Polymorphism of Growth Correlated Genes Associated with Fatness and Muscle Fiber Traits in Chickens Polymorphism of Growth Correlated Genes Associated with Fatness and Muscle Fiber Traits in Chickens. ABSTRACT Thirty single nucleotide polymorphisms (SNP) and one 6bp insertiondeletion (indel) from 8 genes of somatotropic axis were used to study the association with chicken fatness and muscle fibers. The allele frequency difference between Xinghua and White Plymouth Rock chickens was observed, and their effects on fatness and muscle fiber traits were also evaluated by linkage analyses. The G143831A (G+1705A) SNP of the growth hormone (GH) gene was related to fat width, and the G144762A (G+119A) SNP of the GH gene was significantly associated with abdominal fat pad weight, abdominal fat pad ratio, and crude fatty content of the breast muscle. The 6bp indel of the growth hormone secretagogue receptor (GHSR) gene was significantly linked with the fat traits. The C51978309T SNP of the insulinlike factorI (IGFI) gene was significantly linked with the transversal area of the leg muscle fiber and transversal area of the breast muscle fiber. There was significant linkage between the insulin (INS) gene and 2 traits of the transversal area of transversal area of the leg muscle fiber and transversal area of the breast muscle fiber. Association of 30 SNP and one 6bp indel from 8 genes of somatotropic axis with chicken fatness and muscle fiber traits was analyzed in the present study. The GH, GHSR, and leptin receptor genes were significantly related to chicken fatness. The INS and IGFI genes were linked with muscle fiber density. Therefore, the genes of somatotropic axis not only affected chicken growth and body composition but also were associated with fatness and muscle fiber traits.
Polymorphism of Growth-Correlated Genes Associated with Fatness and Muscle Fiber Traits in Chickens M Lei, C Luo, X Peng, M Fang, Q Nie, D Zhang, G Yang, and X Zhang1 Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China insulin-like factor-I (IGF-I) gene was significantly linked with the transversal area of the leg muscle fiber and transversal area of the breast muscle fiber There was significant linkage between the insulin (INS) gene and traits of the transversal area of transversal area of the leg muscle fiber and transversal area of the breast muscle fiber Association of 30 SNP and one 6-bp indel from genes of somatotropic axis with chicken fatness and muscle fiber traits was analyzed in the present study The GH, GHSR, and leptin receptor genes were significantly related to chicken fatness The INS and IGF-I genes were linked with muscle fiber density Therefore, the genes of somatotropic axis not only affected chicken growth and body composition but also were associated with fatness and muscle fiber traits Key words: fatness, muscle fiber trait, linkage disequilibrium, single nucleotide polymorphism, linkage analysis 2007 Poultry Science 86:835–842 al., 2006) Compared with linkage analyses, candidate approaches were less widely used The genes of somatotropic axis play a central role in the regulation of growth and development (Mao et al., 1997; Buyse and Decuypere, 1999; Vasilatos-Younken et al., 2000) Previous studies showed that variation of these genes affected gene expression at the transcription and translation levels (Lo et al., 2003; Wyszynska-Koko et al., 2006) Variation in the genes of somatotropic axis could function as candidates for the evaluation of their effects on chicken growth and development traits Previous studies have shown that some single nucleotide polymorphisms (SNP) of the somatotropic axis genes indeed affected growth traits significantly (Feng et al., 1997; Kuhnlein et al., 1997; Amills et al., 2003; Lei et al., 2005; Nie et al., 2005b; Fang et al., 2006; Qiu et al., 2006) On the other hand, recent studies have shown that there was significant association of growth and body composition with meat quality characteristics (Le Bihan-Duval et al., 2001; Zerehdaran et al., 2004), especially fat deposition and muscle fiber density and sizes (Bruns et al., 2004; Scheuermann et al., 2004) In human, mutations in prepoghrelin/ghrelin gene were associated with obesity (Ukkola et al., 2001) However, few studies on association of growth-correlated genes with meat quality have been reported in chickens INTRODUCTION Meat quality is a complex structural and functional process that depends on species, genetic background, metabolic status of the antemortem animal, the protein complement of the muscle, and environmental factors Meat quality relies on several important characteristics, including appearance, color, taste, fat content, texture, and tenderness Fatness and muscle fiber traits are the major components of meat quality The QTL mapping for meat quality such as fatness and muscle fiber traits was widely studied in the past decade (Ovilo et al., 2002; Nii et al., 2005; Stearns et al., 2005) In chickens, several studies on meat quality QTL mapping were completed with linkage analyses using microsatellite DNA (Jennen et al., 2004, 2005; Abasht et al., 2006; Lagarrigue et al., 2006) Not only linkage analyses with markers were used in studies on meat quality, but also candidate approaches were applied (Amills et al., 2005; Guyonnet-Dupe´rat et ©2007 Poultry Science Association Inc Received December 4, 2006 Accepted January 16, 2007 Corresponding author: xqzhang@scau.edu.cn 835 Downloaded from http://ps.oxfordjournals.org/ at National Chung Hsing University Library on April 10, 2014 ABSTRACT Thirty single nucleotide polymorphisms (SNP) and one 6-bp insertion-deletion (indel) from genes of somatotropic axis were used to study the association with chicken fatness and muscle fibers The allele frequency difference between Xinghua and White Plymouth Rock chickens was observed, and their effects on fatness and muscle fiber traits were also evaluated by linkage analyses The G143831A (G+1705A) SNP of the growth hormone (GH) gene was related to fat width, and the G144762A (G+119A) SNP of the GH gene was significantly associated with abdominal fat pad weight, abdominal fat pad ratio, and crude fatty content of the breast muscle The 6-bp indel of the growth hormone secretagogue receptor (GHSR) gene was significantly linked with the fat traits The C51978309T SNP of the 27 Z 26 GH GHR GHSR IGF-I IGFBP-2 INS LEPR TSH-β G143831A G143978A G142167T G145086A A144762G G6622190A C6622516T A6626579G G18790036A T18791236C 18792785 to 1879075913 C18793056T C18793131T C51978309T C51983354T C51978771T C52028084T G23967395T T23966786A C23966654T T23966559G G23966484A G11303145A C11304264T T11306685C C11306451T T28573025C A28573100G C2541870G C2543216T A2543276T Location2 (nt) 5′-tcccaggctgcgttttgttactc-3′; 5′-acgggggtgagccaggactg-3′ 5′-gccctggcagccctgttaacc-3′; 5′-caccccaccatcgtatcccatc-3′ 5′-cccaacagtgccacgattccatg-3′; 5′-tgcgcaggtggatgtcgaacttg-3′ 5′-atccccaggcaaacatcctc-3; 5′-cctcgacatccagctcacat-3′ 5′-atccccaggcaaacatcctc-3; 5′-cctcgacatccagctcacat-3′ 5′-cccttccattatgcattttatc-3; 5′-gggggtacactctagtcacttg-3′ 5′-gcaacatcagaatcgctttt-3; 5′-tcccatcgtacttgaatatcc-3′ 5′-gaacccaggctctcaacagtg-3; 5′-tggaggttgaggtttatctgtc-3′ 5′-gtcgcctgcgtcctcctctt-3; 5′-acgggcaggaaaaagaagatg-3′ 5′-cccacaaagttagctgcagac-3; 5′-cacctctccatctggctcat-3′ 5′-aggtggaaaaactgcaaaaag-3; 5′-aggcaccccataacttttcag-3′ 5′-tggttgaaaagagagaatgct-3; 5′-ccacacgtctccttttatattc-3′ 5′-tggttgaaaagagagaatgct-3; 5′-ccacacgtctccttttatattc-3′ 5′-ctgggctacttgagttactacat-3; 5′-cacggaaaataagggaatg-3′ 5′-ctgggctacttgagttactacat-3; 5′-cacggaaaataagggaatg-3′ 5′-gccacccgaaagttaaccagaat-3; 5′-tccattgcggctctatct-3′ 5′-tgaaagggtctggccaaaaca-3; 5′-gggaagagtgaaaatggcagagg-3′ 5′-tttggttgagtcctaggcttg-3; 5′-aggcgtactacactgcagag-3′ 5′-accggtctgagagcatccttg-3; 5′-gggaaaaagggtgtgcaaaag-3′ 5′-gggcatttatatctgaggaacac-3; 5′-ggcaaagagcaacccaacac-3′ 5′-tttgttgtcgtggcttttttcag-3; 5′-gcttgtcacagttggggaag-3′ 5′-tttgttgtcgtggcttttttcag-3; 5′-gcttgtcacagttggggaag-3′ 5′-cgtgtctcctttgcttcctac-3; 5′-tggagctttctgtgacaattc-3′ 5′-tgttctgcatttggcccatac-3; 5′-gcagaatgtcagctttttgtcc-3′ 5′-ctccatgtggcttccctgta-3; 5′-ggcttcttggctagttgcagt-3′ 5′-ggtatctgaaaagcgggtctc-3; 5′-aatgctttgaaggtgcgatag-3′ 5′-atgctgcttgattcttcctcct-3; 5′-ccctaggcaaatggtaatgaac-3′ 5′-atgctgcttgattcttcctcct-3; 5′-ccctaggcaaatggtaatgaac-3′ 5′-cccttcttcatgatgtctctcc-3; 5′-ggtccttagttccatctgtgc-3′ 5′-gagcacggtgagcattactgg-3; 5′-ggaggtacatttctgccacgt-3′ 5′-gagcacggtgagcattactgg-3; 5′-ggaggtacatttctgccacgt-3′ Primer 60 60 59 58 57 58 58 56 61 60 58 58 57 58 59 60 59 64 64 60 55 56 58 59 60 61 56 58 60 61 59 Annealing temperature (°C) Downloaded from http://ps.oxfordjournals.org/ at National Chung Hsing University Library on April 10, 2014 PCR-RFLP PCR-RFLP PCR-RFLP PCR-RFLP PCR-RFLP PCR-RFLP PCR-RFLP PCR-RFLP PCR-RFLP PCR-RFLP PCR-RFLP PCR-RFLP PCR-RFLP PCR-RFLP PCR-RFLP PCR-RFLP PCR-RFLP PCR-SSCP PCR-SSCP PCR-RFLP PCR-RFLP PCR-RFLP PCR-RFLP PCR-RFLP PCR-RFLP PCR-RFLP PCR-RFLP PCR-RFLP PCR-RFLP PCR-RFLP PCR-RFLP Genotyping method Eco72 I Bsh136 I Pvu I Nde I Msp I Msp I Msp I Bsh136 I Bsh136 I Csp6 I Hin6 I Msp I Eco RV Pag I Bsh136 I Msp I Msp I Eco72 I Bsu R Eco105 I Msp I Hin6 I Csp6 I Bsp119 I Hin6 I Tas I Bsp119 I Hinf I Mph1103 Enzyme GH = growth hormone gene; GHR = growth hormone receptor gene; GHSR = growth hormone secretagogue receptor gene, IGF-I = insulin-like growth factor-I gene; IGFBP-2 = insulin-like growth factor binding protein-2 gene; INS = insulin gene; LEPR = leptin receptor gene; TSH-β = thyroid-stimulating hormone beta subunit gene; and SSCP = single strand conformational polymorphism Location on chromosome where gene is found (http://mgc.ucsc.edu/cgi-bin/hgBlat) (2004) There was one insertion-deletion GGTACA for 18792785 to 187907591 in the chicken GHSR gene Chromosome Gene Table Details of single nucleotide polymorphism markers, genes, and primers1 836 LEI ET AL 837 GROWTH-CORRELATED GENES AND CHICKEN FATNESS Table Single nucleotide polymorphism allele frequencies and the chi-square test Loci Allele XH2 WRR3 F-value GH G142167T G143831A G143978A A144762G G145086A G6622190A C6622516T A6626579G G18790036A T18791236C 18792785 to 1879075914 C18793056T C18793131T C51978309T C51983354T C51978771T C52028084T G23967395T T23966786A C23966654T T23966559G G23966484A G11303145 A C11304264T T11306685C C11306451T T28573025C A28573100G C2541870G C2543216T A2543276T G G G A G G C A G T I C C C C C C G T C T G G C T C T A C C A 0.53 0.67 0.79 1.00 0.74 1.00 0.38 0.93 0.75 0.74 0.92 0.76 0.50 0.88 0.96 0.50 0.74 1.00 0.31 1.00 0.65 1.00 0.65 0.82 0.57 0.58 0.46 0.78 0.79 0.77 0.78 1.00 0.85 0.64 0.57 1.00 0.94 1.00 0.53 0.65 0.79 0.60 0.50 0.46 0.78 0.50 0.89 1.00 0.67 1.00 0.79 1.00 0.82 0.86 0.70 1.00 1.00 0.83 0.93 0.78 15.512** 36.000** 17.379** 7.433* 0.130 0.000 31.482** 5.373* 10.697** 1.070 4.810 5.560 0.000 32.112** 12.083** 0.000 5.230 0.000 20.355** 0.000 5.130 0.00 8.5895* 0.65 3.21 51.428** 38.297** 2.940 6.923** 16.639** GHR GHSR IGF-I IGFBP-2 INS LEPR TSH-β GH = growth hormone; GHR = growth hormone receptor; GHSR = growth hormone secretagogue receptor; IGF-I = insulin-like growth factor-I; IGFBP-2 = insulin-like growth factor binding protein-2; INS = insulin; LEPR = leptin receptor; and TSH-β = thyroid-stimulating hormone beta subunit XH = Xinghua chickens WRR = White Plymouth Rock chickens There was one insertion-deletion GGTACA for 18792785 to 187907591 in the chicken GHSR gene *P < 0.05; **P < 0.01 The purpose of the present study was to observe the effect of the growth-correlated genes on fatness and muscle fiber traits in chickens Thirty SNP and one 6-bp indel were selected from genes of the somatotropic axis, the growth hormone (GH), growth hormone receptor (GHR), growth hormone secretagogue receptor (GHSR), insulinlike growth factor-I (IGF-I), insulin-like growth factor binding protein-2 (IGFBP-2), insulin (INS), leptin receptor (LEPR), and thyroid-stimulating hormone beta subunit (TSH-β) The linkage of the SNP with fatness and muscle fiber traits was evaluated with linkage analyses and linkage disequilibria in unrelated populations MATERIALS AND METHODS Chicken Populations and the Observation of Chicken Fatness and Muscle Fiber Traits A F2 resource population was constructed by crossing the White Plymouth Rock chickens (WRR) with Xinghua chickens (XH; Lei et al., 2005) Nine WRR males were crossed to XH females, and WRR females were crossed to XH males, producing 17 F1 families and 454 F2 fullsib individuals (221 males and 233 females) The resource population was from hatches Ten fatness and muscle fiber traits [abdominal fat pad weight (AFW), abdominal fat pad ratio (AFPR), fat thickness under skin (FTS), fat width (FW), transversal area of the leg muscle fiber (TALMF), transversal area of the breast muscle fiber (TABMF), CP content of the breast muscle (CPCBM), CP content of the leg muscle (CPCLM), crude fatty content of the breast muscle (CFCBM), and crude fatty content of the leg muscle (CFCLM)] were measured Two unrelated populations, consisting of 36 XH individuals and 36 WRR individuals, respectively, were sampled for a genetic diversity investigation in the present study The XH and WRR were parents of the F2 resource population, both from Guangdong Wens Foodstuff Corporation Ltd (Guangdong, China) The XH was a Chinese native breed with slow growth rate, and WRR was a breed with fast growth rate There were significant differences in fatness and muscle traits between the XH and WRR chickens SNP Markers from the Growth-Correlated Genes and Genotyping Thirty SNP and one 6-bp indel from the growthcorrelated genes (Table 1) were selected to genotype the Downloaded from http://ps.oxfordjournals.org/ at National Chung Hsing University Library on April 10, 2014 Gene1 838 LEI ET AL Table Linkage analyses of 30 single nucleotide polymorphisms and one 6-bp insertion-deletion with chicken fatness and muscle fiber traits Loci AFW2 AFPR FTS FW TALMF TABMF CPCBM CPCLM CFCBM CFCLM GH G142167T G143831A G143978A G145086A A144762G G6622190A A6626579G G18790036A T18791236C 18792785 to 1879075913 C18793056T C18793131T C51978309T C51983354T C51978771T C52028084T G23967395T T23966786A C23966654T T23966559G G23966484A G11303145A C11304264T T11306685C C11306451T T28573025C A28573100G C2541870G C2543216T A2543276T 0.209 0.277 0.789 0.002** 0.524 0.105 0.496 0.275 0.932 0.034* 0.835 0.42 0.354 0.561 0.501 0.91 0.812 0.873 0.33 0.832 0.787 0.672 0.729 0.748 0.707 0.027* 0.137 0.26 0.71 0.513 0.227 0.371 0.71 0.005** 0.318 0.121 0.712 0.189 0.886 0.017* 0.729 0.491 0.521 0.618 0.397 0.814 0.775 0.853 0.323 0.731 0.545 0.536 0.695 0.829 0.532 0.197 0.164 0.235 0.661 0.59 0.023* 0.093 0.783 0.622 0.948 0.861 0.020* 0.801 0.48 0.032* 0.609 0.427 0.521 0.812 0.865 0.781 0.267 0.697 0.448 0.21 0.038* 0.438 0.642 0.315 0.531 0.402 0.618 0.277 0.494 0.589 0.807 0.000** 0.148 0.378 0.67 0.003 0.652 0.000** 0.662 0.482 0.826 0.253 0.7 0.52 0.326 0.751 0.077 0.752 0.437 0.875 0.864 0.524 0.729 0.002** 0.668 0.007** 0.11 0.776 0.326 0.612 0.669 0.898 0.000** 0.068 0.000** 0.322 0.007** 0.853 0.725 0.027* 0.796 0.013* 0.000** 0.249 0.859 0.308 0.74 0.902 0.693 0.808 0.673 0.002** 0.804 0.782 0.835 0.306 0.614 0.832 0.501 0.934 0.574 0.778 0.297 0.788 0.045* 0.458 0.000** 0.058 0.866 0.285 0.44 0.729 0.011* 0.796 0.85 0.758 0.755 0.443 0.068 0.755 0.446 0.016* 0.587 0.881 0.943 0.651 0.669 0.745 0.614 0.895 0.443 0.82 0.594 0.043* 0.085 0.725 0.024* 0.114 0.759 0.773 0.74 0.133 0.698 0.69 0.935 0.396 0.489 0.827 0.71 0.133 0.023* 0.507 0.428 0.851 0.951 0.784 0.778 0.467 0.089 0.549 0.55 0.33 0.547 0.585 0.569 0.994 0.468 0.566 0.951 0.848 0.725 0.717 0.591 0.303 0.707 0.000** 0.623 0.644 0.825 0.033* 0.007** 0.268 0.909 0.834 0.836 0.853 0.531 0.609 0.929 0.725 0.447 0.226 0.757 0.531 0.632 0.504 0.833 0.279 0.603 0.376 0.126 0.125 0.459 0.013* 0.689 0.67 0.457 0.734 0.791 0.757 0.744 0.634 0.786 0.835 0.614 0.461 0.434 0.759 0.236 0.076 0.343 0.205 0.010** 0.32 0.446 0.375 0.000** 0.609 0.308 0.000** 0.763 0.219 0.197 0.94 0.481 0.001** 0.917 0.377 0.935 0.194 0.237 0.581 0.609 0.000** 0.043* 0.582 0.796 0.437 0.515 0.379 GHR GHSR IGF-I IGFBP-2 INS LEPR TSH-β GH = growth hormone; GHR = growth hormone receptor; GHSR = growth hormone secretagogue receptor; IGF-I = insulin-like growth factorI; IGFBP-2 = insulin-like growth factor binding protein-2; INS = insulin; LEPR = leptin receptor; and TSH-β = thyroid-stimulating hormone beta subunit AFW = abdominal fat pad weight (g); AFPR = abdominal fat pad ratio; FTS = fat thickness under skin (mm); FW fat width = (mm); TALMF = transversal area of the leg muscle fiber; TABMF = transversal area of the breast muscle fiber; CPCBM = CP content of the breast muscle; CPCLM = CP content of the leg muscle; CFCBM = crude fatty content of the breast muscle; and CFCLM = crude fatty content of the leg muscle There was one insertion-deletion GGTACA for 18792785 to 187907591 in the chicken GHSR gene *P < 0.05; **P < 0.01 454 F2, 31 F1, and 30 parental chickens by RFLP and single strand conformational polymorphism (SSCP) The PCR was performed in a final volume of 25 L containing L of genomic DNA (2.5 ng/L), 0.25 L of each primer (25 M), 0.5 L of deoxynucleotide triphosphates (10 M) mixture, 1.5 L of MgCl2 (25 mM), 0.2 L of DNA polymerase (5 U/L; Takara, Tokyo, Japan), and 2.5 L of 10 × reaction buffer on an ABI 2700 (Applied Biosystems, Foster City, CA) Thermal Cycle with the following profile: initial denaturation at 94°C for min, 35 cycles of 94°C for 30 s, Y°C for 30 s, 72°C for 30 s, and a final elongation at 72°C for where Y refers to a different annealing temperature for each primer (Table 1) Eight-microliter PCR products were digested with 3.0 U of enzyme at 37°C overnight Restriction patterns were visualized in a to 4% agarose gel electrophoresis stained with ethidium bromide The A23966559T and G23966484A SNP were genotyped with SSCP by a 12% polyacrylamide gel electrophoresis Statistical Analyses The difference of allele frequencies between the unrelated chicken populations was tested using SAS 8.1 FREQ (SAS Institute Inc., Cary, NC) The linkage disequilibria D′ value between each pair of SNP and the haplotype structure of SNP within each gene were estimated by Haploview (Daly et al., 2001) Linkage analyses of single SNP with chicken fatness and muscle fiber traits were performed with SAGE/SIBPAL package (http://darwin.cwru.edu/sage/index.php) (SAGE, 2006) RESULTS Allele Frequency in the Unrelated Populations Allele frequencies of 30 SNP and one 6-bp indel in the populations are shown in Table Allele A of the G18790036A SNP of the GHSR gene, allele A of the G143831A SNP of the GH gene, allele C of the T28573025C SNP, and allele G of the A28573100G SNP of the LEPR gene were all absent in WRR chickens In the XH and WRR chickens, allele A of the G11303145A SNP of the INS gene, allele A of the G6622190A SNP and allele T of the C6622516T SNP of the GHR gene, and allele A of the T23966786A SNP and allele G of the T23966559G SNP of the IGFBP-2 gene were not found There was a significant difference for allele frequencies of C11304264T of the INS gene between the XH and WRR Downloaded from http://ps.oxfordjournals.org/ at National Chung Hsing University Library on April 10, 2014 Gene1 GROWTH-CORRELATED GENES AND CHICKEN FATNESS 839 chickens, but there was no difference for the 18792785 to 187907591 indel, and the C18793056T and C18793131T SNP of the GHSR gene Highly significant differences were found for the C2543216T and A2543276T SNP of the TSH-β gene and the A6626579G SNP of the GHR gene No significant difference was observed in the G143978A SNP of the GH gene, and C51978309T SNP and the C52028084T SNP of the IGF-I gene (P > 0.05) A highly significant difference was found in the C23966654T SNP of the IGFBP-2 gene (P < 0.01) Linkage Disequilibria of the SNP in the Growth-Correlated Genes Linkage Analyses Results from the 2-point linkage analyses are shown in Table There were significant associations of the G11303145A SNP of the INS gene with TALMF and TABMF Positive additive genetic effects were observed at a highly significant level for the TALMF, and highly significant negative additive genetic effects were observed for TABMF (Table 4) The A6626579G SNP of the GHR gene was highly significantly associated with the fatness and muscle fiber traits (P < 0.01) The G145086A SNP of the GH gene was related to fatness traits such as AFW and AFPR The C51978309T of the IGF-I gene was related to chicken TALMF and TABMF The 6-bp indel of the GHSR gene was significantly associated with fatness traits such as AFW, AFPR, FTS, and CFCLM There were highly significant positive additive effects for the fatness traits and CFCLM DISCUSSION In the present study, 30 SNP and one 6-bp indel selected from the 283 SNP in 12 genes of somatotropic axis (Nie et al., 2005a) were associated with some fatness and muscle fiber traits Analyses of variance revealed highly sig- Figure Haplotype structures of the chicken growth hormone (GH) and insulin-like growth factor binding protein-2 (IGFBP-2) gene, as estimated by using the Haploview soft package |D| values × 100 are shown in the boxes, with empty boxes being 100 (or |D| = 1) A Haplotype structure of the GH gene The G143831A SNP deviated from HardyWeinberg equilibrium in White Plymouth Rock (WRR) chickens, but not in the Xinghua (XH) chickens B Haplotype structure of the IGFBP2 gene The G23966484A SNP was located in different block in the XH and WRR chickens nificant additive genetic effects In 14 of the 30 SNP and one 6-bp indel, there were significant differences for allele frequencies between the XH and WRR chickens Such differences suggested that the 14 SNP could be associated with chicken fatness and muscle fiber traits Among the 14 SNP, were linked significantly with one or more chicken fatness and muscle fiber traits The G142167T and G143831A SNP of the GH gene and the G18790036A SNP of the GHSR gene were associated with trait, such as FTS, FW, and FW, and the C51983354T SNP of the IGFI gene were related with CFCBM The remaining SNP Downloaded from http://ps.oxfordjournals.org/ at National Chung Hsing University Library on April 10, 2014 To further define the haplotype structures of the growth-correlated genes and multiloci association of each gene, haplotype blocks were analyzed between the XH and WRR chickens using the Haploview program Only SNP were genotyped so that haplotype blocks and multiloci association were not analyzed for the GHR and LEPR genes According to the 4-gamete testing, different haplotype blocks appeared between the XH and WRR chickens excluding SNP deviation from Hardy-Weinberg equilibrium separately within each population, but only the GH and IGFBP-2 genes were interesting For the IGFBP-2 gene, there was main block in the XH chickens, which showed that no recombination was observed in the C23966654T and G23967395T SNP (D′ = 1), and a different block appeared in WRR chickens, which showed that the G23966484A, C23966654T, and G23967395T SNP were linked (Figure 1) For the IGF-I gene, the G143831A deviated from Hardy-Weinberg equilibrium in the WRR chickens, but not in the XH chickens 840 LEI ET AL Table Gene effects on chicken fatness and muscle fiber traits A6626579G of GHR2 Trait1 AFW AFPR FTS FW TALMF TABMF CPCBM CPCLM CFCBM CFCLM Additive effect ± SE4 −2.20 0.13 0.19 −0.97 −234.10 4,521.60 −0.59 0.16 −0.02 −1.03 ± ± ± ± ± ± ± ± ± ± 0.177 0.013 0.015 0.033 75.664 96.305 0.016 0.009 0.006 0.019 18792785 to 187907591 indel3 of GHSR Dominance effect ± SE5 8.20 1.56 1.32 −1.69 −481.45 259.60 −0.78 −0.51 0.70 0.58 ± ± ± ± ± ± ± ± ± ± 0.026 0.003 0.002 0.004 20.45 22.086 0.004 0.01 0.003 0.007 Additive effect ± SE 29.70 2.11 4.76 7.66 632.70 −497.50 −0.19 0.18 0.81 3.28 ± ± ± ± ± ± ± ± ± ± 0.187 0.013 0.025 0.041 71.354 71.236 0.011 0.01 0.01 0.035 Dominance effect ± SE −4.15 −0.29 −1.58 4.82 −495.75 3,368.45 0.71 0.16 0.03 0.50 ± ± ± ± ± ± ± ± ± ± 0.018 0.001 0.002 0.005 11.683 15.401 0.002 0.003 0.001 0.002 G11303145A of the INS Additive effect ± SE −5.30 −0.18 −0.98 −5.79 3,498.90 −2,869.40 −0.27 1.36 0.81 2.36 ± ± ± ± ± ± ± ± ± ± 1.017 0.071 0.117 0.444 577.448 764.012 0.065 0.175 0.098 0.191 Additive effect ± SE 10.75 0.18 −0.05 −5.61 1,992.20 3,465.80 0.05 0.09 −0.56 −2.01 ± ± ± ± ± ± ± ± ± ± 0.057 0.004 0.005 0.019 41.03 40.698 0.007 0.007 0.006 0.019 were associated with or more traits The G143978A SNP of the GH gene was related with TALMF and CFCLM, and the T28573025C SNP of the LEPR gene was associated with AFW and FW The G145086A SNP of the GH gene was related with AFW, AFPR, and CPCBM The A6626579G SNP of the GH gene was associated with FTS, TALMF, TABMF, CPCBM, and CFCLM Considering some associations might be false positives, allele frequency differences partially supported the accuracy of the association analysis It is known that the genes of the growth axis played crucial roles in the regulation of the growth, development, and differentiation There was an important association of the meat quality and growth and body composition (Le Bihan-Duval et al., 1998) Therefore, the genes of the growth axis probably affect the meat quality traits of the animals The G143831A (G+1705A) SNP of the GH gene was significantly associated with growth traits (Nie et al., 2005b) but was only related with fat width The G144762A (G+119A) SNP of the GH gene was significantly related to AFW, AFPR, and CPCBM in the present study, which showed that there was a positive genetic correlation with BW and meat quality traits (Le BihanDuval et al., 2001; Nie et al., 2005b) The C51978309T SNP of the IGF-I gene was linked with TALMF and TABMF, and the correlation (r) of TALMF and TABMF was 0.65 As an important candidate gene that affected the chicken muscle cell development and reproduction, the IGF-I gene was associated with BW, breast weight, and breast yield (Amills et al., 2003) Myofiber numbers and myofiber densities were related to BW, breast weight, and breast yield (Scheuermann et al., 2003, 2004), which suggested that the C51978309T SNP of the IGF-I gene could affect the chicken muscle fiber growth There were different haplotype structures for the IGFBP-2 gene in the XH and WRR chickens, which showed the G23966484A (G+738A) SNP of the IGFBP-2 gene was important In the present study, the G23966484A SNP of the IGFBP-2 gene was associated with CPCBM and CPCLM This SNP, located in the exon 2, possible affected the expression of the IGFBP-2 gene at the transcription and translation levels (Lo et al., 2003; Wyszynska-Koko et al., 2006) These results were consistent with previous results that suggested a potential association of the G23966484A SNP of the IGFBP-2 gene with growth and carcass traits (Besnard et al., 2001; Lei et al., 2005) In the present study, the T28573025C SNP of the LEPR gene was significantly associated with AFW and FW Schenkel et al (2005) found that there was important association of SNP within the leptin gene with fatness (fat yield and subcutaneous fat) Ovilo et al (2005) also showed that the possible QTL was identified on chromosome where the LEPR gene was located As known, there was a significant correlation of AFW and FW (r = 0.63) Therefore, association of the T28573025C SNP of the LEPR gene with fatness possibly was reliable The A6626579G SNP of the GHR gene was associated with traits (FTS, TALMF, TABMF, CPCBM, and CFCLM) To test the accuracy of association of the A6626579G SNP of the GHR gene with traits, a larger population should be used Recently, some QTL that affected meat quality traits have been detected in chickens by use of many kinds of molecular markers The QTL for AFW were found on chromosomes 1, 3, 5, 7, 15, and 28 (Ikeobi et al., 2002; Jennen et al., 2004; Lagarrigue et al., 2006) Some of these QTL with effect on AFW were located on chromosome 7, which contains the IGFBP-2 gene (Jennen et al., 2004, 2005) Meanwhile, QTL for AFW and percentage abdominal fat on chromosome where the IGF-I gene is located were found (Suzuki et al., 2004; Jennen et al., 2005) The QTL affecting fatness in male chickens were mapped to less than Mbp at the distal part of the chromosome 5, which was close to the chicken INS gene (Abasht et al., 2006) All these showed the locations of underlying QTL Downloaded from http://ps.oxfordjournals.org/ at National Chung Hsing University Library on April 10, 2014 AFW= abdominal fat pad weight (g); AFPR = abdominal fat pad ratio; FTS = fat thickness under skin (mm); FW fat width = (mm); TALMF = transversal area of the leg muscle fiber; TABMF = transversal area of the breast muscle fiber; CPCBM = CP content of the breast muscle; CPCLM = CP content of the leg muscle; CFCBM = crude fatty content of the breast muscle; and CFCLM = crude fatty content of the leg muscle GHR = growth hormone receptor gene; GHSR = growth hormone secretagogue receptor gene; and INS = insulin gene There was one insertion-deletion GGTACA for 18792785 to 187907591in the chicken GHSR gene Estimated by subtracting the solution for the BB genotype from that for the AA genotype, A = A and B = G for the A11303145G SNP, and the A11303145G SNP of the INS gene, and A = A and B = G for the G6626579A SNP of the GHR gene, and A = I and B = D for the 18792785 to 187907591 indel of the GHSR gene Estimated by subtracting the average of solutions for homozygous genotypes from that for the heterozygous genotype GROWTH-CORRELATED GENES AND CHICKEN FATNESS ACKNOWLEDGMENTS The current work was funded by projects under the Major State Basic Research 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96:698–703 Nii, M., T Hayashi, S Mikawa, F Tani, A Niki, N Mori, Y Uchida, N Fujishima–Kanaya, M Komatsu, and T Awata Downloaded from http://ps.oxfordjournals.org/ at National Chung Hsing University Library on April 10, 2014 affecting fatness and muscle fiber traits were often mapped to, or close to, regions harboring candidate functional genes of somatotropic axis The candidate genes of the somatotropic axis may affect chicken fatness deposition and muscle fiber traits Linkage disequilibria in the unrelated populations were analyzed for the genes Only the GH and IGFBP2 genes appeared as haplotype blocks in the XH and WRR chickens by using Haploview software package (Daly et al., 2001) For the other genes, no haplotype blocks were found in both the XH and WRR chickens and, therefore, fail to exhibit disequilibrium with fatness and muscle fiber traits However, haplotype blocks in the XH and WRR chickens were consistent with the association Meanwhile difference for haplotype blocks in 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traits in pigs J Appl Genet 47:131–138 Zerehdaran, S., A L Vereijken, J A van Arendonk, and E H van der Waaijt 2004 Estimation of genetic parameters for fat deposition and carcass traits in broilers Poult Sci 83:521–525 Downloaded from http://ps.oxfordjournals.org/ at National Chung Hsing University Library on April 10, 2014 2005 Quantitative trait loci mapping for meat quality and muscle fiber traits in a Japanese wild boar × Large White intercross J Anim Sci 83:308–315 Ovilo, C., A Crop, J L Noguera, M A Oliver, L Barragan, C Rodriguez, L Silio, M A Toro, A Coll, J M Folch, A Sanchez, D Babot, L Varona, and M Perez-Encisco 2002 Quantitative trait locus mapping for meat quality traits in an Iberian × Landrace F2 pig population J Anim Sci 80:2801–2808 Ovilo, C., A Fernandez, J L Noguera, C Barragan, R Leton, C Rodriguez, A Mercade, E Alves, J M Folch, L Varona, and M Toro 2005 Fine mapping of porcine chromosome QTL and LEPR effects on body composition in multiple generations of an Iberian by Landrace intercross Genet Res 85:57–67 Qiu, F F., Q H Nie, C L Luo, D X Zhang, S M Lin, and X Q Zhang 2006 Association of single nucleotide polymorphisms of the insulin gene with chicken early growth and fat deposition Poult Sci 85:980–985 SAGE 2006 Statistical Analysis for Genetic Epidemiology, Release 5.2 http://genepi.cwru.edu/ Accessed Aug 2006 Schenkel, F S., S P Miller, X Ye, S S Moore, J D Nkrumah, C Li, J Yu, I B Mandell, J W Wilton, and J L Williams 2005 Association of single nucleotide polymorphisms in the leptin gene with carcass and meat quality traits of beef cattle J Anim Sci 83:2009–2020 Scheuermann, G N., S F Bilgili, J B Hess, and D R Mulvaney 2003 Breast muscle development in commercial broiler chickens Poult Sci 82:1648–1658 Scheuermann, G N., S F Bilgili, S Tuzun, and D R Mulvaney 2004 Comparison of chicken genotypes: Myofiber number ... (IGF-I), insulin-like growth factor binding protein-2 (IGFBP-2), insulin (INS), leptin receptor (LEPR), and thyroid-stimulating hormone beta subunit (TSH-β) The linkage of the SNP with fatness and muscle. .. Sanchez, and J Estany 2003 Identification of three single nucleotide polymorphisms in the chicken insulin–like growth factor and genes and their associations with growth and feeding traits Poult... summary, association of 30 SNP and one 6-bp indel from genes of somatotropic axis with chicken fatness and muscle fiber traits was analyzed in the present study Three genes, GH, GHSR, and LEPR, were