Variation at the insulin-like growth factor 1 gene and its association with body weight traits in the chicken

Whole Genome Resequencing Revealed the Genetic Relationship and Selected Regions among Baicheng-You, Beijing-You, and European-Origin Broilers

As the only two You-chicken breeds in China, Baicheng-You (BCY) and Beijing-You (BJY) chickens are famous for their good meat quality. However, so far, the molecular basis of germplasm of the two You-chicken breeds is not yet clear. The genetic relationship among BCY, BJY, and European-origin broilers (BRs) was analyzed using whole genome resequencing data to contribute to this issue. A total of 18,852,372 single nucleotide polymorphisms (SNPs) were obtained in this study. After quality control, 8,207,242 SNPs were applied to subsequent analysis. The data indicated that BJY chickens possessed distant distance with BRs (genetic differentiation coefficient (FST) = 0.1681) and BCY (FST = 0.1231), respectively, while BCY and BRs had a closer relationship (FST = 0.0946). In addition, by using FST, cross-population extended haplotype homozygosity (XP-EHH), and cross-population composite likelihood ratio (XP-CLR) methods, we found 374 selected genes between BJY and BRs chickens and 279 selected genes between BCY and BJY chickens, respectively, which contained a number of important candidates or genetic variations associated with feather growth and fat deposition of BJY chickens and potential disease resistance of BCY chickens. Our study demonstrates a genome-wide view of genetic diversity and differentiation among BCY, BJY, and BRs. These results may provide useful information on a molecular basis related to the special characteristics of these broiler breeds, thus enabling us to better understand the formation mechanism of Chinese-You chickens.

A Novel SNP in the Promoter Region of IGF1 Associated With Yunshang Black Goat Kidding Number via Promoting Transcription Activity by SP1

IGF1, a member of the insulin-like growth factor (IGF) superfamily, is also known as the growth-promoting factor (somatomedin C). IGF1 is involved in vertebrate growth and development, immunity, cell metabolism, reproduction, and breeding. However, there are relatively few studies on the relationship between IGF1 and goat reproduction. In this study, a new transcription factor SP1 bound to the IGF1 g. 64943050T>C promoted granulosa cell (GC) proliferation. A mutation g.64943050T>C located in the promoter region of IGF1 was identified. Association analysis revealed that the kidding number in the first and second litters and the average number of first three litters of the CC genotype (2.206 ± 0.044, 2.254 ± 0.056, and 2.251 ± 0.031) were significantly higher than those in the TC genotype (1.832 ± 0.049, 1.982 ± 0.06, and 1.921 ± 0.034) and TT genotype (1.860 ± 0.090, 1.968 ± 0.117, and 1.924 ± 0.062) (p < 0.05). The kidding number in the third litter of the CC genotype (2.355 ± 0.057) was significantly higher than that in the TT genotype (2.000 ± 0.107) (p < 0.05). Then, the function of this mutation was validated by the dual-luciferase reporter assay and EMSA. The results showed that the luciferase activity of IGF1-mutant-C was significantly higher than that of IGF1-Wild-T (p < 0.05). The EMSA also showed that the binding ability of IGF1-mutant-C was higher than that of IGF1-Wild-T (p < 0.05). Subsequently, the transcription factor SP1 was predicted to bind to the mutation of IGF1 (g.64943050T>C). Overexpression of SP1 promotes the expression of IGF1 in the primary granulosa cells (GCs). The results of the CCK-8 assay and the expression of GC proliferation factors (CDK4, cyclin D1, and cyclin D2) demonstrated that SP1 promoted GC proliferation by regulating IGF1 expression. Our results suggested that the IGF1 g.64943050T>C was significantly associated with the kidding number of Yunshang black goats, and SP1 as a transcription factor of IGF1 binding to the mutation T>C regulated the expression of IGF1. Furthermore, SP1 promoted goat GC proliferation by regulating the expression of IGF1, which provides a new insight for the goat fertility trait.

Associations of Transcription Factor 21 Gene Polymorphisms with the Growth and Body Composition Traits in Broilers

Simple Summary

The functional SNPs discovered in this work will give helpful information on the crucial molecular markers that may be employed in breeding efforts to improve the heart development of broiler chickens.

Abstract

This study aims to identify molecular marker loci that could be applied in broiler breeding programs. In this study, we used public databases to locate the Transcription factor 21 (TCF21) gene that affected the economically important traits in broilers. Ten single nucleotide polymorphisms were detected in the TCF21 gene by monoclonal sequencing. The polymorphisms of these 10 SNPs in the TCF21 gene were significantly associated (p < 0.05) with multiple growth and body composition traits. Furthermore, the TT genotype of g.-911T>G was identified to significantly increase the heart weight trait without affecting the negative traits, such as abdominal fat and reproduction by multiple methods. Thus, it was speculated that the g.-911T>G identified in the TCF21 gene might be used in marker-assisted selection in the broiler breeding program.

Association of insulin-like growth factor 1 (IGF1) gene polymorphism with the reproductive performance of three dual-purpose chicken breeds

The study was designed to investigate the association of Insulin-like growth factor 1 (IGF1) gene polymorphism with the reproductive performance of FUNAAB-Alpha, Sasso, and Kuroiler dual-purpose chicken breeds. To achieve this, a total of 250 healthy hens were selected at 12 wk of age and were intensively managed in cages for 52 wk. Blood sample was taken from each chicken at the 34th week and genomic DNA was extracted using Qiagentm DNA extraction kit, PCR was used to amplify the DNA fragments, and the PCR products were electrophoresed. Amplicons obtained were digested with restriction enzyme hinf1, and were further electrophoresed on 1.5% agarose gel. Data obtained were analyzed using the General linear model of SAS (2002) version 9.0 to determine the effect of IGF1 gene polymorphism and the distribution of alleles within the breeds. Results show polymorphism of the IGF1 gene and the restriction analysis indicated two alleles; A 58% and C 42% with the identification of genotypes AA, AC, and CC, and genotypic frequency of 22%, 43%, and 35%, respectively. Significant associations were observed between the polymorphism of the IGF1 gene, age of the bird at first lay, and weight of the hen at first lay. Chickens with haplotype CC came earlier into lay compared to those with the other two haplotypes (AA and AC). Therefore, the study suggests that haplotype CC could be used as a genetic marker to select for an improved laying performance in chickens.

Polymorphism analysis and expression patterns of the IGF1 gene in the Shitou goose

Insulin-like growth factor 1 (IGF1) is one of the endocrine hormones that plays an important role in regulating growth and development of animals. In this study, polymorphism in the 5′UTR and 3′UTR coding region and of the IGF1 gene was detected by DNA sequencing technology, and the abundance of IGF1 mRNA in various tissues at three growth stages of the Shitou goose was determined by quantitative real-time polymerase chain reaction (qRT-PCR). Moreover, the differential expression of IGF1 in various tissues between the Shitou goose and Wuzong goose was revealed. Two single nucleotide polymorphisms (SNPs) were found in the exon3 region of IGF1 in the Shitou goose. IGF1 mRNA was extensively expressed in various tissues of Shitou geese with high abundant expression in the liver, breast muscle and leg muscle at three growth stages. IGF1 mRNA expression showed a trend of first increase and then decrease in the pituitary, liver, subcutaneous fat and abdominal fat tissues, but it decreased in the breast muscle and leg muscle of a Shitou goose with growing age. Expression of IGF1 in the liver, leg muscle and pituitary tissues of the Shitou goose was significantly higher than that of the Wuzong goose. This provides a foundation for further study of regulatory mechanisms of IGF1 in the growth and development of geese.

A functional variant in the promoter region of IGF1 gene is associated with chicken abdominal fat deposition

Insulin-like growth factor 1 (IGF1) plays an important role in the regulation of cell growth, proliferation, differentiation, and apoptosis. Previously several studies revealed that genotypes of chicken IGF1 c.-366A > C were significantly associated with abdominal fat weight and body weight in chickens. But the underlying mechanism is still unknown. To investigate the mechanism underlying the association, herein, we performed IGF1 gene mRNA expression profiling, a dual-luciferase reporter assay and electrophoretic mobility shift assay (EMSA). Quantitative real-time PCR results showed that IGF1 gene was widely expressed in 14 tissues. The mRNA expression levels of IGF1 gene in both abdominal fat and jejunum were significantly higher in fat broilers than in lean broilers. However, the opposite results were observed in the pancreas. The reporter gene assay showed that the promoter luciferase activity of allele A was significantly higher than that of allele C (P < 0.05). In addition, the luciferase activity of allele A promoted by the transcription factor AP1 and OCT1 was higher than that of allele C (P < 0.05). Electrophoretic mobility shift assay result showed that allele A binding to the transcription factor AP1 and OCT1 was stronger than that of allele C. All in all, our data indicated that the IGF1 gene c.-366A > C is a functional SNP responsible for chicken adipose deposition.

Associations between IGF1, IGFBP2 and TGFß3 Genes Polymorphisms and Growth Performance of Broiler Chicken Lines

Marker-assisted selection based on fast and accurate molecular analysis of individual genes is considered an acceptable tool in the speed-up of the genetic improvement of production performance in chickens. The objective of this study was to detect the single nucleotide polymorphisms (SNPs) in the IGF1, IGFBP2 and TGFß3 genes, and to investigate their associations with growth performance (body weight (BW) and average daily gain (ADG) at 14, 21, 28, 35 and 42 days of age) and carcass traits in broilers. Performance (carcass) data (weight before slaughter; weights of the trunk, giblets, abdominal fat, breast muscle and thigh muscle; slaughter value and slaughter percentage), as well as blood samples for DNA extraction and SNP analysis, were obtained from 97 chickens belonging to two different lines (Hubbard F15 and Cobb E) equally divided between the two sexes. The genotypes were detected using polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP) methods with specific primers and restrictase for each gene. The statistical analysis discovered significant associations (p < 0.05) between the TGFβ3 SNP and the following parameters: BW at 21, 28 and 35 days, trunk weight and slaughter value. Association analysis of BWs (at 21, 28 and 35 days) and SNPs was always significant for codominant, dominant and overdominant genetic models, showing a possible path for genomic selection in these chicken lines. Slaughter value was significant for codominant, recessive and overdominant patterns, whereas other carcass traits were not influenced by SNPs. Based on the results of this study, we suggested that the TGFβ3 gene could be used as a candidate gene marker for chicken growth traits in the Hubbard F15 and Cobb E population selection programs, whereas for carcass traits further investigation is needed.

Identification of selection signatures involved in performance traits in a paternal broiler line

BACKGROUND

Natural and artificial selection leads to changes in certain regions of the genome resulting in selection signatures that can reveal genes associated with the selected traits. Selection signatures may be identified using different methodologies, of which some are based on detecting contiguous sequences of homozygous identical-by-descent haplotypes, called runs of homozygosity (ROH), or estimating fixation index (FST) of genomic windows that indicates genetic differentiation. This study aimed to identify selection signatures in a paternal broiler TT line at generations 7th and 16th of selection and to investigate the genes annotated in these regions as well as the biological pathways involved. For such purpose, ROH and FST-based analysis were performed using whole genome sequence of twenty-eight chickens from two different generations.

RESULTS

ROH analysis identified homozygous regions of short and moderate size. Analysis of ROH patterns revealed regions commonly shared among animals and changes in ROH abundance and size between the two generations. Results also suggest that whole genome sequencing (WGS) outperforms SNPchip data avoiding overestimation of ROH size and underestimation of ROH number; however, sequencing costs can limited the number of animals analyzed. FST-based analysis revealed genetic differentiation in several genomic windows. Annotation of the consensus regions of ROH and FST windows revealed new and previously identified genes associated with traits of economic interest, such as APOB, IGF1, IGFBP2, POMC, PPARG, and ZNF423. Over-representation analysis of the genes resulted in biological terms of skeletal muscle, matrilin proteins, adipose tissue, hyperglycemia, diabetes, Salmonella infections and tyrosine.

CONCLUSIONS

Identification of ROH and FST-based analyses revealed selection signatures in TT line and genes that have important role in traits of economic interest. Changes in the genome of the chickens were observed between the 7th and 16th generations showing that ancient and recent selection in TT line may have acted over genomic regions affecting diseases and performance traits.

Insulinlike Growth Factor 1 Gene Variation in Vertebrates

IGF1-a small, single-chain, secreted peptide in mammals-is essential for normal somatic growth and is involved in a variety of other physiological and pathophysiological processes. IGF1 expression appears to be controlled by several different signaling mechanisms in mammals, with GH playing a key role by activating an inducible transcriptional pathway via the Jak2 protein kinase and the Stat5b transcription factor. Here, to understand aspects of Igf1 gene regulation over a substantially longer timeline than is discernible in mammals, Igf1 genes have been examined in 21 different nonmammalian vertebrates representing five different classes and ranging over ∼500 million years of evolutionary history. Parts of vertebrate Igf1 genes resemble components found in mammals. Conserved exons encoding the mature IGF1 protein are detected in all 21 species studied and are separated by a large intron, as seen in mammals; the single promoter contains putative regulatory elements that are similar to those functionally mapped in human IGF1 promoter 1. In contrast, GH-activated Stat5b-binding enhancers found in mammalian IGF1 loci are completely absent, there is no homolog of promoter 2 or exon 2 in any nonmammalian vertebrate, and different types of "extra" exons not present in mammals are found in birds, reptiles, and teleosts. These data collectively define properties of Igf1 genes and IGF1 proteins that were likely present in the earliest vertebrates and support the contention that common structural and regulatory features in Igf1 genes have a long evolutionary history.

Polymorphism of insulin-like growth factor 1 gene and its association with litter size in Small Tail Han sheep

The insulin-like growth factor 1 (IGF1) gene was studied as a candidate gene for high prolificacy in sheep. Polymorphisms of 5' regulatory region and all four exons of IGF1 gene were detected in Small Tail Han (n = 277), Hu (n = 58), Texel (n = 48) and Dorset (n = 46) sheep by PCR-RFLP and PCR-SSCP analysis. A microsatellite polymorphic site and a restriction fragment length polymorphism were shown in the 5' regulatory region of IGF1 gene. The ewes with genotype 123/123 bp had 0.81 (P < 0.05) or 1.03 (P < 0.01) lambs more than those with genotype 125/125 bp or 125/127 bp, the ewes with genotype 123/125 bp had 0.46 (P < 0.05) or 0.68 (P < 0.01) lambs more than those with genotype 125/125 bp or 125/127 bp. In addition, there were two mutations (C1511G and A1513G) in 5' regulatory region of IGF1 gene. The ewes with genotype BB or AB had 0.96 (P < 0.05) or 0.38 (P < 0.05) lambs more than those with genotype AA, but there were no significant differences between BB and AB genotypes (P > 0.05) in Small Tail Han sheep. These results preliminarily indicated that these polymorphisms of IGF1 gene could be used in molecular marker-assisted selection for sheep breeding programs.

Insulin-like growth factor-I gene polymorphism and its association with growth and slaughter characteristics in broiler chickens

Chicken insulin-like factor 1 gene (IGF1) is a biological candidate gene for the investigation of growth, body composition, and metabolic and skeletal traits, and is also a positional candidate gene for growth and fat deposition in chickens. Two broiler populations Ross 308 and Cobb 500 were used to study the relationship between IGF1 gene polymorphism and phenotypic traits. A single nucleotide polymorphism (SNP) was identified in 132 individuals using the PCR-RFLP technique. Genotypical frequencies were, for genotype AA: 0.83-0.86, and for AC: 0.14-0.17. Associations between IGF1 promotor polymorphism and liver weight (P≤0.05) and liver weight as a percentage of the weight of the poultry carcass with the giblets (P≤0.05), were found in the AC genotype in a comparison of broiler homozygous chickens AA in the Cobb 500 line. In these broilers, the breast muscle and leg muscle weight in the AC genotype were higher, and abdominal fat weight lower compared with AA genotype chickens, but these differences were not significant.

Polymorphisms in the IGF1 gene and their effect on growth traits in Mexican beef cattle

The IGF1 gene (insulin-like growth factor 1) is a candidate gene for marker-assisted selection strategies. A single nucleotide polymorphism in the promoter region (IGF1/SnaBI) has been reported to be associated with production traits in several cattle breeds. Here, we report its allelic frequencies in Charolais and Beefmaster breeds; we confirm its association with three growth traits: weaning weight, weaning weight adjusted to 210 days and preweaning weight gain in the Charolais breed. In addition, we designed a strategy to search these breeds for new polymorphisms in four coding regions of the gene. A C/A transversion was detected in intron 4, but it was not associated with the growth traits. A single nucleotide polymorphism (IGF1/SnaBI) is proposed as a selection marker for Mexican Charolais cattle; validation of its association with weaning weight, weaning weight adjusted to 210 days and preweaning weight gain, could complement the genetic evaluations of this breed through marker-assisted management strategies.

Perspectives on the endocrinology of poultry growth and metabolism

Birds have rapid pre- and post-hatching growth rates. The major hormones required to support normal growth are growth hormone (GH), triiodothyronine (T(3)) and insulin-like growth factor-I (IGF-I). Optimal growth requires a "set-point" concentration of both IGF-I and T(3) in the circulation. Pituitary GH plays a role in controlling the circulating concentrations of both IGF-I and T(3). Nutritional restriction (energy, protein) leads to reductions in circulating concentrations of both IGF-I and T(3) with increased GH secretion due removal of negative feedback. Similarly, there is un-coupling of the GH-IGF-I axis in stunting disease. A critical control point is at the level of the liver and GH receptor/signal transduction. The major hormones controlling metabolism include glucagon, insulin, adrenal glucocorticoid hormone, corticosterone and potentially somatostatin. Chickens and turkeys have higher circulating concentrations of glucose than those of livestock mammals. What are not known include the following: the biological basis for the high basal glucose concentrations; the quantitative fluxes of key metabolites in the fed and fasted state through growth and development; the relative contribution of different organs to gluconeogenesis; the relative importance of insulin and somatostatin in controlling lipolysis and the role of gastro-intestinal hormones in the control of metabolism.