Comparison of genomic prediction accuracy using different models for egg production traits in Taiwan country chicken.

In local chickens targeted for niche markets, genotyping costs are relatively high due to the small population size and diverse breeding goals. The single-step genomic best linear unbiased prediction (ssGBLUP) model, which combines pedigree and genomic information, has been introduced to increase the accuracy of genomic estimated breeding value (GEBV). Therefore, this model may be more beneficial than the genomic BLUP (GBLUP) model for genomic selection in local chickens. Additionally, the single-step genome-wide association study (ssGWAS) can be used to extend the ssGBLUP model results to animals with available phenotypic information but without genotypic data. In this study, we compared the accuracy of (G)EBVs using the pedigree-based BLUP (PBLUP), GBLUP, and ssGBLUP models. Moreover, we conducted single-SNP GWAS (SNP-GWAS), GBLUP-GWAS, and ssGWAS methods to identify genes associated with egg production traits in the NCHU-G101 chicken to understand the feasibility of using genomic selection in a small population. The average prediction accuracy of (G)EBV for egg production traits using the PBLUP, GBLUP, and ssGBLUP models is 0.536, 0.531, and 0.555, respectively. In total, 22 suggestive- and 5% Bonferroni genome-wide significant-level SNPs for total egg number (EN), average laying rate (LR), average clutch length, and total clutch number are detected using 3 GWAS methods. These SNPs are mapped onto Gallus gallus chromosomes (GGA) 4, 6, 10, 18, and 25 in NCHU-G101 chicken. Furthermore, through SNP-GWAS and ssGWAS methods, we identify 2 genes on GGA4 associated with EN and LR: ENSGALG00000023172 and PPARGC1A. In conclusion, the ssGBLUP model demonstrates superior prediction accuracy, performing on average 3.41% than the PBLUP model. The implications of our gene results may guide future selection strategies for Taiwan Country chickens. Our results highlight the applicability of the ssGBLUP model for egg production traits selection in a small population, specifically NCHU-G101 chicken in Taiwan.

Contrasting metal bioaccumulation in marine benthic invertebrate groups in polluted harbor sediments.

This study examined the sediment metal fractions and availability to infer bioaccumulation in marine harbor benthic organisms. Total metals were analyzed using atomic absorption spectrometry and inductively coupled plasma-optical emission spectrometry for chemical fractions and organisms. The results showed similar metal concentrations and distribution driven by rivers and harbor pollution. We found significant differences in metal accumulation in marine benthic groups, highest in scavenger species. Their metal concentrations in decreasing order were 1.97-4568, 0.10-1260, 1.64-159, and 0.105-112 µg g-1 dw for hermit crabs, forams, bivalves, and polychaetes. Moreover, certain organisms, such as tusk shells, sea pens, bivalves, forams, and isopods, may exhibit selective metal accumulation. Biota-sediment accumulation factors (>1) were highest for essential metals like Cu, Zn, and Mn, while toxic metals like As, Cr, Co, and Ni increased. This concurrent assessment provides more comprehensive data for metal bioaccumulation in marine benthic ecosystems.

Sediment organic matter predicts polycyclic aromatic hydrocarbon distribution in port sediments.

We evaluated the influence of organic matter in polycyclic aromatic hydrocarbons (PAHs) in port sediments using multiple linear regression (MLR) and prediction models. Total sediment PAHs ranged between 45 and 3230 ng/g dw (average: 557 ± 962 ng/g dw), with PAHs primarily originating from river inputs, confined to areas near the estuaries. Coal/biomaterial combustion and petroleum mainly contribute to the presence of PAHs along estuaries, with medium-high to high ecological risks. MLR TPAHs prediction model included variables, namely, the marine-derived total organic carbon (TOCmar), terrestrial fraction of organic matter (Fterr), and carbon-to­nitrogen ratio (CNR). Results indicate that mainly marine- followed by terrestrially-derived organic matter influenced sediment PAH distribution. Total organic nitrogen and CNR were variables in the toxic equivalent (TEQ) prediction model, demonstrating that terrestrial pollution sources primarily influenced TEQ. The study analyzes and predicts the impact of organic matter and its sources on the fate and transport of PAHs in port sediments.

Potential risks of accumulated microplastics in shells and soft tissues of cultured hard clams (Meretrix taiwanica) and associated metals.

Microplastics (MPs) pose risks to both aquatic ecosystems and human health. This study investigated MPs in the shells and soft tissues of hard clams (Meretrix taiwanica) cultured in the inland waters of Taiwan. This study further developed two novel risk indices for assessing the potential ecological and health consequences of MPs. Moreover, the metal concentrations in the clam's soft tissues and the associated consumption health risks were investigated. Clamshells contained significant amounts of MPs with an average abundance of 16.6 ± 6.9 MPs/ind., which was higher than in the soft tissues (2.7 ± 1.7 MPs/ind.). The distribution and sizes of MPs in shells and soft tissues were similar, primarily small-sized (<2 mm, >99 %), blue (>65 %), and fibrous (>99 %). Dominant MP polymer types included rayon (83.5 %), polyethylene terephthalate (11.8 %), and polyacrylonitrile (3.6 %). The proposed MP potential ecological risk index indicates a higher potential ecological MP risk in soft tissues (302-423) than in shells (270-278) of the clams. The MP potential hazard risk index showed that the risk of exposure to MP through shellfish consumption decreased with age. The total hazard index (THI) value suggested negligible health hazards from metal exposure through shellfish consumption. Moreover, there was no significant correlation between MPs and metal concentrations in soft tissues, suggesting that metals bound to MPs contribute minimally to the total accumulated metals in clam's soft tissues. This study confirms the presence of MPs in clam shells and provides a novel tool to assess the potential ecological and health risks associated with MPs in shellfish.

Microplastics and phthalate esters contamination in top oceanic predators: A study on multiple shark species in the Pacific Ocean.

Marine organisms, especially top predators such as sharks, are susceptible to environmental pollutants like microplastics (MPs) and phthalate esters (PAEs), leading to ecosystem risks. Research on contamination in these apex species is, however, still limited. This study investigated MPs and PAEs in multiple shark species (Isurus oxyrinchus, Alopias superciliosus, Alopias pelagicus, Carcharhinus brevipinna, and Sphyrna zygaena) off Taiwan's eastern coast. Gastric tissue analyses revealed ubiquitous microplastics (2-31 particles), which positively correlated with body lengths and weights for Isurus oxyrinchus. Blue, fiber-shaped (1-2 mm), and rayon-based MPs are likely associated with textile fiber pollution. The PAEs concentration mean was 7035 ± 6829 ng/g, ww, having DEHP and DiNP as primary compounds. This study highlights pervasive contamination in Pacific Ocean sharks, emphasizing anthropogenic impact on top oceanic predators and providing essential insights for food safety and MP accumulation.

Seasonal dynamics of polycyclic aromatic hydrocarbons in microplankton from Kaohsiung Harbor (Taiwan Strait, northeastern South China Sea).

The impact of polycyclic aromatic hydrocarbons (PAHs) on the marine food web is crucially understudied in the primary trophic system. We evaluated the seasonal dynamics of PAHs in microplankton in a polluted environment (Taiwan), northeastern South China Sea. Replicate size-fractionated microplankton (55-1000 µm) were freeze-dried, and PAHs were extracted with a 1:1 v/v ratio of acetone: n-hexane, then analyzed using GC-MS. Total PAHs ranged between 68 and 2548 ng/g dw in microplankton, greatest during spring (130-2548 ng/g), followed by autumn (135-772 ng/g) and summer (44-423 ng/g). Spatial distribution varied through seasons but was higher in the southern part (S6 > S4 > S5 > S2 > S3 > S1 > S7), dominated by higher-ring PAHs from mixed pyrogenic and petrogenic sources. PAHs are significantly correlated with environmental factors, especially in colder seasons and lower salinity areas. Suspended matter and plankton influenced PAH transport and partitioning seasonally. Plankton's PAHs seasonal changes and environmental influences are revealed in an anthropic environment.

Controlling effects of terrestrial organic matter on metal contamination and toxicity risks in port sediments.

The contents of metals, total carbon, total nitrogen (TN), total organic carbon (TOC), and stable isotope composition (δ13Corg and δ15N) of sediment organic matter (SOM) were investigated to explore the sources and spatial distribution of metals and SOM in the surface sediments (Kaohsiung Port, Taiwan). Results showed that TOC and metals in estuarine sediments are high, gradually decreasing toward the port entrances. The δ13Corg, δ15N, and TOC/TN ratios indicate that SOM comes mainly from terrestrial sources. This study proposes a befitting model between metal pollution and toxicity risk index and SOM sources in port sediments by combining stable isotope composition, correlation matrix, and multiple linear regression analysis. The model indicates that the degree of metal pollution and toxicity risk in sediments are mainly affected by TOCterr content and SOM source. The results help to understand the influence of organic matter sources in port sediments on metal concentration distribution.

Phthalate esters and nonylphenol concentrations correspond with microplastic distribution in anthropogenically polluted river sediments.

This paper presents the phthalate esters (PAEs), nonylphenol (NPs), and microplastics (MPs) in river sediments. Results showed that sediments near residential areas were mainly composed of fine particles, potentially influencing the adsorption of PAEs and NPs in the area. The concentrations of Σ10 PAEs in the sediments ranged between 2448 and 63,457 µg/kg dw, dominated by DEHP and DnOP. Microplastics were detected in all samples, with higher abundances found in sediments near residential areas dominated by polypropylene. Toxicological risk assessment indicated potential risks to sensitive aquatic organisms exposed to the sediments. Correlations between MPs, PAEs, and NPs suggest that MPs may serve as possible sources of PAEs in the sediments. Principal component analysis explained 95.4 % of the pollutant variability in the sediments. Overall, this study emphasizes the significance of monitoring and understanding the presence and interactions of PAEs and MPs in river sediments to assess their potential impacts on aquatic ecosystems.

Polycyclic aromatic hydrocarbons in 55-120 µm phytoplankton.

A baseline study was undertaken on polycyclic aromatic hydrocarbons (PAHs) in phytoplankton. Plankton samples from six stations (duplicates) in Kaohsiung Harbor (KH), Taiwan along with a phytoplankton control sample afar from the harbor, were collected. We applied size-fractionation to isolate phytoplankton (55-120 µm), followed by sedimentation and centrifugation to remove abiogenic particulates. The phytoplankton was freeze-dried, extracted with acetone: n-hexane (1:1, v/v), and analyzed using GC-MS. ΣPAHs in phytoplankton ranged between 5204 and 28,903 ng/g dry weight (mean: 12,150 ng/g). The ΣPAHs in KH were >7 times than the control site (C1: 3972 ng/g). Cluster analysis showed spatial gradients (northern < southern KH). Accumulated PAHs in phytoplankton were from petrogenic (fishing ports and ships) and pyrogenic (river outflows), dominated by lower-ring PAHs, likely due to their higher bioavailability in the dissolved phase. We present a practical phytoplankton isolation technique for more accurate phytoplankton PAH concentrations with insights into their distribution and sources.

Microplastics in coastal farmed oyster (Crassostrea angulata) shells: Abundance, characteristics, and diversity.

One of the most concerning emerging pollutants is microplastics (MPs), which can infiltrate soft tissues of organisms by ingestion, adhesion, and fusing and may even become embedded in biominerals. However, very little evidence is available about MPs in biominerals found in the wild. This study detected the abundance and characteristics of MPs in the shells of farmed oysters (Crassostrea angulata) off the coast of Taiwan and discussed the distribution, accumulation, and diversity in the oyster shells. The results showed that MPs were ubiquitous in oyster shells, with an average abundance of 0.70 ± 0.40 MPs/g. MPs abundance was significantly (p < 0.01) higher in small oyster shells (shell length < 6.5 cm, weight 5-10 g) and inorganic (CaCO3) fraction (HCl digestion) than in large oyster shells (>6.5 cm, 10-25 g) and an organic fraction (H2O2 digestion), respectively. However, there was no significant difference in MPs abundance between the top and bottom shells (p > 0.05). MPs with a size <2 mm accounted for 78.5 %, fibrous MPs for 93.7 %, and rayon for 89.5 %. The MPs diversity integrated index (MPDII) in oyster shells was low (0.27), and the small and fibrous MPs seemed more easily embedded in biominerals. The findings confirm the presence of MPs in oyster shells in coastal environments. In addition, oyster shells may contain higher amounts of MPs than soft tissues 4-5 times, which needs to be confirmed. Further revealing the distribution and accumulation of MPs in water/terrestrial biominerals will help to understand the fate of MPs in the environment.

Microplastics in coral reef sediments underestimated? They may hide in biominerals.

Microplastics (MPs) may be underestimated in coral reef sediments. Current pretreatments for determining MPs in the sediments are mainly density separation and organic matter removal, ignoring MPs that may be embedded or encrusted in biominerals. This could lead to discrepancies in assessing the potential risk of MPs contamination. To confirm whether MPs in coral reef sediments are underestimated, a two-step sequential digestion, including organic matter removal (H2O2 digestion) and biomineral removal (HCl digestion), was performed on sediments from the coral reef area of the South Penghu Marine National Park (SPMNP, Taiwan). The MPs abundance and characteristics of the two steps were analyzed separately. The results showed that the average MPs abundance after HCl digestion (78 ± 42 MPs/kg) was significantly higher than that of H2O2 digestion (38 ± 25 MPs/kg). The MPs diversity integrated index (MPDII) in coral reef sediments was low (MPDII = 0.35), and MPs were mainly small (<2.0 mm, 91.3 %), fibrous (93.5 %), colored (60.9 %), and rayon polymers (73.9 %). Correlation analysis showed that MPs in biominerals mainly dominated MPs in the sediments. These results confirm that current assessments of MPs contamination levels in biomineral-rich sediments may be underestimated and uncertain. In addition, the mineralization of organisms in SPMNP reef regions was affected by MPs from moderate to high levels, depending on the proportion of MPs in biominerals.

Comprehensive assessment of metals and organic pollutants in pelagic fishing port sediments.

Fishing ports are among the environments that accumulate pollutants along the coast but often lack environmental data and scientific research. This study investigated 8 metals, 16 polycyclic aromatic hydrocarbons (PAHs), 10 phthalate esters (APs), and 2 alkylphenols (APs) in the surface sediments of Qianzhen Fishing Port, the largest pelagic fishing port in Taiwan. Indicator compounds, pollution hotspots, potential ecological risk levels, and pollution sources were evaluated. Results showed that copper, zinc, and bis(2-ethylhexyl) phthalate (DEHP) in surface sediments were pollution indicators posing potential toxicological risks. Metals and PAHs in sediments were mainly from ship-related sources, while PAEs and APs were related to dockland activities. Combining metal and organic pollutants, the sediments had a moderate potential ecological risk, with metals higher than organic pollutants. Cluster analysis and color geographic map of risks indicate sediment pollution hotspots and areas requiring immediate intervention. In the future, sustainable operation and management can be carried out by using metal-free antifouling paint, improving sewage treatment rate, and regular environmental dredging of fishing port.

Comparison of Immune-Related Gene Expression in Two Chicken Breeds Following Infectious Bronchitis Virus Vaccination.

This study aims to identify the immune-related genes and the corresponding biological pathways following infectious bronchitis virus vaccination in Taiwan Country and White Leghorn chicken breeds. Transcriptomic analyses of the spleen of these two breeds were conducted by next-generation sequencing. Compared to White Leghorn chicken, Taiwan Country chicken showed a significantly higher level of anti-infectious bronchitis virus (IBV) antibodies at 14 and 21 days pos vaccination. At 7 days post vaccination, in the Taiwan Country chicken, higher expression of mitogen-activated protein kinase 10, Major histocompatibility complex class 1, and V-set pre-B cell surrogate light chain 3 were found. In contrast, the White Leghorn chicken had a high expression of interleukin 4 induced 1, interleukin 6, and interleukin 22 receptor subunit alpha 2. These findings have highlighted the variations in immune induction between chickens with distinct genetic background and provided biological pathways and specific genes involved in immune responses against live attenuated IBV vaccine.

A novel pollution index to assess the metal bioavailability and ecological risks in sediments.

The chemical forms of metals in sediments of ports around Taiwan were investigated using sequential extraction. Based on the availability of different chemical forms, novel indices such as bioavailability, mobility, availability, and availability risk of metals in sediments were developed. The results showed that Co, Zn, Pb, Mn, and Cu were mainly present in available forms (49-84 %), and the proportion of oxidative or reductive fractionation was the highest. This suggests that the redox potential is a major factor for metal mobility in the sediments. The results from the proposed indexes showed that metals in sediments have low bioavailability but high to very high mobility and availability. Primarily, the proposed index is more appropriate, as the current index for assessing total metal content may overestimate the level of risk. The indexes established can comprehensively evaluate the bioavailability, mobility, availability, and ecological risk of metals in sediments.

Chicken HOXC8 and HOXC10 genes may play a role in the altered skull morphology associated with the Crest phenotype.

One of the most intriguing traits found in domestic chickens is the Crest phenotype. This trait, characterized by a tuft of elongated feathers sprouted from the head, is found in breeds such as Polish chickens and Silkie chickens. Moreover, some crested chicken breeds also exhibit a protuberance in their anterodorsal skull region. Previous studies have strived to identify the causative factors of this trait. This study aimed to elucidate the role of chicken HOXC8 and HOXC10 in the formation of the Crest phenotype. We explored the effect of ectopic expression of HOXC8 or HOXC10 on the chicken craniofacial morphology using the RCAS retrovirus transformation system. Microcomputed tomography scanning was conducted to measure the 3D structure of the cranial bone of transgenic embryos for geometric morphometric analysis. We found that the ectopic expression of HOXC8 or HOXC10 in chicken heads caused mild morphological changes in the skull compared with the GFP-transgenic control group. Geometric morphometric analysis showed that HOXC8 and HOXC10 transgenic groups expressed a mild upward shape change in the frontal region of the skull compared with the control group, which is similar to what is seen in the crested chicken breeds. In conclusion, this study supports findings in previous studies in which HOX genes play a role in the formation of the altered skull morphology related to the Crest phenotype. It also supports that mutations in HOX genes may contribute to intra- and inter-specific variation in morphological traits in vertebrates.

Occurrence and emission of polycyclic aromatic hydrocarbons from water treatment plant sludge in Taiwan.

The concentrations level and distribution of 16 US EPA polycyclic aromatic hydrocarbon (PAHs) from the water treatment plant (WTP), sewage treatment plant (STP), and industrial water treatment plant (ITP) sludge in Taiwan were determined and then assessed the sources, and potential toxicity (carcinogenic polycyclic aromatic hydrocarbons [CPAHs] and toxic BaP equivalent [TEQ]). Results indicated that the total concentrations of PAHs ranged between 58 and 16,436 µg/kg dw. Among the 17 samples, the 2-4 ring of total PAHs were the predominant compound in three kinds of treatment plant (> 60%). Especially, ITP1 owns 95.8% of 2-4 ring of total PAHs and ITP3 owns 54% of five- and six-ring of total PAHs. The molecular indices and principal component analysis (PCA) were used to determine the source contributions, with the results showing that the contributions of combustion/grass, coal or wood combustion and combustion/ liquid (oil) fossil fuel combustion. A PAH toxicity indicated by TEQ was 2.5-506 µg TEQ/g dw. Although, the results indicated that these were not recommended for land applications, but analyses are beneficial to develop effective management strategies for controlling PAH discharge in treatment plants and establishing strategies for its reuse in managing pollutants.

Monitoring changes in the genetic structure of Brown Tsaiya duck selected for feeding efficiency by microsatellite markers.

OBJECTIVE: Few studies have genetically monitored chickens over time, and no research has been conducted on ducks. To ensure the sustainable management of key duck breeds, we used microsatellite markers to monitor Brown Tsaiya ducks over time genetically. METHODS: The second, fourth, sixth to eighth generations of the Brown Tsaiya duck selected for feeding efficiency and control lines were included in this study to investigate the genetic variations, effective population size, population structure and the differentiation between populations over time with 11 microsatellite markers derived from Brown Tsaiya duck. RESULTS: The results showed there were a slight decrease in the genetic variations and an increase in within-population inbreeding coefficient (FIS) in both lines, but no consistent increase in FIS was observed in each line. The effective population size in the second and eighth generations was 27.2 for the selected line and 23.9 for the control line. The change in allele richness showed a downward trend over time, and the selected line was slightly lower than the control line in each generation. The number of private alleles (Np) in the selected line were higher than in the control line. Moderate differentiation was observed between the second and eighth generations in the selected line (FST = 0.0510) and the control line (FST = 0.0606). Overall, differentiation tended to increase with each generation, but genetic variation and structure did not change considerably after six generations in the two lines. CONCLUSION: This study provides a reference for poultry conservation and helps to implement cross-generation genetic monitoring and breeding plans in other duck breeds or lines to promote sustainable management.

Development of alternative disposals for waste rice husk and dredged harbor sediment by sintering as lightweight aggregates.

This study developed the alternative disposals for dredged harbor sediments by co-sintering with waste rice husk into lightweight aggregates (LWA) to benefit resource sustainability and waste valorization. The effects of rice husk addition and sintering temperature on LWA performances such as water absorption, particle density, crushing strength, weight loss, volume shrinkage, and open porosity were investigated. The key parameters (e.g. C/Fe ratio in raw materials) controlling the LWA performances and engineering applications were determined. Results showed that dredged harbor sediments could be made into suitable LWA for engineering applications from the controlled rice husk addition and sintering temperature. The addition of rice husk led to lower LWA particle density, but raised water absorption and reduced crushing strength. The increase of sintering temperature reduced water absorption and improved crushing strength. The aggregates with 10-15% rice husk, sintered at 1150 °C had appropriate particle density (1.60-1.73 g/cm3), water absorption (11.8-16.6%), and crushing strength (6.0-10.6 MPa), which could be suitable for lightweight concrete applications. Low water-soluble chloride and heavy metals leachabilities aligned with Taiwan's regulatory standards for concrete aggregates. Co-treating waste rice husk and dredged harbor sediment into LWA can benefit the waste reduction and circular economy, and reduce the environmental impacts associated with their disposals.

Comparing the applicability of ecological risk indices of metals based on PCA-APCS-MLR receptor models for ports surface sediments.

This study collected surface sediments from seven ports in Taiwan and analyzed their characteristics along with 10 metals. Enrichment factor (EF), relative EF (REF), potential ecological risk index (PERI), and mean effect range median quotient (m-ERM-q) were used to evaluate the levels of metal contamination and ecological risks in sediments. Principal component analysis (PCA) and the absolute principal component score-multiple linear regression (APCS-MLR) model were applied to quantify the main factors affecting the variations in sediment metals. The different normalization techniques that vary between indexes significantly affect the estimates of risk levels for sediment metals. APCS-MLR model confirmed the significant difference among the sediment quality indices in the degree of anthropogenic pollution, ranging in the order of REF (normalized with reference site and Fe, 97.0 %), PERI (normalized with reference site, 85.5 %), EF (normalized with crust and Fe, 79.4 %), and m-ERM-q (not normalized, 56.6 %).

Non-proportional distribution and bioaccumulation of metals between phytoplankton and zooplankton in coastal waters.

Metal concentrations were concurrently quantified in seawater, phytoplankton, and zooplankton from a heavily impacted coast of southern Taiwan. Combined size and density fractionation were used to accurately quantify metal concentrations in phytoplankton. Cr, Co, Ni, Cu, As, and Pb were analyzed using an inductively coupled plasma mass spectrometer (ICP-MS). As expected, metals significantly increased with an order of seawater < phytoplankton < zooplankton (p < 0.05); but did not differ between estuarine, nearshore, and offshore sites (p > 0.05). Metals were higher along Kaohsiung Harbor and marine outfall diffusion sites, highlighting their major impacts on plankton metal contamination. Notably, phytoplankton (Cr BCF > 100; half of the sites) significantly accumulated more metals contrary to zooplankton (BAF < 10). Metal concentrations and bioaccumulation factors between phytoplankton and zooplankton showed significant negative correlations. This demonstrates a non-proportional distribution and bioaccumulation of metals in phytoplankton and zooplankton-corroborating laboratory findings on zooplankton ability to control metals, irrespective of significantly high bioaccumulation in phytoplankton.