Expression of variant transcripts of the potassium channel tetramerization domain-containing 15 (KCTD15) gene and their association with fatness traits in chickens

Identification of Key Candidate Genes in Runs of Homozygosity of the Genome of Two Chicken Breeds, Associated with Cold Adaptation

Simple Summary

The search for genomic regions related to adaptive abilities preserved in the chicken gene pool of two breeds, which have not been under intensive selection pressure, is of great importance for breeding in the future. This study aimed to identify key candidate genes associated with the adaptation of chickens to cold environments (using the example of the Russian White breed) by using molecular genetic methods. A total of 12 key genes on breed-specific ROH (runs of homozygosity) islands were identified, which may be potential candidate genes associated with the high level of adaptability of chickens to cold environments in the early postnatal period. These genes were associated with lipid metabolism, maintaining body temperature in cold environments, non-shivering thermogenesis and muscle development and are perspectives for further research.

Abstract

It is well known that the chicken gene pools have high adaptive abilities, including adaptation to cold environments. This research aimed to study the genomic distribution of runs of homozygosity (ROH) in a population of Russian White (RW) chickens as a result of selection for adaptation to cold environments in the early postnatal period, to perform a structural annotation of the discovered breed-specific regions of the genome (compared to chickens of the Amroks breed) and to suggest key candidate genes associated with the adaptation of RW chickens to cold environments. Genotyping of individual samples was performed using Illumina Chicken 60K SNP BeadChip^® chips. The search for homozygous regions by individual chromosomes was carried out using the PLINK 1.9 program and the detectRuns R package. Twelve key genes on breed-specific ROH islands were identified. They may be considered as potential candidate genes associated with the high adaptive ability of chickens in cold environments in the early postnatal period. Genes associated with lipid metabolism (SOCS3, NDUFA4, TXNRD2, IGFBP 1, IGFBP 3), maintaining body temperature in cold environments (ADIPOQ, GCGR, TRPM2), non-shivering thermogenesis (RYR2, CAMK2G, STK25) and muscle development (METTL21C) are perspectives for further research. This study contributes to our understanding of the mechanisms of adaptation to cold environments in chickens and provides a molecular basis for selection work.

Association of KCTD15 gene with fat deposition in pigs

KCTD15 is associated with body mass index and fat deposition in humans, mice and chickens. However, the function of KCTD15 in pig fat deposition remains unclear. In this study, we cloned and analysed the cDNA sequence of porcine KCTD15. The full length of the mRNA sequence of KCTD15 is 4,091 bp, encoding 283 amino acids. The protein is hydrophilic, it has a relative molecular mass of about 31.9 kDa and an isoelectric point of 7.09 with no signal peptide sequence or transmembrane structure. Expression analysis showed that KCTD15 expression level was significantly higher in the tissues of Large White pigs (LW) than in those of Tibetan pigs (TP) and Diannan Small-ear pigs (DN) at 6 months of age, whereas its expression level in embryonic tissues of LW at 60 days was lower than that in tissues of TP and Wujin pigs (WJ). In pig primary adipocytes, the expression level of KCTD15 is high in the early stage of differentiation and gradually decreases in later stages. Additionally, the single-nucleotide polymorphism (SNP) site T-2030C (T/C mutation, located 2,030 bp upstream of the start codon) showed a dominant allele T with high promoter activity in the LW population and a dominant allele C in the TP and WJ populations. Our results indicate that KCTD15 is involved in pig fat deposition and that T-2030C is an important regulatory site for transcriptional activity, affecting fat deposition.

miR-381 Targets KCTD15 to Regulate Bovine Preadipocyte Differentiation In Vitro

MicroRNAs (miRNAs) are small, single-stranded, noncoding RNAs ~21 to ~23 nucleotides in length and have become a popular research topic in recent years due to their regulation of gene expression and many physiological processes, including fat metabolism; however, the precise functional mechanisms underlying their regulation of fat metabolism are not fully understood. Here, we identified miR-381, which specifically targets the 3' untranslated region (3' UTR) of potassium channel tetramerization-domain-containing 15 (KCTD15) , and verified the mechanism regulating its expression and participation in adipogenesis. We used a dual luciferase-reporter assay and transfection-mediated miR-381 overexpression and inhibition in Yanbian yellow cattle preadipocytes to investigate the role of miR-381 in adipogenesis. The results showed that miR-381 directly targets the 3' UTR of KCTD15 and downregulates its expression. Additionally, miR-381 overexpression using an miRNA mimic promoted triglyceride accumulation and upregulated adipogenic peroxisome proliferator-activated receptor γ (PPARγ) and CCAAT enhancer-binding protein α (C/EBPα) at both the protein and mRNA levels, whereas miR-381 inhibition produced the opposite effect. These results indicated that miR-381 regulates the differentiation of Yanbian yellow cattle preadipocytes by inhibiting KCTD15 expression, thereby highlighting the importance of miRNA-mediated regulation of adipogenesis. Furthermore, our findings suggested that miR-381 and its target gene(s) might represent new targets for investigating intramuscular fat deposits in cattle and treating human obesity.

Evaluation of Waste Mushroom Compost as a Feed Supplement and Its Effects on the Fat Metabolism and Antioxidant Capacity of Broilers

Simple Summary

Mushroom waste compost is the main byproduct when cultivating mushrooms. Due to its high mycelium content, mushroom waste compost may improve animal health by increasing antioxidant capacity. Furthermore, increasing evidence suggests that supplementing animal diets with fiber could improve body composition and health. The results showed that supplementation with mushroom waste compost accelerates adipolysis and enhances the antioxidant capacity of broilers. Among all treatment groups, broilers given dietary supplementation with 0.5% mushroom waste compost showed improved feed conversion rate and the highest adipose metabolism.

Abstract

Pennisetum purpureum Schum No. 2 waste mushroom compost (PWMC) is the main byproduct when cultivating Pleurotus eryngii. Due to the high mycelium levels in PWMC, it may have potential as a feed supplement for broilers. This study investigated the effects of PWMC supplementation on antioxidant capacity and adipose metabolism in broilers. In the study, 240 broilers were randomly allocated to one of four treatment groups: basal diet (control), 0.5%, 1%, or 2% PWMC supplementation. Each treatment group had 60 broilers, divided into three replicates. The results showed that supplementation with 0.5% PWMC decreased the feed conversion rate (FCR) from 1.36 to 1.28, compared to the control. Supplementation with 0.5% or 2% PWMC decreased glucose and triglyceride levels, compared to the control (p < 0.0001), the concentrations of adiponectin and oxytocin increased from 5948 to 5709, 11820, and 7938 ng/ mL; and 259 to 447, 873, and 963 pg/ mL, respectively. Toll-like receptor 4 was slightly increased in the 0.5% and 1% PWMC groups. Both interferon-γ (IFN-γ) and interleukin-1ß (IL-1ß) were significantly decreased, by about three to five times for IFN-γ (p < 0.0001) and 1.1 to 1.6 times for IL-1ß (p = 0.0002). All antioxidant-related mRNA, including nuclear factor erythroid 2–related factor 2 (Nrf-2) and superoxidase dismutase-1 (SOD-1), increased significantly following PWMC supplementation. Both claudin-1 and zonula occludens 1 increased, especially in the 2% PWMC group. Excitatory amino acid transporter 3 (EAAT3) significantly increased by about 5, 12, and 11 times in the 0.5%, 1%, and 2% PWMC groups. All adipolysis-related mRNA were induced in the PWMC treatment groups, further enhancing adipolysis. Overall, 0.5% PWMC supplementation was recommended due to its improving FCR, similar antioxidant capacity, and upregulated adipolysis.

Genomic Insights Into the Multiple Factors Controlling Abdominal Fat Deposition in a Chicken Model

Genetic selection for an increased growth rate in meat-type chickens has been accompanied by excessive fat accumulation particularly in abdominal cavity. These progressed to indirect and often unhealthy effects on meat quality properties and increased feed cost. Advances in genomics technology over recent years have led to the surprising discoveries that the genome is more complex than previously thought. Studies have identified multiple-genetic factors associated with abdominal fat deposition. Meanwhile, the obesity epidemic has focused attention on adipose tissue and the development of adipocytes. The aim of this review is to summarize the current understanding of genetic/epigenetic factors associated with abdominal fat deposition, or as it relates to the proliferation and differentiation of preadipocytes in chicken. The results discussed here have been identified by different genomic approaches, such as QTL-based studies, the candidate gene approach, epistatic interaction, copy number variation, single-nucleotide polymorphism screening, selection signature analysis, genome-wide association studies, RNA sequencing, and bisulfite sequencing. The studies mentioned in this review have described multiple-genetic factors involved in an abdominal fat deposition. Therefore, it is inevitable to further study the multiple-genetic factors in-depth to develop novel molecular markers or potential targets, which will provide promising applications for reducing abdominal fat deposition in meat-type chicken.

The Association between Obesity-Risk Genes and Gestational Weight Gain Is Modified by Dietary Intake in African American Women

Obesity-risk genes have been associated with dietary intake, appetite regulation, and gestational weight gain (GWG). The purpose of this study was to examine whether dietary intake including total energy intake and macronutrients modify or mediate the association between obesity-risk genes and GWG. An observational study was conducted with 85 African American pregnant women. Sociodemographic, medical, and lifestyle factors and dietary recalls were collected during pregnancy. Seven obesity-risk genetic variants were genotyped. Regression analyses with bootstrapping methods were used to examine the moderation and mediation effects of dietary intake. The mean GWG was 14.2 kg, and 55.3% of the women gained above the Institute of Medicine GWG guidelines. A nominally significant association was found between rs17782313 (close to MC4R) and percentage of energy intake from fat (P=0.043). A variant downstream of KCTD15 (rs11084753) was nominally significantly related to GWG (P=0.023). There was a significant interaction between the KCTD15 polymorphism and dietary fat intake (P=0.048). Women with the AG genotype gained more weight during pregnancy with more dietary fat consumption. In conclusion, our results indicate that dietary macronutrients, especially fat intake, may modify the effect of the KCTD15 gene on GWG. Improved knowledge of gene-diet interactions can facilitate the development of personalized interventions.

Generation and characterization of Kctd15 mutations in zebrafish

Potassium channel tetramerization domain containing 15 (Kctd15) was previously found to have a role in early neural crest (NC) patterning, specifically delimiting the region where NC markers are expressed via repression of transcription factor AP-2a and inhibition of Wnt signaling. We used transcription activator-like effector nucleases (TALENs) to generate null mutations in zebrafish kctd15a and kctd15b paralogs to study the in vivo role of Kctd15. We found that while deletions producing frame-shift mutations in each paralog showed no apparent phenotype, kctd15a/b double mutant zebrafish are smaller in size and show several phenotypes including some affecting the NC, such as expansion of the early NC domain, increased pigmentation, and craniofacial defects. Both melanophore and xanthophore pigment cell numbers and early markers are up-regulated in the double mutants. While we find no embryonic craniofacial defects, adult mutants have a deformed maxillary segment and missing barbels. By confocal imaging of mutant larval brains we found that the torus lateralis (TLa), a region implicated in gustatory networks in other fish, is absent. Ablation of this brain tissue in wild type larvae mimics some aspects of the mutant growth phenotype. Thus kctd15 mutants show deficits in the development of both neural crest derivatives, and specific regions within the central nervous system, leading to a strong reduction in normal growth rates.

Influence of TFAP2B and KCTD15 genetic variability on personality dimensions in anorexia and bulimia nervosa

INTRODUCTION

TFAP2B and KCTD15 are obesity-related genes that interact to regulate feeding behavior. We hypothesize that variability in these loci, isolated or in combination, could also be related to the risk of eating disorders (ED) and/or associated psychological traits.

METHODS

We screened 425 participants (169 ED patients, 75 obese subjects, and 181 controls) for 10 clinically relevant and tag single-nucleotide polymorphisms (SNPs) in KCTD15 and TFAP2B by the Sequenom MassARRAY platform and direct sequencing. Psychometric evaluation was performed with EDI-2 and SCL-90R inventories.

RESULTS

The KCTD15 rs287103 T variant allele was associated with increased risk of bulimia nervosa (BN) (OR = 4.34 [1.47-29.52]; p = .003) and with scores of psychopathological scales of these patients. Haplotype *6 in KCTD15 was more frequent in controls (OR = 0.40 [0.20-0.80], p = .009 for anorexia nervosa), while haplotype *4 in TFAP2B affected all three scales of the SCL-90R inventory in BN patients (p ≤ .01). Epistasis analyses revealed relevant interactions with body mass index of BN patients (p < .001). Genetic profiles in obese patients did not significantly differ from those found in ED patients.

CONCLUSIONS

This is the first study that evaluates the combined role of TFAP2B and KCTD15 genes in ED. Our preliminary findings suggest that the interaction of genetic variability in these loci could influence the risk for ED and/or anthropometric and psychological parameters.

A Genome-Wide mRNA Screen and Functional Analysis Reveal FOXO3 as a Candidate Gene for Chicken Growth

Chicken growth performance provides direct economic benefits to the poultry industry. However, the underlying genetic mechanisms are unclear. The objective of this study was to identify candidate genes associated with chicken growth and investigate their potential mechanisms. We used RNA-Seq to study the breast muscle transcriptome in high and low tails of Recessive White Rock (WRR_h, WRR_l) and Xinghua chickens (XH_h, XH_l). A total of 60, 23, 153 and 359 differentially expressed genes were detected in WRR_h vs. WRR_l, XH_h vs. XH_l, WRR_h vs. XH_h and WRR_l vs. XH_l, respectively. GO, KEGG pathway and gene network analyses showed that CEBPB, FBXO32, FOXO3 and MYOD1 played key roles in growth. The functions of FBXO32 and FOXO3 were validated. FBXO32 was predominantly expressed in leg muscle, heart and breast muscle. After decreased FBXO32 expression, growth-related genes such as PDK4, IGF2R and IGF2BP3 were significantly down-regulated (P < 0.05). FBXO32 was significantly (P < 0.05) associated with carcass and meat quality traits, but not growth traits. FOXO3 was predominantly expressed in breast and leg muscle. In both of these tissues, the FOXO3 mRNA level in XH was significantly higher than that in WRR chickens with normal body weight (P < 0.05). In DF-1 cells, siRNA knockdown of FOXO3 significantly (P < 0.01) inhibited the MYOD expression and significantly up-regulated (P < 0.01 or P < 0.05) the expression of growth-related genes including CEBPB, FBXO32, GH, GHR, IGF1R, IGF2R, IGF2BP1, IGF2BP3, INSR, PDK1 and PDK4. Moreover, 18 SNPs were identified in FOXO3. G66716193A was significantly (P < 0.05) associated with growth traits. The sites C66716002T, C66716195T and A66716179G were significantly (P < 0.05) associated with growth or carcass traits. These results demonstrated that FOXO3 is a candidate gene influencing chicken growth. Our observations provide new clues to understand the molecular basis of chicken growth.