Understanding the genomic basis of indigenous livestock is essential for both conservation and sustainable improvement. Korean native chickens (KNCs), although representing a small fraction of the poultry industry in Korea, are distinguished by their unique meat quality, robustness, and adaptability. Recent genomic studies have investigated their genetic diversity, evolutionary history, and economically important traits. High-density SNP arrays and population structure analyses have clarified the distinct identity of KNC lines, while runs of homozygosity have provided insights into inbreeding, conservation progress, and functional loci. Selection signature analyses have identified candidate genes related to growth, metabolism, reproduction, and immune function, reflecting line-specific adaptation. Genome-wide association studies have further identified variants associated with taste-active compounds, fatty acid composition, and growth traits, offering a foundation for genomic selection. Moreover, research on disease-related genes, such as the major histocompatibility complex B genes, has documented substantial genetic variability in KNCs, establishing important genomic resources for subsequent studies on avian immunity and pathogen response. Together, these findings highlight KNCs as valuable reservoirs of genetic variation with implications for both conservation and breeding. More broadly, the genomic insights obtained from KNCs provide a cautious yet informative model for indigenous livestock worldwide, demonstrating how genomic tools can support sustainable breeding programs that balance biodiversity preservation with productivity.

TAPBP is a key chaperone of the peptide-loading complex that facilitates peptide loading onto major histocompatibility complex class I (MHC I) molecules. This study characterized TAPBP alleles in Korean Native Chickens (KNCs), identified novel variants, and evaluated allelic associations with BF2. Thirty-six samples representing six KNC lines were genotyped using LEI0258 and the MHC-B SNP panel, and individuals homozygous at both markers were classified into 16 groups. The same samples were subjected to Sanger sequencing of TAPBP exons 3-8. Sequences were assembled and aligned against MHC-B reference alleles of the TAPBP gene and the Red Junglefowl reference. Additional comparisons with “tapasin allele” datasets enabled the identification of novel variants. Six novel nucleotide variants were detected across exons 3-6, including one nonsynonymous substitution in exon 4 (D251H). This residue corresponds to position Q265 in human TAPBP and lies adjacent to residues involved in MHC I interaction, suggesting potential functional relevance. Furthermore, TAPBP exhibited high haplotype diversity (Hd = 0.93) and moderate nucleotide diversity (π = 0.00892), with exon 5 showing the highest diversity (π = 0.01). B9 was the most frequent allele at the nucleotide level, whereas B6/B24 predominated at the amino acid level. Comparison with BF2 data revealed allele-dependent pairing patterns: BF2-B9 consistently matched TAPBP-B9, whereas BF2-B6 was associated with distinct TAPBP nucleotide variants, indicating allelic diversification. Homozygosity at LEI0258 and the SNP panel corresponded with TAPBP homozygosity, supporting marker-based prediction. These findings highlight potential BF2-TAPBP associations and provide a foundation for understanding variation in MHC I peptide loading.

Objective The major histocompatibility complex (MHC) is central to immunological protection. This study represents the assessment of MHC-B haplotype diversity in Indonesian native chickens. Methods Six Indonesian native chicken populations were selected as study populations: Merawang (MRG), Pelung (PLG), Black Kedu (KJM), Sentul (STL), Nunukan (NNK), and Gaga (GAG), with 24, 17, 30, 16, 14, and 20 birds from each population, respectively. Samples were genotyped using the MHC-B single-nucleotide polymorphism (SNP) panel. To explore haplotype diversity, the results were analyzed using PHASE 2.1 software. Results Genotyping of six Indonesian native chicken populations revealed high haplotype diversity, with a total of 126 distinct haplotypes: 38, 25, 19, 21, 11, and 12 from the MRG, PLG, KJM, STL, NNK, and GAG populations, respectively. Three haplotypes have been identified to be shared: BSNP-IND14 (KJM and STL populations), BSNP-IND26 (KJM, NNK, and MRG populations), and BSNP-IND31 (KJM and MRG populations). Accordingly, all haplotypes obtained from the GAG and PLG populations were unique. Phylogenetic analysis of the results did not reveal a distinct pattern for any population; nonetheless, three subclades were identified, with all six populations represented in each clade. A comparison of MHC-B haplotypes in Indonesian native chickens with MHC-B standard haplotypes shows no distinct clades; however, three possible subclades were also identified. Nevertheless, no Indonesian MHC-B haplotypes matched 100% with the known standard haplotypes, indicating that all Indonesian haplotypes identified in this study are novel. Furthermore, the comparison of Indonesian MHC-B haplotypes to those from other Asian regions reveals that the majority of Indonesian haplotypes cluster with those from Bangladesh, suggesting a shared evolutionary background among South and Southeast Asian chickens. Conclusion This study identified unique MHC-B haplotypes in Indonesian native chickens, suggesting that the observed populations are diverse in the MHC-B region and may have variation in immune responses.

Objective: Domestication alters the phenotypes of wild animals to meet human demands and leaves characteristic patterns in their genomes. Various selection signature analysis methods have been developed to identify these characteristic patterns left in the genome. The Korean native duck (KND) is one of the domesticated species in Korea. KND is categorized into two populations based on plumage color; colored KND (KNDC) and white KND (KNDW). To enhance the competitiveness of native ducks, it is necessary to establish a KNDW line. In this study, we conducted selection signature analysis to identify candidate genes associated with white plumage color in KNDs. Methods: We generated whole genome resequencing data from 22 KNDCs, 22KNDWs, and 10 Pekin ducks (PKDs). To detect distinct genomic regions between KND populations with different plumage colors, we analyzed three types of selection signature analysis: the fixation index (Fst), nucleotide diversity(pi), and cross-population extended haplotype heterozygosity (XP-EHH). Results: Population structure analysis showed that although KNDC and KNDW are distinct from PKD, they form a single group sharing a common ancestor. The results of Fst and pi analyses revealed that compared to KNDC, there were strong selection signals in the MITF gene in KNDW, with a 6,641 bp insertion in the intron 2 region. This variant is a transposable element insertion that causes white plumage in PKD. In addition, XP-EHH analysis identified DCT, KIT, TYR, and ADCY9 as major candidate genes associated with pigmentation in the KND population. Conclusion: White plumage in KNDW is caused by a transposable element insertion in the MITF gene. This finding improves our understanding of plumage color in KND and supports the establishment of KNDW breeding programs.

Genome-wide association studies (GWAS) have identified numerous single nucleotide polymorphisms (SNPs) associated with complex traits in poultry. However, most GWAS-identified variants reside in non-coding regions, making their functional relevance to their phenotypes unclear. Emerging evidence suggests that many of these markers overlap cis-regulatory elements, yet experimental validation of their biological function remains limited. Here, we investigated non-coding GWAS variants associated with nucleotide-related compounds in chicken breast muscle by targeting SNP-containing genomic regions using a CRISPR activation (CRISPRa) system in DF-1 cells and profiling transcriptomic responses via bulk RNA sequencing to assess the functional impact of activating these regions. Based on chicken muscle-specific epigenetic profiles and chromatin state annotations, we identified three significant GWAS variants on chromosome five associated with nucleotide metabolism. These variants are situated within cis-regulatory elements, specifically in intron three of DUSP8, intron one of SLC25A22, and upstream of FBXO3. To understand their functional impact, we employed an in vitro CRISPRa system with targeted guide RNAs to activate each non-coding SNP region in DF-1 cells. This activation resulted in significant changes at the transcriptomic level. Subsequent functional enrichment analysis of the differentially expressed genes consistently highlighted muscle-related pathways across all SNPs, including MAPK signaling, cytoskeletal remodeling, and ECM-receptor interactions, which are potentially involved in regulating nucleotide metabolism and deposition in muscle. Furthermore, transcript-level analysis of RNA-seq reads revealed that the non-coding SNP region within the intron three of DUSP8 may function as an alternative promoter, resulting in significantly higher expression of a shorter transcript that could generate a non-canonical protein isoform. Our study demonstrates that activating genomic regions harboring specific non-coding GWAS SNPs can modulate gene expression, suggesting that these SNPs may contribute to gene regulatory functions. Importantly, this work underscores the powerful utility of CRISPRa as a functional genomics tool for linking GWAS signals to their biological roles in chickens by targeting SNP-containing regions and uncovering consequential molecular phenotypes.

Recent advances in photolithography have significantly reduced the size of transistors on integrated circuits (ICs). However, the performance demands of new technologies such as machine learning, 5G networks, and the Internet of Things are no longer fulfilled by transistor scaling alone. Accordingly, the focus has shifted from traditional scaling to three-dimensional (3D) packaging techniques that offer advanced heterogeneous integration. Copper (Cu)/dielectric hybrid bonding is a highly practical and promising technology in 3D packaging techniques that allows finer pitches in interconnections. This paper reviews the development and implications of Cu/dielectric hybrid bonding, particularly with SiO2 and alternative materials such as SiCN and polymers. To address the challenges of fine-pitch hybrid structures, detailed assessments through experimental methods are introduced to enhance connection reliability and resolve coplanarity issues in fine-pitch applications. In addition, this paper presents a comprehensive overview of the simulation approach for Cu/dielectric hybrid bonding, which mitigates the drawbacks of high costs and time consumption associated with experimental approaches. The primary challenge identified in Cu/dielectric hybrid bonding involves achieving precise surface cleanliness and uniformity and managing interfacial stress due to thermal expansion mismatches between copper and dielectric materials, which adversely affect overall bonding reliability. Advancement of surface preparation techniques along with innovative dielectric materials and structures, which reduce the residual stress and enhance alignment accuracy, will facilitate reliable interconnections at ultra-fine pitches in Cu/dielectric hybrid bonding.

Objective Chickens and ducks represent the most important poultry species within the livestock industry. However, the availability of single nucleotide polymorphism (SNP) chips for these species is limited, and development of separate chips for each species requires considerable expense. To address this limitation, we developed the first poultry SNP chip applicable to both species simultaneously. The 60K SNP chip comprises 30,816 SNPs for chickens and 35,209 SNPs for ducks. The performance of the chip was evaluated using non-pooled datasets (chicken only and duck only) and a pooled dataset combining chicken and duck DNA to verify that genotyping accuracy was maintained without cross-species interference. Methods DNA was extracted from 28 Korean native chickens and 28 Korean native ducks. Genotyping was performed using the Illumina platform, employing chicken-only, duck-only, and pooled chicken-duck SNP panels. Genotype accuracy and concordance were evaluated with PLINK. Sample and SNP quality were assessed in accordance with the Illumina genotyping protocol. Principal component analysis (PCA) was conducted to evaluate and compare the chicken-duck pooled dataset with the non-pooled datasets. Results The mean genotype concordance of non-pooled (chicken only and duck only) datasets exceeded 99%, while concordance between non-pooled and chicken-duck pooled datasets surpassed 97.8%. All datasets satisfied quality thresholds for call rate, GenCall score, 10% GenCall score, and cluster separation. PCA revealed consistent clustering patterns, with no significant differences observed between non-pooled and pooled datasets. Conclusion The first, at the best of our knowledge, poultry SNP chip incorporating chicken-duck pooled samples, has been successfully developed and validated. This chip provides reliable genotyping performance for both species and presents a cost-effective option for large-scale SNP chip development in the livestock industry.

Runs of homozygosity (ROHs) are caused by identical haplotypes inherited from ancestors. ROHs provide useful information regarding the inbreeding rate, demographics, and selection history. The Yeonsan Ogye (YO) breed is an indigenous chicken in Korea that is characterized by a completely black body. In this study, we investigated ROH in the YO genome to determine ROH-based inbreeding coefficients and their correlations with other inbreeding estimators, then analyzed their genetic characteristics. Using 600K single nucleotide polymorphism (SNP) chip information for 189 chickens, we found 20,339 ROHs in the YO population. The average number of ROHs was 107, the total average ROH length was 165 Mb, and the average ROH length was 1.542 Mb. Most ROHs were short (< 8 Mb), suggesting a past population bottleneck. The average inbreeding coefficient (FROH) calculated based on ROHs was 0.184 and this was correlated with other inbreeding coefficients estimated using allele frequencies. 17 ROH islands were detected and these regions exceeded the threshold of the top 1% of SNPs among SNPs present in ROHs. In the ROH islands, 152 genes were annotated, some of which were genes associated with meat production traits and hyperpigmentation in chickens. A comparison of overlapping regions between ROH islands and quantitative trait loci (QTLs) indicated that most QTLs were related to color traits. These results will help to optimize conservation strategies for the YO breed.

A crack-free and residue-free transfer technique for large-area, atomically-thin 2D transition metal dichalcogenides (TMDCs) such as MoS2 and WS2 is critical for their integration into next-generation electronic devices, either as channel materials replacing silicon or as back-end-of-line (BEOL) components in 3D-integrated nano-systems on CMOS platforms. However, cracks are frequently observed during the debonding of TMDCs from their growth substrates, and polymer or metal residues are often left behind after the removal of adhesive support layers via wet etching. These issues stem from excessive angular strain accumulated during debonding and the incomplete removal of support layers due to their low solubility. In this study, we developed a novel debonding strategy along with an optimized etching protocol to address these challenges. Characterization using Raman spectroscopy, photoluminescence (PL), X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), and optical microscopy (OM) confirmed that the optimized process enables clean, crack-free, and morphologically intact MoS2 films. The success of the crack-free and residual-free transfer is attributed to two key factors: (1) the suppression of mechanical bending during debonding, which eliminates bending-induced crack formation; and (2) the precise control of etchant concentration, reaction duration, and post-etch rinsing steps, which ensures the complete removal of the support layer without damaging the MoS2 film. Using commercially available fab tools such as wafer bonders and debonders, we successfully demonstrated the clean transfer of a 2-inch monolayer MoS2 film with a high transfer yield of 95%, highlighting the practical applicability of this process for scalable device fabrication.

Avian influenza (AI) is a serious global threat to poultry and public safety, although some native chicken varieties show resilience, such as the Ri chicken in Vietnam. Major histocompatibility complex B (MHC-B), a critical component of the chicken immune system, has been shown to influence disease resistance. This study examined the MHC-B haplotype diversity in a Ri chicken population that is sensitive to AI. Ri chickens were genotyped for MHC-B single nucleotide polymorphisms (SNPs) using the Kompetitive Allele Specific Polymerase Chain Reaction (KASP). Statistical tests revealed no significant differences in allele frequencies of the SNPs between resistant (R) and susceptible (S) groups. Haplotype analysis identified 32 unique haplotypes, with only one shared haplotype between the R and S groups. However, a phylogenetic analysis did not find distinct clustering of MHC-B alleles of the Ri chicken groups. Further research with a larger sample size is recommended to establish representative group-specific haplotypes and enhance our comprehension of the intricate genetic mechanisms underlying disease resistance in poultry. The implications of this research extend to improving disease resistance strategies and guiding selective breeding practices in the poultry industry.

Objective Yellow Korean native chicken (KNC-Y) is one of the five pure Korean indigenous chicken breeds that were restored through a government project in 1992. KNC-Y is recognized for its superior egg production performance compared to other KNC lines. In this study, we performed runs of homozygosity (ROH) analysis to discover selection signatures associated with egg production traits in the KNC-Y population. Methods A total of 675 DNA samples from KNC-Y were genotyped to generate single nucleotide polymorphism (SNP) data using custom 60K Affymetrix SNP chips. ROH analysis was performed using PLINK software, with predefined parameters set for the analysis. The threshold of ROH island was defined as the top 1% frequency of SNPs withing the ROH among the population. Results In the KNC-Y population, a total of 29,958 runs of homozygosity (ROH) fragments were identified. The average total length of ROH was 120.84 Mb, with each ROH fragment having an average length of 2.71 Mb. The calculated ROH-based inbreeding coefficient (FROH) was 0.13. Furthermore, we revealed the presence of ROH islands on chromosomes 1, 2, 4, 5, 7, 8, and 11. Within the identified regions, a total of 111 genes were annotated, and among them were genes related to economic traits, including PRMT3, ANO5, HDAC4, LSS, PLA2G4A, and PTGS2. Most of the overlapping quantitative trait locus regions with ROH islands were found to be associated with production traits. Conclusion This study conducted a comprehensive analysis of ROH in the KNC-Y population. Notably, among the findings, the PTGS2 gene is believed to play a crucial role in influencing the laying performance of KNC-Y.

Runs of homozygosity (ROHs) are caused by identical haplotypes inherited from ancestors. ROHs provide useful information regarding the inbreeding rate, demographics, and selection history. The Yeonsan Ogye (YO) breed is an indigenous chicken in Korea that is characterized by a completely black body. In this study, we investigated ROH in the YO genome to determine ROH-based inbreeding coefficients and their correlations with other inbreeding estimators, then analyzed their genetic characteristics. Using 600K single nucleotide polymorphism (SNP) chip information for 189 chickens, we found 20,339 ROHs in the YO population. The average number of ROHs was 107, the total average ROH length was 165 Mb, and the average ROH length was 1.542 Mb. Most ROHs were short (< 8 Mb), suggesting a past population bottleneck. The average inbreeding coefficient (FROH) calculated based on ROHs was 0.184 and this was correlated with other inbreeding coefficients estimated using allele frequencies. 17 ROH islands were detected and these regions exceeded the threshold of the top 1% of SNPs among SNPs present in ROHs. In the ROH islands, 152 genes were annotated, some of which were genes associated with meat production traits and hyperpigmentation in chickens. A comparison of overlapping regions between ROH islands and quantitative trait loci (QTLs) indicated that most QTLs were related to color traits. These results will help to optimize conservation strategies for the YO breed.

Objective: The analysis of runs of homozygosity (ROH) has been applied to assess the level of inbreeding and identify selection signatures in various livestock species. The objectives of this study were to characterize the ROH pattern, estimate the rate of inbreeding, and identify signatures of selection in the red-brown Korean native chickens. Methods: The Illumina 60K single nucleotide polymorphism chip data of 651 chickens was used in the analysis. Runs of homozygosity were analysed using the PLINK v1.9 software. Inbreeding coefficients were estimated using the GCTA software and their correlations were examined. Genomic regions with high levels of ROH were explored to identify selection signatures. Results: A total of 32,176 ROH segments were detected in this study. The majority of the ROH segments were shorter than 4 Mb. The average ROH inbreeding coefficients ( F ROH ) varied with the length of ROH segments. The means of inbreeding coefficients calculated from different methods were also variable. The correlations between different inbreeding coefficients were positive and highly variable ( r = 0.18-1). Five ROH islands harbouring important quantitative trait loci were identified. Conclusion: This study assessed the level of inbreeding and patterns of homozygosity in Red-brown native Korean chickens. The results of this study suggest that the level of recent inbreeding is low which indicates substantial progress in the conservation of red-brown Korean native chickens. Additionally, Candidate genomic regions associated with important production traits were detected in homozygous regions.

A string of FTO films with different film thicknesses varying from 35 to 1225 nm has been fabricated on borosilicate glass substrates by ultrasonic spray pyrolysis. The film thickness evaluation on the morphological, structural, electrical, optical, and nanomechanical properties of the FTO coatings has been studied. As the film thickness is increased, surface roughness and grain size also increase. The formation of structural defects, including grain boundaries and crystal twinning, have been observed using Field Emission Scanning Electron Microscopy (FE-SEM) and Atomic Force Microscopy (AFM). X-ray Diffraction (XRD) results reveal a texture evaluation from the (310) to the (200) diffraction peak as a function of film thickness. Changes in surface morphology have also been found to affect electrical, optical, and mechanical performance. As a result, an experiment enhances FTO thin film's electrical and optical properties, showing the sheet resistance of 4.85 +/- 0.15 to 1490 +/- 122.70 Ohm/sq and visible transmittance in the range of 78-96 %. The optimized conditions for the growth of FTO thin film via ultrasonic spray pyrolysis have been determined through this experiment, enabling the use of FTO thin film as a transparent electrode for various device applications.

OBJECTIVE:The major histocompatibility complex in chicken demonstrates a great range of variations within varities, breeds, populations and that can eventually influence their immuneresponses. The preset study was conducted to understand the major histocompatibility complex-B (MHC-B) variability in five major populations of Bangladesh native chicken: Aseel, Hilly, Junglefowl, Non-descript Deshi, and Naked Neck.METHODS:These five major populations of Bangladesh native chicken were analyzed with a subset of 89 single nucleotide polymorphisms (SNPs) in the high-density MHC-B SNP panel and Kompetitive Allele-Specific polymerase chain reaction genotyping was applied. To explore haplotype diversity within these populations, the results were analyzed both manually and computationally using PHASE 2.1 program. The phylogenetic investigations were also performed using MrBayes program.RESULTS:A total of 136 unique haplotypes were identified within these five Bangladesh chicken populations, and only one was shared (between Hilly and Naked Neck). Phylogenetic analysis showed no distinct haplotype clustering among the five populations, although they were shared in distinct clades; notably, the first clade lacked Naked Neck haplotypes.CONCLUSION:The present study discovered a set of unique MHC-B haplotypes in Bangladesh chickens that could possibly cause varied immune reponses. However, further investigations are required to evaluate their relationships with global chicken populations.

Transparent conductive oxides (TCOs) are in high demand by optoelectronic devices such as light-emitting diodes, phototransistors, touchscreens, solar cells, and low-emissivity windows. Tin-doped indium oxide (ITO) material is the most predominant in the market and is utilised among the various TCO materials. However, the lack of raw materials and the high cost of indium materials have necessitated the exploration of cost-effective TCOs that can serve as viable alternatives without compromising the desired optical and electrical properties. Tin oxide (SnO2) films emerge as a promising candidate, offering several benefits, including abundant material sources, inexpensiveness, and non-toxicity. It anticipates producing a higher visible transmittance, excellent electrical conductivity, and good mechanical properties compared to ITO. Moreover, SnO2 can increase its electrical conductivity by introducing representative dopant elements such as Sb, and F. However, structural, optical, and mechanical properties can affect additional dopant elements. Herein, we have demonstrated fluorine-doped tin oxide (FTO) thin films as a function of F dopant concentration by ultrasonic spray pyrolysis. The FTO thin films achieved excellent properties for FTO coatings such as polycrystalline structure, electrical conductivity (ρ = 9.1 × 10–5 Ω cm), transmittance in the visible region (average visible transmittance up to 85.0

Delafossite CuCrO 2 thin films are synthesized controlling the Cu : Cr ratio and doped with Mg, to provide enhanced transparency and conductivity.