Early embryonic polarity establishment and implications for lineage differentiation.

Polarity establishment is one of the key factors affecting early embryonic development. Polarity establishment begins with myosin phosphorylation in the 8-cell embryo, and phosphorylation activates actin leading to its initiation of contractility. Subsequently, actin undergoes reorganization to form an apical domain rich in microvilli on the non-contacting surface of each blastomere, and form the actomyosin ring that marks the maturation of the apical domain in conjunction with polar protein complexes and others. From the process of polarity establishment, it can be seen that the formation of the apical domain is influenced by actin-related proteins and polar protein complexes. Some zygote genome activation (ZGA) and lineage-specific genes also regulate polarity establishment. Polarity establishment underlies the first cell lineage differentiation during early embryonic development. It regulates lineage segregation and morphogenesis by affecting asymmetric cell division, asymmetric localization of lineage differentiation factors, and activity of the Hippo signaling pathway. In this review, we systematically summarize the mechanisms of early embryonic polarity establishment and its impact on lineage differentiation in mammals, and discuss the shortcomings of the currently available studies in terms of regulatory mechanisms and species, thereby providing clues and systematic perspectives for elucidating early embryonic polarity establishment.

Usefulness of estimated pulse wave velocity for identifying prevalent coronary heart disease: findings from a general Chinese population.

BACKGROUND: Aortic stiffness and coronary heart disease (CHD) share a similar spectrum of risk factors; previous studies have identified the association between aortic stiffness and CHD. Recent studies have demonstrated estimated pulse wave velocity (ePWV) as a simple and easy-acquired indicator of aortic stiffness. Our work aims to evaluate the association between ePWV and the prevalence of CHD and assess the value of ePWV for the identification of prevalent CHD. METHODS: The current cross-sectional work included 7012 subjects from rural areas of southeastern China between September 2020 and February 2021. ePWV was calculated from age and mean blood pressure by specific algorithm. RESULTS: The prevalence of CHD in our population was 3.58% (251 patients among 7012 subjects). After adjusting for age, sex, education, income and exercise level, current smoking and drinking status, body mass index, waist circumference, fasting plasma glucose, total cholesterol, high density lipoprotein, estimated glomerular filtration rate and cerebrovascular diseases, each standard deviation increment of ePWV would produce an additional 37.8% risk of prevalent CHD. Moreover, after dividing ePWV into quartiles, the 4th quartile of ePWV showed a significant risk of prevalent CHD (OR (95% CI): 3.567 (1.963-6.479)) when compared with the 1st quartile. Additionally, the subgroup analysis showed the association between ePWV and prevalent CHD was robust to several common risk factors of CHD, including age, sex, body mass index, hypertension, diabetes and reduced estimated glomerular filtration rate. Finally, the area under curve (AUC) displayed an improvement when adding ePWV into common CHD risk factors (0.705 vs. 0.718. P = 0.044). Consistently, net reclassification index (0.436, 95% CI: 0.301-0.571, P < 0.001) and integrated discrimination index (0.004, 95% CI: 0.001-0.006, P = 0.002) demonstrated the value of ePWV to optimize the identification of prevalent CHD in the general population. CONCLUSION: The present analysis implicates the robust association between ePWV, a simple, rapid, and practical marker of aortic stiffness, and prevalent CHD in the general Chinese population. More importantly, the results suggest the value of ePWV as a potential marker to improve the identification of prevalent CHD.

Genetic parameters estimation and genome-wide association studies for internal organ traits in an F2 chicken population.

Chicken internal organs are indispensable parts of the body, but their genetic architectures have not been commonly understood. Herein, we estimated the genetic parameters for heart weight (HW), liver weight (LW), spleen weight (SpW), testis weight (TW), glandular stomach weight (GSW), muscular stomach weight (MSW) and identified single nucleotide polymorphisms (SNPs) and potential candidate genes associated with internal organ weights in an F2 population constructed by crossing broiler cocks derived from Arbor Acres with high abdominal fat content and Baier layer dams (a Chinese native breed). The restricted maximum likelihood (REML) method was applied for genetic parameters estimation of internal organ weights using GCTA software. The results showed that heritabilities of internal organ traits ranged from 0.336 to 0.673 and most of the genetic and phenotypic correlations amongst internal organs weights were positive. A genome-wide association study (GWAS) was performed based on a mixed linear model (MLM) in GEMMA software. Genotypic data were produced from the whole genome re-sequenced (26 F0 individuals were re-sequenced at 10 × coverage; 519 F2 individuals were re-sequenced at 3 × coverage). A total of 7,890,258 SNPs remained to be analysed after quality control and genotype imputation. The GWAS results indicated that significant SNPs responsible for internal organ traits were scattered on the different chicken chromosomes 1-5, 8, 11, 14, 16, 18, 19 and 27. Amongst the annotated genes, fibronectin type III domain containing 3A (FNDC3A), LOC101748122, membrane palmitoylated protein 6 (MPP6), LOC107049584 and KAT8 regulatory NSL complex subunit 1 (KANSL1) were the most promising candidates for internal organ traits. The findings will provide instrumental information for understanding the genetic basis of internal organ development.

A phenome database (NEAUHLFPD) designed and constructed for broiler lines divergently selected for abdominal fat content.

Effective management and analysis of precisely recorded phenotypic traits are important components of the selection and breeding of superior livestocks. Over two decades, we divergently selected chicken lines for abdominal fat content at Northeast Agricultural University (Northeast Agricultural University High and Low Fat, NEAUHLF), and collected large volume of phenotypic data related to the investigation on molecular genetic basis of adipose tissue deposition in broilers. To effectively and systematically store, manage and analyze phenotypic data, we built the NEAUHLF Phenome Database (NEAUHLFPD). NEAUHLFPD included the following phenotypic records: pedigree (generations 1-19) and 29 phenotypes, such as body sizes and weights, carcass traits and their corresponding rates. The design and construction strategy of NEAUHLFPD were executed as follows: (1) Framework design. We used Apache as our web server, MySQL and Navicat as database management tools, and PHP as the HTML-embedded language to create dynamic interactive website. (2) Structural components. On the main interface, detailed introduction on the composition, function, and the index buttons of the basic structure of the database could be found. The functional modules of NEAUHLFPD had two main components: the first module referred to the physical storage space for phenotypic data, in which functional manipulation on data can be realized, such as data indexing, filtering, range-setting, searching, etc.; the second module related to the calculation of basic descriptive statistics, where data filtered from the database can be used for the computation of basic statistical parameters and the simultaneous conditional sorting. NEAUHLFPD could be used to effectively store and manage not only phenotypic, but also genotypic and genomics data, which can facilitate further investigation on the molecular genetic basis of chicken adipose tissue growth and development, and expedite the selection and breeding of broilers with low fat content.

Differential expression of six chicken genes associated with fatness traits in a divergently selected broiler population.

A genome-wide association study has shown a number of chicken (Gallus gallus) single nucleotide polymorphism (SNP) markers to be significantly associated with abdominal fat content in Northeast Agricultural University (NEAU) broiler lines selected divergently for abdominal fat content (NEAUHLF). The six significant SNPs are located in the kinase insert domain receptor (KDR), tumor suppressor candidate 3 (TUSC3), phosphoribosyl pyrophosphate amidotransferase (PPAT), exocyst complex component 1 (EXOC1), v-myb myeloblastosis viral oncogene homolog (avian)-like 2 (MYBL2) and KIAA1211 (undefined) genes. In this study, the expression levels of these genes were investigated in both abdominal fat and liver tissues using 32 14th generation chickens from the NEAUHLF. The levels of expression of KDR in abdominal fat and KDR and TUSC3 in liver differed significantly between the two lines. The expression level of KDR in the abdominal fat was significantly correlated with the abdominal fat weight (AFW) and abdominal fat percentage (AFP). The expression levels of KDR, TUSC3 and PPAT in liver were significantly correlated with AFW and AFP, indicating that the six genes, especially KDR and TUSC3, could be associated with fat traits in domestic chickens. This study could provide insight into the mechanisms underlying the formation of abdominal fat in chickens.

Divergent selection-induced obesity alters the composition and functional pathways of chicken gut microbiota.

BACKGROUND: The gastrointestinal tract is populated by a complex and vast microbial network, with a composition that reflects the relationships of the symbiosis, co-metabolism, and co-evolution of these microorganisms with their host. The mechanism that underlies such interactions between the genetics of the host and gut microbiota remains elusive. RESULTS: To understand how genetic variation of the host shapes the gut microbiota and interacts with it to affect the metabolic phenotype of the host, we compared the abundance of microbial taxa and their functional performance between two lines of chickens (fat and lean) that had undergone long-term divergent selection for abdominal fat pad weight, which resulted in a 4.5-fold increase in the fat line compared to the lean line. Our analysis revealed that the proportions of Fusobacteria and Proteobacteria differed significantly between the two lines (8 vs. 18% and 33 vs. 24%, respectively) at the phylum level. Eight bacterial genera and 11 species were also substantially influenced by the host genotype. Differences between the two lines in the frequency of host alleles at loci that influence accumulation of abdominal fat were associated with differences in the abundance and composition of the gut microbiota. Moreover, microbial genome functional analysis showed that the gut microbiota was involved in pathways that are associated with fat metabolism such as lipid and glycan biosynthesis, as well as amino acid and energy metabolism. Interestingly, citrate cycle and peroxisome proliferator activated receptor (PPAR) signaling pathways that play important roles in lipid storage and metabolism were more prevalent in the fat line than in the lean line. CONCLUSIONS: Our study demonstrates that long-term divergent selection not only alters the composition of the gut microbiota, but also influences its functional performance by enriching its relative abundance in microbial taxa. These results support the hypothesis that the host and gut microbiota interact at the genetic level and that these interactions result in their co-evolution.

Identification and characterization of transcript variants of chicken peroxisome proliferator-activated receptor gamma.

Peroxisome proliferator-activated receptor gamma regulates adipogenesis. The genomic structure of the chicken peroxisome proliferator-activated receptor gamma (cPPARγ) gene has not been fully characterized, and only one cPPARγ gene mRNA sequence has been reported in genetic databases. Using 5' rapid amplification of cDNA ends, we identified five different cPPARγ mRNAs that are transcribed from three transcription initiation sites. The open reading frame analysis showed that these five cPPARγ transcript variants (cPPARγ1 to 5) could encode two cPPARγ protein isoforms (cPPARγ1 and cPPARγ2), which differ only in their N-terminal region. Quantitative real-time RT-PCR analysis showed that, of these five cPPARγ transcript variants, cPPARγ1 was ubiquitously highly expressed in various chicken tissues, including adipose tissue, liver, kidney, spleen and duodenal; cPPARγ2 was exclusively highly expressed in adipose tissue; cPPARγ3 was highly expressed in adipose tissue, kidney, spleen and liver; cPPARγ4 and cPPARγ5 were ubiquitously weakly expressed in all the tested tissues, and comparatively, cPPARγ5 was highly expressed in adipose tissue, heart, liver and kidney. The comparison of the expression of the five cPPARγ transcript variants showed that adipose tissue cPPARγ1 expression was significantly higher in the fat line than in the lean line from 2 to 7 wk of age (P < 0.05 or P < 0.01). Adipose tissue cPPARγ3 expression was significantly higher in the fat line than in the lean line at 3, 5 and 6 wk of age (P < 0.01, P < 0.05), but lower at 4 wk of age (P < 0.05). Adipose tissue cPPARγ5 expression was significantly higher in the fat line than in the lean line at 3, 4, and 6 wk of age (P < 0.01) and at 2 and 7 wk of age (P < 0.05). This is the first report of transcript variants and protein isoforms of cPPARγ gene. Our findings provided a foundation for future investigations of the function and regulation of cPPARγ gene in adipose tissue development.

[Preliminary Analysis of the Genetic Loci of SAG1 and SAG3, the Surface Antigens of Toxoplasma gondii, in HIV-positive People in Dali of Yunnan Province].

OBJECTIVE: To identify the genotypes of Toxoplasma gondii that infects HIV-positive people in Dali of Yunnan Province through analyzing the genetic loci of the surface antigens SAG1 and SAG3. METHODS: A total of 291 blood samples from HIV-positive cases were collected from the HIV/AIDS Prevention and Control Institution in Yunnan. Nested PCR was used to amplify SAGI and SAG3 genes in the blood samples. The products were digested with restriction enzymes Sau96 I, Hae II and Nci I, and sequenced. RESULTS: Of the 291 HIV-positive blood samples, 64 showed successful amplification of SAGI gene, and 42 of SAG3 gene, with product sizes of 390 bp and 225 bp, respectively. Enzymetic digestion of the PCR products resulted in fragments of 350 bp and 50 bp for SAGI, and -200 bp band for SAG3, consistent with RH, a particular type I strain of T. gondii. Sequencing of the SAG1 and SAG3 PCR products showed that their sequence identities with SAGI (Accession No. GQ253073) and SAG3 (Accession No. JX218225.1) of the type I strain of T. gondii were 99.98%-100% and 99.96% -99.98% respectively. CONCLUSION: The Toxoplasma gondii in HIV-positive cases in Dali of Yunnan Province is the type I strain of T. gondii.

Comparative analyses of laying performance and follicular development characteristics between fat and lean broiler lines.

The deposition of high levels of fat in broiler breeder hens can have a profound impact on follicular development and laying performance. This study was formulated with the goal of comparing egg production and follicular development characteristics at different laying stages in the Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF). The egg production was analyzed using the birds from the 19th to 24th generations of NEAUHLF; the follicular development characteristics were analyzed by hematoxylin-eosin staining and quantitative real-time polymerase chain reaction using the birds from the 24th generation of NEAUHLF. The results showed that the age at first egg of lean hens was significantly earlier than that of fat hens in this study. While no significant differences in total egg output from the first egg to 50 wk of age were noted when comparing these 2 chicken lines, lean hens laid more eggs from the first egg to 35 wk of age relative to fat hens, whereas fat hens laid more eggs from wk 36 to 42 and 43 to 50 relative to their lean counterparts. No differences in ovarian morphology and small yellow follicle (SYF) histological characteristics were noted when comparing these 2 chicken lines at 27 wk of age. At 35 and 52 wk of age, however, lean hens exhibited significantly lower ovarian weight, ovarian proportion values, numbers of hierarchical follicles, hierarchical follicle weight, and SYF granulosa layer thickness as compared to fat hens, together with a significant increase in the number of prehierarchical follicles relative to those in fat hens. Gene expression analyses suggested that follicle selection was impaired in the fat hens in the early laying stage, whereas both follicle selection and maturation were impaired in the lean hens in the middle and late laying stages. Overall, these data highlight that fat deposition in broiler hens can have a range of effects on follicular development and egg production that are laying stage-dependent.

HBP1 promotes chicken preadipocyte proliferation via directly repressing SOCS3 transcription.

Preadipocyte proliferation is an essential process in adipose development. During proliferation of preadipocytes, transcription factors play crucial roles. HMG-box protein 1 (HBP1) is an important transcription factor of cellular proliferation. However, the function and underlying mechanisms of HBP1 in the proliferation of preadipocytes remain unclear. Here, we found that the expression level of HBP1 decreased first and then increased during the proliferation of chicken preadipocytes. Knockout of HBP1 could inhibit the proliferation of preadipocytes, while overexpression of HBP1 could promote the proliferation of preadipocytes. ChIP-seq data showed that HBP1 had the unique DNA binding motif in chicken preadipocytes. By integrating ChIP-Seq and RNA-Seq, we revealed a total of 3 candidate target genes of HBP1. Furthermore, the results of ChIP-qPCR, RT-qPCR, luciferase reporter assay and EMSA showed that HBP1 could inhibit the transcription of suppressor of cytokine signaling 3 (SOCS3) by binding to its promoter. Moreover, we confirmed that SOCS3 can mediate the regulation of HBP1 on the proliferation of preadipocytes through RNAi and rescue experiments. Altogether, these data demonstrated that HBP1 directly targets SOCS3 to regulate chicken preadipocyte proliferation. Our findings expand the transcriptional regulatory network of preadipocyte proliferation, and they will be helpful in formulating a molecular breeding scheme to control excessive abdominal fat deposition and to improve meat quality in chickens.

A Study on the Growth and Development Characteristics of Lindian Chickens.

As an excellent chicken breed found in a high-altitude zone of northern China, Lindian chickens are characterized by good egg and meat production, strong adaptability, cold tolerance, rough feeding resistance, excellent egg quality, and delicious meat quality. To facilitate the exploitation of the unique qualities of the Lindian chicken, the varying patterns and correlations of various body size and carcass traits of 3-22-week-old Lindian chickens were analyzed in this study. The optimal growth model of these traits was determined by growth curve fitting analysis. The results showed that most traits of Lindian chickens increased steadily with increasing age, and most of them increased rapidly before 10 weeks of age. In addition, the inflection point age of each trait was predicted to be between 4 and 10 weeks. Furthermore, this study revealed that body size traits were closely related to carcass traits in Lindian chickens. In summary, Lindian chickens are in a rapid growth stage before the age of 10 weeks, and better slaughter performance can be achieved through good feeding management during this stage. The reproductive traits and muscles are the main developmental focus after the age of 19 weeks, so it is important to adequately meet their energy requirements for subsequent good breeding performance.

A Functional Variant Alters the Binding of Bone morphogenetic protein 2 to the Transcription Factor NF-κB to Regulate Bone morphogenetic protein 2 Gene Expression and Chicken Abdominal Fat Deposition.

In this study, we employed a dual-luciferase reporter assay and electrophoretic mobility shift analysis (EMSA) in vitro to explore whether a 12-base pair (bp) insertion/deletion (InDel) variant (namely g.14798187_14798188insTCCCTGCCCCCT) within intron 2 of the chicken BMP2 gene, which was significantly associated with chicken abdominal fat weight and abdominal fat percentage, is a functional marker and its potential regulatory mechanism. The reporter analysis demonstrated that the luciferase activity of the deletion allele was extremely significantly higher than that of the insertion allele (p < 0.01). A bioinformatics analysis revealed that compared to the deletion allele, the insertion allele created a transcription factor binding site of nuclear factor-kappa B (NF-κB), which exhibited an inhibitory effect on fat deposition. A dual-luciferase reporter assay demonstrated that the inhibitory effect of NF-κB on the deletion allele was stronger than that on the insertion allele. EMSA indicated that the binding affinity of NF-κB for the insertion allele was stronger than that for the deletion allele. In conclusion, the 12-bp InDel chicken BMP2 gene variant is a functional variant affecting fat deposition in chickens, which may partially regulate BMP2 gene expression by affecting the binding of transcription factor NF-κB to the BMP2 gene.

Whole genome analyses reveal novel genes associated with chicken adaptation to tropical and frigid environments.

INTRODUCTION: Investigating the genetic footprints of historical temperature selection can get insights to the local adaptation and feasible influences of climate change on long-term population dynamics. OBJECT: Chicken is a significative species to study genetic adaptation on account of its similar domestication track related to human activity with the most diversified varieties. Yet, few studies have demonstrated the genetic signatures of its adaptation to naturally tropical and frigid environments. METHOD: Here, we generated whole genome resequencing of 119 domesticated chickens in China including the following breeds which are in order of breeding environmental temperature from more tropical to more frigid: Wenchang chicken (WCC), green-shell chicken (GSC), Tibetan chicken (TBC), and Lindian chicken (LDC). RESULTS: Our results showed WCC branched off earlier than LDC with an evident genetic admixture between WCC and LDC, suggesting their closer genetic relationship. Further comparative genomic analyses solute carrier family 33 member 1 (SLC33A1) and thyroid stimulating hormone receptor (TSHR) genes exhibited stronger signatures for positive selection in the genome of the more tropical WCC. Furthermore, genotype data from about 3,000 African local ecotypes confirmed that allele frequencies of single nucleotide polymorphisms (SNPs) in these 2 genes appeared strongly associated with tropical environment adaptation. In addition, the NADH:ubiquinone oxidoreductase subunit S4 (NDUFS4) gene exhibited a strong signature for positive selection in the LDC genome, and SNPs with marked allele frequency differences indicated a significant relationship with frigid environment adaptation. CONCLUSION: Our findings partially clarify how selection footprints from environmental temperature stress can lead to advantageous genomic adaptions to tropical and frigid environments in poultry and provide a valuable resource for selective breeding of chickens.

A genome-wide scan of selective sweeps in two broiler chicken lines divergently selected for abdominal fat content.

BACKGROUND: Genomic regions controlling abdominal fatness (AF) were studied in the Northeast Agricultural University broiler line divergently selected for AF. In this study, the chicken 60KSNP chip and extended haplotype homozygosity (EHH) test were used to detect genome-wide signatures of AF. RESULTS: A total of 5357 and 5593 core regions were detected in the lean and fat lines, and 51 and 57 reached a significant level (P<0.01), respectively. A number of genes in the significant core regions, including RB1, BBS7, MAOA, MAOB, EHBP1, LRP2BP, LRP1B, MYO7A, MYO9A and PRPSAP1, were detected. These genes may be important for AF deposition in chickens. CONCLUSIONS: We provide a genome-wide map of selection signatures in the chicken genome, and make a contribution to the better understanding the mechanisms of selection for AF content in chickens. The selection for low AF in commercial breeding using this information will accelerate the breeding progress.

Identification of biomarkers associated with the feed efficiency by metabolomics profiling: results from the broiler lines divergent for high or low abdominal fat content.

BACKGROUND: Improving feed efficiency (FE) is one of the main objectives in broiler breeding. It is difficult to directly measure FE traits, and breeders hence have been trying to identify biomarkers for the indirect selection and improvement of FE traits. Metabolome is the "bridge" between genome and phenome. The metabolites may potentially account for more of the phenotypic variation and can suitably serve as biomarkers for selecting FE traits. This study aimed to identify plasma metabolite markers for selecting high-FE broilers. A total of 441 birds from Northeast Agricultural University broiler lines divergently selected for abdominal fat content were used to analyze plasma metabolome and estimate the genetic parameters of differentially expressed metabolites. RESULTS: The results identified 124 differentially expressed plasma metabolites (P < 0.05) between the lean line (high-FE birds) and the fat line (low-FE birds). Among these differentially expressed plasma metabolites, 44 were found to have higher positive or negative genetic correlations with FE traits (|rg| ≥ 0.30). Of these 44 metabolites, 14 were found to display moderate to high heritability estimates (h2 ≥ 0.20). However, among the 14 metabolites, 4 metabolites whose physiological functions have not been reported were excluded. Ultimately, 10 metabolites were suggested to serve as the potential biomarkers for breeding the high-FE broilers. Based on the physiological functions of these metabolites, reducing inflammatory and improving immunity were proposed to improve FE and increase production efficiency. CONCLUSIONS: According to the pipeline for the selection of the metabolite markers established in this study, it was suggested that 10 metabolites including 7-ketocholesterol, dimethyl sulfone, epsilon-(gamma-glutamyl)-lysine, gamma-glutamyltyrosine, 2-oxoadipic acid, L-homoarginine, testosterone, adenosine 5'-monophosphate, adrenic acid, and calcitriol could be used as the potential biomarkers for breeding the "food-saving broilers".

Profiling of RNA N 6 -Methyladenosine Methylation Reveals the Critical Role of m6A in Chicken Adipose Deposition.

One of the main objectives of broiler breeding is to prevent excessive abdominal adipose deposition. The role of RNA modification in adipose deposition is not clear. This study was aimed to map m6A modification landscape in chicken adipose tissue. MeRIP-seq was performed to compare the differences in m6A methylation pattern between fat and lean broilers. We found that start codons, stop codons, coding regions, and 3'-untranslated regions were generally enriched for m6A peaks. The high m6A methylated genes (fat birds vs. lean birds) were primarily associated with fatty acid biosynthesis and fatty acid metabolism, while the low m6A methylated genes were mainly involved in processes associated with development. Furthermore, we found that the mRNA levels of many genes may be regulated by m6A modification. This is the first comprehensive characterization of m6A patterns in the chicken adipose transcriptome, and provides a basis for studying the role of m6A modification in fat deposition.

Integrated transcriptome and proteome analysis reveals potential mechanisms for differential abdominal fat deposition between divergently selected chicken lines.

Genetic selection for meat production performance of broilers concomitantly causes excessive abdominal fat deposition, accompanied by several adverse effects, such as the reduction of feed conversion efficiency and reproduction performance. Our previous studies have identified important genes regulating chicken fat deposition, using the Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF) as an animal model. However, the molecular mechanism underlying fat deposition differences between fat and lean broilers remains largely unknown. Here, we integrated the transcriptome (RNA-Seq) and quantitative proteome (isobaric tags for relative and absolute quantitation, iTRAQ) profiling analyses on abdominal fat tissues from NEAUHLF chicken lines. Differentially expressed genes (2167 DEGs, corrected p-value < 0.01) and differentially abundant proteins (199 DAPs, corrected p-value < 0.05) were identified in lean line compared to fat line. Down-regulated DEGs and DAPs mainly enriched in pathways related to fatty acid metabolism, fatty acid biosynthesis, and PPAR signaling, and interestingly, up-regulated DEGs and DAPs enriched both in lysosome pathway. Moreover, numerous key DEGs and DAPs involved in long-chain fatty acid uptake, in situ lipogenesis (fatty acid and cholesterol synthesis), and lipid droplet accumulation were discovered after integrated transcriptome and proteome analysis. SIGNIFICANCE: Excessive abdominal fat deposition critically affects the health of broilers and causes economic loss to broiler producers, but the molecular mechanism of abdominal fat deposition is still unclear in chicken. We identified key DEGs/DAPs and potential pathways through an integration of chicken abdominal fat tissues transcriptome and proteome analyses. Our findings will facilitate a better revealing the mechanism and provide a novel insight into abdominal fat content discrepancy between the fat and lean chicken lines.

Estimation of the genetic parameters of traits relevant to feed efficiency: result from broiler lines divergent for high or low abdominal fat content.

Feed consumption represents a major cost in poultry production and improving feed efficiency is one of the important goals in breeding strategies. The present study aimed to analyze the relationship between feed efficiency and relevant traits and find the proper selection method for improving feed efficiency by using the Northeast Agricultural University High and Low Fat broiler lines that were divergently selected for abdominal fat content. A total of 899 birds were used to measure the feed intake (FI), abdominal fat weight (AFW), and body weight traits. The abdominal fat percentage (AFP), feed conversion ratio (FCR), and the residual feed intake (RFI) were calculated for each individual broiler. The differences in the AFW, AFP, and in traits relevant to feed efficiency, such as FCR and RFI, between the fat line and the lean line were analyzed, and the genetic parameters were estimated for AFW, AFP, and feed efficiency relevant traits. The results showed that AFW, AFP, body weight gain (BWG), FI, FCR, and RFI were significantly higher in the fat line compared with the lean line. The heritability of FI, BWG, FCR, RFI, AFW, and AFP were 0.45, 0.28, 0.36, 0.38, 0.33, and 0.30, respectively. Both FCR and RFI showed high positive genetic correlations with FI, AFW, and AFP and relatively low, negative genetic correlations with BWG. The RFI showed much higher positive genetic correlation with the abdominal fat traits than FCR. In addition, the FCR showed negative genetic correlation with body weight of 4 wk (BW4) and 7 wk (BW7), whereas RFI showed positive genetic correlation with BW4 and BW7. The results showed that both RFI and FCR could be used for improving feed efficiency. When selecting against RFI, the AFP could be significantly reduced, and by selecting against FCR, the body weight could be improved simultaneously.

Multi-Omics Association Reveals the Effects of Intestinal Microbiome-Host Interactions on Fat Deposition in Broilers.

Growing evidence indicates that gut microbiota factors cannot be viewed as independent in the occurrence of obesity. Because the gut microbiome is highly dimensional and complex, studies on interactions between gut microbiome and host in obesity are still rare. To explore the relationship of gut microbiome-host interactions with obesity, we performed multi-omics associations of gut metagenome, intestinal transcriptome, and host obesity phenotypes in divergently selected obese-lean broiler lines. Metagenomic shotgun sequencing generated a total of 450 gigabases of clean data from 80 intestinal segment contents of 20 broilers (10 of each line). The microbiome comparison showed that microbial diversity and composition in the duodenum, jejunum, ileum, and ceca were altered variously between the lean- and fat-line broilers. We identified two jejunal microbes (Escherichia coli and Candidatus Acetothermia bacterium) and four cecal microbes (Alistipes sp. CHKCI003, Ruminococcaceae bacterium CPB6, Clostridiales bacterium, and Anaeromassilibacillus sp. An200), which were significantly different between the two lines (FDR < 0.05). When comparing functional metagenome, the fat-line broilers had an intensive microbial metabolism in the duodenum and jejunum but degenerative microbial activities in the ileum and ceca. mRNA-sequencing identified a total of 1,667 differentially expressed genes (DEG) in the four intestinal compartments between the two lines (| log2FC| > 1.5 and FDR < 0.05). Multi-omics associations showed that the 14 microbial species with abundances that were significantly related with abdominal fat relevant traits (AFRT) also have significant correlations with 155 AFRT-correlated DEG (p < 0.05). These DEG were mainly involved in lipid metabolism, immune system, transport and catabolism, and cell growth-related pathways. The present study constructed a gut microbial gene catalog of the obese-lean broiler lines. Intestinal transcriptome and metagenome comparison between the two lines identified candidate DEG and differential microbes for obesity, respectively. Multi-omics associations suggest that abdominal fat deposition may be influenced by the interactions of specific gut microbiota abundance and the expression of host genes in the intestinal compartments in which the microbes reside. Our study explored the interactions between gut microbiome and host intestinal gene expression in lean and obese broilers, which may expand knowledge on the relationships between obesity and gut microbiome.

A single nucleotide polymorphism of chicken acetyl-CoA carboxylase A gene associated with fatness traits.

Acetyl-CoA carboxylase alpha (ACCalpha) is a major rate-limiting enzyme in the biogenesis of long-chain fatty acids. It can catalyze the carboxylation of acetyl-CoA to form malonyl-CoA that plays a key role in the regulation of fatty acid metabolism. The objective of the present study was to investigate the associations of ACCalpha gene polymorphisms with chicken growth and body composition traits. The Northeast Agricultural University broiler lines divergently selected for abdominal fat content and the Northeast Agricultural University F(2) Resource Population were used in the current study. Body weight and body composition traits were measured in the aforementioned two populations. A synonymous mutation was detected in the exon 19 region of ACCalpha gene, then polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was developed to genotype all the individuals derived from the aforementioned populations. Association analysis revealed that the polymorphism was associated with abdominal fat weight and percentage of abdominal fat in the two populations. The results suggested that ACCalpha gene could be a candidate locus or linked to a major gene that affects abdominal fat content in the chicken.