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Volumn 4, Issue NOV, 2013, Pages

Identification of candidate genes and mutations in QTL regions for chicken growth using bioinformatic analysis of NGS and SNP-chip data

Author keywords

Candidate genes; Functional prediction; Genetic divergence; Growth; QTL; Resequencing; SNP

Indexed keywords


EID: 84890303173     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2013.00226     Document Type: Article
Times cited : (31)

References (30)
  • 1
    • 33745003913 scopus 로고    scopus 로고
    • Fibroblast growth factor 16 and 18 are expressed in human cardiovascular tissues and induce on endothelial cells migration but not proliferation
    • doi: 10.1016/j.bbrc.2006.05.105
    • Antoine, M., Wirz, W., Tag, C. G., Gressner, A. M., Wycislo, M., Muller, R., et al. (2006). Fibroblast growth factor 16 and 18 are expressed in human cardiovascular tissues and induce on endothelial cells migration but not proliferation. Biochem. Biophys. Res. Commun. 346, 224-233. doi: 10.1016/j.bbrc.2006.05.105.
    • (2006) Biochem. Biophys. Res. Commun. , vol.346 , pp. 224-233
    • Antoine, M.1    Wirz, W.2    Tag, C.G.3    Gressner, A.M.4    Wycislo, M.5    Muller, R.6
  • 2
    • 79955007478 scopus 로고    scopus 로고
    • Fine mapping and replication of QTL in outbred chicken advanced intercross lines
    • doi: 10.1186/1297-9686-43-3
    • Besnier, F., Wahlberg, P., Rönnegård, L., Weronica, E. K., Andersson, L., Siegel, P. B., et al. (2011). Fine mapping and replication of QTL in outbred chicken advanced intercross lines. Genet. Sel. Evol. 43, 3. doi: 10.1186/1297-9686-43-3.
    • (2011) Genet. Sel. Evol. , vol.43 , pp. 3
    • Besnier, F.1    Wahlberg, P.2    Rönnegård, L.3    Weronica, E.K.4    Andersson, L.5    Siegel, P.B.6
  • 3
    • 0020573729 scopus 로고
    • Genetic selection for growth rate alters hypothalamic satiety mechanisms in chickens
    • doi: 10.1007/BF01071874
    • Burkhart, C. A., Cherry J. A., Van Krey H. P., and Siegel, P. B. (1983). Genetic selection for growth rate alters hypothalamic satiety mechanisms in chickens. Behav. Genet. 13, 295-300. doi: 10.1007/BF01071874.
    • (1983) Behav. Genet. , vol.13 , pp. 295-300
    • Burkhart, C.A.1    Cherry, J.A.2    Van Krey, H.P.3    Siegel, P.B.4
  • 4
    • 20944448106 scopus 로고    scopus 로고
    • Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis
    • doi: 10.1186/gb-2004-6-1-r6
    • Caldwell, R. B., Kierzek, A. M., Arakawa, H., Bezzubov, Y., Zaim, J., Fiedler, P., et al. (2005). Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis. Genome Biol. 6, R6. doi: 10.1186/gb-2004-6-1-r6.
    • (2005) Genome Biol. , vol.6
    • Caldwell, R.B.1    Kierzek, A.M.2    Arakawa, H.3    Bezzubov, Y.4    Zaim, J.5    Fiedler, P.6
  • 5
    • 0035877608 scopus 로고    scopus 로고
    • The yeast ALG11 gene specifies addition of the terminal alpha 1,2-Man to the Man(5)GlcNAc(2)-PP-dolichol N-glycosylation intermediate formed on the cytosolic side of the endoplasmic reticulum
    • doi: 10.1074/jbc.M010896200
    • Cipollo, J. F., Trimble, R. B., Chi, J. H., Yan, Q., and Dean, N. (2001). The yeast ALG11 gene specifies addition of the terminal alpha 1,2-Man to the Man(5)GlcNAc(2)-PP-dolichol N-glycosylation intermediate formed on the cytosolic side of the endoplasmic reticulum. J. Biol. Chem. 276, 21828-21840. doi: 10.1074/jbc.M010896200.
    • (2001) J. Biol. Chem. , vol.276 , pp. 21828-21840
    • Cipollo, J.F.1    Trimble, R.B.2    Chi, J.H.3    Yan, Q.4    Dean, N.5
  • 6
    • 0030256396 scopus 로고    scopus 로고
    • Long-term divergent selection for eight-week body weight in White Plymouth Rock chickens
    • doi: 10.3382/ps.0751168
    • Dunnington, E. A., and Siegel, P. B. (1996). Long-term divergent selection for eight-week body weight in White Plymouth Rock chickens. Poult. Sci. 75, 1168-1179. doi: 10.3382/ps.0751168.
    • (1996) Poult. Sci. , vol.75 , pp. 1168-1179
    • Dunnington, E.A.1    Siegel, P.B.2
  • 7
    • 84879155080 scopus 로고    scopus 로고
    • Phenotypic responses of chickens to long-term, bidirectional selection for juvenile body weight-historical perspective
    • doi: 10.3382/ps.2013-03069
    • Dunnington, E. A., Honaker, C. F., McGilliard, M. L., and Siegel, P. B. (2013). Phenotypic responses of chickens to long-term, bidirectional selection for juvenile body weight-historical perspective. Poult. Sci. 92, 1724-1734. doi: 10.3382/ps.2013-03069.
    • (2013) Poult. Sci. , vol.92 , pp. 1724-1734
    • Dunnington, E.A.1    Honaker, C.F.2    McGilliard, M.L.3    Siegel, P.B.4
  • 9
    • 0033304640 scopus 로고    scopus 로고
    • Overexpression of insulin-like growth factor-binding protein-2 in transgenic mice reduces postnatal body weight gain
    • doi: 10.1210/en.140.12.5488
    • Hoeflich, A., Wu, M., Mohan, S., Foll, J., Wanke, R., Froehlich, T., et al. (1999). Overexpression of insulin-like growth factor-binding protein-2 in transgenic mice reduces postnatal body weight gain. Endocrinology 140, 5488-5496. doi: 10.1210/en.140.12.5488.
    • (1999) Endocrinology , vol.140 , pp. 5488-5496
    • Hoeflich, A.1    Wu, M.2    Mohan, S.3    Foll, J.4    Wanke, R.5    Froehlich, T.6
  • 10
    • 20544460666 scopus 로고    scopus 로고
    • Grb10 and Grb14: enigmatic regulators of insulin action-and more?
    • doi: 10.1042/BJ20050216
    • Holt, L. J., and Siddle, K. (2005). Grb10 and Grb14: enigmatic regulators of insulin action-and more? Biochem. J. 388, 393-406. doi: 10.1042/BJ20050216.
    • (2005) Biochem. J. , vol.388 , pp. 393-406
    • Holt, L.J.1    Siddle, K.2
  • 11
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
    • doi: 10.1093/nar/gkn923
    • Huang, D. W., Sherman, B. T., and Lempicki, R. A. (2009a). Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37, 1-13. doi: 10.1093/nar/gkn923.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 1-13
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 12
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • doi: 10.1038/nprot.2008.211
    • Huang, D. W., Sherman, B. T., and Lempicki, R. A. (2009b). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57. doi: 10.1038/nprot.2008.211.
    • (2009) Nat. Protoc. , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 13
    • 29244437178 scopus 로고    scopus 로고
    • Many QTLs with minor additive effects are associated with a large difference in growth between two selection lines in chickens
    • doi: 10.1017/S0016672305007767
    • Jacobsson, L., Park, H. B., Wahlberg, P., Fredriksson, R., Perez-Enciso, M., Siegel, P. B., et al. (2005). Many QTLs with minor additive effects are associated with a large difference in growth between two selection lines in chickens. Genet. Res. 86, 115-125. doi: 10.1017/S0016672305007767.
    • (2005) Genet. Res. , vol.86 , pp. 115-125
    • Jacobsson, L.1    Park, H.B.2    Wahlberg, P.3    Fredriksson, R.4    Perez-Enciso, M.5    Siegel, P.B.6
  • 14
    • 78649395355 scopus 로고    scopus 로고
    • Genome-Wide Effects of Long-Term Divergent Selection
    • doi: 10.1371/journal.pgen.1001188
    • Johansson, A. M., Pettersson, M. E., Siegel, P. B., and Carlborg, ö. (2010). Genome-Wide Effects of Long-Term Divergent Selection. PLoS Genet. 6:e1001188. doi: 10.1371/journal.pgen.1001188.
    • (2010) PLoS Genet. , vol.6
    • Johansson, A.M.1    Pettersson, M.E.2    Siegel, P.B.3    Carlborg, ö.4
  • 15
    • 60549114890 scopus 로고    scopus 로고
    • Extremely different behaviours in high and low body weight lines of chicken are associated with differential expression of genes involved in neuronal plasticity
    • doi: 10.1111/j.1365-2826.2009.01819.x
    • Ka, S., Lindberg, J., Strömstedt, L., Fitzsimmons, C., Lindqvist, N., Lundeberg, J., et al. (2009). Extremely different behaviours in high and low body weight lines of chicken are associated with differential expression of genes involved in neuronal plasticity. J. Neuroendocrinol. 21, 208-216. doi: 10.1111/j.1365-2826.2009.01819.x.
    • (2009) J. Neuroendocrinol. , vol.21 , pp. 208-216
    • Ka, S.1    Lindberg, J.2    Strömstedt, L.3    Fitzsimmons, C.4    Lindqvist, N.5    Lundeberg, J.6
  • 16
    • 0035793557 scopus 로고    scopus 로고
    • Livin, a novel inhibitor of apoptosis protein family member
    • doi: 10.1074/jbc.M003670200
    • Kasof, G. M., and Gomes, B. C. (2001). Livin, a novel inhibitor of apoptosis protein family member. J. Biol. Chem. 276, 3238-3246. doi: 10.1074/jbc.M003670200.
    • (2001) J. Biol. Chem. , vol.276 , pp. 3238-3246
    • Kasof, G.M.1    Gomes, B.C.2
  • 17
    • 0033989153 scopus 로고    scopus 로고
    • CRIM1, a novel gene encoding a cysteine-rich repeat protein, is developmentally regulated and implicated in vertebrate CNS development and organogenesis
    • doi: 10.1016/S0925-4773(99)00248-8
    • Kolle, G., Georgas, K., Holmes, G. P., Little, M. H., and Yamada, T. (2000). CRIM1, a novel gene encoding a cysteine-rich repeat protein, is developmentally regulated and implicated in vertebrate CNS development and organogenesis. Mech. Dev. 90, 181-193. doi: 10.1016/S0925-4773(99)00248-8.
    • (2000) Mech. Dev. , vol.90 , pp. 181-193
    • Kolle, G.1    Georgas, K.2    Holmes, G.P.3    Little, M.H.4    Yamada, T.5
  • 18
    • 0028360062 scopus 로고
    • Elevated blood pressure and craniofacial abnormalities in mice deficient in endothelin-1
    • doi: 10.1038/368703a0
    • Kurihara, Y., Kurihara, H., Suzuki, H., Kodama, T., Maemura, K., Nagai, R., et al. (1994). Elevated blood pressure and craniofacial abnormalities in mice deficient in endothelin-1. Nature 368,703-710. doi: 10.1038/368703a0.
    • (1994) Nature , vol.368 , pp. 703-710
    • Kurihara, Y.1    Kurihara, H.2    Suzuki, H.3    Kodama, T.4    Maemura, K.5    Nagai, R.6
  • 20
    • 84876071035 scopus 로고    scopus 로고
    • PASE: a novel method for functional prediction of amino acid substitutions based on physicochemical properties
    • doi: 10.3389/fgene.2013.00021
    • Li, X., Kierczak, M., Shen, X., Ahsan, M., Carlborg, ö., and Marklund, S. (2013). PASE: a novel method for functional prediction of amino acid substitutions based on physicochemical properties. Front. Genet. 4:21. doi: 10.3389/fgene.2013.00021.
    • (2013) Front. Genet. , vol.4 , pp. 21
    • Li, X.1    Kierczak, M.2    Shen, X.3    Ahsan, M.4    Carlborg, ö.5    Marklund, S.6
  • 21
    • 78649330039 scopus 로고    scopus 로고
    • SNP detection and prediction of variability between chicken lines using genome resequencing of DNA pools
    • doi: 10.1186/1471-2164-11-665
    • Marklund, S., and Carlborg, ö. (2010). SNP detection and prediction of variability between chicken lines using genome resequencing of DNA pools. BMC Genomics 11, 655. doi: 10.1186/1471-2164-11-665.
    • (2010) BMC Genomics , vol.11 , pp. 655
    • Marklund, S.1    Carlborg, ö.2
  • 22
    • 78649430777 scopus 로고    scopus 로고
    • Genetic diversity and population structure in lines of chickens divergently selected for high and low 8-week body weight
    • doi: 10.3382/ps.2010-01034
    • Marquez, G. C., Siegel, P. B., and Lewis, R. M. (2010). Genetic diversity and population structure in lines of chickens divergently selected for high and low 8-week body weight. Poult. Sci. 89, 2580-2588. doi: 10.3382/ps.2010-01034.
    • (2010) Poult. Sci. , vol.89 , pp. 2580-2588
    • Marquez, G.C.1    Siegel, P.B.2    Lewis, R.M.3
  • 23
    • 0032706623 scopus 로고    scopus 로고
    • A general approach to single-nucleotide polymorphism discovery
    • doi: 10.1038/70570
    • Marth, G. T., Korf, I., Yandell, M. D., Yeh, R. T., Gu, Z. J., Zakeri, H., et al. (1999). A general approach to single-nucleotide polymorphism discovery. Nat. Genet. 23, 452-456. doi: 10.1038/70570.
    • (1999) Nat. Genet. , vol.23 , pp. 452-456
    • Marth, G.T.1    Korf, I.2    Yandell, M.D.3    Yeh, R.T.4    Gu, Z.J.5    Zakeri, H.6
  • 24
    • 77955405475 scopus 로고    scopus 로고
    • Deriving the consequences of genomic variants with the Ensembl API and SNP effect predictor
    • doi: 10.1093/bioinformatics/btq330
    • McLaren, W., Pritchard, B., Rios, D., Chen, Y. A., Flicek, P., and Cunningham, F. (2010). Deriving the consequences of genomic variants with the Ensembl API and SNP effect predictor. Bioinformatics 26, 2069-2070. doi: 10.1093/bioinformatics/btq330.
    • (2010) Bioinformatics , vol.26 , pp. 2069-2070
    • McLaren, W.1    Pritchard, B.2    Rios, D.3    Chen, Y.A.4    Flicek, P.5    Cunningham, F.6
  • 25
    • 0029147486 scopus 로고
    • Cloning and functional analysis of the promoter for KDR/flk-1, a receptor for vascular endothelial growth factor
    • doi: 10.1074/jbc.270.39.23111
    • Patterson, C., Perrella, M. A., Hsieh, C. M., Yoshizumi, M., Lee, M. E., and Haber, E. (1995). Cloning and functional analysis of the promoter for KDR/flk-1, a receptor for vascular endothelial growth factor. J. Biol. Chem. 270, 23111-23118. doi: 10.1074/jbc.270.39.23111.
    • (1995) J. Biol. Chem. , vol.270 , pp. 23111-23118
    • Patterson, C.1    Perrella, M.A.2    Hsieh, C.M.3    Yoshizumi, M.4    Lee, M.E.5    Haber, E.6
  • 26
    • 45849148191 scopus 로고    scopus 로고
    • An improved method for quantitative trait loci detection and identification of within-line segregation in F-2 intercross designs
    • doi: 10.1534/genetics.107.083162
    • Rönnegård, L., Besnier, F., and Carlborg, ö. (2008). An improved method for quantitative trait loci detection and identification of within-line segregation in F-2 intercross designs. Genetics 178, 2315-2326. doi: 10.1534/genetics.107.083162.
    • (2008) Genetics , vol.178 , pp. 2315-2326
    • Rönnegård, L.1    Besnier, F.2    Carlborg, ö.3
  • 27
    • 77950080740 scopus 로고    scopus 로고
    • Whole-genome resequencing reveals loci under selection during chicken domestication
    • doi: 10.1038/nature08832
    • Rubin, C. J., Zody, M. C., Eriksson, J., Meadows, J. R. S., Sherwood, E., Webster, M. T., et al. (2010). Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464, 587-591. doi: 10.1038/nature08832.
    • (2010) Nature , vol.464 , pp. 587-591
    • Rubin, C.J.1    Zody, M.C.2    Eriksson, J.3    Meadows, J.R.S.4    Sherwood, E.5    Webster, M.T.6
  • 28
    • 84876348105 scopus 로고    scopus 로고
    • Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity
    • doi: 10.1093/nar/gks1205
    • Shabalina, S. A., Spiridonov, N. A., and Kashina, A. (2013). Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity. Nucleic Acids Res. 41, 2073-2094. doi: 10.1093/nar/gks1205.
    • (2013) Nucleic Acids Res. , vol.41 , pp. 2073-2094
    • Shabalina, S.A.1    Spiridonov, N.A.2    Kashina, A.3
  • 29
    • 77953630340 scopus 로고    scopus 로고
    • The role of gut hormones and the hypothalamus in appetite regulation
    • doi: 10.1507/endocrj.K10E-077
    • Suzuki, K., Simpson, K. A., Minnion, J. S., Shillito, J. C., and Bloom, S. R. (2010). The role of gut hormones and the hypothalamus in appetite regulation. Endocr. J. 57, 359-372. doi: 10.1507/endocrj.K10E-077.
    • (2010) Endocr. J. , vol.57 , pp. 359-372
    • Suzuki, K.1    Simpson, K.A.2    Minnion, J.S.3    Shillito, J.C.4    Bloom, S.R.5
  • 30
    • 16844386223 scopus 로고    scopus 로고
    • Insulin-like growth factor signaling in fish
    • doi: 10.1016/S0074-7696(05)43004-1
    • Wood, A. W., Duan, C., and Bern, H. A. (2005). Insulin-like growth factor signaling in fish. Int. Rev. Cytol. 243, 215-285. doi: 10.1016/S0074-7696(05)43004-1.
    • (2005) Int. Rev. Cytol. , vol.243 , pp. 215-285
    • Wood, A.W.1    Duan, C.2    Bern, H.A.3


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