Large-scale genomic and transcriptomic analyses elucidate the genetic basis of high meat yield in chickens.

INTRODUCTION: Investigating the genetic markers and genomic signatures related to chicken meat production by combing multi-omics methods could provide new insights into modern chicken breeding technology systems. OBJECT: Chicken is one of the most efficient and environmentally friendly livestock, especially the fast-growing white-feathered chicken (broiler), which is well known for high meat yield, but the underlying genetic basis is poorly understood. METHOD: We generated whole-genome resequencing of three purebred broilers (n = 748) and six local breeds/lines (n = 114), and sequencing data of twelve chicken breeds (n = 199) were obtained from the NCBI database. Additionally, transcriptome sequencing of six tissues from two chicken breeds (n = 129) at two developmental stages was performed. A genome-wide association study combined with cis-eQTL mapping and the Mendelian randomization was applied. RESULT: We identified > 17 million high-quality SNPs, of which 21.74% were newly identified, based on 21 chicken breeds/lines. A total of 163 protein-coding genes underwent positive selection in purebred broilers, and 83 genes were differentially expressed between purebred broilers and local chickens. Notably, muscle development was proven to be the major difference between purebred broilers and local chickens, or ancestors, based on genomic and transcriptomic evidence from multiple tissues and stages. The MYH1 gene family showed the top selection signatures and muscle-specific expression in purebred broilers. Furthermore, we found that the causal gene SOX6 influenced breast muscle yield and also related to myopathy occurrences. A refined haplotype was provided, which had a significant effect on SOX6 expression and phenotypic changes. CONCLUSION: Our study provides a comprehensive atlas comprising the typical genomic variants and transcriptional characteristics for muscle development and suggests a new regulatory target (SOX6-MYH1s axis) for breast muscle yield and myopathy, which could aid in the development of genome-scale selective breeding aimed at high meat yield in broiler chickens.

Assessment the effect of genomic selection and detection of selective signature in broilers.

Due to high selection advances and shortened generation interval, genomic selection (GS) is now an effective animal breeding scheme. In broilers, many studies have compared the accuracy of different GS prediction methods, but few reports have demonstrated phenotypic or genetic changes using GS. In this study, the paternal chicken line B underwent continuous selection for 3 generations. The chicken 55 k SNP chip was used to estimate the genetic parameters and detect genomic response regions by selective sweep analysis. The heritability for body weight (BW), meat production, and abdominal fat traits were ranged from 0.12 to 0.38. A high genetic correlation was found between BW and meat production traits, while a low genetic correlation (<0.1) was found between meat production and abdominal fat traits. Selection resulted in an increase of about 516 g in BW and 140 g in breast muscle weight. Percentage of breast muscle and whole thigh were increased 0.8 to 1.5%. No change was observed in abdominal fat percentage. The genomic estimated breeding value advances was positive for BW and meat production (except whole thigh percentage), while negative for abdominal fat percentage. By selective sweep analysis, 39 common chromosomal regions and 102 protein coding genes were found to be influenced, including MYH1A, MYH1B, and MYH1D of the MYH gene family. Tight junction pathway as well as myosin complex related terms were enriched. This study demonstrates the effective use of GS for improvements in BW and meat production in chicken line B. Further, genomic regions, responsive to intensive genetic selection, were identified to contain genes of the MYH family.

Integrated metabolomics and lipidomics evaluate the alterations of flavor precursors in chicken breast muscle with white striping symptom.

White striping (WS) is the most common myopathy in the broiler chicken industry. To reveal flavor changes of WS meat objectively, flavor precursors of WS breast muscle were evaluated systematically with integrated metabolomics and lipidomics. The results showed that WS could be distinguished from normal controls by E-nose, and four volatile compounds (o-xylene, benzene, 1,3-dimethyl, 2-heptanone and 6-methyl and Acetic acid and ethyl ester) were detected as decreased compounds by gas chromatography-mass spectrometry. Lipidomic analysis showed that WS breast fillets featured increased neutral lipid (83.8%) and decreased phospholipid molecules (33.2%). Targeted metabolomic analysis indicated that 16 hydrophilic metabolites were altered. Thereinto, some water-soluble flavor precursors, such as adenosine monophosphate, GDP-fucose and L-arginine increased significantly, but fructose 1,6-bisphosphate and L-histidine significantly decreased in the WS group. These results provided a systematic evaluation of the flavor precursors profile in the WS meat of broiler chickens.

Identification of Major Loci and Candidate Genes for Meat Production-Related Traits in Broilers.

BACKGROUND: Carcass traits are crucial characteristics of broilers. However, the underlying genetic mechanisms are not well understood. In the current study, significant loci and major-effect candidate genes affecting nine carcass traits related to meat production were analyzed in 873 purebred broilers using an imputation-based genome-wide association study. RESULTS: The heritability estimates of nine carcass traits, including carcass weight, thigh muscle weight, and thigh muscle percentage, were moderate to high and ranged from 0.21 to 0.39. Twelve genome-wide significant SNPs and 118 suggestively significant SNPs of 546,656 autosomal variants were associated with carcass traits. All SNPs for six weight traits (body weight at 42 days of age, carcass weight, eviscerated weight, whole thigh weight, thigh weight, and thigh muscle weight) were clustered around the 24.08 Kb region (GGA24: 5.73-5.75 Mb) and contained only one candidate gene (DRD2). The most significant SNP, rs15226023, accounted for 4.85-7.71% of the estimated genetic variance of the six weight traits. The remaining SNPs for carcass composition traits (whole thigh percentage and thigh percentage) were clustered around the 42.52 Kb region (GGA3: 53.03-53.08 Mb) and contained only one candidate gene (ADGRG6). The most significant SNP in this region, rs13571431, accounted for 11.89-13.56% of the estimated genetic variance of two carcass composition traits. Some degree of genetic differentiation in ADGRG6 between large and small breeds was observed. CONCLUSION: We identified one 24.08 Kb region for weight traits and one 42.52 Kb region for thigh-related carcass traits. DRD2 was the major-effect candidate gene for weight traits, and ADGRG6 was the major-effect candidate gene for carcass composition traits. Our results supply essential information for causative mutation identification of carcass traits in broilers.

Identification of QTL regions and candidate genes for growth and feed efficiency in broilers.

BACKGROUND: Feed accounts for about 70% of the total cost of poultry meat production. Residual feed intake (RFI) has become the preferred measure of feed efficiency because it is phenotypically independent of growth rate and body weight. In this study, our aim was to estimate genetic parameters and identify quantitative trait loci (QTL) for feed efficiency in 3314 purebred broilers using a genome-wide association study. Broilers were genotyped using a custom 55 K single nucleotide polymorphism (SNP) array. RESULTS: Estimates of genomic heritability for seven growth and feed efficiency traits, including body weight at 28 days of age (BW28), BW42, average daily feed intake (ADFI), RFI, and RFI adjusted for weight of abdominal fat (RFIa), ranged from 0.12 to 0.26. Eleven genome-wide significant SNPs and 15 suggestively significant SNPs were detected, of which 19 clustered around two genomic regions. A region on chromosome 16 (2.34-2.66 Mb) was associated with both BW28 and BW42, and the most significant SNP in this region, AX_101003762, accounted for 7.6% of the genetic variance of BW28. The other region, on chromosome 1 (91.27-92.43 Mb) was associated with RFI and ADFI, and contains the NSUN3 and EPHA6 as candidate genes. The most significant SNP in this region, AX_172588157, accounted for 4.4% of the genetic variance of RFI. In addition, a genomic region containing the gene AGK on chromosome 1 was found to be associated with RFIa. The NSUN3 and AGK genes were found to be differentially expressed in breast muscle, thigh muscle, and abdominal fat between male broilers with high and low RFI. CONCLUSIONS: We identified QTL regions for BW28 and BW42 (spanning 0.32 Mb) and RFI (spanning 1.16 Mb). The NSUN3, EPHA6, and AGK were identified as the most likely candidate genes for these QTL. These genes are involved in mitochondrial function and behavioral regulation. These results contribute to the identification of candidate genes and variants for growth and feed efficiency in poultry.

New insights into the associations among feed efficiency, metabolizable efficiency traits and related QTL regions in broiler chickens.

BACKGROUND: Improving the feed efficiency would increase profitability for producers while also reducing the environmental footprint of livestock production. This study was conducted to investigate the relationships among feed efficiency traits and metabolizable efficiency traits in 180 male broilers. Significant loci and genes affecting the metabolizable efficiency traits were explored with an imputation-based genome-wide association study. The traits measured or calculated comprised three growth traits, five feed efficiency related traits, and nine metabolizable efficiency traits. RESULTS: The residual feed intake (RFI) showed moderate to high and positive phenotypic correlations with eight other traits measured, including average daily feed intake (ADFI), dry excreta weight (DEW), gross energy excretion (GEE), crude protein excretion (CPE), metabolizable dry matter (MDM), nitrogen corrected apparent metabolizable energy (AMEn), abdominal fat weight (AbF), and percentage of abdominal fat (AbP). Greater correlations were observed between growth traits and the feed conversion ratio (FCR) than RFI. In addition, the RFI, FCR, ADFI, DEW, GEE, CPE, MDM, AMEn, AbF, and AbP were lower in low-RFI birds than high-RFI birds (P < 0.01 or P < 0.05), whereas the coefficients of MDM and MCP of low-RFI birds were greater than those of high-RFI birds (P < 0.01). Five narrow QTLs for metabolizable efficiency traits were detected, including one 82.46-kb region for DEW and GEE on Gallus gallus chromosome (GGA) 26, one 120.13-kb region for MDM and AMEn on GGA1, one 691.25-kb region for the coefficients of MDM and AMEn on GGA5, one region for the coefficients of MDM and MCP on GGA2 (103.45-103.53 Mb), and one 690.50-kb region for the coefficient of MCP on GGA14. Linkage disequilibrium (LD) analysis indicated that the five regions contained high LD blocks, as well as the genes chromosome 26 C6orf106 homolog (C26H6orf106), LOC396098, SH3 and multiple ankyrin repeat domains 2 (SHANK2), ETS homologous factor (EHF), and histamine receptor H3-like (HRH3L), which are known to be involved in the regulation of neurodevelopment, cell proliferation and differentiation, and food intake. CONCLUSIONS: Selection for low RFI significantly decreased chicken feed intake, excreta output, and abdominal fat deposition, and increased nutrient digestibility without changing the weight gain. Five novel QTL regions involved in the control of metabolizable efficiency in chickens were identified. These results, combined through nutritional and genetic approaches, should facilitate novel insights into improving feed efficiency in poultry and other species.

Phase-shifted type-IIa fiber Bragg gratings for high-temperature laser applications.

Phase-shifted Bragg gratings have been extensively implemented in superior in-fiber bandpass filters or wavelength selectors, although high-temperature operation remains a challenge. We propose a phase-shifted type-IIa fiber Bragg grating (PSBG-IIa), which can conduct a notch signal as narrow as 4.8 pm within the stopband. The notch's spectrum and wavelength can be adjusted according to the flexible design of the phase-mask translation. Using the thermal resistance as well as the narrow band notch, the PSBG-IIa is implemented in a distributed Bragg reflector laser structure to demonstrate a single longitudinal mode and single polarization laser output that can stabilize robustly at 500 °C. The results demonstrate that the proposed device qualifies as a high-quality optical regulator, without compromise, in the high-temperature region.

Dual-color distributed Bragg reflector fiber laser with simultaneous emission at 1.06 µm and 1.55 µm wavebands.

A dual-wavelength fiber laser is proposed by the use of Er/Yb co-doped active fiber and a pair of novel Bragg-grating reflectors. The Bragg grating presents strong reflections of both third and second harmonics in accordance with the gain of ytterbium and erbium ion, respectively, enabling the laser emitted at 1.06 µm and 1.55 µm wavebands simultaneously with a short linear cavity structure. Adjusting reflectivity of the harmonics in the grating can influence the intensity contrast of the two lasing signals. Optimization on the compactness and brightness of the laser is achieved by adapting the harmonic wavelengths with the optimal gain windows of the ytterbium and erbium ions.

Formation and Applications of the Secondary Fiber Bragg Grating.

Being one of the most proven fiber optic devices, the fiber Bragg grating has developed continually to extend its applications, particularly in extreme environments. Accompanying the growth of Type-IIa Bragg gratings in some active fibers, a new resonance appears at the shorter wavelength. This new type of grating was named "secondary Bragg grating" (SBG). This paper describes the formation and applications of the SBGs. The formation of the SBG is attributed to the intracore Talbot-type-fringes as a result of multi-order diffractions of the inscribing beams. The SBG presents a variety of interesting characteristics, including dip merge, high-temperature resistance, distinct temperature response, and the strong higher-order harmonic reflection. These features enable its promising applications in fiber lasers and fiber sensing technology.

1-µm-wavelength ytterbium-doped fiber laser based on the third harmonic reflection in secondary-type-In Bragg gratings.

In this Letter, a 1-µm-wavelength fiber laser is proposed through the use of the ytterbium-doped active fiber and the third harmonic Bragg reflectors. Benefiting from the ratio below 0.5 between the core diameter of the fiber and the Talbot length of the UV fringes, enabling the formation of the secondary-type-In grating, the reflector with reflectivity higher than 95% at two-thirds of the designing Bragg wavelength can be fabricated within 2 min. Inherited by the lower temperature and strain sensitivity of the third harmonic grating, the laser has good wavelength stability and could be used as a reliable laser resource. In addition, this Letter can also be expected to provide great flexibility in fiber laser wavelength design.

Thermally triggered fiber lasers based on secondary-type-In Bragg gratings.

The secondary-type-In grating formed in a small-core photosensitivity active fiber is discovered and investigated. Due to the different grating types, the transmission dip of a secondary grating structure chases and integrates with the type-In grating structure as the temperature increases, which strengthens the reflectivity of the grating. By use of these secondary-type-In gratings as Bragg reflectors, a thermally activated distributed Bragg reflector (DBR) fiber laser is proposed, which can be potentially used in high-temperature alarms and sensors.

Spectral tuning of the diameter-dependent-chirped Bragg gratings written in microfibers.

Chirped fiber Bragg gratings can straightforwardly and efficiently be fabricated onto microfibers with a uniform phase mask. Due to the variation of the propagating constant, which depends on the fiber diameter, the broadband spectrum of the grating can be formed. Depending on the different responses to the ambient refractive index in different parts of the grating, the bandwidth of the grating can be tuned by changing the surrounding solution. In addition, by being partly immersed in a liquid, the diameter-chirped Bragg grating can act as a broadband Fabry-Perot interferometer, whose spectrum can be tuned by means of controlling the liquid level and ambient refractive index.

Type IIa Bragg grating based ultra-short DBR fiber laser with high temperature resistance.

We report on the fabrication of a thermally resistant ultra-short distributed Bragg reflector (DBR) fiber laser based on the photo inscription of two wavelength-matched type IIa gratings in a thin-core Er-doped fiber. With continuous UV exposure, each Bragg reflector initially grows as a type I grating, followed by decay in strength, and then re-grows as a type IIa grating with enhanced thermal resistance. The DBR laser, with an entire length of 13 mm, can stably operate at 600°C with single longitude mode, which provides potential applications in high temperature environments.

[Clinical study on treatment of acute paraquat poisoning].

OBJECTIVE: To investigate the clinical therapeutic effect of methylprednisolone combined with cyclophosphamide and Etanercept method on acute paraquat poisoning. METHODS: 136 patients with acute paraquat poisoning were divided into the normal therapy group and the intensive therapy group randomly. Methylprednisolone, cyclophosphamide and Etanercept were used in the intensive therapy group. Methylprednisolone 500 mg was given intravenously per day for continuous three days followed by 200 mg intravenous per day. Then methylprednisolone was decreased gradually 14 d or 21 d later according to the patient's condition. Cyclophosphamide 600 mg was given intravenously twice weekly for 2 weeks and Etanercept 25 mg was given hypodermic injection twice weekly for 3 weeks. Curative effect evaluation was done at 7, 14, 21 d and 12 weeks after therapy. RESULTS: The survival rate of the intensive therapy group was obviously higher than that of the normal therapy group (P<0.01) on 7, 4, 21 d and 12 weeks. The cure rate of the intensive group were 94.6% (intake dose<50 ml 20% paraquat solution), 75.0% (intake dose 50 approximately 100 ml 20% paraquat solution), 12.5% (intake dose>100 ml 20% paraquat solution) respectively, while the cure rate of the normal group were 16.7% (intake dose<50 ml 20% paraquat solution), 8.3% (intake dose 50 approximately 100 ml 20% paraquat solution), 0% (intake dose>100 ml 20% paraquat solution) respectively. The total cure rate of the intensive therapy group (78.3%) 12 weeks later was higher than that of the normal group (11.9%). CONCLUSION: Methylprednisolone combined with cyclophosphamide and Etanercept intensive therapy has the curative effect on acute paraquat poisoning.