Identification of Avai polymorphisms in the third intron of GH gene and their associations with abdominal fat in chickens

Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds

BACKGROUND

The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by, and formed due to, past and current admixture events. Adaptation to diverse environments, including acclimation to harsh climatic conditions, has also left selection footprints in breed genomes.

RESULTS

Using the Chicken 50K_CobbCons SNP chip, we genotyped four divergently selected breeds: two aboriginal, cold tolerant Ushanka and Orloff Mille Fleur, one egg-type Russian White subjected to artificial selection for cold tolerance, and one meat-type White Cornish. Signals of selective sweeps were determined in the studied breeds using three methods: (1) assessment of runs of homozygosity islands, (2) F_ST based population differential analysis, and (3) haplotype differentiation analysis. Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds. In these regions, we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies. Amongst them, SOX5, ME3, ZNF536, WWP1, RIPK2, OSGIN2, DECR1, TPO, PPARGC1A, BDNF, MSTN, and beta-keratin genes can be especially mentioned as candidates for cold adaptation. Epigenetic factors may be involved in regulating some of these important genes (e.g., TPO and BDNF).

CONCLUSION

Based on a genome-wide scan, our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds. These include genes representing the sine qua non for adaptation to harsh environments. Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals, and this warrants further investigation.

Molecular characterization and analysis of the association of growth hormone 1 gene with growth traits in Chinese indigenous yak (Bos grunniens)

This study aimed to investigate the effects of polymorphisms in growth hormone 1 (GH1) gene on the growth traits in Chinese indigenous yak. Using the polymerase chain reaction-restriction fragment length polymorphism (PCR-PFLP) approach, one novel single-nucleotide polymorphism (SNP), termed as g.1721G>A, was identified in the exon 4 of GH1 gene in 423 individuals of yak population. Based on the chi-square (χ²) test, the frequencies of g.1721G>A alleles agreed with Hardy-Weinberg equilibrium (HWE) (P < 0.05). A significant association was observed between this SNP and several growth traits (P < 0.01 or P < 0.05), in which the genotype GG exhibited the best values. The present study suggested that the identified SNP was a useful genetic marker for the improvement of growth traits in Chinese indigenous yak.

Expression Signatures of microRNAs and Their Targeted Pathways in the Adipose Tissue of Chickens during the Transition from Embryonic to Post-Hatch Development

As the chick transitions from embryonic to post-hatching life, its metabolism must quickly undergo a dramatic switch in its major energy source. The chick embryo derives most of its energy from the yolk, a lipid-rich/carbohydrate-poor source. Upon hatching, the chick’s metabolism must then be able to utilize a lipid-poor/carbohydrate-rich source (feed) as its main form of energy. We recently found that a number of hepatically-expressed microRNAs (miRNAs) help facilitate this shift in metabolic processes in the chick liver, the main site of lipogenesis. While adipose tissue was initially thought to mainly serve as a lipid storage site, it is now known to carry many metabolic, endocrine, and immunological functions. Therefore, it would be expected that adipose tissue is also an important factor in the metabolic switch. To that end, we used next generation sequencing (NGS) and real-time quantitative PCR (RT-qPCR) to generate miRNome and transcriptome signatures of the adipose tissue during the transition from late embryonic to early post-hatch development. As adipose tissue is well known to produce inflammatory and other immune factors, we used SPF white leghorns to generate the initial miRNome and transcriptome signatures to minimize complications from external factors (e.g., pathogenic infections) and ensure the identification of bona fide switch-associated miRNAs and transcripts. We then examined their expression signatures in the adipose tissue of broilers (Ross 708). Using E18 embryos as representative of pre-switching metabolism and D3 chicks as a representative of post-switching metabolism, we identified a group of miRNAs which work concordantly to regulate a diverse but interconnected group of developmental, immune and metabolic processes in the adipose tissue during the metabolic switch. Network mapping suggests that during the first days post-hatch, despite the consumption of feed, the chick is still heavily reliant upon adipose tissue lipid stores for energy production, and is not yet efficiently using their new energy source for de novo lipid storage. A number of core master regulatory pathways including, circadian rhythm transcriptional regulation and growth hormone (GH) signaling, likely work in concert with miRNAs to maintain an essential balance between adipogenic, lipolytic, developmental, and immunological processes in the adipose tissue during the metabolic switch.

Effects of dietary supplementation with Taiwanese tea byproducts and probiotics on growth performance, lipid metabolism, and the immune response in red feather native chickens

Objective

This study compared the catechin composition of different tea byproducts and investigated the effects of dietary supplementation with green tea byproducts on the accumulation of abdominal fat, the modulation of lipid metabolism, and the inflammatory response in red feather native chickens.

Methods

Bioactive compounds were detected, and in vitro anti-obesity capacity analyzed via 3T3-L1 preadipocytes. In animal experiments, 320 one-day-old red feather native chickens were divided into 4 treatment groups: control, basal diet supplemented with 0.5% Jinxuan byproduct (JBP), basal diet supplemented with 1% JBP, or basal diet supplemented with 5×10⁶ colony-forming unit (CFU)/kg Bacillus amyloliquefaciens+5×10⁶ CFU/kg Saccharomyces cerevisiae (BA+SC). Growth performance, serum characteristics, carcass characteristics, and the mRNA expression of selected genes were measured.

Results

This study compared several cultivars of tea, but Jinxuan showed the highest levels of the anti-obesity compound epigallocatechin gallate. 3T3-L1 preadipocytes treated with Jinxuan extract significantly reduced lipid accumulation. There were no significant differences in growth performance, serum characteristics, or carcass characteristics among the groups. However, in the 0.5% JBP group, mRNA expression of fatty acid synthase (FAS) and acetyl-CoA carboxylase (ACC) were significantly decreased. In the 1% JBP group, FAS, ACC and peroxisome proliferator-activated receptor γ levels were significantly decreased. Moreover, inflammation-related mRNA expression levels were decreased by the addition of JBP.

Conclusion

JBP contained abundant catechins and related bioactive compounds, which reduced lipid accumulation in 3T3-L1 preadipocytes, however there was no significant reduction in abdominal fat. This may be due to a lack of active anti-obesity compounds or because the major changes in fat metabolism were not in the abdomen. Nonetheless, lipogenesis-related and inflammation-related mRNA expression were reduced in the 1% JBP group. In addition, dietary supplementation with tea byproducts could reduce the massive amount of byproducts created during tea production and modulate lipid metabolism and the inflammatory response in chickens.

Polymorphisms of the growth hormone gene and their association with growth traits and sex in Sarcocheilichthys sinensis

The growth hormone gene (gh) of Sarcocheilichthys sinensis was cloned and characterized in this study. The cDNA length of gh was 973 bp, containing a 5'-UTR of 15 bp, a 3'-UTR of 325 bp and an open reading frame of 633 bp. The genomic DNA of gh was 2135 bp in length containing five exons and four introns. The precursor peptide of gh contained 210 amino acids (aa), including a signal peptide of 22 aa (Met¹-Ala²²) and a mature region of 188 aa (Ser²³-Leu²¹⁰). The similarity and identity ranges of the gh precursor peptide with those of other cyprinids were 88.6%-99.0% and 84.8%-98.6%, respectively. The gh of S. sinensis expressed at the highest level in the pituitary, and its expression was also detected in muscle and brain. Six polymorphic sites were detected in intron 1 (g.51InDel, g.64InDel and g.242InDel), intron 2 (g.864T>C), intron 3 (g.1017InDel) and intron 4 (g.1541A>G). Among these sites, g.242InDel was significantly associated with condition factor, g.1541A>G was associated with all six growth traits, while g.864T>C was associated with sex. The data obtained herein provide useful information for further studies on the regulation mechanisms of growth and sexual growth differences in S. sinensis.

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.

Expression of Potential Regulatory Genes in Abdominal Adipose Tissue of Broiler Chickens during Early Development

The identities of genes that underlie population variation in adipose tissue development in farm animals are poorly understood. Previous studies in our laboratory have suggested that increased fat tissue involves the expression modulation of an array of genes in broiler chickens. Of special interest are eight genes, FGFR3, EPHB2, IGFBP2, GREM1, TNC, COL3A1, ACBD7, and SCD. To understand their expression regulation and response to dietary manipulation, we investigated their mRNA levels after dietary manipulation during early development. Chickens were fed either a recommended standard or a high caloric diet from hatch to eight weeks of age (WOA). The high caloric diet markedly affected bodyweight of the broiler birds. mRNA levels of the eight genes in the abdominal adipose tissue were assayed at 2, 4, 6, and 8 WOA using RT-qPCR. Results indicate that (1) FGFR3 mRNA level was affected significantly by diet, age, and diet:age interaction; (2) COL3A mRNA level was repressed by high caloric diet; (3) mRNA levels of EPHB2, ACBD7, and SCD were affected by age; (4) mRNA level of TNC was modulated by age:diet interaction; (5) changes in GREM1 and IGFBP2 mRNA levels were not statistically different.

Association of polymorphisms of exon 2 of the growth hormone gene with production performance in Huoyan goose

Primers based on the cDNA sequence of the goose growth hormone (GH) gene in GenBank were designed to amplify exon 2 of the GH gene in Huoyan goose. A total of 552 individuals were brooded in one batch and raised in Liaoning and Jiangsu Provinces, China. Single nucleotide polymorphisms (SNPs) of exon 2 in the GH gene were detected by the polymerase chain reaction (single strand conformation polymorphism method). Homozygotes were subsequently cloned, sequenced and analyzed. Two SNP mutations were detected, and 10 genotypes (referred to as AA, BB, CC, DD, AB, AC, AD, BC, BD and CD) were obtained. Allele D was predominant, and the frequencies of the 10 genotypes fit the Hardy-Weinberg equilibrium in the male, female and whole populations according to the chi-square test. Based on SNP types, the 10 genotypes were combined into three main genotypes. Multiple comparisons were carried out between different genotypes and production traits when the geese were 10 weeks old. Some indices of production performance were significantly (p < 0.05) associated with the genotype. Particularly, geese with genotype AB or BB were highly productive. Thus, these genotypes may serve as selection markers for production traits in Huoyan geese.

Green tea polyphenols alleviate obesity in broiler chickens through the regulation of lipid-metabolism-related genes and transcription factor expression

The current study investigated the effects of green tea polyphenols (GTPs) on lipid metabolism and its mechanisms using broiler chickens (Gallus gallus domesticus). A total of 36 male chickens (35 days old) had been subjected to an oral administration of GTPs at a dosage of 0, 50 (low), and 100 (high) mg/kg of body weight for 20 days. Our results showed that GTPs significantly decreased the abdominal and subcutaneous fat masses of broilers and reduced the serum triglyceride, total cholesterol, and low-density lipoprotein cholesterol levels compared to those of the control. Furthermore, the expression levels for lipid anabolism genes were significantly downregulated, while the expression levels of fat transportation and catabolism-related genes, carnitine palmitoyl transferase I (CPT-I), acyl-CoA oxidase 1 (ACOX1), and peroxisome proliferator-activated receptor-α (PPARα) in liver, adipose triglyceride lipase (ATGL) in abdominal fat, and lipoprotein lipase (LPL) in skeletal muscles, were notably upregulated. Our data have revealed that GTPs alleviate obesity and serum lipid levels in broiler chickens by suppressing fatty acid synthesis and stimulating lipolysis.

Tissue-specific expression of the chicken adipose differentiation-related protein (ADP) gene

Adipose differentiation-related protein gene (ADP) plays an important role in controlling lipid accumulation in mammals. It may also affect lipid deposition in birds. However, the molecular mechanism of its actions in birds remains unknown. In the present study, the coding sequence of ADP cDNA for Chinese native breed Sichuan Mountainous Black-bone chicken (MB) was first cloned from abdominal fat using reverse transcription-PCR (RT-PCR). This putative MB ADP cDNA (1,881 bp) encodes an open reading frame of 438 amino acids (AA) and shares high AA sequence identity with that of red jungle fowl (99%), duck (92%), house mouse (70%), human (70%), chimpanzee (70%), pig (70%), domestic cow (69%) and domestic sheep (68%). Further analysis using bioinformatics shows the deduced MB ADP protein has the typical characters of PAT (Perilipin, Adipophilin and Tip47) family. Quantitative real-time PCR (qRT-PCR) analysis revealed that ADP expresses in chicken leg muscle, whole brain, heart, liver, pectoralis muscle, abdominal fat and subcutaneous fat. Ontogenetic expression studies shows ADP expression levels in abdominal fat, subcutaneous fat and pectoralis muscle were prior to that in leg muscles at posthatch day (P) 84. But, its levels in abdominal fat and subcutaneous fat were less than that in leg muscles at P28, 42, 56 and 70, respectively. The ADP expression levels in subcutaneous fat and abdominal fat were stable from P28 to P70 and both were less than their counterparts at P84. However, it changed greatly in pectoralis muscle, liver, brain, heart and leg muscle at all points. Patterns of ADP expression suggest that ADP plays an important role in fat development, but further study is needed to reconfirm its function in a large population and in other breeds with different genetic backgrounds.