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Genomic insights into local adaptation and phenotypic diversity of Wenchang chickens

Wenchang chicken, a prized local breed in Hainan Province of China renowned for its exceptional adaptability to tropical environments and good meat quality, is deeply favored by the public. However, an insufficient understanding of its population architecture and the unclear genetic basis that governs its typical attributes have posed challenges in the protection and breeding of this precious breed. To address these gaps, we conducted whole-genome resequencing on 200 Wenchang chicken samples derived from 10 distinct strains, and we gathered data on an array of 21 phenotype traits. Population genomics analysis unveiled distinctive population structures in Wenchang chickens, primarily attributed to strong artificial selection for different feather colors. Selection sweep analysis identified a group of candidate genes, including PCDH9, DPF3, CDIN1, and SUGCT, closely linked to adaptations that enhance resilience in tropical island habitats. Genome-wide association studies (GWAS) highlighted potential candidate genes associated with diverse feather color traits, encompassing TYR, RAB38, TRPM1, GABARAPL2, CDH1, ZMIZ1, LYST, MC1R, and SASH1. Through the comprehensive analysis of high-quality genomic and phenotypic data across diverse Wenchang chicken resource groups, this study unveils the intricate genetic backgrounds and population structures of Wenchang chickens. Additionally, it identifies multiple candidate genes linked to environmental adaptation, feather color variations, and production traits. These insights not only provide genetic reference for the purification and breeding of Wenchang chickens but also broaden our understanding of the genetic basis of phenotypic diversity in chickens.

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Open Access
Changes in Soil Chemical Properties and Rhizosphere Bacterial Community Induced by Soil Amendments Associated with Reduction in Cadmium Accumulation by Rice

Soil amendments have been extensively employed for the purpose of remediating soils contaminated with cadmium (Cd). However, the potential impacts of soil amendments on soil chemical properties, soil Cd bioavailability, total Cd accumulation by rice, and rhizosphere bacterial community in Cd-contaminated paddy fields located in a tropical region is still at its infancy. In this study, a commercial MgO-CaO-SiO2 conditioner (A), biochar (B), and a combination of the commercial MgO-CaO-SiO2 conditioner and biochar with a ratio of 1:1 (C) were applied at two different doses [2250 kg ha−1 (A150, B150, C150), 4500 kg ha−1 (A300, B300, C300)] to investigate their impacts on soil Cd stabilization and total Cd uptake of rice straw and grain in a Cd-contaminated remediation field experiment. Rhizosphere bacterial community diversity and composition were also assessed using high-throughput sequencing based on 16S rRNA genes. Compared with non-amendment treatment (CK), soil pH, cation exchange capacity (CEC), organic matter (OM), total nitrogen (TN), available nitrogen (AN), and nitrate (NO3−) concentrations were significantly elevated, whereas ammonium (NH4+) and soil available Cd concentrations were reduced by soil amendment treatments. Meanwhile, soil amendments significantly decreased concentrations of total Cd in both rice straw and grain, with the lowest Cd concentration in the C300 treatment. Soil pH and CEC were significantly and negatively associated with soil Cd availability and rice straw and grain Cd concentrations, while NH4+ concentration was positively correlated with soil available Cd concentration, and OM, TN, and NO3− concentrations were positively linked with rice grain Cd concentration. Soil amendments significantly increased bacterial Chao 1 and Shannon indexes and altered bacterial community composition in rhizosphere soil, due to changes in the composition of the community primarily influenced by variations in soil pH, CEC, and soil available Cd, NH4+, available phosphorous (AP) and available Potassium (AK) concentrations. Furthermore, the abundant bacterial species (Pseudomonas) and rare bacterial species (Bacillus, Candidatus_Solibacter and Streptomyces) have been up-regulated by different soil amendments, which might be in favour of soil Cd immobilization. A structural equation model also showed that soil amendments could improve bacterial diversity and change soil pH and CEC, which were conducive to hindering the removal and conversion of Cd. Overall, these results indicate that biochar-(MgO-CaO-SiO2) mixed amendments at high dosage exerted better performance compared with single application soil amendment A and B. The changes in soil chemical properties, available Cd content, and rhizosphere bacterial community assembly induced by soil amendments are closely correlated with the decrease in rice’s ability to accumulate Cd.

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Open Access
Supplementation of dietary areca nut extract modulates the growth performance, cecal microbiota composition, and immune function in Wenchang chickens.

The study was aimed at evaluating the effects of areca nut extract (ANE) on the growth performance, cecal microbiota, and immunity of Wenchang chickens. For this study, 42-day-old healthy Wenchang chickens (n = 450) with similar body weight were chosen. The animals were randomly divided into five groups, with six replicates per group and 15 chickens per replicate. One group was fed a basal diet (control; CCK). The remaining four groups were fed a basal diet supplemented with varying ANE concentrations: 0.038, 0.063, 0.100, and 0.151 g/kg, with the groups denoted as CNT1, CNT2, CNT3, and CNT4, respectively. The feeding experiment lasted 35 days. The ligated cecum segments of the control and experimental groups were collected for metabolomic and metagenomic analysis, while the bone marrow samples were extracted for tandem mass tag (TMT)-based proteomic analysis. All the experimental groups exhibited significantly higher average daily gain (ADG) and significantly lower feed-to-weight (F/G) ratios than CCK. Metabolomic screening of the cecum contents revealed the presence of 544 differential metabolites, including several gut health-related metabolites, such as xanthine, hydroxy hypoxanthine, 2,5-dimethylhydrazine, ganoderic acid, and 2-aminohexanoic acid. Metagenomic analysis of the cecum contents showed an upregulation in the abundance of Prevotella spp. in the experimental groups. However, we observed no significant differences in the abundances of other cecal microbes at phylum and genus levels. Furthermore, we observed significant associations between Prevotella spp. and the differentially abundant metabolites, such as cherubins, thiaburimamide, and 3,4-dihydroxy-L-phenylalanine, (r)-mevalonate, 5-O-methylalloptaeroxylin, nalidixic acid, and deoxyloganin (p < 0.05). Proteomic analysis revealed that the differentially expressed proteins (such as interferon-induced protein with tetratricopeptide repeats 5 (IFIT5), MHC-BF1, and death domain-associated protein (Daxx)) in the bone marrow of the chickens were primarily enriched in the immune network for IgA production and B cell receptor signaling pathway. In conclusion, dietary ANE supplementation was found to enhance metabolic activity and energy utilization, improve growth performance, modulate cecal microbiota, and strengthen the immunity of Wenchang chickens.

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Open Access
Malic acid inhibits accumulation of cadmium, lead, nickel and chromium by down-regulation of OsCESA and up-regulation of OsGLR3 in rice plant

Malic acid (MA) plays an important role in plant tolerance to toxic metals, but its effect in restricting the transport of harmful metals remains unclear. In this study, japonica rice NPB and its fragile-culm mutant fc8 with low cellulose and thin cell wall were used to investigate the influence of MA on the accumulation of 4 toxic elements (Cd, Pb, Ni, and Cr) and 8 essential elements (K, Mg, Ca, Fe, Mn, Zn, Cu and Mo) in rice. The results showed that fc8 accumulated less toxic elements but more Ca and glutamate in grains and vegetative organs than NPB. After foliar application with MA at rice anthesis stage, the content of Cd, Pb, Ni significantly decreased by 27.9–41.0%, while those of Ca and glutamate significantly increased in both NPB and fc8. Therefore, the ratios between Cd and Ca in grains of NPB (3.4‰) and fc8 (1.5‰) were greatly higher than that in grains of NPB + MA (1.1‰) and fc8+MA (0.8‰) treatments. Meanwhile, the expression of OsCEAS4,7,8,9 for the cellulose synthesis in secondary cell walls were down-regulated and cellulose content in vegetative organs of NPB and fc8 decreased by 16.7–21.1%. However, MA application significantly up-regulated the expression of GLR genes (OsGLR3.1-3.5) and raised the activity of glutamic-oxalacetic transaminease for glutamate synthesis in NPB and fc8. These results indicate that hazard risks of toxic elements in foods can be efficiently reduced through regulating cellulose biosynthesis and GLR channels in plant by combining genetic modification in vivo and malic acid application in vitro.

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Ozone Pollution Characteristics and Formation Mechanism in a Typical Tropical Seaside City

To investigate the pollution characteristics and formation mechanism of ambient air ozone(O3) in a typical tropical seaside city, we conducted an observational experiment on O3 and its precursors at an urban site in Haikou, Hainan Province, from June to October 2019. The O3 pollution characteristics were analyzed comprehensively; the O3-NOx-VOCs sensitivities and key precursors were determined, and the control strategies for O3 pollution were carried out. The results were as follows:1 O3 pollution in Haikou mainly occurred in September and October, with daily maximum 8-h O3 concentrations in the range of 39-190 μg·m-3, and the daily variation in O3 was unimodal, peaking at approximately 14:00. 2 The concentrations of NO2 and VOCs were higher during O3 pollution episodes than their respective mean values in Haikou City. The increased O3 precursor concentrations were an important factor leading to O3 pollution, whereas O3 pollution was also influenced by regional transport, with pollutants mainly transported from the northeastern part of Haikou City. 3 O3-NOx-VOCs sensitivity in Haikou City was in the VOCs and NOx transitional regime, and the most sensitive precursors in various months were different. O3 formation in September was sensitive to anthropogenic VOCs the most; however, in October it was sensitive to NOx. 4 In the future, the reduction ratio of VOCs to NOx should be 1:1-4:1 to control O3 pollution effectively in Haikou.

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Distribution, sources and ecological risks of per- and polyfluoroalkyl substances in overlying water and sediment from the mangrove ecosystem in Hainan Island, China

Since data on Per- and polyfluoroalkyl substances (PFASs) in mangrove ecosystems are very limited. This study investigated the occurrence, distribution, sources, and ecological risk of 24 PFASs in the overlying waters and sediments of mangrove systems in Hainan Island, China. The concentration levels of PFASs in water and sediment ranged from 6.3 to 35.3 ng/L and from 0.33 to 10.2 ng/g dw, respectively. In terms of spatial distribution, firstly, the mangrove forests in Haikou and Sanya contained higher levels of PFASs; secondly, the eastern region contained higher levels of PFASs than the western region. The reasons for this may be related to the population size and development level of the region. For the organic carbon normalized sediment-water partition coefficient (log Koc), the results showed that log Koc decreased with increasing carbon chains for short-chain PFASs (with ≤6 CF2 units) and increased with increasing carbon chains for long-chain PFASs (with ˃6 CF2 units). Principal Component Analysis (PCA) and correlation analysis were employed to pinpoint specific origins of PFASs, namely firefighting, metal plating, food packaging, textiles, and fluoropolymer manufacturing. The risk quotient (RQ) values of PFASs in mangrove ecosystems on Hainan Island were all <1, but the existence of potential risks cannot be excluded. Hence, further investigations related to the bioaccumulation effects of PFASs in organisms in mangrove forests should be conducted to gain a more comprehensive understanding of their environmental behavior.

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Comparative flavor precursors and volatile compounds of Wenchang chickens fed with copra meal based on GC–O–MS

In the Wenchang chicken (WC) feeding process, copra meal is often added to improve chicken quality. To determine the effect of feeding with copra meal on the flavor formation of WCs, the experimental subjects were fed with 4.5 % and 7.5 % copra meal, and the control group was fed without copra meal. The electronic nose combined with gas chromatography–olfactometry mass spectrometry (GC–O–MS) was used to identify the volatile compounds from the samples. Compared with the control group, the pH of chickens fed copra meal was significantly decreased (P < 0.05) after slaughter. Aldehydes and alcohols were the main volatile compounds in muscle, among which hexanal and 1-octen-3-ol were the highest. Thirty-two and thirty-six compounds were identified in breast muscle and drumstick muscle, respectively. Twelve new volatile compounds were added, including 1-octanol, butanal, 1-heptanol, 3-ethylbenzaldehyde, 2,2-dimethylpentanal, hexanoic acid, 3-heptanone, 2,5-heptanedione, 2-ethylfuran, 2-propylfuran, 2-ethynylpyridine, and 1,2,4,5-tetrazine. The types and contents of volatile compounds in drumstick muscle increased with an increasing proportion of copra meal in the diet. In summary, the addition of copra meal changed the quality of WCs and increased the types and contents of volatile compounds. This study provides a reference for understanding the flavor profile of WC fed copra meal.

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