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The introduction of exotic breeds and the cultivation of new lines by breeding companies have posed challenges to native chickens in South China, including loss of breed characteristics, decreased genetic diversity, and declining purity. Understanding the population genetic structure and genetic diversity of native chickens in South China is crucial for further advancements in breeding efforts. In this study, we analyzed the population genetic structure and genetic diversity of 321 individuals from 10 different breeds in South China. By comparing commercial chickens with native ones, we identified selection signatures occurring between local chickens and commercial breeds. The analysis of population genetic structure revealed that the native chicken populations in South China exhibited a considerable level of genetic diversity. Moreover, the commercial lines of Xiaobai chicken and Huangma chicken displayed even higher levels of genetic diversity, which distinguished them from other native varieties at the clustering level. However, certain individuals within these commercial varieties showed a discernible genetic relationship with the native populations. Notably, both commercial varieties also retained a significant degree of genetic similarity to their respective native counterparts. In order to investigate the genomic changes occurring during the commercialization of native chickens, we employed 4 methods (Fst, ROD, XPCLR, and XPEHH) to identify potential candidate regions displaying selective signatures in Southern Chinese native chicken population. A total of 168 (identified by Fst and ROD) and 86 (identified by XPCLR and XPEHH) overlapping genes were discovered. Functional annotation analysis revealed that these genes may be associated with reproduction and growth (SAMSN1, HYLS1, ROBO3, FGF14, PRSS23), musculoskeletal development (DNER, MYBPC1, DGKB, ORC1, KLF10), disease resistance and environmental adaptability (PUS3, CRB2, CALD1, USP15, SGCD, LTBP1), as well as egg production (ADGRB3, ACSF3). Overall, native chickens in South China harbor numerous selective sweep regions compared to commercial chickens, enriching valuable genomic resources for future genetic research and breeding conservation. [ABSTRACT FROM AUTHOR]

Meat quality traits are essential for producing high-quality broilers, but the genetic improvement has been limited by the complexity of measurement methods and the numerous traits involved. To systematically understand the meat quality characteristics of different broiler breeds, this study collected data on slaughter performance, skin color, fat deposition, and meat quality traits of 434 broilers from 12 different breeds in South China. The results showed that there was no significant difference in the live weight and slaughter weight of various broiler breeds at their respective market ages. Commercial broiler breeds such as Xiaobai and Huangma chickens had higher breast muscle and leg muscle rates. The skin and abdominal fat of Huangma chickens cultivated in the consumer market in South China exhibited significantly higher levels of yellowness compared to other varieties. Concerning fat traits, we observed that Wenchang chickens exhibited a strong ability to fat deposition, while the younger breeds showed lower fat deposition. Additionally, there were significant positive correlations found among different traits, including traits related to weight, traits related to fat, and skin color of different parts. Hierarchical clustering analysis revealed that fast-growing and large broiler Xiaobai chickens formed a distinct cluster based on carcass characteristics, skin color, and meat quality traits. Principal component analysis (PCA) was used to extract multiple principal components as substitutes for complex meat quality indicators, establishing a chicken meat quality evaluation model to differentiate between different breeds of chickens. At the same time, we identified 46, 22, and 20 SNP loci and their adjacent genes that were significantly associated with muscle mass traits, fat deposition, and skin color through genome-wide association studies (GWAS). The above results are helpful for systematically understanding the differences and characteristics of meat quality traits among different breeds. [ABSTRACT FROM AUTHOR]

As a Chinese local chicken breed, Hongshan chickens have 2 kinds of tail feather phenotypes, normal and taillessness. Our previous studies showed that taillessness was a sex-linked dominant trait. Abnormal development of the tail vertebrae could be explained this phenomenon in some chicken breeds. However, the number of caudal vertebrae in rumpless Hongshan chickens was normal, so rumplessness in Hongshan chicken was not related to the development of the caudal vertebrae. Afterwards, we found that rumplessness in Hongshan was due to abnormal development of tail feather rather than abnormal development of caudal vertebrae. In order to understand the genetic foundation of the rumplessness of Hongshan chickens, we compared and reanalyzed 2 sets of data in normal and rumpless Hongshan chickens from our previous studies. By joint analysis of genome-wide selection signature analysis and genome-wide association approach, we found that 1 overlapping gene (EDIL3) and 16 peak genes (ENSGALG00000051843, ENSGALG00000053498, ENSGALG00000054800, KIF27, PTPRD, ENSGALG00000047579, ENSGALG00000041052, ARHGEF28, CAMK4, SERINC5, ENSGALG00000050776, ERCC8, MCC, ADAMTS19, ENSGALG00000053322, CHRNA8) located on the Z chromosome was associated with the rumpless trait. The results of this study furtherly revealed the molecular mechanism of the rumpless trait in Hongshan chickens, and identified the candidate genes associated with this trait. Our results will help to improve the shape of chicken tail feathers and to rise individual economic value in some specific market in China. [ABSTRACT FROM AUTHOR]

• Constructed an operation architecture of the coupling of energy supply and demand. • Established the comprehensive demand response mechanism based on time-sharing energy prices. • Established the minimum carbon emission cost economic scheduling model as an objective function. • The scheduling method could achieve the goal of low-carbon economic dispatch. Aiming at the problems of low energy utilization and environmental pollution in China's livestock and poultry breeding industry under the carbon peaking and carbon neutralization goals, this paper proposes an optimal scheduling model for multi-energy coupling integrated energy system with ladder-type carbon trading mechanism and demand response. First, based on the construction of a reward and punishment model with ladder-type carbon trading mechanism, this paper explores the potential interaction between the coupling ability of multiple heterogeneous energy sources and carbon emissions in consideration of the impact of carbon capture equipment on carbon emissions. Second, in view of the diversity and complexity of demands for agricultural energy supply, the energy supply side equipment model and the comprehensive demand response model of electricity, heat, and gas are established, and a low-carbon economic scheduling model of integrated agricultural energy system is proposed, aiming at minimizing the total operation cost of the system. Finally, the model is solved by CPLEX, and the coupling system of a 6-node power distribution network, a 6-node gas network, and a 4-node heat supply network is used to verify the effectiveness of the proposed model and method and optimize the operation of the integrated agricultural energy system. [ABSTRACT FROM AUTHOR]

Yellow-feather broilers take a large portion of poultry industry in China due to its meat characteristics. Improving the growth traits of yellow-feathered broilers will have great significance for the Chinese poultry market. The current study was designed to investigate the potential genetic factors using the weighted single-step genome-wide association study (wssGWAS) method, which takes consideration of more factors including pedigree, sex, environment and has more accuracy than traditional GWAS. The yellow-feather dwarf chickens from Wens Nanfang Poultry Breeding Co. Ltd. were revolved to recode 9 growth traits: Average daily gain (ADG), body weight (BW) at 45 d, 49 d, 56 d, 63 d, 70 d, 77 d, 84 d, 91 d for analysis. For the results, the region 4.63 to 5.03 Mb on chromosome 15, which was the QTL overlapped in BW45, BW49, BW56, BW63, BW84, might be the crucial genetic region for growth traits. Seven GO terms and 3 KEGG pathways, GO:0005200, GO:0005882, GO:0045111, GO:0099513, GO:0099081, GO:0099512, GO:0099080, KEGG:gga04020, KEGG:gga04540, KEGG:gga04210, were detected to relevant with growth traits. The genes enriched in these biological processes (NRAS, TUBB1, ADORA2B, NTRK3, NGF, TNNC2, F-KER, LOC429492, LOC431325, LOC431324, LOC396480) might have the function in growth of yellow-feather broilers. [ABSTRACT FROM AUTHOR]

Ornithobacterium rhinotracheale (ORT) has been associated with avian respiratory disease. On coinfection with other pathogens, ORT can cause serious health problems in avian species, leading to financial losses. To monitor the serologic prevalence of ORT in chicken flocks in China, 1,280 sera were collected to determine ORT antibodies among 64 flocks from 15 provinces of China using a commercial ELISA kit. The overall seroprevalence of ORT among the birds tested was 44.06%. In younger chickens, the serum positive rate was lower than that in older chickens, and with increased age, the serum positive rates increased. Older chickens had not only higher positive rates but also higher antibody levels. These data indicated that ORT infections were common in China. Because an ORT vaccine is currently not available, good disease management and biosecurity measures are required for effective disease control. [ABSTRACT FROM AUTHOR]

The large economic losses caused by leg disorders have raised concerns in the broiler industry. Several types of leg disorders in broilers have been identified, such as tibial dyschondroplasia (TD), femoral head necrosis (FHN), and valgus-varus deformity (VVD). In this study, phenotypic changes associated with VVD were examined using clinical diagnosis, anatomical examination, measured growth performance, bone traits, and serum indicators. The incidence of VVD among the chicken population at a commercial facility in Tangshan China was 1.75% (n = 52,000), distributed about 1:1 (n = 122), between females and males. A majority of chickens were characterized by a unilaterally abnormality, while appropriately 17.6% by bilateral abnormality. Approximately 97.9% of affected broilers were classified as the "valgus" type. Growth traits, including body weight, shank length, and shank girth, were significantly lower in chickens with VVD, while tibia and metatarsal bone indexes were about 1.3-fold higher in the affected birds than in the normal birds. Bone mineral density, bone breaking strength, and several serum indicators were significantly different between affected and normal broilers. Sparse and disarranged bony trabecular was observed in abnormal broilers by histological analysis. Generally, leg disorders are associated with compromised growth, bone quality, bone structure, and lipid metabolism. This study provides a reference for clinical diagnosis of VVD and lays a foundation for exploring its underlying mechanisms. [ABSTRACT FROM AUTHOR]

Lack of clean energy supply remains a challenge in China, particularly in rural areas with large population. Biogas production from anaerobic digestion of biomass is an efficient technology for energy strategy in China. This paper reviews the importance of household biogas in China and discusses the regional differentiation of rural household biogas (RHB), and related driving factors. Gray correlation analysis showed that regional differentiation of RHB exhibited the highest correlation degree with temperature (0.889), followed by raw materials, rural population, and levels of income and education. According to the total biogas production in China, the development regions of RHB was separated into Region 1, Region 2 and Region 3. The highest development level of RHB was found in Region 2 with a total biogas production of 1.2×10 10 m 3 , accounting for 77.6% of the total TBP of China in 2012. Moreover, the RHB development levels in Region 1 and Region 3 were 1.84×10 9 and 1.69×10 9 m 3 , respectively. Basing on the results of regional differentiation of RHB and characteristic of the primary influence factors in different regions, this study proposes that RHB development must be further promoted by combining actual situation of different regions to avoid blind development. [ABSTRACT FROM AUTHOR]

Subgroup K avian leukosis virus (ALV-K) is a new subgroup of avian leukosis virus (ALV) first identified in Chinese indigenous chickens in recent years. In this study, an ALV-K strain was isolated from Luhua chicken in Shandong province, China, and designated SD20LH01. The full-length genomic sequence of SD20LH01 was 7491 bp, which had the highest homology with ALV-K reference strains GDFX0601, GDFX0602 and GDFX0603. The nucleotide homology of env gene of SD20LH01 with reference strains of subgroup A, B, C, D, E, and J was ranged from 57.1 to 93.2%, while 94.1 to 99.4% with other ALV-K reference strains. The nucleotide difference of SD20LH01 mainly clustered with gp85 gene and U3 sequence when compared with the reference strain of ALV-K. In order to investigate the pathogenicity of SD20LH01, SPF chicken embryos were infected by yolk sac inoculation, and 1-day-old chickens were infected by intraperitoneal inoculation of SD20LH01. The results showed that yolk sac inoculation of SD20LH01 could induce persistent viremia, growth retardation and reduce the immune response to NDV and AIV-H9 vaccines. However, intraperitoneal inoculation in 1-day-old chickens could only induce a low level of viremia. In addition, no tumors were found in infected chickens during the animal experiments. This study enriched the genomic sequence data of ALV-K isolated in Chinese indigenous chickens, and laid a foundation for further study on the pathogenesis and prevention of ALV-K. [ABSTRACT FROM AUTHOR]

In 2013, Tembusu virus (TMUV) infection was successively observed on several breeding duck farms in Shandong province, China. Affected ducks showed consistently acute anorexia, diarrhea and egg production drop. 125 hatching eggs produced by TMUV infected breeding ducks from four duck farms were collected. Among them, 35 hatching eggs were selected randomly from all before incubation for vitelline membrane samples collection. The rest of 90 hatching eggs were incubated routinely. As a result, 16 hatching eggs were found non-embryonated, 28 duck embryos died during incubation and 46 newly hatched ducklings were obtained. Vitelline membranes of non-embryonated hatching eggs, vitelline membrane, brain or liver samples of dead embryos and brain samples of newly hatched ducklings were collected for virus detection. Samples collected from one egg, embryo or duckling were treated as one. Consequently, 18 of 35 (51.43%) hatching eggs, 2 of 16 (12.50%) non-embryonated duck eggs, 17 of 28 (60.71%) dead duck embryos and 5 of 46 (10.87%) newly hatched ducklings were detected positive for TMUV using NS3-based RT-PCR. Overall, 42 of 125 (33.6%) eggs were positive for TMUV. A virus strain, designated as TMUV-SDDE, was isolated from one of these dead duck embryos which were detected TMUV positive. The results of phylogenetic analysis showed that E gene of TMUV-SDDE virus was closely related to other TMUV strains isolated in China during 2010–2013. Pathogenicity studies showed that TMUV-SDDE strain was virulent to ducklings. This is the first report that TMUV is isolated from duck embryos. The findings provide evidence of possible vertical transmission of TMUV from breeding ducks to ducklings. [ABSTRACT FROM AUTHOR]

China is the world's largest livestock and poultry breeding country. Heavy metal trace element additives are widely used to prevent animal diseases and promote their growth. China produces approximately 3.8 billion tons of livestock and poultry manure annually, and untreated livestock and poultry manure causes a large amount of heavy metal elements to enter the soil environment. Currently, there is limited research on the accumulation of heavy metals in the soil due to the continuous application of livestock and poultry manure, the resulting pollution risk and the negative effects on soil ecology sustainability. This study thoroughly investigated the effects of livestock and poultry manure on the composition and function of soil microbial, and heavy metal resistance genes using 16S and metagene sequencing and 6 years of field experiments. The application of livestock and poultry manure for 6 consecutive years increased the accumulation of zinc (Zn), copper (Cu), mercury (Hg), and chromium (Cr) in the soil at the experimental sites, and cadmium (Cd) and Hg had higher potential risk levels (single potential ecological risk coefficients (E r i) of Hg and Cd were 190.49–336.52 and 385.43–468.52, respectively). Firmicutes and Zoopagomycota were significantly correlated with the soil Zn and Cd contents and pH. After continuous application of manure, the relative abundance of Hg resistance genes (merA) in soil increased by 7.3–8.2 times compared with inorganic feitilizer treatment (IF), and Cu resistance genes (copF and actP) increased by 2.45–5.45 times and 3.8–4.6 times. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) and metagenomic function prediction indicated that resistance genes, antioxidant response, and metal output played an important role in heavy metal bioresistance and biotransformation. This work presented heavy metal contents, microbial composition and resistance genes in continuous application of livestock and poultry manure in China, and these data will be of great use in the surveillance, maintenance, and biological removal of heavy metals in manure. [Display omitted] • Continuous application of manure, soil Cd and Hg had higher potential risk levels. • The relative abundance of soil Mortierella was increased. • Relative abundance of merA and actP was increased by 7.3–8.2 and 3.8–4.6 times. • Resistance genes, etc. played an important role in heavy metal biotransformation. [ABSTRACT FROM AUTHOR]

Pullorum disease is characterized by white diarrhea resulting from infection by S. Pullorum, but arthritis associated with S. Pullorum infection has become increasingly frequent recently, especially in Chinese native chicken flocks. In this study, we isolated and identified 4 S. Pullorum strains from the Qingjiaoma chicken breeders with arthritis symptoms. The LD 50 of the isolate 20JS04 was 1.33 × 106 CFU, which was considered as a highly virulent strain in chicks. Reproducible arthritis symptoms were observed in the experimentally chickens infected with the isolate 20JS04, and the disease occurrence was 27.78% (5/18). In addition to the characteristics of high virulence and induced-arthritis, our results confirmed that the arthritis-causing isolate 20JS04 had greater negative impact on BW, ADFI, and ADG, compared with the white diarrhea-causing S. Pullorum standard strain CVCC526 (P < 0.05). These results suggest that the pathogenic diversity of S. Pullorum in China deserves more attention and stringent measures should be taken to control salmonellosis. [ABSTRACT FROM AUTHOR]

[Display omitted] • In-situ synthesis/purification integration (ISSPI) strategy was adopted for NH 4 + and PO 4 3- removal. • The strategy was achieved based on constructing Mg-doped tricalcium aluminate (Mg-C 3 A). • Mg-C 3 A exhibited excellent capacities for NH 4 + (43.0 mg·g−1) and PO 4 3- (20.2 mg·g−1). • The hydration properties of Mg-C 3 A played vital roles in the ions removal/recovery. • ISSPI strategy using Mg-C 3 A was compelling for authentic wastewater treatment. Simultaneous capture of ammonium (NH 4 +-N) and phosphate (PO 4 3−-P) in digested piggery wastewater is of great urgency yet remains a challenge. Recently, the in-situ synthesis/purification integration (ISSPI) strategy, with the essence of converting contaminations to high value-added products, has aroused great enthusiasm in the environmental remediation realm. In the present work, we employed ISSPI method for simultaneous elimination and recovery of NH 4 + and PO 4 3- from digested piggery wastewater based on the construction of a novel material system, i.e. , Mg-doped tricalcium aluminate (Mg-C 3 A), which coupled the features of cement-based material tricalcium aluminate (Ca 3 Al 2 O 6 , C 3 A) and Mg dopants. The released metal cations (Ca2+, Mg2+, and Al(OH) 4 −) of Mg-C 3 A were expected to act as precipitation agents to capture NH 4 + and PO 4 3− via the formation of Ca(NH 4) 2 (HPO 4) 2, MgHPO 4 ·3H 2 O or AlPO 4 ; OH− established an alkaline environment for the enhancement of NH 4 + removal via neutralization; Mg2+ played a major role in the recovery of NH 4 + and PO 4 3−, with the formation of valuable struvite as fertilizer. Benefited by these functions, Mg-C 3 A exhibited superior removal capacity for NH 4 + (43.0 mg·g−1) and PO 4 3− (20.2 mg·g−1). More importantly, the ISSPI method using Mg-C 3 A was prospective to be applied for authentic effluent treatment as demonstrated by response surface methodology (RSM), with the concentration of both ions down to the discharge standard of livestock and poultry breeding, China (80 mg·L−1 for NH 4 +; 8 mg·L−1 for PO 4 3−). This research provided an alternative and promising approach for the simultaneous removal and recovery of NH 4 + and PO 4 3− from digested piggery effluent, shedding light on environmental remediation. [ABSTRACT FROM AUTHOR]

• A total of 147 S. Enteritidis were isolated from a poultry breeding enterprise. • All S. Enteritidis belonged to ST11, and further divided into 4 rSTs and 64 cgSTs. • SNPs typing suggested the presence of vertical transmission of S. Enteritidis. • Heterogeneous antimicrobial resistance was present in clonally related strains. • One bla CTX-M-14 -carrying plasmid and two virulence-resistance plasmids were characterized. Human salmonellosis caused by the consumption of eggs and chicken meat contaminated with Salmonella Enteritidis has become a continuing public health concern worldwide. In this study we adopted whole genome sequencing (WGS) to determine the genetic relationship and antimicrobial resistance of S. enterica strains isolated from a poultry breeding enterprise that consists of one breeding chicken farm, one egg hatchery and one commercial chicken farm. A total of 148 S. enterica including 147 S. Enteritidis strains were isolated from 2100 fecal swab samples, with 16 (5.3 %, 16/300) from breeding chicken farm, 38 (4.2 %, 38/900) from egg hatchery and 94 (10.4 %, 94/900) from commercial chicken farm. WGS revealed that all 147 S. Enteritidis strains belonged to ST11, and further divided into 4 different ribosomal STs and 64 core genome STs. Single nucleotide polymorphism typing suggested the presence of the vertical transmission of S. Enteritidis from breeding chicken to commercial chicken. Three different antimicrobial-resistant plasmids including one bla CTX-M-14 -carrying plasmid and two virulence-resistance plasmids were characterized, resulting in the heterogeneous antimicrobial resistance of clonally related S. Enteritidis strains. Routine surveillance in breeding chicken farms is conducive to the control of S. Enteritidis from farm to fork. [ABSTRACT FROM AUTHOR]