Gastrocnemius transcriptome analysis reveals domestication induced gene expression changes between wild and domestic chickens

Genomics

Volumn 100, Issue 5, 2012, Pages 314-319

  Li, Qinghe ^a   Wang, Nan ^a   Du, Zhuo ^a   Hu, Xiaoxiang ^a   Chen, Li ^b   Fei, Jing ^a   Wang, Yuanyuan ^a   Li, Ning ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

^b INSTITUTE OF PLANT PROTECTION AND MICROBIOLOGY   (China)

Author keywords

Domestic chicken; Domestication; Gene expression profile; Wild chicken

Indexed keywords

CONNECTIN; TRANSCRIPTOME; TRANSFORMING GROWTH FACTOR BETA RECEPTOR 3; UBIQUITIN;

ANIMAL TISSUE; ARTICLE; ARTIFICIAL SELECTION; BIOLOGICAL ACTIVITY; BREEDING; BROILER; CHICKEN; CONTROLLED STUDY; DNA BINDING; DOMESTICATION; EXTRACELLULAR MATRIX; FEMALE; GASTROCNEMIUS MUSCLE; GENE EXPRESSION PROFILING; GENE FUNCTION; GENETIC VARIABILITY; IMMUNE SYSTEM; JUNGLE FOWL; LAST COMMON ANCESTOR; MYOSTATIN UBIQUITIN RELATED GENE; NONHUMAN; PRIORITY JOURNAL; WILD ANIMAL; WILD VERSUS DOMESTICATED SPECIES;

ANIMALS; ANIMALS, DOMESTIC; ANIMALS, WILD; CHICKENS; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; MUSCLE, SKELETAL; SELECTION, GENETIC; SPECIES SPECIFICITY;

ANIMALIA; AVES; GALLUS GALLUS;

EID: 84867909759     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2012.07.008     Document Type: Article

References (36)

1. Burt D.W. Chicken genome: current status and future opportunities. Genome Res. 2005, 15:1692-1698.
2. Fumihito A., Miyake T., Sumi S., Takada M., Ohno S., Kondo N. One subspecies of the red junglefowl (Gallus gallus gallus) suffices as the matriarchic ancestor of all domestic breeds. Proc. Natl. Acad. Sci. U. S. A. 1994, 91:12505-12509.
3. Rubin C.J., et al. Differential gene expression in femoral bone from red junglefowl and domestic chicken, differing for bone phenotypic traits. BMC Genomics 2007, 8:208.
4. Jensen P. Domestication-from behaviour to genes and back again. Appl. Anim. Behav. Sci. 2006, 97:3-15.
5. Kanginakudru S., Metta M., Jakati R.D., Nagaraju J. Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken. BMC Evol. Biol. 2008, 8:174.
6. McPherron A.C., Lawler A.M., Lee S.J. Regulation of skeletal muscle mass in mice by a new TGF-beta superfamily member. Nature 1997, 387:83-90.
7. Cockett N.E., et al. Polar overdominance at the ovine callipyge locus. Science 1996, 273:236-238.
8. Grobet L., et al. A deletion in the bovine myostatin gene causes the double-muscled phenotype in cattle. Nat. Genet. 1997, 17:71-74.
9. Amaral A.J., et al. Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA. PLoS One 2011, 6:e14782.
10. Palmiter R.D., et al. Dramatic growth of mice that develop from eggs microinjected with metallothionein-growth hormone fusion genes. Nature 1982, 300:611-615.
11. Jeon J.T., et al. A paternally expressed QTL affecting skeletal and cardiac muscle mass in pigs maps to the IGF2 locus. Nat. Genet. 1999, 21:157-158.
12. Nezer C., et al. An imprinted QTL with major effect on muscle mass and fat deposition maps to the IGF2 locus in pigs. Nat. Genet. 1999, 21:155-156.
13. I.c.g.s. consortium, Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 2004, 432:695-716.
14. Bao W., et al. Analysis of genetic diversity and phylogenetic relationships among red jungle fowls and Chinese domestic fowls. Sci. China C Life Sci. 2008, 51:560-568.
15. Mortazavi A., Williams B.A., McCue K., Schaeffer L., Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 2008, 5:621-628.
16. Rock K.L., et al. Inhibitors of the proteasome block the degradation of most cell proteins and the generation of peptides presented on MHC class I molecules. Cell 1994, 78:761-771.
17. Kee A.J., et al. Ubiquitin-proteasome-dependent muscle proteolysis responds slowly to insulin release and refeeding in starved rats. J. Physiol. 2003, 546:765-776.
18. Zhao W., Wu Y., Zhao J., Guo S., Bauman W.A., Cardozo C.P. Structure and function of the upstream promotor of the human Mafbx gene: the proximal upstream promotor modulates tissue-specificity. J. Cell. Biochem. 2005, 96:209-219.
19. Rubin C.J., et al. Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 2010, 464:587-591.
20. Andersson L., Georges M. Domestic-animal genomics: deciphering the genetics of complex traits. Nat. Rev. Genet. 2004, 5:202-212.
21. Johansson Moller M., Chaudhary R., Hellmen E., Hoyheim B., Chowdhary B., Andersson L. Pigs with the dominant white coat color phenotype carry a duplication of the KIT gene encoding the mast/stem cell growth factor receptor. Mamm. Genome 1996, 7:822-830.
22. Fang M., Larson G., Ribeiro H.S., Li N., Andersson L. Contrasting mode of evolution at a coat color locus in wild and domestic pigs. PLoS Genet. 2009, 5:e1000341.
23. Kijas J.M., Andersson L. A phylogenetic study of the origin of the domestic pig estimated from the near-complete mtDNA genome. J. Mol. Evol. 2001, 52:302-308.
24. Devlin R.H., Sakhrani D., Tymchuk W.E., Rise M.L., Goh B. Domestication and growth hormone transgenesis cause similar changes in gene expression in coho salmon (Oncorhynchus kisutch). Proc. Natl. Acad. Sci. U. S. A. 2009, 106:3047-3052.
25. Favier R.P., Mol J.A., Kooistra H.S., Rijnberk A. Large body size in the dog is associated with transient GH excess at a young age. J. Endocrinol. 2001, 170:479-484.
26. Eigenmann J.E., Amador A., Patterson D.F. Insulin-like growth factor I levels in proportionate dogs, chondrodystrophic dogs and in giant dogs. Acta Endocrinol (Copenh) 1988, 118:105-108.
27. Porter T.E. Differences in embryonic growth hormone secretion between slow and fast growing chicken strains. Growth Horm. IGF Res. 1998, 8:133-139.
28. Beccavin C., Chevalier B., Cogburn L.A., Simon J., Duclos M.J. Insulin-like growth factors and body growth in chickens divergently selected for high or low growth rate. J. Endocrinol. 2001, 168:297-306.
29. Kruger M., Linke W.A. The giant protein titin: a regulatory node that integrates myocyte signaling pathways. J. Biol. Chem. 2011, 286:9905-9912.
30. Schuelke M., et al. Myostatin mutation associated with gross muscle hypertrophy in a child. N. Engl. J. Med. 2004, 350:2682-2688.
31. Lee S.J. Regulation of muscle mass by myostatin. Annu. Rev. Cell Dev. Biol. 2004, 20:61-86.
32. Beattie J., Allan G.J., Lochrie J.D., Flint D.J. Insulin-like growth factor-binding protein-5 (IGFBP-5): a critical member of the IGF axis. Biochem. J. 2006, 395:1-19.
33. Kollias H.D., McDermott J.C. Transforming growth factor-beta and myostatin signaling in skeletal muscle. J. Appl. Physiol. 2008, 104:579-587.
34. Schneyer A., Tortoriello D., Sidis Y., Keutmann H., Matsuzaki T., Holmes W. Follistatin-related protein (FSRP): a new member of the follistatin gene family. Mol. Cell. Endocrinol. 2001, 180:33-38.
35. Glaser C., Heinrich J., Koletzko B. Role of FADS1 and FADS2 polymorphisms in polyunsaturated fatty acid metabolism. Metabolism 2010, 59:993-999.
36. Lattka E., Illig T., Heinrich J., Koletzko B. Do FADS genotypes enhance our knowledge about fatty acid related phenotypes?. Clin. Nutr. 2010, 29:277-287.