in full-sibling hybrid broilers at different ages. Gene. 2022;842:146801.
   PubMed Web of Science ®Google Scholar
• Hiltunen JK, Qin Y. strategies for the metabolism of a wide variety of acyl-CoA esters. Biochim Biophys Acta. 2000;1484(2–3):117–128.
   PubMed Web of Science ®Google Scholar
• Houten SM, Violante S, Ventura FV, Wanders RJ. The biochemistry and physiology of mitochondrial fatty acid β-oxidation and its genetic disorders. Annu Rev Physiol. 2016;78:23–44.
   PubMed Web of Science ®Google Scholar
• Fu S, Zhao Y, Li Y, et al. Characterization of miRNA transcriptome profiles related to breast muscle development and intramuscular fat deposition in chickens. J Cell Biochem. 2018;119(8):7063–7079.
   PubMed Web of Science ®Google Scholar
• Chen L, Peng T, Luo Y, et al. ACAT1 and metabolism-related pathways are essential for the progression of clear cell renal cell carcinoma (ccRCC), as determined by co-expression network analysis. Front Oncol. 2019;9:957.
   PubMed Web of Science ®Google Scholar
• Yun-Feng LU, Ji-Bao C, Bo Z, et al. Cloning, expression, and polymorphism of the ECI1 gene in various pig breeds. Journal of Integrative Agriculture. 2017;16(8):1789–1799.
   Web of Science ®Google Scholar
• Alphey MS, Yu W, Byres E, Li D, Hunter WN. Structure and reactivity of human mitochondrial 2,4-dienoyl-CoA reductase: enzyme-ligand interactions in a distinctive short-chain reductase active site. J Biol Chem. 2005;280(4):3068–3077.
   PubMed Web of Science ®Google Scholar
• Chen L, Toke NH, Luo S, et al. A reinforcing HNF4–SMAD4 feed-forward module stabilizes enterocyte identity. Nat Genet. 2019;51(5):777–785.
   PubMed Web of Science ®Google Scholar
• Xepapadaki E, Nikdima I, Sagiadinou EC, Zvintzou E, Kypreos KE. HDL and type 2 diabetes: the chicken or the egg? Diabetologia. 2021;64(9):1917–1926.
   PubMed Web of Science ®Google Scholar
• Zhang J, Cao J, Geng A, et al. Comprehensive proteomic characterization of the pectoralis major at three chronological ages in Beijing-You chicken. Front Physiol. 2021;12:658711.
   PubMed Web of Science ®Google Scholar
• Su J, Lei H, Xiao T, Cui S. Ci-AMBP: a highly conserved member of the microglobulin superfamily of proteinase inhibitors in grass carp, Ctenopharyngodon idellus. Genes Genet Syst. 2018;92(5):251–256.
   PubMed Web of Science ®Google Scholar
• Bekeova C, Anderson-Pullinger L, Boye K, et al. Multiple mitochondrial thioesterases have distinct tissue and substrate specificity and CoA regulation, suggesting unique functional roles. J Biol Chem. 2019;294(50):19034–19047.
   PubMed Web of Science ®Google Scholar
• Quijano C, Trujillo M, Castro L, Trostchansky A. Interplay between oxidant species and energy metabolism. Redox Biol. 2016;8:28–42.
   PubMed Web of Science ®Google Scholar
• Surai PF, Kochish II, Fisinin VI, Kidd MT. Antioxidant defence systems and oxidative stress in poultry biology: An update. Antioxidants. 2019;8(7):235.
   Web of Science ®Google Scholar
• Hatori Y, Lutsenko S. The role of copper chaperone Atox1 in coupling redox homeostasis to intracellular copper distribution. Antioxidants. 2016;5(3):25:25.
   Web of Science ®Google Scholar
• Romer LH, Birukov KG, Garcia JG. Focal adhesions: paradigm for a signaling nexus. Circ Res. 2006;98(5):606–616.
   PubMed Web of Science ®Google Scholar
• Thomas K, Engler AJ, Meyer GA. Extracellular matrix regulation in the muscle satellite cell niche. Connect Tissue Res. 2015;56(1):1–8.
   PubMed Web of Science ®Google Scholar
• Saltiel AR, Pessin JE. Insulin signaling pathways in time and space. Trends Cell Biol. 2002;12(2):65–71.
   PubMed Web of Science ®Google Scholar
• Zhang Z, Du H, Yang C, et al. Comparative transcriptome analysis reveals regulators mediating breast muscle growth and development in three chicken breeds. Anim Biotechnol. 2019;30(3):233–241.
   PubMed Web of Science ®Google Scholar
• Luo N, Shu J, Yuan X, et al. Differential regulation of intramuscular fat and abdominal fat deposition in chickens. BMC Genomics. 2022;23(1):308.
   PubMed Web of Science ®Google Scholar
• Zhang M, Li F, Ma XF, et al. Identification of differentially expressed genes and pathways between intramuscular and abdominal fat-derived preadipocyte differentiation of chickens in vitro. BMC Genomics. 2019;20(1):743.
   PubMed Web of Science ®Google Scholar
• Gonzalez FJ. Regulation of hepatocyte nuclear factor 4a-mediated transcription. Drug Metab Pharmacokinet. 2008;23(1):2–7.
   PubMed Web of Science ®Google Scholar
• Li Y, Chen Y, Jin W, et al. Analyses of microRNA and mRNA expression profiles reveal the crucial interaction networks and pathways for regulation of chicken breast muscle development. Front Genet. 2019;10:197.
   PubMed Web of Science ®Google Scholar
• Cam H, Griesmann H, Beitzinger M, et al. p53 family members in myogenic differentiation and rhabdomyosarcoma development. Cancer Cell. 2006;10(4):281–293.
   PubMed Web of Science ®Google Scholar
• Kamada R, Toguchi Y, Nomura T, Imagawa T, Sakaguchi K. Tetramer formation of tumor suppressor protein p53: Structure, function, and applications. Biopolymers. 2016;106(4):598–612.
   PubMed Web of Science ®Google Scholar
• Barclay RD, Burd NA, Tyler C, Tillin NA, Mackenzie RW. The role of the IGF-1 signaling cascade in muscle protein synthesis and anabolic resistance in aging skeletal muscle. Front Nutr. 2019;6:146.
   PubMed Web of Science ®Google Scholar
• Hiroyuki L, Tadahiko K, Yuichiro S, et al. DNA maintenance methylation enzyme DNMT1 in satellite cells is essential for muscle regeneration. Biochem Biophys Res Commun. 2021;534:79–85.
   PubMed Web of Science ®Google Scholar
• Rodríguez-Fdez S, Bustelo XR. Rho GTPases in skeletal muscle development and homeostasis. Cells. 2021;10(11):2984.
   PubMed Web of Science ®Google Scholar