Animal Bioscience最新文献

{"title":"Combined transcriptome and metabolome analysis of chicken follicles in Tengchong Snow Chicken follicle selection.","authors":"Yanli Du, Xiannian Zi, Kun Wang, Jinshan Ran, Hanyi Xiang, Li Lei, Yong Liu","doi":"10.5713/ab.24.0861","DOIUrl":"https://doi.org/10.5713/ab.24.0861","url":null,"abstract":"<p><strong>Objective: </strong>The development of pre-hierarchical follicles (PHFs), especially small yellow follicles (SYFs), directly affects the recruitment of dominant follicles and thus affects the egg-laying performance of chickens. However, the development of PHFs, especially SYFs, and their regulatory mechanism remain unclear.</p><p><strong>Methods: </strong>We performed transcriptomic and metabolomic analyses of large white follicles (LWFs) and SYFs in chickens.</p><p><strong>Results: </strong>Transcriptome sequencing revealed 258 differentially expressed genes (DEGs) between SYFs and LWFs, of which 172 were upregulated and 86 were downregulated. The DEGs were mapped to 17 KEGG pathways, including Glutathione metabolism, Ferroptosis, Calcium signaling pathway, and Neuroactive ligand-receptor interactions, etc. The metabolome analysis revealed 129 significant differential metabolites (DMs), including 36 upregulated DMs and 93 downregulated DMs. The DMs were mapped to nine KEGG pathways, including Glutathione metabolism, alpha-Linolenic acid metabolism, and Linoleic acid metabolism, etc. The combined transcriptional and metabolic analysis revealed significantly enriched pathways. Five KEGG pathways associated with follicular development were identified, including Glutathione metabolism, Ferroptosis, alpha-Linolenic acid metabolism, Linoleic acid metabolism, and Pyrimidine metabolism.</p><p><strong>Conclusion: </strong>Glutathione metabolism may directly inhibit Ferroptosis, which can induce apoptosis of granulosa cells (GCs), thereby regulating SYFs development in chickens. These findings provided a reference for improving the egg-laying performance of Tengchong snow chickens.</p>","PeriodicalId":7825,"journal":{"name":"Animal Bioscience","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143954065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of nitrate in combination with lactate on rumen fermentation, and methane production in an in vitro batch culture.","authors":"Beomseok Bae, Logan Pope, Kiyeon Park, Chanhee Lee","doi":"10.5713/ab.25.0020","DOIUrl":"https://doi.org/10.5713/ab.25.0020","url":null,"abstract":"<p><strong>Objective: </strong>This in vitro study determined the combination effect of nitrate and lactate on nitrate reduction, rumen fermentation and methane production. We hypothesized that the combination decreases methane production and enhances nitrate reduction.</p><p><strong>Methods: </strong>An in vitro batch culture was conducted to determine the 2 main factors of nitrate and lactate in 2 × 2 factorial arrangement: a basal diet (CON), the basal diet supplemented with nitrate (2.2% in dietary DM; Nit), lactate (2.2%; Lact), or the combination of nitrate and lactate (Nit-Lact). Rumen fluids from lactating Holstein cows were obtained and mixed with McDougall's buffer for the in vitro batch culture. Total gas production, methane production, pH, VFA, NH₃-N, NO3-N and NO2-N concentration, and dry matter (DM) digestibility were determined.</p><p><strong>Results: </strong>A trend of interaction between nitrate and lactate was observed for DM digestibility (p=0.06), which occurred because DM digestibility tended to decrease for Nit compared with CON (42.2 vs. 45.3%) but did not for Nit-Lact. Nitrate decreased (p<0.05) methane (25.6 vs. 31.0 mL at 24 h) and total gas production (296 vs. 313 mL at 24 h). Total VFA production was not affected by treatments. However, nitrate increased the proportion of acetate (p<0.01) and decreased (p<0.01) proportions of propionate, butyrate and valerate at 24 h of incubation. However, lactate increased valerate at 24 h of incubation (p<0.01). The concentration of NO3-N for Nit-Lact was lower than that of Nit (41.2 vs. 51.0 mg/L; p<0.01) at 3 h of incubation.</p><p><strong>Conclusion: </strong>Nitrate decreased methane production. The combination of nitrate and lactate had beneficial effects on DM digestibility and nitrate reduction, compared with nitrate alone although no interaction between nitrate and lactate was shown for VFA production and methane production. Changes in the major VFA by nitrate indicated that nitrate acted as an alternative electron acceptor to decrease methane production.</p>","PeriodicalId":7825,"journal":{"name":"Animal Bioscience","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143958503","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Beneficial Impact of Pomegranate Oil Nanoemulsion on the Quality of Cryopreserved Bovine Sperm: Antioxidant and Anti-Apoptotic Effects.","authors":"Fatma Mohsen Shalaby, Soha A Hassan, Ali Ali El-Raghi, Fatemah Enad Alajmi, Mohamed G Alfayoumi, Kandil Abd El Hai Attia","doi":"10.5713/ab.25.0067","DOIUrl":"https://doi.org/10.5713/ab.25.0067","url":null,"abstract":"<p><strong>Objective: </strong>This study was conducted to investigate the effect of Pomegranate oil nano-emulsion (PO-NE) supplementation in semen extender on semen quality, redox status and apoptotic genes of cryopreserved bovine semen.</p><p><strong>Methods: </strong>Seven proven fertility Holstein cattle bulls (4-6 years) were involved, and the semen samples were collected using the artificial vagina method. Semen was pooled and cryopreserved in tris extender containing PO-NE at 0 (PO-NE0), 1 (PO-NE1), 2 (PO-NE 2) and 4 μg/mL (PO-NE4), respectively.</p><p><strong>Results: </strong>Incorporating 2 or 4 μg/mL PO-NE into freezing media significantly increased sperm progressive motility, viability, membrane integrity, and kinematic parameters. Furthermore, the aforementioned two treated concentrations demonstrated superior anti-oxidative activities (total antioxidant capacity and super oxide dismutase) and higher nitric oxide levels compared to the control group (p < 0.05). The levels of hydrogen peroxide, malondialdehyde, and Nuclear Factor-Kappa B were notably lower in the PO-NE4 treated group compared to the control group. The addition of 2 or 4 μg/mL of PO-NE to the freezing media significantly downregulated pro-apoptotic genes (caspase 3, Bax), while significantly induced the expression of anti-apoptotic gene Bcl2. The addition of PO-NE preserved plasma membrane and acrosome integrity and maintained the ultrastructure of sperm, contrasting with PO-NE0, which exhibited the most damage.</p><p><strong>Conclusion: </strong>supplementing the bovine freezing extender with 2 - 4 μg/mL of PO-NE enhanced post-thawed sperm characteristics by reducing oxidative stress, improving antioxidant indices and apoptotic genes expression, and preserving the ultrastructure integrity of frozen-thawed cattle sperm.</p>","PeriodicalId":7825,"journal":{"name":"Animal Bioscience","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143962874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Longitudinal Investigation of Gut Microbiota Dynamics in Laying Hens from Birth to Egg-Laying Stages.","authors":"Seojin Choi, Eun Bae Kim","doi":"10.5713/ab.24.0889","DOIUrl":"https://doi.org/10.5713/ab.24.0889","url":null,"abstract":"<p><strong>Objective: </strong>Laying hens are a critical resource in global agriculture, valued for their egg production, which provides an economical and nutritious source of protein. This study aims to comprehensively characterize the developmental changes in the gut microbiota of Hy-Line Brown laying hens from birth to post-laying stages.</p><p><strong>Methods: </strong>A total of 100 Hy-Line Brown laying hens were reared under controlled conditions, and feces and ileal contents were collected at three post-laying stages (151, 302, and 422 days). DNA was extracted from the samples and the V4 region of the 16S rRNA gene was sequenced using an Illumina MiSeq platform. The Random Forest algorithm was applied to identify microbial predictors and explore their relationships with age.</p><p><strong>Results: </strong>The rapid increase in body weight continued until day 151, after which it stabilized through day 422. Fecal microbiome diversity increased until day 302, whereas in the ileal content, it grew until day 101 before declining. Throughout all stages, Firmicutes, Proteobacteria, and Bacteroidetes were the predominant phyla. Lactobacillus abundance peaked on day 10 (33.75%) across all sampling sites, whereas Escherichia-Shigella reached its maximum on day 21 but gradually diminished to 2.88% by day 422 (p < 0.05). Machine learning analysis revealed that Candidatus Arthromitus and Clostridia vadinBB60 group consistently had the highest importance scores across all sample sites. At 302 day, body weight exhibited negative relationships with feces Brevibacterium (R=-0.87; p < 0.05) and Brachybacterium (R=-0.79; p < 0.05).</p><p><strong>Conclusion: </strong>This study examined gut microbiota changes in Hy-Line Brown hens from birth to one-year post-laying, highlighting the impact of calcium-rich layer diets. The findings provide insights into microbiota dynamics and their relationship with age, which can be applied to optimize dietary strategies and improve laying hen productivity and health.</p>","PeriodicalId":7825,"journal":{"name":"Animal Bioscience","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143956568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Preparation of two kinds of immunocastration vaccines and their immune effects on male goats.","authors":"Fuqiang Pan, Yumeng Guo, Panpan Cheng, Wei Qian, Mengdi Han, Qing Yi, Huihui Xie, Meng Cao, Yanqiuhong Li, Yuke Jia, Jiankun Cui, Xinbao Gong, Ziye Zhu, Fugui Fang, Yinghui Ling, Yunsheng Li, Jian Li, Ya Liu","doi":"10.5713/ab.24.0811","DOIUrl":"https://doi.org/10.5713/ab.24.0811","url":null,"abstract":"<p><strong>Objective: </strong>After sexual maturity, male goats will exhibit fighting and mounting behaviors due to the increase of testosterone level, resulting in slower growth rate and mutton odor. However, traditional castration methods will cause significant stress. In contrast, immunocastration is a welfare-friendly and gentler approach to replace mechanical castration. Therefore, it is important to develop immunocastration vaccines with good immune effects.</p><p><strong>Methods: </strong>GnRH octamer vaccine (G8), LHR and GnRH octamer tandem vaccine (LG) were designed and prepared for this study. Forty 3-month-old male goats were randomly divided into four groups: surgical castration (SC group), immunization with the G8 vaccine (G8 group), immunization with the LG vaccine (LG group), or left intact (non- castration, NC group). After the first immunization, serum antibodies and testosterone levels, as well as body weight, body size, and scrotal size, were measured at different times. Testicular size and slaughter rate were measured at slaughter.</p><p><strong>Results: </strong>Both vaccines successfully elicited the corresponding antibodies in male goats; the testosterone levels in the G8 and LG groups were significantly lower than those in the NC group (p< 0.01) 4 weeks after the first immunization and this trend continued until the end of the experiment; the testicular organ index and size of G8 group were significantly smaller than those of NC group at slaughter (p < 0.05). Compared with the NC group, the seminiferous tubule diameter in the G8 and LG groups was significantly reduced (p < 0.01), with a notable decrease in Leydig Cells and various stages of spermatogenic cells, and the weight gain of goats in the SC group was significantly lower than that of other groups 2 weeks after the first immunization (p < 0.05).</p><p><strong>Conclusion: </strong>The two immunocastration vaccines developed can effectively inhibit the development of testes and spermatogenesis in male goats and reduce testosterone levels.</p>","PeriodicalId":7825,"journal":{"name":"Animal Bioscience","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143968470","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chitinase improves the effective energy value, amino acids digestibility of black soldier fly and intestinal microbiota of growing pigs.","authors":"Yuansen Yang, Shenrui Xu, Wenjun Gao, Yu Wei, Lu Wang, Changhua Lai","doi":"10.5713/ab.24.0920","DOIUrl":"https://doi.org/10.5713/ab.24.0920","url":null,"abstract":"<p><strong>Objective: </strong>The main objective of this study was to determine the energy value and digestibility of amino acids in growing pigs fed black soldier fly (BSF) with chitinase supplementation and its effect on intestinal microbiota.</p><p><strong>Methods: </strong>In Exp. 1, eighteen barrows with initial body weight (BW) of 31.57 ± 1.24 kg were randomly assigned to 3 treatments with 6 replicates per treatment to determine the DE, ME, and nutrients digestibility, including the corn-soybean meal basal group, the BSF with or without chitinase groups. In Exp. 2, six barrows (36.72 ± 4.2 kg BW) with ileal T-cannulas were randomly assigned to 3 dietary treatments in 3 periods in a Latin square design to determine the digestibility of the amino acids, including the nitrogen-free group, the BSF with or without chitinase groups.</p><p><strong>Results: </strong>We observed that that adding chitinase increased the BSF's digestive and metabolic energy by 2.34MJ/kg and 1.37MJ/kg, respectively. Chitinase supplementation had no adverse effects on piglets and could improve the composition of intestinal microbiota, promote the colonisation of beneficial bacteria, and inhibit the proliferation of potentially pathogenic bacteria. Moreover, adding chitinase increased the abundance and homogeneity of intestinal microorganisms in growing pigs. Adding chitinase enhanced the apparent ileal digestibility and standardized ileal digestibility of most amino acids in BSF, such as methionine, leucine, and glutamate.</p><p><strong>Conclusion: </strong>Adding chitinase can increase the effective energy value and amino acid ileal digestibility of BSF, regulate the composition of intestinal microorganisms and improve the intestinal health of growing pigs, which can provide a reference for developing novel protein feed.</p>","PeriodicalId":7825,"journal":{"name":"Animal Bioscience","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143958703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rapid determination of nutrient composition and mineral element content of common vetch (Vicia sativa L.) using Near-infrared spectroscopy.","authors":"Tao Wang, Li Wang, Tao Guo, Yanli Shi, Baocang Liu, Fei Li","doi":"10.5713/ab.24.0872","DOIUrl":"https://doi.org/10.5713/ab.24.0872","url":null,"abstract":"<p><strong>Objective: </strong>This study aims to establish an accurate and reliable near-infrared spectroscopy to enable rapid, efficient, and non-destructive evaluation of the nutritional quality of common vetches across different regions and varieties.</p><p><strong>Methods: </strong>A total of 190 samples from various regions and varieties were selected for this study, which were divided into a calibration set (4:1 ratio) and validation set. The original spectrum of the calibration set is subjected to 10 different pretreatment techniques in combination with first and second derivatives, while the prediction model was established by combining the measured value of common vetch with the modified partial least squares method (MPLS).</p><p><strong>Results: </strong>The results indicate that the calibration root-mean-square error (REMSEC) and cross-validation root-mean-square error (REMSECV) values range from 0.01 to 1.25 and 0.01 to 1.37, respectively. The determination coefficients of cross-validation (R2CV) for phosphorus (P), potassium (K), magnesium (Mg), and iron (Fe) are relatively low at 0.82, 0.86, 0.82, and 0.74 respectively; however, all other indicators have R2CV values above 0.90. The predicted root means square errors (RMSEP) for common vetch indexes range from 0.01 to 1.87 with RMSEP values higher than 1.0 observed for crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF), and ash indices, whereas RMSEP values lower than or equal to 1.0 were obtained for other indicators. The measured coefficient of determination (R2p) demonstrates that the R2p values for each nutrient element and mineral element vary from 0.70 to 0.96. The residual prediction deviation (RPD) values for Mg exhibit relatively low levels, while the RDP values for other indicators exceed 2.0.</p><p><strong>Conclusion: </strong>These findings suggest that this study provides a viable approach to evaluate the nutritional composition and mineral element content of different varieties and regions of common vetch.</p>","PeriodicalId":7825,"journal":{"name":"Animal Bioscience","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143952175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigation of the Genetic Determinism of Amino Acid Digestibility Traits in Duroc x Landrace x Yorkshire Crossbred Pigs.","authors":"Yancan Wang, Xin Wang, Qiye Wang, Kang Xu, Zhi Li, Qin Zeng, Jianzhong Li, Yulong Yin, Huansheng Yang","doi":"10.5713/ab.24.0765","DOIUrl":"https://doi.org/10.5713/ab.24.0765","url":null,"abstract":"<p><strong>Objective: </strong>The objective of this study was to delineate the genetic architecture of ileal amino acid digestibility in Duroc × (Landrace × Yorkshire) hybrid (DLY) pigs through genome-wide association study (GWAS), aiming to identify associated Single nucleotide polymorphisms (SNPs) and candidate genes to inform precision breeding strategies for enhanced nutrient utilization and environmental sustainability.</p><p><strong>Methods: </strong>We conducted a GWAS on 600 DLY pigs to identify genetic markers associated with ileal amino acid digestibility, employing the GGP Porcine 50K SNP Chip and analyzing fifteen amino acid digestibility traits. GLM and FarmCPU-based GWAS approaches were utilized to detect SNP associations, followed by gene annotation to identify candidate genes near significant SNP loci.</p><p><strong>Results: </strong>We identified two SNPs, chr3:33019982 and Chr17:34715741, significantly associated with the digestibility of multiple amino acids. SNP chr3:33019982 was linked to threonine, leucine, histidine, proline, and arginine digestibility, while Chr17:34715741 was associated with arginine. Gene annotation revealed Trans-Golgi network vesicle protein 23 homolog A (TVP23A) and Synapse differentiation-induced gene I (SynDIG1) as potential candidates for amino acid metabolism in the terminal ileum.</p>","PeriodicalId":7825,"journal":{"name":"Animal Bioscience","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143959529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Heated drinking water in winter improves growth performance of male Hu sheep by modulating rumen quorum sensing and metabolites, and enhancing serum antioxidant capacity.","authors":"Chang Liu, Lingyan Li, Jiaqi Dai, Mingren Qu, Kehui Ouyang, Qinghua Qiu","doi":"10.5713/ab.24.0821","DOIUrl":"https://doi.org/10.5713/ab.24.0821","url":null,"abstract":"<p><strong>Objective: </strong>This study aimed to explore the mechanism by which increasing the temperature of drinking water in winter promotes sheep growth from a microbial perspective.</p><p><strong>Methods: </strong>A total of 12 healthy male Hu sheep were evenly divided into two groups: one with drinking water at 12°C (WT12) and the other at 25°C (WT25), and they were raised for 60 days in the cold winter.</p><p><strong>Results: </strong>The WT25 group exhibited higher average daily gain, serum immunoglobulin G, total antioxidant capacity, glutathione peroxidase, and superoxide dismutase, along with lower feed-to-gain ratio, serum cortisol, malondialdehyde, reactive oxygen species, and oxidative stress index when compared to the WT12 group (p<0.05). The concentrations of microbial crude protein, microbial density, autoinducer-2 (AI-2) signaling molecule concentration, and biofilm formation were higher in the WT25 group, while the ammonia nitrogen concentration was lower (p<0.05). The relative abundances of Muribaculum and Clostridia UCG-014, as well as the predicted metabolic pathways related to lipid metabolism, were lower in the WT25 group, whereas the metabolism of other amino acids showed increased abundances (p<0.05). Both principal coordinates analysis (PCoA) and analysis of similarities (ANOSIM) revealed no significant differences in rumen microbial communities between the WT12 and WT25 groups (p>0.05). Metabolomics analysis identified 12 differential metabolites, four of which were correlated with Muribaculum, Raoultibacter, and Coriobacteriales Incertae Sedis.</p><p><strong>Conclusion: </strong>These results indicate that heated drinking water in winter could improve growth performance by increasing rumen bacterial biofilm formation and enhancing serum antioxidant capacity in Hu sheep. This study establishes correlations between rumen microbial quorum sensing and key factors such as animal growth phenotypes, rumen metabolic characteristics, and specific bacterial genera. It offers innovative perspectives on enhancing animal feed efficiency through the modulation of rumen bacterial quorum sensing.</p>","PeriodicalId":7825,"journal":{"name":"Animal Bioscience","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143968530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of imputation performance based on the SNP panel density and the reference population size in Korean native chicken(R).","authors":"Minjun Kim, Hyo Jun Choo, Sunghyun Cho, Doo Ho Lee, Jun Heon Lee, Dongwon Seo","doi":"10.5713/ab.24.0815","DOIUrl":"https://doi.org/10.5713/ab.24.0815","url":null,"abstract":"<p><strong>Objective: </strong>This study aimed to identify the optimal single nucleotide polymorphism (SNP) panel density for accurate imputation in the Korean native chicken (KNC) and Yeonsan Ogye (YO) populations. The primary focus was on evaluating how the reference population size and SNP density influence imputation performance and accuracy.</p><p><strong>Methods: </strong>Data were collected from five purebred lines of KNC and the YO population, comprising a total of 256 KNC and 199 YO chickens. Imputed genotype ratio and accuracy were evaluated across various scenarios using SNP densities of 2.5K, 5K, 10K, and 50K in both populations. Additionally, for the YO dataset, reference population sizes of 50, 100, and 150 were analyzed to assess their impact on imputation outcomes.</p><p><strong>Results: </strong>Higher SNP densities notably improved imputation performance. Specifically, when SNP panel density reached 10K or greater, the ratio of imputed SNPs exceeded 70% and the accuracy increased substantially, regardless of the reference population size. However, imputation efficiency decreased markedly when either the reference or test population size was around 50 individuals.</p><p><strong>Conclusion: </strong>A test SNP density of at least 10K was determined to be essential for accurate genotype imputation. Additionally, imputation efficiency was observed to decline when either the reference or test population included around 50 individuals. These findings provide important data that can guide the genetic improvement of indigenous livestock populations.</p>","PeriodicalId":7825,"journal":{"name":"Animal Bioscience","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143956926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}