GC-IMS and multivariate analyses of volatile organic components in different Chinese breeds of chickens.

This study examined the difference in volatile flavor characteristics among four different local breeds of chicken by headspace gas chromatography-ion mobility spectrometry (HS-GC-IMS) combined with multivariate analysis. In total, 65 volatile organic compounds (VOCs) were identified (17 aldehydes, 12 alcohols, 7 ketones, 5 esters, 2 acids, and 22 unidentified, i.e., 26.15% aldehydes, 18.46% alcohols, 10.77% ketones, 7.69% esters, 3.08% acids, and 33.84% unidentified), of which 43 were annotated. The chicken meats from the four breeds exhibited good separation in topographic plots, VOC fingerprinting, and multivariate analysis. Meanwhile, 20 different volatile components, with variable importance in projection value > 1, were selected as potential markers to distinguish different breeds of chicken by partial least squares discriminant analysis (PLS-DA). These findings provide insights into the flavor traits of chicken meat. Also, HS-GC-IMS combined with multivariate analysis can be a convenient and powerful method for characterizing different meats.

Effects of L-Leu-L-Leu peptide on growth, proliferation, and apoptosis in broiler intestinal epithelial cells.

Small peptides are nutrients and bioactive molecules that have dual regulatory effects on nutrition and physiology. They are of great significance for maintaining the intestinal health and production performance of broilers. We here cultured the primary small intestinal epithelial cells (IEC) of chicken in a medium containing L-Leu (Leu) and L-Leu-L-Leu (Leu-Leu) for 24 h. The untreated cells were considered as the control group. The growth, proliferation, and apoptosis of IEC were examined. By combining RNA-seq and label-free sequencing technology, candidate genes, proteins, and pathways related to the growth, proliferation, and apoptosis of IEC were screened. Immunofluorescence detection revealed that the purity of the isolated primary IEC was >90%. The Leu-Leu group significantly promoted IEC growth and proliferation and significantly inhibited IEC apoptosis, and the effect was better than those of the Leu and control groups. Using transcriptome sequencing, four candidate genes, CCL20, IL8L1, IL8, and IL6, were screened in the Leu group, and one candidate gene, IL8, was screened in the Leu-Leu group. Two candidate genes, IL6 and RGN, were screened in the Leu-Leu group compared with the Leu group. Nonquantitative proteomic marker sequencing results revealed that through the screening of candidate proteins and pathways, found one growth-related candidate protein PGM3 and three proliferation-related candidate proteins RPS17, RPS11, and RPL23, and two apoptosis-related candidate proteins GPX4 and PDPK1 were found in the Leu-Leu group compared with Leu group. In short, Leu-Leu could promote IEC growth and proliferation and inhibit IEC apoptosis. On combining transcriptome and proteome sequencing technologies, multiple immune- and energy-related regulatory signal pathways were found to be related to IEC growth, proliferation, and apoptosis. Three candidate genes of IL8, IL6, and RGN were identified, and six candidate proteins of PGM3, RPS17, RPS11, RPL23, GPX4, and PDPK1 were involved in IEC growth, proliferation, and apoptosis. The results provide valuable data for preliminarily elucidating small peptide-mediated IEC regulation pathways, improving the small peptide nutrition theoretical system, and establishing small peptide nutrition regulation technology.

Aerial parts of Angelica sinensis supplementation for improved broiler growth and intestinal health.

This research examined the impact of incorporating Angelica sinensis's aerial components (APA), commonly referred to as "female ginseng", into broilers' diet. Two hundred eighty-eight 1-day-old Cobb 500 broilers were randomly assigned to the 4 experimental groups with 6 replications and 12 birds/replicate. The 4 groups were fed the diets included 4 concentrations of APA (0, 1, 2, and 3%, respectively). The study spanned 42 d, categorized as the starter phase (1-21 d) and the finisher phase (22-42 d). Notably, broilers fed with 3% APA demonstrated a pronounced surge in feed consumption and weight gain during the 22 to 42 d and over the full 42-d period (P < 0.05). Furthermore, when examining the broilers' intestinal structure, there was a notable increase in the villus height and villi ratio across the duodenum, jejunum, and ileum, with a decrease in crypt depth upon 3% APA inclusion (P < 0.05). On a molecular note, certain genes connected to the intestinal mechanical barrier, such as Zona Occludens 1 and Claudin-2, saw significant elevation in the jejunum (P < 0.05). The jejunum also displayed heightened levels of antimicrobial peptides like lysozyme, mucin 2, sIgA, IgG, and IgM, showcasing an enhanced chemical and immune barrier (P < 0.05). Delving into the 16SrDNA sequencing of intestinal content, a higher microbial diversity was evident with a surge in beneficial bacteria, particularly Firmicutes, advocating a resilient and balanced microecosystem. The findings imply that a 3% APA dietary addition bolsters growth metrics and fortifies the intestinal barrier's structural and functional integrity in broilers.

Quantitative Proteomics Reveals Manganese Alleviates Heat Stress of Broiler Myocardial Cells via Regulating Nucleic Acid Metabolism.

Heat stress threatens severely cardiac function by caused myocardial injury in poultry. Our previous study has showed that manganese (Mn) has a beneficial effect on heat-stress resistance of broiler. Therefore, we tried to confirm the alleviation mechanism through proteomic analysis after heat stress exposure to primary broiler myocardial cells pretreated with Mn. The experiment was divided into four groups: CON group (37 °C, cells without any treatment), HS group (43 °C, cells treatment with heat stress for 4 h), HS+MnCl2 group (cells treated with 20 µM MnCl2 before heat stress), and HS+Mn-AA group (cells treated with 20 µM Mn compound amino acid complex before heat stress). Proteome analysis using DIA identified 300 differentially expressed proteins (DEPs) between CON group and HS group; 93 and 121 DEPs were identified in inorganic manganese treatment group and organic manganese treatment group, respectively; in addition, there were 53 DEPs identified between inorganic and organic manganese group. Gene Ontology (GO) analysis showed that DEPs were mainly involved in binding, catalytic activity, response to stimulus, and metabolic process. DEPs of manganese pretreatment involved in a variety of biological regulatory pathways, and significantly influenced protein processing and repair in endoplasmic reticulum, apoptosis, and DNA replication and repair. These all seem to imply that manganese may help to resist cell damage induced by heat stress by regulating key node proteins. These findings contribute to a better understanding of the effects of manganese on overall protein changes during heat-stress and the possible mechanisms, as well as how to better use manganese to protect heart function in high temperature.

Effects of Jujube Powder on Growth Performance, Blood Biochemical Indices, and Intestinal Microbiota of Broiler.

In total, 576 Cobb broilers were randomized into 6 treatment groups, with 8 replicates in each treatment group and 12 broilers in each replicate. Each treatment group was fed six different experimental diets containing 0%, 2%, 4%, 6%, 8%, and 10% jujube powder. The group receiving 0% jujube powder was considered the blank control group. The experimental period was 42 days and was divided into two periods: starter (0-21 days) and finisher (22-42 days). Compared with the control group, the addition of 8% jujube powder significantly improved the ADG of broilers (p < 0.05), and 8% and 10% jujube powder significantly improved the total tract apparent digestibility of organic matter in broilers (p < 0.05). Adding 10% jujube powder significantly improved the apparent metabolic energy of broilers (p < 0.05). Compared with the control group, 4-10% jujube powder significantly increased IgA, IgG, IgM, and sCD4 levels (p < 0.05) and T-AOC and SOD contents, and it reduced the MDA content in the serum of broilers (p < 0.05). In addition, the relative abundance of Firmicutes, Bacteroidetes, Lactobacillus, and Romboutsia significantly increased in the broiler ileum, whereas that of Proteobacteria and Enterobacter decreased significantly (p < 0.05) when 8% jujube powder was added to the diet. The relative abundance of Proteobacteria, Bacteroides, and Faecalibacterium in the cecum increased significantly (p < 0.05), whereas that of Bacteroidetes decreased significantly (p < 0.05).

Dietary zinc supplementation in breeding pigeons improves the carcass traits of squabs through regulating antioxidant capacity and myogenic regulatory factor expression.

The purpose of this experiment was to explore the effects of zinc supplementation in breeding pigeons diet on carcass traits, meat quality, antioxidant capacity and mRNA expressions of myogenic regulatory factors of squabs. A total of 120 healthy White King pigeons were randomly assigned to 5 treatments, each involving 8 replicates. The experiment lasted for 46 d (18-d incubation period of eggs and 28-d growth period of squabs). The 5 groups were 0, 30, 60, 90, and 120 mg/kg zinc addition. Results showed that the 28-d body weight, breast muscle yield, zinc content in crop milk and myogenic factor 6 (MyF6) abundance of breast muscle were linearly increased (P < 0.050), but the abdominal fat yield linearly decreased (P = 0.040) with increasing dietary zinc supplementation. Both the linear (P < 0.050) and quadratic responses (P < 0.001) were observed in copper zinc superoxide dismutase (Cu-Zn SOD), total antioxidant capacity (T-AOC) and malondialdehyde (MDA) contents in liver and breast muscle. The 28-d body weight was increased by 90 mg/kg zinc supplementation (P < 0.05), and there is no significant difference between 90 and 120 mg/kg zinc addition. The breast muscle yield, Cu-Zn SOD and T-AOC contents in breast muscle and liver, zinc contents in crop milk and breast muscle, MyF6 mRNA expression in breast muscle were higher (P < 0.05) in the group supplemented with 120 mg/kg zinc than the control. The abdominal fat yield was numerically lowest, and MDA contents in breast muscle and liver were significantly lowest in the group fed 120 mg/kg zinc (P < 0.05). However, the meat quality traits were not affected (P > 0.05) by zinc supplementation, except for shear force. It should be stated dietary zinc supplementation at the level of 120 mg/kg for breeding pigeons increased body weight and breast muscle yield of squabs, which may be associated with the up-regulating MyF6 mRNA expression and antioxidant capacity in liver and breast muscle.

Effects of Processing Methods and Conditioning Temperatures on the Cassava Starch Digestibility and Growth Performance of Broilers.

As an important food crop, cassava is rich in nutrients and high in starch content and is widely used in the production of industrial raw materials. However, the utilization value of cassava is limited due to the reduction of planting area and the existence of anti-nutritional factors. Therefore, we evaluated in vitro cassava starch digestibility and in vivo growth performance of broilers in a 3 × 3 factorial arrangement of treatments using three processing methods (mechanical crushing (MC), steam conditioning (SC), and puffing conditioning (PU)) and three conditioning temperatures (60, 75, and 90 °C) to screen for the optimal processing method and conditioning temperature to improve the utilization of cassava. In the in vitro cassava starch digestion study, the digestibility and digestion rate (p < 0.01) were higher at conditioned 90 °C than that at 60 or 75 °C, and PU was higher than SC and MC (p < 0.01) (0.25-2 h). The amylose content and amylose/amylopectin at conditioned 60 °C or PU were lower (p < 0.01) than that of 75 or 90 °C or SC, whereas the opposite was true for amylopectin content (p < 0.01). The resistant starch content of SC or PU was lower (p < 0.01) than MC. In the in vivo study, broilers fed diets conditioned at 60 °C or SC had a lower (p < 0.05) feed-to-gain ratio than those fed diets conditioned at 90 °C or PU diets. The ileum apparent digestibility of starch and AME were higher (p < 0.05) for broilers fed SC diets than for those fed MC diets. These results indicate that cassava starch promoted starch digestion rate by reducing amylose content and amylose/amylose under PU combined with a conditioning temperature of 60 °C, ileum digestibility of starch in broilers fed SC diets was higher than MC diets regardless of conditioning temperature, and SC diets increased AME and decreased F/G to promote growth performance of broilers.

Manganese alleviates heat stress of primary cultured chick embryonic myocardial cells via enhancing manganese superoxide dismutase expression and attenuating heat shock response.

Manganese (Mn) is an essential trace element that has been shown to attenuate the adverse effects of heat stress in the heart of broiler breeders and embryos. However, the underlying molecular mechanisms involving this process remain unclear. Therefore, two experiments were conducted to investigate the possible protective mechanisms of Mn on primary cultured chick embryonic myocardial cells exposed to heat challenge. In experiment 1, the myocardial cells were exposed to 40 °C (normal temperature, NT) and 44 °C (high temperature, HT) for 1, 2, 4, 6 or 8 h. In experiment 2, the myocardial cells were preincubated with no Mn supplementation (CON), 1 mmol/L of Mn as the inorganic MnCl2 (iMn) or organic Mn proteinate (oMn) under NT for 48 h, and then continuously incubated under NT or HT for another 2 or 4 h. The results from experiment 1 showed that the myocardial cells incubated for 2 or 4 h had the highest (P < 0.0001) heat-shock protein 70 (HSP70) or HSP90 mRNA levels than those incubated for other incubation times under HT. In experiment 2, HT increased (P < 0.05) the heat-shock factor 1 (HSF1) and HSF2 mRNA levels as well as Mn superoxide dismutase (MnSOD) activity of myocardial cells compared with NT. Furthermore, supplemental iMn and oMn increased (P < 0.02) HSF2 mRNA level and MnSOD activity of myocardial cells compared with the CON. Under HT, the HSP70 and HSP90 mRNA levels were lower (P < 0.03) in iMn group than in the CON group, in oMn group than in iMn group; and the MnSOD mRNA and protein levels were higher (P < 0.05) in oMn group than in the CON and iMn groups. These results from the present study indicate that supplemental Mn, especially oMn, could enhance the MnSOD expression and attenuate heat shock response to protect against heat challenge in primary cultured chick embryonic myocardial cells.

A quantitative proteomic analyses of primary myocardial cell injury induced by heat stress in chicken embryo.

In this study, the model of heat stress was constructed in primary chick embryonic myocardial cells at 42 °C for 4 h. Proteome analysis using DIA identified 245 differentially expressed proteins (DEPs) (Q-value <0.05, fold change >1.5), of which 63 proteins were up-regulated and 182 proteins were down-regulated. Many were related to metabolism, oxidative stress, oxidative phosphorylation and apoptosis. Gene Ontology (GO) analysis showed that many DEPs under heat stress were involved in regulating metabolites and energy, cellular respiration, catalytic activity and stimulation. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that DEPs were enriched in metabolic pathways, oxidative phosphorylation, citrate cycle (TCA cycle), cardiac muscle contraction, and carbon metabolism. The results could help understanding of the effect of heat stress on myocardial cells and even the heart and possible action mechanism at the protein level.

Effects of Dietary Supplementation with Iron in Breeding Pigeons on the Blood Iron Status, Tissue Iron Content, and Full Expression of Iron-Containing Enzymes of Squabs.

This study was aimed at investigating the effects of diet iron levels on the blood iron status, tissue iron content, mRNA levels, and the activity of iron-containing enzymes in different tissues of squabs. A total of 120 pairs of healthy Silver Feather King parental pigeons with similar average body weight and egg production were randomly divided into 5 groups with 8 replicates and 3 pairs of pigeons per replicate. The five groups of breeding pigeons were fed an iron-unsupplemented basal diet and basal diet supplemented with 75, 150, 300, and 600 mg iron/kg, respectively. The diets were fed in the form of granular feed based on corn, soybean meal, wheat, and sorghum. A broken line model was used for regression analysis. The results showed that plasma iron (PI), serum ferritin, iron contents in crop milk and liver, liver catalase (CAT) activity, and heart succinate dehydrogenase (SDH) activity were affected by iron levels (P < 0.05). And PI, serum ferritin, iron content in crop milk, and heart SDH activity increased quadratically (P < 0.05), but the iron content and CAT activity in the liver decreased quadratically (P < 0.005) as dietary iron level increased. According to the broken-line model of serum ferritin fitting (P < 0.002), the optimal dietary iron level of breeding pigeons was estimated to be 193 mg/kg. In conclusion, serum ferritin is a sensitive index to evaluate the iron requirement of the breeding pigeon with two squabs, and the recommended iron supplemental level is 193 mg/kg.

Analysis of the antioxidant activity of toons sinensis extract and their biological effects on broilers.

Plant extracts are rich in a variety of nutrients and contain a large number of bioactive compounds, and compared with traditional feed additives, they have advantages such as wide sources, natural safety and rich nutrition. This study employed in vitro antioxidant and animal experiments to comprehensively evaluate the use of Toona sinensis extract (TSE) in broiler production. 508 1-day-old Cobb 500 broilers were randomly assigned to the 7 experimental groups with 6 replications and 12 birds/replicate. Two groups received Vitamin C (VC) 300 g/t and Vitamin E 500 g/t, and five dose groups of TSE received 0, 300, 600, 900, and 1,200 g/t of TSE in their feed. The study spanned 42 days, with a starter phase (1-21 days) and a finisher phase (22-42 days). The results showed that compared to ascorbic acid, TSE had the scavenging ability of 2,2-Diphenyl-1-picrylhydrazyl and hydroxyl radical, with IC50 values of 0.6658 mg/mL and 33.1298 mg/mL, respectively. Compared to TSE 0 group, broilers fed with 1,200 g/t TSE showed significant weight gain during the starter phase and increased the feed-to-weight gain ratio during both the starter and finisher phases. Additionally, broilers receiving 1,200 g/t TSE had enhanced dry matter and organic matter utilization. Concerning meat quality, broilers in the 1,200 g/t TSE group demonstrated increased cooked meat yield, and pH value, as well as higher antioxidant capacity (T-AOC), dismutase (SOD), and glutathione peroxidase (GSH-PX) in serum. In addition, there was no significant difference in ileal microflora due to TSE supplementation. In summary, this study confirms the positive impact of a dietary inclusion of 1,200 g/t TSE on broiler growth, meat quality, and serum antioxidants.

Smad4 mediates Bmf involvement in sheep granulosa cell apoptosis.

Bcl-2-modifying factor (Bmf) functions to mediate follicular atresia and oocyte growth in mice. It has been proven that TGF-ß can induce Bmf expression via the Smad4 pathway in a variety of cells, and then induce cell apoptosis. Based on this, we hypothesized that Smad4 and Bmf may play important roles in the apoptosis of granulosa cells (GCs) in domestic animals. This study used small-tailed Han sheep follicular GCs cultured in vitro as a model system, and overexpression or interference experiments, to explore the biological roles of Bmf and reveal the preliminary regulatory mechanisms between Smad4 and Bmf in the process of GCs' apoptosis. We found that the proliferation rate of sheep GCs was significantly increased after the knockdown of Bmf, whereas overexpressing Bmf increased the apoptosis rate of GCs, results also verified by the expression patterns of PCNA, Bcl-2, and Bax genes. After the Smad4 knockdown, the apoptosis rate of GCs was increased, while the mRNA and protein expression of Bmf was significantly up-regulated. A rescue experiment verified that the Bmf knockdown could alleviate GCs' apoptosis induced by Smad4 knockdown. In conclusion, our study not only elucidated an important role for Bmf in the apoptosis of sheep GCs but also revealed a new regulatory pathway between Smad4 and Bmf in this process.

Manganese Mitigates Heat Stress-Induced Apoptosis by Alleviating Endoplasmic Reticulum Stress and Activating the NRF2/SOD2 Pathway in Primary Chick Embryonic Myocardial Cells.

Heat stress leads to oxidative stress and induces apoptosis in various cells. Endoplasmic reticulum (ER) stress is an important apoptosis pathway. Manganese (Mn) has been shown to enhance the activity of manganese superoxide dismutase (MnSOD). To explore the potential effect of Mn on ER stress and apoptosis induced by heat stress, we examined crucial factors associated with heat stress, ER stress, and apoptosis in cultured primary chick embryonic myocardial cells that had been pretreated with 20 µM Mn for 24 h and then subjected to 4 h of heat stress. The results showed that Mn decreased (P < 0.05) heat stress-induced reactive oxygen species (ROS) production and exerted antiapoptotic effects by increasing MnSOD enzymatic activity. The heat stress-induced accumulation of intracellular calcium was dramatically reduced (P < 0.05). Mn treatment significantly decreased (P < 0.05) the expression levels of the apoptosis-related gene Bax and ER stress markers glucose-regulated protein 78 (GRP78) and CCAAT/enhancer binding protein homologous protein (CHOP) in primary chick embryonic myocardial cells. Additionally, Mn reduced oxidative stress by activating the nuclear factor E2-related factor 2 (NRF2)/SOD2 signaling pathway. Taken together, our findings indicate that Mn attenuates heat stress-induced apoptosis by inhibiting ROS generation, intracellular calcium accumulation, and the ER stress pathway and activating the NRF2/SOD2 signaling pathway to protect myocardial cells from oxidative stress during chick embryonic development.

Protective Effect of Manganese on Apoptosis and Mitochondrial Function of Heat-Stressed Primary Chick Embryonic Myocardial Cells.

Heat stress, as a kind of oxidative stress, induces cell apoptosis. Apoptosis is a form of programmed cell death, and mitochondria play an important role in apoptosis. Manganese (Mn) has an antioxidant capacity by enhancing the activity of manganese superoxide dismutase (MnSOD). To investigate the potential effect of Mn on heat stress-induced apoptosis and mitochondrial function, we examined crucial related factors in the context of heat stress using primary chick embryonic myocardial cells pretreated with Mn for 24 h. The results showed that Mn restored the heat stress-induced decrease in cell viability and reduced the activities of caspase-3 (P < 0.05). The repression of the Δψm and intracellular ATP content caused by heat stress was reversed dramatically in the Mn pretreatment group (P < 0.05). Additionally, Mn inhibited heat stress-induced mitochondrial fission, as shown by decreased mitochondrial fission-related protein dynamin-related protein 1 (Drp1) expression and increased mitochondrial fusion-related protein optic atrophy 1 (Opa1) and mitofusin 1 (Mfn1) (P < 0.05) in primary chick embryonic myocardial cells. It was concluded that Mn attenuates the mitochondrial-mediated apoptosis pathway and sustains mitochondrial structure and function under heat stress in primary chick embryonic myocardial cells.

Mouse Organ-Specific Proteins and Functions.

Organ-specific proteins (OSPs) possess great medical potential both in clinics and in biomedical research. Applications of them-such as alanine transaminase, aspartate transaminase, and troponins-in clinics have raised certain concerns of their organ specificity. The dynamics and diversity of protein expression in heterogeneous human populations are well known, yet their effects on OSPs are less addressed. Here, we used mice as a model and implemented a breadth study to examine the panorgan proteome for potential variations in organ specificity in different genetic backgrounds. Using reasonable resources, we generated panorgan proteomes of four in-bred mouse strains. The results revealed a large diversity that was more profound among OSPs than among proteomes overall. We defined a robustness score to quantify such variation and derived three sets of OSPs with different stringencies. In the meantime, we found that the enriched biological functions of OSPs are also organ-specific and are sensitive and useful to assess the quality of OSPs. We hope our breadth study can open doors to explore the molecular diversity and dynamics of organ specificity at the protein level.

Baseline Gut Metagenomic Functional Gene Signature Associated with Variable Weight Loss Responses following a Healthy Lifestyle Intervention in Humans.

Recent human feeding studies have shown how the baseline taxonomic composition of the gut microbiome can determine responses to weight loss interventions. However, the functional determinants underlying this phenomenon remain unclear. We report a weight loss response analysis on a cohort of 105 individuals selected from a larger population enrolled in a commercial wellness program, which included healthy lifestyle coaching. Each individual in the cohort had baseline blood metabolomics, blood proteomics, clinical labs, dietary questionnaires, stool 16S rRNA gene sequencing data, and follow-up data on weight change. We generated additional targeted proteomics data on obesity-associated proteins in blood before and after intervention, along with baseline stool metagenomic data, for a subset of 25 individuals who showed the most extreme weight change phenotypes. We built regression models to identify baseline blood, stool, and dietary features associated with weight loss, independent of age, sex, and baseline body mass index (BMI). Many features were independently associated with baseline BMI, but few were independently associated with weight loss. Baseline diet was not associated with weight loss, and only one blood analyte was associated with changes in weight. However, 31 baseline stool metagenomic functional features, including complex polysaccharide and protein degradation genes, stress-response genes, respiration-related genes, and cell wall synthesis genes, along with gut bacterial replication rates, were associated with weight loss responses after controlling for age, sex, and baseline BMI. Together, these results provide a set of compelling hypotheses for how commensal gut microbiota influence weight loss outcomes in humans. IMPORTANCE Recent human feeding studies have shown how the baseline taxonomic composition of the gut microbiome can determine responses to dietary interventions, but the exact functional determinants underlying this phenomenon remain unclear. In this study, we set out to better understand interactions between baseline BMI, metabolic health, diet, gut microbiome functional profiles, and subsequent weight changes in a human cohort that underwent a healthy lifestyle intervention. Overall, our results suggest that the microbiota may influence host weight loss responses through variable bacterial growth rates, dietary energy harvest efficiency, and immunomodulation.

Detection of copy number variation and selection signatures on the X chromosome in Chinese indigenous sheep with different types of tail.

OBJECTIVE: Chinese indigenous sheep breeds can be classified into the following three categories by their tail morphology: fat-tailed, fat-rumped and thin-tailed sheep. The typical sheep breeds corresponding to fat-tailed, fat-rumped, and thin-tailed sheep are large-tailed Han, Altay, and Tibetan sheep, respectively. Detection of copy number variation (CNV) and selection signatures provides information on the genetic mechanisms underlying the phenotypic differences of the different sheep types. METHODS: In this study, PennCNV software and F-statistics (FST) were implemented to detect CNV and selection signatures, respectively, on the X chromosome in three Chinese indigenous sheep breeds using ovine high-density 600K single nucleotide polymorphism arrays. RESULTS: In large-tailed Han, Altay, and Tibetan sheep, respectively, a total of six, four and 22 CNV regions (CNVRs) with lengths of 1.23, 0.93, and 7.02 Mb were identified on the X chromosome. In addition, 49, 34, and 55 candidate selection regions with respective lengths of 27.49, 16.47, and 25.42 Mb were identified in large-tailed Han, Altay, and Tibetan sheep, respectively. The bioinformatics analysis results indicated several genes in these regions were associated with fat, including dehydrogenase/reductase X-linked, calcium voltage-gated channel subunit alpha1 F, and patatin like phospholipase domain containing 4. In addition, three other genes were identified from this analysis: the family with sequence similarity 58 member A gene was associated with energy metabolism, the serine/arginine-rich protein specific kinase 3 gene was associated with skeletal muscle development, and the interleukin 2 receptor subunit gamma gene was associated with the immune system. CONCLUSION: The results of this study indicated CNVRs and selection regions on the X chromosome of Chinese indigenous sheep contained several genes associated with various heritable traits.