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Abstract Background Although multiple chicken genomes have been assembled and annotated, the numbers of protein-coding genes in chicken genomes and their variation among breeds are still uncertain due to the low quality of these genome assemblies and limited resources used in their gene annotations. To fill these gaps, we recently assembled genomes of four indigenous chicken breeds with distinct traits at chromosome-level. In this study, we annotated genes in each of these assembled genomes using a combination of RNA-seq- and homology-based approaches. Results We identified varying numbers (17,497–17,718) of protein-coding genes in the four indigenous chicken genomes, while recovering 51 of the 274 “missing” genes in birds in general, and 36 of the 174 “missing” genes in chickens in particular. Intriguingly, based on deeply sequenced RNA-seq data collected in multiple tissues in the four breeds, we found 571 ~ 627 protein-coding genes in each genome, which were missing in the annotations of the reference chicken genomes (GRCg6a and GRCg7b/w). After removing redundancy, we ended up with a total of 1,420 newly annotated genes (NAGs). The NAGs tend to be found in subtelomeric regions of macro-chromosomes (chr1 to chr5, plus chrZ) and middle chromosomes (chr6 to chr13, plus chrW), as well as in micro-chromosomes (chr14 to chr39) and unplaced contigs, where G/C contents are high. Moreover, the NAGs have elevated quadruplexes G frequencies, while both G/C contents and quadruplexes G frequencies in their surrounding regions are also high. The NAGs showed tissue-specific expression, and we were able to verify 39 (92.9%) of 42 randomly selected ones in various tissues of the four chicken breeds using RT-qPCR experiments. Most of the NAGs were also encoded in the reference chicken genomes, thus, these genomes might harbor more genes than previously thought. Conclusion The NAGs are widely distributed in wild, indigenous and commercial chickens, and they might play critical roles in chicken physiology. Counting these new genes, chicken genomes harbor more genes than originally thought.

Abstract Background Although many studies have been done to reveal artificial selection signatures in commercial and indigenous chickens, a limited number of genes have been linked to specific traits. To identify more trait-related artificial selection signatures and genes, we re-sequenced a total of 85 individuals of five indigenous chicken breeds with distinct traits from Yunnan Province, China. Results We found 30 million non-redundant single nucleotide variants and small indels (

Abstract Many lines of evidence indicate that red jungle fowl (RJF) is the primary ancestor of domestic chickens. Although multiple versions of RJF (galgal2-galgal5 and GRCg6a) and commercial chickens (GRCg7b/w and Huxu) genomes have been assembled since 2004, no high-quality indigenous chicken genomes have been assembled, hampering the understanding of chicken domestication and evolution. To fill the gap, we sequenced the genomes of four indigenous chickens with distinct morphological traits in southwest China, using a combination of short, long and Hi-C reads. We assembled each genome (~1.0 Gb) into 42 chromosomes with chromosome N50 90.5–90.9 Mb, amongst the highest quality of chicken genome assemblies. To provide resources for gene annotation and functional analysis, we also sequenced transcriptomes of 10 tissues for each of the four chickens. Moreover, we corrected many mis-assemblies and assembled missing micro-chromosomes 29 and 34–39 for GRCg6a. Our assemblies, sequencing data and the correction of GRCg6a can be valuable resources for studying chicken domestication and evolution.

Chicken soup is popular among consumers because of its delicious taste, strong flavor, and abundant nutritional value. Twenty-four Yunnan local hens were stewed by adding different amounts of NaCl [1.5, 2, 2.5, 3%, m/m, calculated based on chicken carcass weight; chicken: water = 1:2 (m/m)] to study the effect of salt addition on taste- and flavor-related compounds in chicken soup. Sensory evaluation results showed that the 2 and 2.5% NaCl treatment groups had higher scores. Water-soluble small molecule compounds were detected by LC-Q/TOF-MS based metabolomics approach, among which amino acids and their derivatives, nucleic acids, and small peptides were the main components. The concentration of Water-soluble small molecule substances in chicken soup samples with different salt additions showed a clear trend of separation and reached the highest in the 2.5% NaCl treatment group. Volatile flavor compounds in the chicken soup were analyzed by HS-SPME-GC–MS, including aldehydes, and alcohols, and the relative concentration of flavor compounds in the 2.5% salt treatment group was the highest. In summary, the addition of salt could improve the overall flavor of chicken broth, and the optimal salt addition of NaCl in chicken soup is 2.5%.

Objective: To investigate the flavor difference of chicken bone homogenate before and after enzymatic hydrolysis. Methods: On the basis of single factor experiments, response surface experimental design was used to optimize the enzymatic hydrolysis process of chicken bone homogenate. Then, the amino acid automatic analyzer and headspace solid phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS) combined with taste activity value (TAV) and odor activity value (OAV) were used to carry out the key free amino acids and volatile aroma compounds for the flavor. Results: The optimal process was as follows: Time 5.1 h, enzyme addition 0.61%, solid-liquid ratio 1:3 g/mL, hydrolysis degree 33.68%±1.53%. The degree of hydrolysis was verified (33.24%±0.61%). A total of 13 free amino acids had TAV greater than 1, among which 8 free amino acids had TAV greater than 10, which made great contribution to the taste of chicken bone homogenate. A total of 92 volatile compounds were identified, 63 before and 66 after enzymatic hydrolysis. The 13 and 16 compounds of OAV≥1 was found before and after enzymatic hydrolysis, including 4 alcohols, 2 esters, 2 furans and 9 aldehydes. Before the enzymatic hydrolysis, the chicken bone homogenate had a strong fat flavor, but after the enzymatic hydrolysis, the fat flavor was weakened, and the roasted, bean and melon and meat flavor were increased at the same time, which increased the overall flavor. Conclusion: This paper would provide experimental basis for the study of flavor components of chicken bone homogenate before and after enzymatic hydrolysis.

Abstract Background Melanin is an important antioxidant in food and has been used in medicine and cosmetology. Chicken meat with high melanin content from black-boned chickens have been considered a high nutritious food with potential medicinal properties. The molecular mechanism of melanogenesis of skeletal muscle in black-boned chickens remain poorly understood. This study investigated the biological gene-metabolite associations regulating the muscle melanogenesis pathways in Wuliangshan black-boned chickens with two normal boned chicken breeds as control. Results We identified 25 differentially expressed genes and 11 transcription factors in the melanogenesis pathways. High levels of the meat flavor compounds inosine monophosphate, hypoxanthine, lysophospholipid, hydroxyoctadecadienoic acid, and nicotinamide mononucleotide were found in Wuliangshan black-boned chickens. Conclusion Integrative analysis of transcriptomics and metabolomics revealed the dual physiological functions of the PDZK1 gene, involved in pigmentation and/or melanogenesis and regulating the phospholipid signaling processes in muscle of black boned chickens.

Host defense peptides (HDPs) are an important first line of defense with antimicrobial and immunomodulatory properties. Selection for increased body weight is hypothesized to be related to reduced immune response. We studied the relationships among body weight, age, and the HDP expression patterns in intestine and immune organs. We used chickens with marked differences of body sizes. The non-selected Daweishan mini chickens showed the highest indexes of immune organs and the lowest concentrations of the plasma immune parameters C3, C4, IgA, and IgY, while the commercial Avian broiler showed the opposite results. The Daweishan mini chickens showed the highest mRNA expressions of HDP genes in small intestine followed by the semi-selected Wuding chickens. Compared with local breeds, broiler chickens showed higher mRNA expression of HDP genes in spleen, thymus, and bursa. Body weight and HDP expression levels were negatively correlated in the intestine and positively in the immune organs. Our results indicated that the HDP immune regulatory roles in small intestine acted as first line of defense in innate immunity in local breeds, and as an adaptive immunity in broiler chickens. Selection was associated with different expression expressions of HDP genes in breed-, age-, and organ-specific manners.

Abstract Background Intensive selection has resulted in increased growth rates and muscularity in broiler chickens, in addition to adverse effects, including delayed organ development, sudden death syndrome, and altered metabolic rates. The biological mechanisms underlying selection responses remain largely unknown. Non-artificially-selected indigenous Chinese chicken breeds display a wide variety of phenotypes, including differential growth rate, body weight, and muscularity. The Wuding chicken breed is a fast growing large chicken breed, and the Daweishan mini chicken breed is a slow growing small chicken breed. Together they form an ideal model system to study the biological mechanisms underlying broiler chicken selection responses in a natural system. The objective of this study was to study the biological mechanisms underlying differential phenotypes between the two breeds in muscle and liver tissues, and relate these to the growth rate and body development phenotypes of the two breeds. Results The muscle tissue in the Wuding breed showed higher expression of muscle development genes than muscle tissue in the Daweishan chicken breed. This expression was accompanied by higher expression of acute inflammatory response genes in Wuding chicken than in Daweishan chicken. The muscle tissue of the Daweishan mini chicken breed showed higher expression of genes involved in several metabolic mechanisms including endoplasmic reticulum, protein and lipid metabolism, energy metabolism, as well as specific immune traits than in the Wuding chicken. The liver tissue showed fewer differences between the two breeds. Genes displaying higher expression in the Wuding breed than in the Daweishan breed were not associated with a specific gene network or biological mechanism. Genes highly expressed in the Daweishan mini chicken breed compared to the Wuding breed were enriched for protein metabolism, ABC receptors, signal transduction, and IL6-related mechanisms. Conclusions We conclude that faster growth rates and larger body size are related to increased expression of genes involved in muscle development and immune response in muscle, while slower growth rates and smaller body size are related to increased general cellular metabolism. The liver of the Daweishan breed displayed increased expression of metabolic genes.

The growth hormone / insulin-like growth factor-1 (GH/IGF-1) pathway of the somatotropic axis is the major controller for growth rate and body size in vertebrates, but the effect of selection on the expression of GH/IGF-1 somatotropic axis genes and their association with body size and growth performance in farm animals is not fully understood. We analyzed a time series of expression profiles of GH/IGF-1 somatotropic axis genes in two chicken breeds, the Daweishan mini chickens and Wuding chickens, and the commercial Avian broilers hybrid exhibiting markedly different body sizes and growth rates. We found that growth rate and feed conversion efficiency in Daweishan mini chickens were significantly lower than those in Wuding chickens and Avian broilers. The Wuding and Daweishan mini chickens showed higher levels of plasma GH, pituitary GH mRNA but lower levels of hepatic growth hormone receptor (GHR) mRNA than in Avian broilers. Daweishan mini chickens showed significantly lower levels of plasma IGF-1, thigh muscle and hepatic IGF-1 mRNA than did Avian broilers and Wuding chickens. These results suggest that the GH part of the somatotropic axis is the main regulator of growth rate, while IGF-1 may regulate both growth rate and body weight. Selection for growth performance and body size have altered the expression profiles of somatotropic axis genes in a breed-, age-, and tissue-specific manner, and manner, and alteration of regulatory mechanisms of these genes might play an important role in the developmental characteristics of chickens.

Abstract Landslide in reservoirs imposes challenges to reservoir operation and dam safety management practices. The understanding of the landside mechanism during reservoir operation is crucial to landslide‐related risk migration. During the reservoir operation from 2018 to 2021, a massive landslide occurred with over 107 m3 in total volume on the bank of the NE reservoir. The surface movement characteristics before and after the occurrence of landslides in the NE reservoir in the region scale were detected and interpreted by Sentinel‐2 time series images. Experimental studies were conducted to investigate the geotechnical properties of the fine‐grained soil. The slope stability was evaluated for a typical slope profile considering the rising water level using the extended Bishop's simplified method, which was implemented in the code STAB‐UNSAT. It can be found that the landslide in the fine‐grained soil occurred simultaneously when the water level rose. The cumulative area of soil slope failure on the left bank of the NE reservoir increased continuously during the reservoir operation from 2018 to 2020, especially had a remarkable increment from August to October in 2019. The extended Bishop's simplified method provides a more rational method to evaluate the soil slope stability. The slope failure mechanism of the studied soil, that is, collapse–erosion–slide upon the rising reservoir water has been proposed.

The muscle composition of fatty acid has appeared as economically important traits due to their profound effect in meat quality. It has been shown that breed and age are most important factors effect on the muscle fatty acid composition in chickens. However, the molecular mechanism of fatty acid composition between the local Chinese chicken and commercial broiler which showed different growing rate is still unclear. To address the molecular mechanism underlying of muscle fatty acid composition, we comparably analyzed the fatty acid (FA) compositions in breast and thigh muscle with different ages by using an Agilent 6890 Series EGC system gas chromatograph equipped with a HP Innowax (30 m × 0.32 mm inside diameter) crosslinked polyethylene glycol column and FID detector (Agilent Technologies, USA) in Chinese native Wuding chickens and fast-growing Cobb broiler. Furthermore, quantitative reverse transcription PCR (Polymerase Chain Reaction) (RT-qPCR) was performed to investigate expression pattern of related candidate genes of fatty acid composition including D9D (Delta-9- Desaturase), FADS-2 (Fatty Acid Desaturase-2), FASN (Fatty Acid Synthatase), FATP-1 (fatty acid transport protein-1) and LPL (lipoprotein lipase) in relative breast and thigh muscles. The results showed that Wuding chickens showed both higher levels of SFA and USFA in two type muscles and two time points due to higher muscle lipid contents compare with Cobb broiler. Thus, Wuding chickens had approximately twice to three folds amount of MUFA (monounsaturated fatty acid) and PUFA (polyunsaturated fatty acid) and association with higher abundance expression of FADS-2, D9D and FATP-1 mRNA in two type of muscles and at two time points compare to broilers. In contrast, broiler showed low amount of MUFA and PUFA and association with higher abundance expression LPL mRNA in two type muscles and at two time points. Similar with reports in fish, rat and human, the FADS-2 and D9D gene code protein might played important role in operation as Δ6 or Δ9 desaturases to synthesis USFAs, including Oleic acid (C18:1), Linoleic acid (LA, C18:2n-6), a-Linolenic acid (ALA, C18:3 n-6) and Docosahexaenoic acid (C22:6n-3, DHA) in chicken muscles. Breed, age and muscle type had significantly influence on the muscle fatty acids composition and expression profiling of related lipid metabolism or fatty acid synthase gene. It is obviously that FADS-2, D9D, FATP-1, FASN and LPL genes play important role in regulating muscle fatty acid synthase and influence in meat quality in chicken. [ABSTRACT FROM AUTHOR]

Chemical composition traits, for instance, intramuscular fat (IMF) are an important meat quality trait. However, the molecular mechanisms related to IMF deposition in skeletal muscle have not previously been discussed for the native Yunnan (Wuding, Mini, and Wuliangshan) chicken breeds. In order to determine important discrepancies in IMF content, the chemical composition, and phenotypical variations in the gene expression of different breeds, five genes related to fat metabolism were analyzed in the muscle tissues of twenty-week-old native Yunnan breeds and the commercial broiler breed through quantitative reverse transcription PCR (qRT-PCR). The results were a clear statement that breeds had significant effects on LPL, UCP, FAS, FATP1, and PPAR-a gene expression. Higher (P<0.05) LPL gene, UCP gene, and FAS gene expression were observed in the muscles of the Wuding chicken. In comparison, higher (P<0.05) muscle FATP1 gene expression was found in the Mini chicken. The levels of PPAR-a gene (PPAR-a) mRNA were greatest (P<0.05) in the Wuding, moderate (P<0.05) in the Mini, and lowest in the Wuliangshan and the broiler. Chemical composition exhibited the lowest IMF content in the broiler thigh and breast muscle. In the thigh muscles, the Wuding chicken had the highest IMF content, while the Mini chicken had higher crude protein levels and ash content. In comparison, the breast muscles of the Wuliangshan had higher crude fat, protein, and ash content followed by those of the Wuding and the Mini. Variations in gene expression in different breeds and their relationship to chemical composition could contribute to the distinct fatty phenotype and characteristic flavor of native Yunnan chicken. The identification of variations in gene expression could facilitate targeted sequencing and genotyping efforts for advanced studies. [ABSTRACT FROM AUTHOR]

This project used a driving simulator to investigate patterns of drivers’ behavior during rainfall events using different geometries. We conducted a literature review of previous transportation studies using driving simulators and selected and analyzed extensive field data on major highway sections throughout Florida. The driving simulator at the University of Central Florida simulated the parameters such as speed and rainfall intensity observed in the field.Based on our analysis, we found that drivers are not affected by light rainfall events. However, heavy rainfall has a significant impact on their speed; on average they reduced their speed by 6 to 12 mph. Also, there is no interaction between rainfall intensity and either gender or age group. The female participants appeared to drive faster as compared to their male counterparts and the age group ranging from 16 to 21 year olds to be the most aggressive drivers. Eighty percent (80%) of the participants reported on the survey that they have experienced some level of hydroplaning while driving on the road. The simulator appears to provide identical results to the field data analysis, lending credence to the validity of using a driving simulator to investigate the pattern of drivers’ behavior during rainfall events.The researchers recommend further validation and refinement of this study. Continuation of this project may also help Florida Department of Transportation and other agencies with future decision making, such as Variable Message Signs, determining appropriate corrective measures on existing roadway sections, and/or designing future roadway sections to reduce hydroplaning.

The level of service is an important aspect of the operation and management at a railway passenger station. Particularly, the level of service in waiting room (LOSWR) is one of the most important influential factors in deciding passengers’ satisfaction. This paper proposes a model for finding the LOSWR based on the maximum number of passengers, and an Arena simulation model that simulates passengers’ aggregation behaviors in the waiting room is presented for analyzing the LOSWR. Through the simulation, we demonstrate how the passenger advanced arrival time and the accompany rate influence the maximum number of passengers and the LOSWR. In addition, the simulation also illustrates the effect utilities and the priority of different measures that can be used to improve the LOSWR. In detail, the simulation results demonstrate that the passenger advanced arrival time and advanced check-out time have much stronger effect utilities on the maximum number of passengers and the LOSWR than other discussed factors. The simulation suggests that the Arena is an effective simulation platform for analyzing complex passengers-related behaviors at railway passenger station.

The present study aims to evaluate the effects of enzyme, ultrasound, and ultrasound-assisted enzyme treatments at different ultrasound times on the quality of the spent-hen breast meat (SHBM). The enzyme, ultrasound, and ultrasound-assisted enzyme treatments had a slight adverse effect on the color and pH, significantly reduced shear force, and increased water holding capacity (WHC) (P < 0.05), but the shear force and WHC gradually worsened with the extension of ultrasound radiation time over 20 min. Low-field NMR results showed that ultrasound-assisted treatment increases the percentage of immobilized water (T21) in the meat by promoting the migration and uniform distribution of water; thus, improving the WHC of meat. Myofibrillar fragmentation index (MFI), myofibril microstructure and rupture status revealed that enzymes and ultrasound softened meat texture by destroying muscle fiber structure. These results indicated that ultrasound technology is a promising auxiliary method to improve meat quality, and ultrasound with enzymes has a synergistic effect on the improvement of meat quality. [ABSTRACT FROM AUTHOR]