1,039
Views
0
CrossRef citations to date
0
Altmetric
Articles

Blood transcriptome comparison between sexes and their function in 4-week Rhode Island red chickens

, , , , , , , , , , , , & show all
Pages 358-368 | Received 10 May 2022, Accepted 31 Oct 2022, Published online: 29 Nov 2022

References

  • Abdullah AY, Al-Beitawi NA, Rjoup MMS, Qudsieh RI, Ishmais MAA. 2010. Growth performance, carcass and meat quality characteristics of different commercial crosses of broiler strains of chicken. J Poult Sci. 47(1):13–21.
  • Amberger JS, Bocchini CA, Schiettecatte F, Scott AF, Hamosh A. 2015. OMIM.org: online Mendelian inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders. Nucleic Acids Res. 43:D789–D798.
  • Anh NTL, Kunhareang S, Duangjinda M. 2015. Association of chicken growth hormones and insulin-like growth factor gene polymorphisms with growth performance and carcass traits in Thai broilers. Asian-Australas J Anim Sci. 28(12):1686–1695.
  • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. 2000. Gene ontology: tool for the unification of biology. Nat Genet. 25:25–29.
  • Ayers KL, Davidson NM, Demiyah D, Roeszler KN, Grützner F, Sinclair AH, Oshlack A, Smith CA. 2013. RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome. Genome Biol. 14:R26.
  • Bai D-P, Chen Y, Hu Y-Q, He W-F, Shi Y-Z, Fan Q-M, Luo R-T, Li A. 2020. Transcriptome analysis of genes related to gonad differentiation and development in Muscovy ducks. BMC Genomics. 21:438.
  • Beck HN, Drahushuk K, Jacoby DB, Higgins D, Lein PJ. 2001. Bone morphogenetic protein-5 (BMP-5) promotes dendritic growth in cultured sympathetic neurons. BMC Neurosci. 2:1–11.
  • Bellott DW, Skaletsky H, Cho T-J, Brown L, Locke D, Chen N, Galkina S, Pyntikova T, Koutseva N, Graves T, et al. 2017. Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators. Nat Genet. 49:387–394.
  • Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman W-H, Pagès F, Trajanoski Z, Galon J. 2009. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 25:1091–1093.
  • Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics. 30:2114–2120.
  • Brothers B, Zhuo Z, Papah MB, Abasht B. 2019. RNA-Seq analysis reveals spatial and sex differences in pectoralis major muscle of broiler chickens contributing to difference in susceptibility to wooden breast disease. Front Physiol. 10:1–14.
  • Ceplitis H, Ellegren H. 2004. Adaptive molecular evolution of HINTW, a female-specific gene in birds. Mol Biol Evol. 21:249–254.
  • Chamruspollert M, Pesti GM, Bakalli RI. 2002. Determination of the methionine requirement of Male and female broiler chicks using an indirect amino acid oxidation method. Poult Sci. 81:1004–1013.
  • Divya D, Bhattacharya TK. 2021. Bone morphogenetic proteins (BMPs) and their role in poultry. Worlds Poult Sci J. 77:539–564.
  • D’Mello SAN, Finlay GJ, Baguley BC, Askarian-Amiri ME. 2016. Signaling pathways in melanogenesis. Int J Mol Sci. 17:1–18.
  • Dridi S, Taouis M, Gertler A, Decuypere E, Buyse J. 2007. The regulation of stearoyl-CoA desaturase gene expression is tissue specific in chickens. J Endocrinol. 192:229–236.
  • Gahr M. 2001. Distribution of sex steroid hormone receptors in the avian brain: functional implications for neural sex differences and sexual behaviors. Microsc Res Tech. 55(1):1–11. doi:10.1002/jemt.1151.
  • Galván I, Solano F. 2016. Bird integumentary melanins: biosynthesis, forms, function and evolution. Int J Mol Sci. 17:520.
  • Graves JAM. 2016. Evolution of vertebrate sex chromosomes and dosage compensation. Nat Rev Genet. 17(1):33–46.
  • He M, Wu P, Chen F, Zhang B, Chen L, Zhang T, Zhang L, Li P, Wang J, Zhang G. 2020. Transcriptome analysis of leg muscles in fast and slow growth Bian chickens. Anim Biotechnol. 31:295–305.
  • Huang DW, Sherman BT, Lempicki RA. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 4:44–57.
  • Jansen R, Batista S, Brooks AI, Tischfield JA, Willemsen G, Gv G, Hottenga J-J, Milaneschi Y, Mbarek H, Madar V, et al. 2014. Sex differences in the human peripheral blood transcriptome. BMC Genomics. 15:33.
  • Jia J, Ahmed I, Liu L, Liu Y, Xu Z, Duan X, Li Q, Dou T, Gu D, Rong H, et al. 2018. Selection for growth rate and body size have altered the expression profiles of somatotropic axis genes in chickens. PLOS ONE. 13(4):e0195378.
  • Johnsson M, Henriksen R, Höglund A, Fogelholm J, Jensen P, Wright D. 2018. Genetical genomics of growth in a chicken model. BMC Genomics. 19(1):72.
  • Julien P, Brawand D, Soumillon M, Necsulea A, Liechti A, Schütz F, Daish T, Grützner F, Kaessmann H. 2012. Mechanisms and evolutionary patterns of mammalian and avian dosage compensation. PLoS Biol. 10(5):e1001328.
  • Kaiser VB, Ellegren H. 2006. Nonrandom distribution of genes with sex-biased expression in the chicken genome. Evolution. 60:1945–1951.
  • Kanehisa M, Goto S. 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28:27–30.
  • Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. 2019. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 37:907–915.
  • Li J, Yuan J, Miao Z, Guo Y. 2017. Effects of age on intestinal phosphate transport and biochemical values of broiler chickens. Asian-Australas J Anim Sci. 30(2):221–228. eng.
  • Liao Y, Smyth GK, Shi W. 2014. Featurecounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 30:923–930.
  • Livak KJ, Schmittgen TD. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods. 25:402–408.
  • Mecklenburg N, Martinez-Lopez JE, Moreno-Bravo JA, Perez-Balaguer A, Puelles E, Martinez S. 2014. Growth and differentiation factor 10 (Gdf10) is involved in Bergmann glial cell development under Shh regulation. Glia. 62(10):1713–1723. eng.
  • Miller AC, Voelker LH, Shah AN, Moens CB. 2015. Neurobeachin is required postsynaptically for electrical and chemical synapse formation. Curr Biol. 25(1):16–28. eng.
  • Mishra SK, Chen B, Zhu Q, Xu Z, Ning C, Yin H, Wang Y, Zhao X, Fan X, Yang M, et al. 2020. Transcriptome analysis reveals differentially expressed genes associated with high rates of egg production in chicken hypothalamic-pituitary-ovarian axis. Sci Rep. 10:1–8.
  • Miyazono K. 2000. Positive and negative regulation of TGF-beta signaling. J Cell Sci. 113:1101–1109.
  • Nam K, Ellegren H. 2008. The chicken (Gallus gallus) Z chromosome contains at least three nonlinear evolutionary strata. Genetics. 180:1131–1136.
  • Ono R, Miyachi H, Usui H, Oguchi R, Nishimura K, Takahashi K, Yamagishi Y, Kawamura N, Matsushita R, Goto T. 2022. Phenotypic analysis of growth and morphological traits in miniature breeds of Japanese indigenous chickens. J Poult Sci. 59(1):38–47.
  • Ons E, Gertler A, Buyse J, Lebihan-Duval E, Bordas A, Goddeeris B, Dridi S. 2010. Visfatin gene expression in chickens is sex and tissue dependent. Domest Anim Endocrinol. 38:63–74.
  • Patzke H, Ernsberger U. 2000. Expression of neurexin Iα splice variants in sympathetic neurons: selective changes during differentiation and in response to neurotrophins. Mol Cell Neurosci. 15(6):561–572. eng.
  • Podisi BK, Knott SA, Burt DW, Hocking PM. 2013. Comparative analysis of quantitative trait loci for body weight, growth rate and growth curve parameters from 3 to 72 weeks of age in female chickens of a broiler–layer cross. BMC Genet. 14(1):22.
  • Rallabandi HR, Yang H, Jo YJ, Lee HC, Byun SJ, Lee BR. 2019. Identification of female specific genes in the W chromosome that are expressed during gonadal differentiation in the chicken. Korean J Poult Sci. 46:287–296.
  • Ramstad KM, Miller HC, Kolle G. 2016. Sixteen kiwi (Apteryx spp) transcriptomes provide a wealth of genetic markers and insight into sex chromosome evolution in birds. BMC Genomics. 17:1–14.
  • Robinson MD, McCarthy DJ, Smyth GK. 2010. Edger: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 26:139–140.
  • Rogers TF, Palmer DH, Wright AE. 2021. Sex-specific selection drives the evolution of alternative splicing in birds. Mol Biol Evol. 38:519–530.
  • Rondelli S, Martinez O, García P. 2003. Sex effect on productive parameters, carcass and body fat composition of two commercial broilers lines. Braz J Poult Sci. 5:169–173.
  • Ross S, Hill CS. 2008. How the Smads regulate transcription. Int J Biochem Cell Biol. 40:383–408.
  • Salim HM, Lee HR, Jo C, Lee SK, Lee BD. 2012. Effect of sex and dietary organic zinc on growth performance, carcass traits, tissue mineral content, and blood parameters of broiler chickens. Biol Trace Elem Res. 147:120–129.
  • Shah TA, Rogers MB. 2018. Unanswered questions regarding sex and BMP/TGF-β signaling. J Dev Biol. 6:1–9.
  • Shimasaki S, Moore RK, Otsuka F, Erickson GF. 2004. The bone morphogenetic protein system in mammalian reproduction. Endocr Rev. 25:72–101.
  • Slominski A, Tobin DJ, Shibahara S, Wortsman J. 2004. Melanin pigmentation in mammalian skin and Its hormonal regulation. Physiol Rev. 84:1155–1228.
  • Storchová R, Divina P. 2006. Nonrandom representation of sex-biased genes on chicken Z chromosome. J Mol Evol. 63:676–681.
  • Thompson CT, Ng L, Menon V, Martinez S, Lee C-K, Glattfelder K, Sunkin Susan M, Henry A, Lau C, Dang C, et al. 2014. A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain. Neuron. 83(2):309–323.
  • Tomaszkiewicz M, Medvedev P, Makova KD. 2017. Y and W chromosome assemblies: approaches and discoveries. Trends Genet. 33:266–282.
  • Uebbing S, Konzer A, Xu L, Backström N, Brunström B, Bergquist J, Ellegren H. 2015. Quantitative mass spectrometry reveals partial translational regulation for dosage compensation in chicken. Mol Biol Evol. 32(10):2716–2725.
  • Umair Z, Kumar S, Rafiq K, Kumar V, Reman ZU, Lee S-H, Kim S, Lee J-Y, Lee U, Kim J. 2020. Dusp1 modulates activin/smad2 mediated germ layer specification via FGF signal inhibition in Xenopus embryos. Animal Cells Syst (Seoul). 24(6):359–370.
  • Wang J, Lan Y, He L, Tang R, Li Y, Huang Y, Liang S, Gao Z, Price M, Yue B, et al. 2021. Sex-specific gene expression in the blood of four primates. Genomics. 113:2605–2613.
  • Wang Y, Jin G, Ma M, Xiang X. 2019. Sex differences in serum steroid hormone levels during embryonic development in hen eggs. Poult Sci. 98(11):6053–6062.
  • Wang Z, Yu D, Wang M, Wang Q, Kouznetsova J, Yang R, Qian K, Wu W, Shuldiner A, Sztalryd C, et al. 2015. Elabela-Apelin receptor signaling pathway is functional in mammalian systems. Sci Rep. 5:8170.
  • Xue Q, Zhang G, Li T, Ling J, Zhang X, Wang J. 2017. Transcriptomic profile of leg muscle during early growth in chicken. PLOS ONE. 12:1–21.
  • Yu S, Wang G, Liao J, Tang M. 2019. Five alternative splicing variants of theTYRgene and their different roles in melanogenesis in the Muchuan black-boned chicken. Br Poult Sci. 60:8–14.
  • Yu-Jiang Y, Xin Z, Hai-Nan L. 2020. JAK2-STAT5 signaling is insensitive to porcine growth hormone (pGH) in hepatocytes of neonatal pig. Animal Cells Syst (Seoul). 24(2):69–78.
  • Zhang L, Wang H, Yu D, Chen J, Xing C, Li J, Li J, Cai Y. 2018. The effects of mouse ovarian granulosa cell function and related gene expression by suppressing BMP/Smad signaling pathway. Animal Cells Syst (Seoul). 22(5):317–323.
  • Zito A, Cartelli D, Cappelletti G, Cariboni A, Andrews W, Parnavelas J, Poletti A, Galbiati M. 2014. Neuritin 1 promotes neuronal migration. Brain Struct Funct. 219(1):105–118.
  • Zuo Q, Jin K, Zhang Y, Song J, Li B. 2017. Dynamic expression and regulatory mechanism of TGF-β signaling in chicken embryonic stem cells differentiating into spermatogonial stem cells. Biosience Rep. 37:1–15.