Association of Single Nucleotide Polymorphisms of the Insulin Gene with Chicken Early Growth and Fat Deposition

Growth performance of Indonesian three-breed cross chicken associated with growth hormone and insulin-like growth factor 2 genes

Background and Aim

Poultry, such as chickens, is an important source of animal protein, producing eggs and meat. Local chickens are able to adapt to the hot weather and become more resistant to disease. However, it has relatively slow growth and low egg production. These problems can be overcome through holding selection and crossing. Local chicken productivity is slow and low based on chicken growth. There is a need to examine the factors that influence growth and productivity. Therefore, this study aimed to evaluate crossbreed chicken growth performance, including body weight (BW), BW gain, feed intake, and feed conversion.

Materials and Methods

DNA was extracted from 40 chickens with the growth hormone (GH) gene and 40 chickens with the insulin-like growth factor 2 (IGF2) gene, followed by a polymerase chain reaction. Genotyping was performed using restriction fragment length polymorphism analysis. In animal selection and phenotypic data collection, 80 chickens from Sentul, Kampung, and Kedu were used to produce the second-generation three-crossbreed chickens (F2) using the GH gene.

Results

Growth hormone is a very relevant gene in chicken performance traits. Growth hormone and IGF2 genes regulate chicken production. This study presents the second-generation growth features of three-crossbreed chickens derived from Sentul, Kampung, and Kedu, all of which are native to Indonesia (F2). A statistically significant (p = 0.05) improvement in BW, weight gain, feed intake, and feed conversion over a 12-week period was observed when the animals were allowed free access to regular feed. Analysis of variance results indicated a significant (p = 0.0001) interaction between the 12-week period and GH and IGF2 gene sensitivities of different chicken breeds.

Conclusion

Crossbreed chicken growth performance increased within 12 weeks. This study highlighted the need to improve the productivity and breeding of domestic crossbred chickens to contribute to the Indonesian conservation and genetic diversity program.

Genome-Wide Association Study on the Content of Nucleotide-Related Compounds in Korean Native Chicken Breast Meat

Meat flavor is an important factor that influences the palatability of chicken meat. Inosine 5'-monophosphate (IMP), inosine, and hypoxanthine are nucleic acids that serve as taste-active compounds, mainly enhancing flavor in muscle tissue. For this study, we performed a genome-wide association study (GWAS) using a mixed linear model to identify single-nucleotide polymorphisms (SNPs) that are significantly associated with changes in the contents of the nucleotide-related compounds of breast meat in the Korean native chicken (KNC) population. The genomic region on chicken chromosome 5 containing an SNP (rs316338889) was significantly (p < 0.05) associated with all three traits. The trait-related candidate genes located in this significant genomic region were investigated through performing a functional enrichment analysis and protein-protein interaction (PPI) database search. We found six candidate genes related to the function that possibly affected the content of nucleotide-related compounds in the muscle, namely, the TNNT3 and TNNT2 genes that regulate muscle contractions; the INS, IGF2, and DUSP8 genes associated with insulin sensitivity; and the C5NT1AL gene that is presumably related to the nucleotide metabolism process. This study is the first of its kind to find candidate genes associated with the content of all three types of nucleotide-related compounds in chicken meat using GWAS. The candidate genes identified in this study can be used for genomic selection to breed better-quality chickens in the future.

Polymorphisms of CRELD1 and DNAJC30 and their relationship with chicken carcass traits

Carcass traits play important roles in the broiler industry and single nucleotide polymorphism (SNP) can be efficient molecular markers for marker-assisted breeding of chicken carcass traits. Based on our previous RNA-seq data (accession number GSE58755), cysteine rich with epidermal growth factor like domains 1 (CRELD1) and DnaJ heat shock protein family member C30 (DNAJC30) are differentially expressed in breast muscle between white recessive rock chicken (WRR) and Xinghua chicken (XH). In this study, we further characterize the potential function and SNP mutation of CRELD1 and DNAJC30 in chicken for the first time. According to protein interaction network and enrichment analysis, CRELD1 and DNAJC30 may play some roles in chicken muscle development and fat deposition. In WRR and XH, the results of the relative tissue expression pattern demonstrated that CRELD1 and DNAJC30 are not only differentially expressed in breast muscle but also leg muscle and abdominal fat. Therefore, we identified 5 SNP sites of CRELD1 and 7 SNP sites of DNAJC30 and genotyped them in an F₂ chicken population. There are 4 sites of CRELD1 and 3 sites of DNAJC30 are associated with chicken carcass traits like breast muscle weight, body weight, dressed weight, leg weight percentage, eviscerated weight with giblet percentage, intermuscular adipose width, shank length, and girth. These results suggest that the SNP sites of CRELD1 and DNAJC30 can be potential molecular markers to improve the chicken carcass traits and lay the foundation for marker-assisted selection.

Growth hormone 1 and insulin 2 gene polymorphism in Egyptian chickens

The genetic polymorphism of two genes related to growth production in four chicken breeds (Dokki 4, Inshas, El-Salam and Mandarah) were studied. PCR-RFLP and single nucleotide polymorphism (SNPs) analysis were studied in the two genes namely GH1 and insulin 2. Blood samples were collected randomly from 84 chickens, DNA was extracted and genotypes for two genes were detected using PCR-RFLP analysis. The locus GH1 (467 bp) showed two genotypes (GG, AG) in four chicken breeds due to the presence of two Msp1 restriction sites (C^CGG) in intron1. The sequence analysis revealed two substitutions (C/T) in Dokki 4 and Inshas breeds, G/A substitution in Dokki 4 and Mandarah breeds and insertion of T nucleotide in four chicken breeds. In insulin 2 gene (371 bp), two genotypes (TT, TC) were recorded in four chicken breeds due to presence of one restriction site in intron1. The nucleotide substitutions (A/G) and (T/C) were observed in all Egyptian chicken breeds except Inshas breed and A/ T transversion was observed in all breeds. The sequences of detected SNPs were submitted to GenBank database with the accession numbers MG906782–MG906789 in GH1 gene and the accession numbers MG906790–MG906791 in insulin 2 gene. In conclusion, the presence of certain polymorphisms could increase the phenotypic variety and will be supportive in selection and breeding programs.

Insulin resistance and metabonomics analysis of fatty liver haemorrhagic syndrome in laying hens induced by a high-energy low-protein diet

Fatty liver haemorrhagic syndrome (FLHS) is a widespread metabolic disease in laying hens that causes a decrease in egg production and even death. Insulin resistance is a major contributor to the pathogenesis of nonalcoholic fatty liver disease. However, the relationship between FLHS and the insulin resistance mechanisms underlying FLHS is not well elucidated. Therefore, we established an FLHS model induced by feeding a high-energy low-protein diet. In the current study, we found that the fasting glucose and insulin concentrations were elevated in the FLHS group compared with the control group during the experimental period. The results of the oral glucose tolerance test (OGTT) and insulin sensitivity test (IST) showed a high level of insulin resistance in the FLHS model. InsR, 4EBP-1, Glut-1 and Glut-3 mRNA expression were decreased, and TOR, S6K1, and FOXO1 were elevated (P < 0.05). Metabolomic analysis with GC/MS identified 46 differentially expressed metabolites between these two groups, and of these, 14 kinds of metabolism molecules and 32 kinds of small metabolism molecules were decreased (P < 0.05). Further investigation showed that glucose, lipid and amino acid metabolism blocks in the progression of FLHS by GO functional and pathway analysis. Overall, these results suggest that insulin resistance participated in FLHS; comprehensively, metabolites participated in the dysregulated biological process.

Associations of SNPs located at candidate genes to bovine growth traits, prioritized with an interaction networks construction approach

Background

For most domestic animal species, including bovines, it is difficult to identify causative genetic variants involved in economically relevant traits. The candidate gene approach is efficient because it investigates genes that are expected to be associated with the expression of a trait and defines whether the genetic variation present in a population is associated with phenotypic diversity. A potential limitation of this approach is the identification of candidates. This study used a bioinformatics approach to identify candidate genes via a search guided by a functional interaction network.

Results

A functional interaction network tool, BosNet, was constructed for Bos taurus. Predictions for candidate genes were performed using the guilt-by-association principle in BosNet. Association analyses identified five novel markers within BosNet-prioritized genes that had significant effects on different growth traits in Charolais and Brahman cattle.

Conclusions

BosNet is an excellent tool for the identification of single nucleotide polymorphisms that are potentially associated with complex traits.

Overview of Genomic Insights into Chicken Growth Traits Based on Genome-Wide Association Study and microRNA Regulation

Over the two past decades, a significant number of studies have observed animal growth traits to examine animal genetic mechanisms due to their ease of measurement and high heritability. Chicken which has a significant impact on fundamental biology is a major source of protein worldwide, making it an ideal model for examining animal growth trait development. The genetic mechanisms of chicken growth traits have been studied using quantitative trait loci mapping through genome-scan and candidate gene approaches, genome-wide association studies (GWAS), comparative genomic strategies, microRNA (miRNA) regulation of growth development analysis, and epigenomic analysis. This review focuses on chicken GWAS and miRNA regulation of growth traits. Several recently published GWAS reports showed that most genome-wide significant single nucleotide polymorphisms are located on chromosomes 1 and 4 in chickens. Chicken growth, particularly skeletal muscle growth and development, is greatly regulated by miRNA. Using dwarf and normal chickens, let-7b was found to be involved in determining chicken dwarf phenotypes by regulating growth hormone receptor gene expression.

Growth hormone and growth?

Pituitary GH is obligatory for normal growth in mammals, but the importance of pituitary GH in avian growth is less certain. In birds, pituitary GH is biologically active and has growth promoting actions in the tibia-test bioassay. Its importance in normal growth is indicated by the growth suppression following the surgical removal of the pituitary gland or after the immunoneutralization of endogenous pituitary GH. The partial restoration of growth in some studies with GH-treated hypophysectomized birds also suggests GH dependency in avian growth, as does the dwarfism that occurs in some strains with GHR dysfunctions. Circulating GH concentrations are also correlated with body weight gain, being high in young, rapidly growing birds and low in slower growing older birds. Nevertheless, despite these observations, there is an extensive literature that concludes pituitary GH is not important in avian growth. This is based on numerous studies with hypophysectomized and intact birds that show only slight, transitory or absent growth responses to exogenous GH-treatment. Moreover, while circulating GH levels correlate with weight gain in young birds, this may merely reflect changes in the control of pituitary GH secretion during aging, as numerous studies involving experimental alterations in growth rate fail to show positive correlations between plasma GH concentrations and the alterations in growth rate. Furthermore, growth is known to occur in the absence of pituitary GH, as most embryonic development occurs prior to the ontogenetic appearance of pituitary somatotrophs and the appearance of GH in embryonic circulation. Early embryonic growth is also independent of the endocrine actions of pituitary GH, since removal of the presumptive pituitary gland does not impair early growth. Embryonic growth does, however, occur in the presence of extrapituitary GH, which is produced by most tissues and has autocrine or paracrine roles that locally promote growth and development. The role of GH in avian growth is therefore still unclear.

Effect of polymorphisms at the ghrelin gene locus on carcass, microstructure and physicochemical properties of longissimus lumborum muscle of Polish Landrace pigs

The influence of RFLP-BsrI polymorphisms at the ghrelin gene locus on carcass, meat quality parameters and muscle fiber characteristics of longissimus lumborum was studied in 168 barrows of the Polish Landrace breed. Analysis revealed a high frequency of the 1 allele (0.60) with the frequencies of the 11, 12 and 22 genotypes being 0.45, 0.30 and 0.25, respectively. The most favorable parameters of meat traits were characteristic of pigs with the 22 genotype, together with a higher carcass and loin weight and lower thermal loss compared to 12 heterozygotes. The highest fat content was found in pigs with the 11 genotype, which had the highest abdominal fat weight and mean backfat thickness. Meanwhile, the 12 heterozygotes were characterized by the largest loin eye areas, highest lightness (L*) and yellowness (b*) values, and lowest redness (a*) values, as well as the greatest hardness and chewiness and largest diameter of type IIB muscle fibers compared to the other genotypes.

A novel single-nucleotide polymorphism of the visfatin gene and its associations with performance traits in the chicken

Visfatin is a peptide that is predominantly expressed in visceral adipose tissue and is hypothesized to be related to obesity and insulin resistance. In this study, a novel silent single-nucleotide polymorphism (SNP) was found in exon 7 of the chicken visfatin gene (also known as PBEF1) by single-stranded conformation polymorphism (SSCP) and DNA sequencing. In total, 836 chickens forming an F2 resource population of Gushi chicken crossed with Anka broiler were genotyped by XbaI forced RFLP, and the associations of this polymorphism with chicken growth, carcass characteristics, and meat quality were analyzed. Significant associations were found between the polymorphism and 4-week body weight (BW4), 6-week body weight (BW6), 4-week body slanting length (BSL4), fat bandwidth (FBW), breast muscle water loss rate (BWLR) and breast muscle fiber density (BFD) (P < 0.05), as well as 4-week breastbone length (BBL4) (P < 0.01). These observations suggested that the polymorphism in exon7 of the visfatin gene had significant effects on the early growth traits of chicken.

Association of resistance to avian coccidiosis with single nucleotide polymorphisms in the zyxin gene

Our previous genetic studies demonstrated that resistance to avian coccidiosis is linked with microsatellite markers LEI0071 and LEI0101 on chromosome 1. In this study, the associations between parameters of resistance to coccidiosis and single nucleotide polymorphisms (SNP) in 3 candidate genes located between LEI0071 and LEI0101 [zyxin, CD4, and tumor necrosis factor receptor super family 1A (TNFRSF1A)] were determined. The SNP were genotyped in 24 F(1) generation and 290 F(2) generation animals. No SNP were identified in the TNFRSF1A gene, whereas 10 were located in the zyxin gene and 4 in the CD4 gene. At various times following experimental infection of the F(2) generation with Eimeria maxima, BW, fecal oocyst shedding, and plasma levels of carotenoid, nitrite plus nitrate (NO(2)(-) + NO(3)(-)), and interferon-gamma (IFN-gamma) were measured as parameters of resistance. Single marker and haplotype-based tests were applied to determine the associations between the 14 SNP and the parameters of coccidiosis resistance. None of the CD4 SNP were correlated with disease resistance. However, by single marker association, several of the zyxin SNP were significantly associated with carotenoid or NO(2)(-) + NO(3)(-) concentrations. These were the SNP at nucleotide 149 associated with carotenoid at d 3 postinfection (PI), nucleotide 187 with carotenoid at d 6 and 9 PI, and nucleotide 159 with carotenoid between d 3 and 9 PI. In addition, the zyxin SNP at nucleotide 191 was significantly associated with increased levels of NO(2)(-) + NO(3)(-) at d 3 PI. By haplotype association, the zyxin SNP also were found to be highly associated with NO(2)(-) + NO(3)(-) at d 3 PI and increased IFN-gamma at d 6 PI. These results suggest that zyxin is a candidate gene potentially associated with increased resistance to experimental avian coccidiosis.

Polymorphism of Growth-Correlated Genes Associated with Fatness and Muscle Fiber Traits in Chickens

Thirty single nucleotide polymorphisms (SNP) and one 6-bp insertion-deletion (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 6-bp indel of the growth hormone secretagogue receptor (GHSR) gene was significantly linked with the fat traits. The C51978309T SNP of the 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 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 6-bp 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 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.