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Poult Sci 2007. 86:1873-1880
© 2007 Poultry Science Association
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GENETICS

Association of Spot14{alpha} Gene Polymorphisms with Body Weight in the Chicken1

Z. P. Cao, S. Z. Wang, Q. G. Wang, Y. X. Wang and H. Li2

College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China

2 Corresponding author: lihui{at}neau.edu.cn or lihui645{at}hotmail.com


   ABSTRACT
TOP
 ABSTRACT
INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
In mammals, thyroid hormone responsive Spot14 (THRSP) is a small acidic protein that responds to thyroid hormone stimulation and, therefore, is thought to play a role in growth. The current study was designed to investigate the associations of Spot14{alpha} gene polymorphisms on chicken growth and body composition traits. The Northeast Agricultural University Resource Population (NEAURP) was used in the present study. The NEAURP was established by crossing broiler sires, derived from Northeast Agricultural University broiler lines divergently selected for abdominal fat content, with Baier layer dams, a local Chinese breed. The F1 birds were intercrossed to produce the F2 population. Body weight and body composition traits were measured in the F2 population. Polymorphisms of the gene were detected between parental lines by DNA sequencing. Primers were designed according to the chicken Spot14{alpha} gene (AY568628 [GenBank] ). The PCR-RFLP and PCR-length polymorphisms methods were then developed to genotype polymorphisms in the NEAURP. The A213C and 9 bp insertion-deletion of the Spot14{alpha} gene in the F2 population was found to be associated with BW, which implied that Spot14{alpha} gene or a tightly linked gene had an important effect on growth in the chicken.

Key Words: chicken • Spot14{alpha} gene • polymorphism • association • body weight


   INTRODUCTION
TOP
 ABSTRACT
 INTRODUCTION
MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
There are 2 basic methods of QTL identification: the candidate gene approach and the whole-genome linkage-disequilibrium scanning (Ikeobi et al., 2002; Kim et al., 2005). The candidate gene approach is a powerful method for finding QTL responsible for genetic variation in the traits of interest in agricultural animal species and determining whether specific genes are related to economic traits in farm animals (Li et al., 2003). Many studies have involved the association between candidate gene single nucleotide polymophisms (SNP) and animal growth and body composition traits (Li et al., 2003; Meng et al., 2005; Zhang et al., 2005).

The Spot14 gene, referred to as thyroid hormone responsive Spot14 (THRSP), encodes a small acidic protein that was discovered in earlier studies of thyroid hormone (TH) action in hepatocytes (Seelig et al., 1981; Jump et al., 1984; Liaw and Towle, 1984). The rat Spot14 gene was one of the first TH-responsive genes characterized at the molecular level (Sudo et al., 1993; Zou et al., 1994; Shih et al., 1995). Identification of the human Spot14 TRE revealed extensive sequence similarity to the rat Spot14 TRE. Thus, it was concluded that the mechanism whereby the Spot14 promoter responds to TH is highly conserved between these 2 species (Campbell et al., 2003). Spot14, which is implicated as a transcription factor involved in control of lipogenic enzymes, is only expressed in lipogenic tissue such as liver, fat, and the mammary gland (Liaw and Towle, 1984; Jump and Oppenheimer, 1985). Although the exact molecular mechanism is not clear, the Spot14 promoter region contains 3 thyroid response elements (TRE) that work synergistically and interact with the far upstream region elements to maximize triiodothyronine (T3) responses in hepatocytes (Liu and Towle, 1994). Spot14 mRNA levels are greatly increased by carbohydrate feeding or insulin injection and decreased by high plasma glucagon levels or by feeding a diet rich in polyunsaturated fatty acids (Jump et al., 1993). The human Spot14 promoter responds more robustly to T3 than to glucose, whereas the rat Spot14 promoter region is more responsive to glucose than to T3 (Campbell et al., 2003).

The chicken Spot14 was first identified by microarray analysis as a differentially expressed sequence tag in livers of chickens divergently selected for fast or slow growth rate (Cogburn et al., 2000, 2003a,Cogburn et al., b). A related expressed sequence tag was revealed by differential mRNA display in the liver of genetically fat and lean chickens and subsequently mapped to 1q41–44 (Carre et al., 2001), which also harbors a QTL for skin fatness (Ikeobi et al., 2002) and abdominal fatness (Lagarrigue et al., 2003). Expression of Spot14 mRNA is regulated by the thyroid hormone status in broiler chickens (Wang et al., 2002). Duplicated polymorphic paralogs of Spot14, Spot14{alpha}, and Spot14ßwere reported in the chicken (Wang et al., 2004). The 9-bp insertion-deletion of Spot14{alpha} was associated with abdominal fat (Wang et al., 2004). Spot14{alpha} and Spot14ßwere composed of 2 exons (442 and 355 bp) and 1 intron (637 bp). Despite low similarity in amino acid sequence between chickens and mammals, other properties of Spot14 (i.e., pI, subcellular localization, transcriptional control, and functional domains) appear to be highly conserved. Furthermore, a synteny group of Spot14 and its flanking genes [reduced form of nicotin-amide-adenine dinucleotide dehydrogenase (NDUFC2) and glucosyltransferase (ALG8)] appears to be conserved among chickens, humans, mice, and rats (Wang et al., 2004). The objectives of the present study were to identify the polymorphisms of the chicken Spot14{alpha} gene, develop the PCR-RFLP and PCR-length polymorphisms methods to genotype the polymorphisms of the individuals in NEAURP, and evaluate the association between Spot14{alpha} gene polymorphism and growth and body composition traits.


   MATERIALS AND METHODS
TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
RESULTS
 DISCUSSION
 REFERENCES
 
Experimental Populations and Management
The NEAURP was established by crossing 4 broiler grandsires, derived from Northeast Agricultural University broiler lines divergently selected for abdominal fat content, with 24 Baier layer granddams, a local Chinese breed. The F1 birds (12 sires and 72 dams) were intercrossed to produce the F2 population. A total of 825 F2 individuals were used in the current study.

All birds had free access to feed and water. Commercial corn-soybean-based diets that met all NRC requirements (National Research Council, 1994) were provided in the study. From hatch to 3 wk of age, birds received a starter feed (3,000 kcal of ME/kg and 210 g/kg of CP) and from 3 to 12 wk of age, birds were fed a grower diet (3,100 kcal of ME/kg and 190 g/kg of CP).

Phenotypic Measurements
Body weight was measured at hatch and weekly up to 12 wk of age. Metatarsus length (ML) and metatarsus circumference (MC) were measured at 2-wk intervals from 4 to 12 wk of age. Body composition traits were recorded at 12 wk of age. These measurements included carcass weight (CW), pectoralis major weight (PMaW), pectoralis minor weight (PMiW), leg muscle weight (LMW), metatarsus length (ML) metatarsus circumference (MC), femur length (FL), femur weight (FW), shank length (SL), shank weight (ShW), shank claw weight (SCW), abdominal fat weight (AFW), spleen weight (SpW), liver weight (LW), and heart weight (HW). All traits were also expressed as percentage of BW at 12 wk of age. The MC was measured with a string that circled the metatarsal bone, and the string length that was the MC was measured with Vernier caliper (Suzhou Sanfeng Measure S and T Co. Ltd., Suzhou, China). The ML, FL, SL, and KL were measured with Vernier caliper directly, and the BW, CW, AFW, FW, ShW, SpW, PMaW, and LMW were measured with an electronic scale.

Development of PCR-RFLP and PCR-Length Polymorphisms Assays
Genomic DNA was extracted using phenol/chloroform from 10 µL of venous blood collected in EDTA-Na2-coated tubes (Axygen Scientific Inc., Union City, CA). All primers were designed according to the chicken Spot14{alpha} gene sequence in the GenBank database (accession no. AY568628 [GenBank] ) by Primer 5.0 (Premier Biosoft International, Palo Alto, CA).

The primers 1 (Table 1Go; SF1, 5'-CAG GAG GGA GCA GAG GGA TA G-3'; SR1, 5'-TCC TTG TCA TCG TGG GCT AAG-3') were designed to amplify a 1,580-bp fragment including exon 1 (442 bp), intron 1 (637 bp), exon 2 (355 bp), and a part of 5' flanking region and 3' flanking region of the chicken Spot14{alpha} gene. The PCR was carried out with DNA from 2 of 4 grandsires and 2 of 24 grand-dams to investigate sequence polymorphisms of the chicken Spot14{alpha} gene. The PCR components included 1x PCR reaction buffer (10 mM Tris-HCl, 50 mM KCl, and 1.5 mM MgCl2 pH 8.3), 200 µM of each deoxynucletide triphosphate, 0.25 µM of each primer, 2 µL of DNA (50 ng/µL), and 1 U of Taq DNA polymerase in a final volume of 25 µL (TaKaRa Biotechnology Co. Ltd., Dalian, China). The thermal profiles were 95°C for 7 min followed by 35 cycles of 95°C for 1 min, 67°C for 1 min, and 72°C for 2 min. The PCR products were purified by Gel Extraction Mini Kit (Watson Biotechnologies Inc., Shanghai, China) and the forward and reverse DNA strand was sequenced with an ABI 3730 sequencer (Bioasia Biotechnology Co., Ltd., Shanghai, China). Restriction enzyme sites in these sequences were detected by the DNAMAN package Version 4.0 (Lynnon BioSoft, Vaudreuil-Dorion, Quebec, Canada).


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  		Table 1. The primers and location of the amplification sites within the Spot14{alpha} gene
 
The primers 2 (Table 1Go; SF1, 5'-CAG GAG GGA GCA GAG GGA TAG-3'; SR2, 3'-CGT CGT CCA AGA CTG GCT GG-5') were designed to amplify a 419-bp fragment. The PCR was carried out with DNA from all the grandsires, parents, and F2 offspring to detect the polymorphisms of the chicken Spot14{alpha} gene. The PCR components were 1x PCR reaction buffer, 200 µM of each deoxy-nucletide triphosphate, 0.25 µM of each primer, 1 µL of genomic DNA (50 ng/µL), and 0.5 U of Taq DNA polymerase in a final volume of 10 µL (TaKaRa Biotechnology Co. Ltd., Dalian, China). The thermal profiles were 94 °C for 7 min followed by 35 cycles of 94°C for 30 s, 65 °C for 30 s, and 72°C for 30 s.

The primers 3 (Table 1Go; SF2, 5'-ATC AAG CCC GTG GTG GAG C-3'; SR2, 3'-CGT CGT CCA AGA CTG GCT GG-5') were designed to amplify a 157-bp exon-region fragment. The PCR was carried out with DNA from all the grandsires, parents, and F2 offspring to detect the polymorphisms of the chicken Spot14{alpha} gene. The PCR components and thermal profiles were same as the primers 1 except that the extension time was 40 s.

Screening of the F2 Population Single Nucleotide Polymorphisms and Length Polymorphisms
For primers 2, the PCR product was digested using 1 U of the Hin1I enzyme at 37°C overnight. Restriction patterns were visualized by electrophoresing the digestion product in a 2.5% agarose gel stained with ethidium bromide. For primers 3, polymorphism patterns were visualized by electrophoresing 1 µL of the PCR product in a 14% nondenaturing polyacrylamide gel stained with silver nitrate.

Linkage Disequilibrium Analysis and Haplotype Construction
The individuals and their parents were used to construct haplotype as introduced by Alex et al. (2002). If the genotypes of the 2 sites of the individual and its parents were all heterozygous, the individual’s phase information was uncertain. Then all the grandparents’ and parents’ genotypes were used to construct individual’s haplotypes using Cyrillic 2.1 (Cyrillic Software, 2000). If the individual’s phase information was still uncertain, then the individual was eliminated from analysis.

Two normalized measures, D' and r2, were used to characterize linkage disequilibrium (LD) patterns within the studied candidate gene. Pairwise D' values are computed as D' = D/Dmax, Dmax = min(f1+f+2, f+1f2+) when D > 0, and Dmax = min(f1+f+1, f+2f2+) when D < 0, where f are sample estimates of SNP frequencies (Lewontin, 1964; note: + represented 1 or 2, e.g., f1+ represented f11 and f12). The r2 was quantified as r2 = (f11f22 – f12f21)2/[(f11 + f12)(f21 + f22)(f11 + f21)(f12 + f22)], where f are sample estimates of haplotype frequencies (Devlin and Risch. 1995). The value of D' > 0.33 and r2 > 0.1 (Kruglyak, 1999) were applied as the criterion for meaningful LD.

Statistical Analysis
The association between the polymorphism and the phenotypic traits was analyzed using the GLM procedure of JMP 4.0 (SAS Institute Inc., 2002). The model was fitted with the genotype (G), sex (S), and hatch (H) as fixed effects; family (f, F1 sires), dam nested within the family (d (f)) as random effects, G x S and G x H as interaction of G x S, and G x H effect, and BW at 12 wk (BW12) as a linear covariate (except for the percentage traits and the BW traits), as follows:


Formula

where Y was the dependent variable, µ was population mean, and e was the random error. The other interactions of each 2 terms in the model were not significant for any of traits and, therefore, were not included in the final model. Significant differences between least squares means of the different genotypes were calculated using a contrast test. Significance was determined as P < 0.05, unless otherwise specified.


   RESULTS
TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
DISCUSSION
 REFERENCES
 
Sequence Variation, PCR-RFLP, and PCR-Length Polymorphisms Analysis
For the primers 1, the amplified 1,580-bp product from the Spot14{alpha} gene was sequenced for 4 individuals that include 2 F0 sires and 2 F0 dams. Two polymorphisms, an A/C at base 213 (A213C) from ATG and a 9-bp insertion-deletion at base 232 from ATG, were found in exon 1.

The PCR-RFLP method was developed successfully for screening the individuals of the F2 population. The primers 2 were used to amplify Spot14{alpha} gene for A213C. The PCR products (419 bp) were the same as expected. The restriction enzyme Hin1I-digested PCR products resulted in 3 genotypes defined as AA (419 bp), AB (419, 319, and 100 bp), and BB (319 and 100 bp; Figure 1Go).


Figure 1
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  		Figure 1. The PCR-RFLP pattern for the Spot14{alpha} gene exon 1 region with Hin1I digestion. M = Marker DL2000; AA = 419 bp; AB = 419 bp/ 319 bp; and BB = 319 bp. The numbers listed on the left and right of the figure are fragment sizes.

 
The PCR-length polymorphisms method was developed successfully for screening the individuals of the F2 population. The primers 3 were used to amplify Spot14{alpha} gene for 9-bp insertion-deletion. The PCR products (157 or 166 bp) were the same as expected. The PCR products resulted in 3 genotypes defined as CC (166 bp), CD (166, 157, and 9 bp), and DD (157 and 9 bp) in the 14% nondenaturing polyacrylamide gel (Figure 2Go).


Figure 2
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  		Figure 2. The PCR-length polymorphisms pattern for Spot14{alpha} gene. The numbers listed on the left of the figure are fragment sizes. CC = 166 bp; CD = 166 bp/157 bp; and DD = 157 bp.

 
Association of Spot14{alpha} Gene Polymorphisms with Growth and Body Composition Traits
The polymorphisms A213C and 9-bp insertion-deletion of the chicken Spot14{alpha} gene were genotyped for 825 F2 individuals in the NEAURP. There were significant associations between the SNP A213C and BW at 5 to 12 wk of age in the F2 offspring of the broiler by Baier cross (Table 2Go). There were significant associations between the 9-bp insertion-deletion and BW at 8 to 12 wk of age in the F2 offspring of the broiler by Baier cross. There was no association between the polymorphisms and body composition traits.


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  		Table 2. The effects (probability value) of the Spot14{alpha} polymorphisms on chicken growth and body composition trait in the F2 birds
 
Effects of the Spot14 Genotype on Growth and Body Composition Traits
Effects (least squares means) of the Spot14{alpha} A213C and 9-bp insertion-deletion on BW and CW in the F2 population are shown in Tables 3Go and 4Go, respectively. The F2 Birds with AA genotype birds had significantly (P < 0.05) lower BW at 4 to 12 wk of age and CW than those with BB genotype (Table 3Go). The F2 birds with CC genotype had significantly (P < 0.05) lower BW at 6 to 12 wk of age and CW than those with DD genotype (Table 4Go).


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  		Table 3. Effects of Spot14 A213C genotypes on BW in grams for the F2 birds (least squares means ± SE)
 

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  		Table 4. Effects of the 9 bp insertion-deletion genotype on body weight in grams for the F2 birds (least squares means ± SE)
 
Linkage Disequilibrium and Haplotype-Traits Association Analysis
In the present study, there were 4 haplotypes in the F2 birds, and 8 diplotypes were detected. Their frequencies are listed in Table 5Go. Two most common LD measures, D' and r2, were used to determine the extent of LD in the Spot14{alpha} gene. The D' and r2 values were 0.53 (>0.33) and 0.14 (>0.1) in the NEAURP, which indicated that the 2 polymorphisms were linked, and this region may be inherited as a unit.


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  		Table 5. Haplotype and diplotype frequencies of the Spot14{alpha} gene
 
The mixed model analysis indicated that there were significant associations between the diplotype and BW at 6 to 12 wk of age in F2 offspring of the broiler by Baier cross (Table 2Go). The F2 birds with AC/AC genotype had significantly (P < 0.05) lower BW at 5 to 12 wk of age and CW than those with BD/BD genotype (Table 6Go).


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  		Table 6. Effects of diplotype genotype on body weight in grams for the F2 birds (least squares means ± SE)
 

   DISCUSSION
TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
REFERENCES
 
Growth is a comprehensive reflection of development of various parts of a chicken body, and its final expression is the result of interaction among genetic, nutritional, and environmental factors (Scanes et al., 1984). Growth is under complex genetic control, and uncovering the molecular mechanisms of growth will contribute to more efficient selection for growth in broiler chickens (Deeb and Lamont, 2002).

Thyroid hormone belongs to the hypothalamic-pituitary-thyroid axis, and the hypothalamic-pituitary-thyroid axis plays an important role in the regulation of energy homeostasis via the effects of TH to increase oxygen consumption and heat generation (de Jesus et al., 2001; Lanni et al., 2001). Disturbance of thyroid function is associated with marked changes in BW and energy expenditure (Belsing et al., 2003).

The rat Spot 14 promoter contains 3 regions responsible for mediating TH-dependent regulation of the gene (Zilz et al., 1990; Zou et al., 1994). The TH regulation of gene expression is achieved through the thyroid hormone receptor, which regulates cognate gene expression by binding the upstream promoters of TH-responsive genes at specific sequences (Chin, 1994). Spot14 can regulate expression of type I deiodinase (Brown et al., 1997), which converts the prohormone thyroxine to metabolically active T3 in most tissues and induces expression of the thyroid hormone receptor (Cogburn et al., 2003b). The mammalian Spot14 gene can respond to thyroid hormones quickly (Seelig et al., 1981; Cogburn et al., 2003b). It seemed likely that Spot14 gene and thyroid hormones played a mutual role.

In chickens, T3 treatment can also upregulate expression of hepatic Spot14 mRNA (Wang et al., 2002). Although the Spot14 amino acid sequence is weakly conserved in vertebrates, an alignment of all members of the Spot14 family clearly shows 3 conserved domains, which include the leucine zipper motif, and 2 hydrophobic domains (Wang et al., 2004). The Spot14 family and its flanking genes that affect growth are conserved among chickens, humans, mice, and rats (Wang et al., 2004).

As a traditional approach, single-marker analysis has created many problems, such as being time consuming and having a lower efficiency to detect QTL (Daly et al., 2001). However, haplotype or haplotype block provided a practical solution to resolve these problems (Daly et al., 2001) and had greater statistical power by using linkage information (Jenny et al., 2004). The linkage disequilibrium between A213C and the 9-bp insertion-deletion was estimated as D' = 0.53 (>0.33) and r2 = 0.14 (>0.1) in the present study, and the space between 2 polymorphism sites was 19 bp in the physical map. A meaningful LD was relatively common in a pairwise physical distance smaller than 8.6 kb (Long et al., 2004). Thus, the 2 polymorphism sites detected in the present study have strong linkage disequilibrium. This region may be inherited as a unit. It was a very unusual finding that there was over 32% of recombinant haplotypes between 2 loci that were only 19 bp apart. It was presumed that this location was a recombination hotspot. Meiotic recombination events are not random and occur more frequently in some regions of the genome (recombination hotspots), where double-stranded DNA breaks are often preferentially induced. This is a universal phenomenon in many eukaryotes in which meiotic recombination has been studied (Lichten and Goldman, 1995). Hotspots are usually small (between 1 to 3 kilobase; Nishant and Rao, 2006).

An A213C and a 9-bp insertion-deletion were found in the exon1 of the Spot14{alpha} gene in the current study. The A213C mutation is a missense mutation, which changes aspartic acid to alanine, and the 9-bp insertion-deletion is a codon mutation, which leads to the insertion or deletion of 3 amino acids (Asp, Gly, and Ile). The Spot14{alpha} gene polymorphisms and diplotypes were predominantly related to BW (5 to 12 wk). The F2 birds with AA, CC, and AC/AC genotypes had a lower BW than the birds with BB, DD, and BD/BD genotypes, respectively. There was disagreement between the results of the current study and a previously published study that showed Spot14{alpha} and fatness association. The 9-bp insertion-deletion have been detected and screened in 2 F2 populations. The association of the Spot14{alpha} locus with abdominal fat traits in the broiler x Leghorn cross have been demonstrated, but not in the broiler x Fayoumi cross. It was presumed that this discrepancy was resulted by a large difference in genetic background between the Leghorn and Fayoumi breeds, as well as between broilers used in different experiments. Grandsires (broilers) used here were derived from the fat line of Northeast Agricultural University broiler lines divergently selected for abdominal fat content. Thus, the disagreement between the current results and the previous reports is not surprising.

Thyroid hormone is one of the most important hormones that are involved in animal growth and development, and the Spot14 gene can respond to TH. Sequence variation in the Spot14 gene may be related to the change in response of the gene to TH. In an F2 population, however, the linkage disequilibrium was substantial. The associations between the Spot14{alpha}-polymorphisms and BW at different ages in the F2 birds might have been produced by linkage disequilibrium between the mutations and another mutation located in the Spot14{alpha} locus or another linked gene directly involved in the regulation of these phenotypic traits.

The results from the current study indicated that the Spot14 gene was associated with BW. The Spot14 gene is, therefore, a potential marker for use in marker-assisted selection programs. To make further progress, there is a need to evaluate polymorphism and traits of growth and body composition in other different breeds and lines of chickens, and conduct further function studies for defining the effects of A213C and the 9-bp insertion/deletion at a molecular level.


   ACKNOWLEDGMENTS
 
The authors gratefully acknowledge the members of the Poultry Breeding group of the College of Animal Science Technology in the Northeast Agricultural University for help in managing the birds and collecting the data. This research was supported by Program for New Century Excellent Talents in University (No. NCET-04-0343), ational Basic Research Program (No. 2006CB102105), and National Natural Science Foundation Key Project (No. 30430510).


   FOOTNOTES
 
1 This research was supported by Program for New Century Excellent Talents in University (No. NCET-04-0343), National Basic Research Program (No. 2006CB102105), and National Natural Science Foundation Key Project (No. 30430510). Back

Received for publication February 28, 2007. Accepted for publication April 30, 2007.


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