cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24968733.v1
title: Effects of selenium-enriched yeast dietary supplementation on egg quality, gut morphology and caecal microflora of laying hens

description: Selenium (Se) is an essential micronutrient for humans and animals and is a powerful antioxidant that can promote reproductive and immune functions. The purpose of this study was to evaluate the effects of supplemental dietary selenium-enriched yeast (SeY) on egg quality, gut morphology and microflora in laying hens. In total, 100 HY-Line Brown laying hens (45-week old) were randomly allocated to two groups with 10 replicates and fed either a basal diet (without Se supplementation) or a basal diet containing 0.2 mg/kg Se in the form of SeY for 8 weeks. The Se supplementation did not have a significant effect on egg quality and intestinal morphology of laying hens. Based on the 16S rRNA sequencing, SeY dietary supplementation effectively modulated the cecal microbiota structure. An alpha diversity analysis demonstrated that birds fed 100 mg/kg SeY had a higher cecal bacterial diversity. SeY dietary addition elevated <i>Erysipelotrichia</i> (class), <i>Lachnospiraceae</i> (family), <i>Erysipelotrichaceae</i> (family) and <i>Ruminococcus_torques_group</i> (genus; <i>p</i> &lt; .05). Analysis of microbial community-level phenotypes revealed that SeY supplementation decreased the microorganism abundance of facultatively anaerobic and potentially pathogenic phenotypes. Overall, SeY supplementation cannot significantly improve intestinal morphology; however, it modulated the composition of cecal microbiota toward a healthier gut.
DOI: 10.6084/m9.figshare.25315876
title: RETRACTED ARTICLE: Thyroid transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in small tail han sheep with <i>FecB BB</i> genotype

description: We, the Editor and Publisher of Animal Biotechnology, have retracted the following article: Chang, C., He, X., Di, R., Wang, X., Han, M., Liang, C., & Chu, M. (2024). Thyroid transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in small tail han sheep with FecB BB genotype. Animal Biotechnology, 35(1), https://doi.org/10.1080/10495398.2024.2312393 Following publication, concerns have been raised about the integrity of the data presented in the article. When approached for an explanation, the authors responded, however, they were unable to address the concerns raised. As verifying the validity of published work is core to the integrity of the scholarly record, we are therefore, retracting the article. The corresponding author listed in this publication has been informed. The authors do not agree with the retraction. We have been informed in our decision-making by our editorial policies and the COPE guidelines. The retracted articles will remain online to maintain the scholarly record, but they will be digitally watermarked on each page as ‘Retracted’.
DOI: 10.6084/m9.figshare.25315876.v2
title: RETRACTED ARTICLE: Thyroid transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in small tail han sheep with <i>FecB BB</i> genotype

description: We, the Editor and Publisher of Animal Biotechnology, have retracted the following article: Chang, C., He, X., Di, R., Wang, X., Han, M., Liang, C., & Chu, M. (2024). Thyroid transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in small tail han sheep with FecB BB genotype. Animal Biotechnology, 35(1), https://doi.org/10.1080/10495398.2024.2312393 Following publication, concerns have been raised about the integrity of the data presented in the article. When approached for an explanation, the authors responded, however, they were unable to address the concerns raised. As verifying the validity of published work is core to the integrity of the scholarly record, we are therefore, retracting the article. The corresponding author listed in this publication has been informed. The authors do not agree with the retraction. We have been informed in our decision-making by our editorial policies and the COPE guidelines. The retracted articles will remain online to maintain the scholarly record, but they will be digitally watermarked on each page as ‘Retracted’.
DOI: 10.6084/m9.figshare.25315876.v1
title: Thyroid transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in small tail han sheep with <i>FecB BB</i> genotype

description: The thyroid gland is an important endocrine gland in animals that secretes thyroid hormones and acts on various organs throughout the body. lncRNAs are long non-coding RNAs that play an important role in animal reproduction; however, there is a lack of understanding of their expression patterns and potential roles in the thyroid gland of the Small Tail Han (STH) sheep. In this study, we used RNA-Seq technology to examine the transcriptome expression pattern of the thyroid from the luteal phase (LP) and follicular phase (FP) of FecB BB (MM) STH sheep. We identified a total of 122 and 1287 differential expression lncRNAs (DELs) and differential expression mRNAs (DEGs), respectively, which were significantly differentially expressed. These DELs target genes and DEGs can be enriched in several signalling pathways related to the animal reproduction process. The expression profiles of DELs and DEGs in thyroid glands provide a more comprehensive resource for elucidating the reproductive regulatory mechanisms of STH sheep.
DOI: 10.6084/m9.figshare.27241924
title: Full-length 16S rRNA gene amplicon analysis of gut microbiota in pigs fed with different diets in growing and finishing stages

description: The present study utilized full-length 16S rRNA gene sequencing to investigate the impact of dietary protein content on the composition and function of gut microbiota, and to analyze the gut microbiota of pigs in the growing (30 kg) and finishing (120 kg) stages under different feeding conditions. The results indicated that the gut microbiota was significantly different between pigs fed high- and low-protein diets. Comparing fecal samples from pigs at 30 and 120 kg, pigs at 30 kg showed a significant increase in the relative abundance of <i>Clostridium butyricum</i>, whereas at 120 kg, the abundance of <i>Lactobacillus reuteri</i> and <i>Lactobacillus johnsonii</i> decreased. To access the functional profiles and metabolic pathways based on amplicon sequence variants (ASVs), the microbiome of the 120 kg exhibited significant enrichments in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to metabolism-related category, including Alanine, aspartate and glutamate metabolism, Tyrosine and Thiamin metabolism, and Inositol phosphate metabolism. Meanwhile, analysis using the MetaCyc database showed that the metabolic pathways of the 30 kg group were significantly distinct when compared to the 120 kg of fecal samples. Overall, the findings indicated that the gut microbiota composition and function in the 30 and 120 kg fecal samples were markedly shaped by different dietary protein levels.
DOI: 10.6084/m9.figshare.27241924.v1
title: Full-length 16S rRNA gene amplicon analysis of gut microbiota in pigs fed with different diets in growing and finishing stages

description: The present study utilized full-length 16S rRNA gene sequencing to investigate the impact of dietary protein content on the composition and function of gut microbiota, and to analyze the gut microbiota of pigs in the growing (30 kg) and finishing (120 kg) stages under different feeding conditions. The results indicated that the gut microbiota was significantly different between pigs fed high- and low-protein diets. Comparing fecal samples from pigs at 30 and 120 kg, pigs at 30 kg showed a significant increase in the relative abundance of <i>Clostridium butyricum</i>, whereas at 120 kg, the abundance of <i>Lactobacillus reuteri</i> and <i>Lactobacillus johnsonii</i> decreased. To access the functional profiles and metabolic pathways based on amplicon sequence variants (ASVs), the microbiome of the 120 kg exhibited significant enrichments in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to metabolism-related category, including Alanine, aspartate and glutamate metabolism, Tyrosine and Thiamin metabolism, and Inositol phosphate metabolism. Meanwhile, analysis using the MetaCyc database showed that the metabolic pathways of the 30 kg group were significantly distinct when compared to the 120 kg of fecal samples. Overall, the findings indicated that the gut microbiota composition and function in the 30 and 120 kg fecal samples were markedly shaped by different dietary protein levels.
DOI: 10.6084/m9.figshare.27900757
title: Core promoter identification and transcriptional regulation of porcine <i>ACSL3</i> gene

description: Intramuscular fat (IMF) content is an important factor that affects the edible and processing quality of pork. Studying the transcriptional regulation mechanisms of genes affecting intramuscular fat deposition can provide theoretical support for genetic improvement in pigs. Long-chain fatty acyl-CoA synthase 3 (<i>ACSL3</i>), as a key enzyme in the process of lipid synthesis in mammals. However, no information about the core promoter of the <i>ACSL3</i> gene and its transcriptional regulation has been reported so far. In this experiment, we successfully cloned 3112 bp of the porcine <i>ACSL3</i> gene promoter region. In order to find out the core promoter of the <i>ACSL3</i> gene. The results indicated that the core promoter region of the <i>ACSL3</i> gene is located from −111 bp to −59 bp upstream of the transcription initiation site (TSS). To identify the interaction between SP1 and the <i>ACSL3</i> gene promoter, we mutated the predicted binding sites of <i>ACSL3</i> gene promoter. The results showed that the activity of the promoter was decreased by site-specific mutagenesis of the SP1 transcription factor binding site, while overexpression of SP1 increased the expression of the <i>ACSL3</i> gene. In summary, our study identified a core promoter region of the porcine <i>ACSL3</i> gene, and the SP1 binding site is responsible for the promoter activity.
DOI: 10.6084/m9.figshare.27900757.v1
title: Core promoter identification and transcriptional regulation of porcine <i>ACSL3</i> gene

description: Intramuscular fat (IMF) content is an important factor that affects the edible and processing quality of pork. Studying the transcriptional regulation mechanisms of genes affecting intramuscular fat deposition can provide theoretical support for genetic improvement in pigs. Long-chain fatty acyl-CoA synthase 3 (<i>ACSL3</i>), as a key enzyme in the process of lipid synthesis in mammals. However, no information about the core promoter of the <i>ACSL3</i> gene and its transcriptional regulation has been reported so far. In this experiment, we successfully cloned 3112 bp of the porcine <i>ACSL3</i> gene promoter region. In order to find out the core promoter of the <i>ACSL3</i> gene. The results indicated that the core promoter region of the <i>ACSL3</i> gene is located from −111 bp to −59 bp upstream of the transcription initiation site (TSS). To identify the interaction between SP1 and the <i>ACSL3</i> gene promoter, we mutated the predicted binding sites of <i>ACSL3</i> gene promoter. The results showed that the activity of the promoter was decreased by site-specific mutagenesis of the SP1 transcription factor binding site, while overexpression of SP1 increased the expression of the <i>ACSL3</i> gene. In summary, our study identified a core promoter region of the porcine <i>ACSL3</i> gene, and the SP1 binding site is responsible for the promoter activity.
DOI: 10.6084/m9.figshare.24118284
title: Thyroid transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in Small Tail Han sheep with <i>FecB<sup>++</sup></i> genotype

description: The thyroid gland is an important endocrine gland in animals, which mainly secretes thyroid hormones and acts on various organs of the body. Long-chain non-coding RNA (lncRNA) plays an important role in animal reproduction. However, there is still a lack of understanding of their expression patterns and potential roles in the thyroid of Small Tail Han (STH) sheep. In this study, RNA-seq was used to examine the transcriptome expression patterns of lncRNAs and mRNAs in the follicular phase (ww_FT) and luteal phase (ww_LT) in <i>FecB<sup>++</sup></i> genotype STH Sheep. A total of 17,217 lncRNAs and 39,112 mRNAs were identified including 96 differentially expressed lncRNAs (DELs) and 1054 differentially expressed mRNAs (DEGs). Functional analysis of genes with significant differences in expression level showed that these genes could be enriched in Ras signalling pathway, hedgehog (HH) signalling pathway, ATP-binding cassette (ABC) transporters and other signalling pathways related to animal reproduction. In addition, through correlation analysis for lncRNA–mRNA co-expression and network construction, we found that LNC_009115 and LNC_005796 trans target NIK-related kinase (<i>NRK</i>) and poly(A)-specific ribonuclease (<i>PARN</i>). LNC_007189 and LNC_002045 trans target progesterone-induced blocking factor 1 (<i>PIBF1</i>), LNC_009013 trans targets small mothers against decapentaplegic (<i>SMAD1</i>) are related to animal reproduction. These genes add new resources for elucidating the regulatory mechanisms of reproduction in sheep with different reproductive cycles of the <i>FecB<sup>++</sup></i> genotype STH sheep.
DOI: 10.6084/m9.figshare.24118284.v1
title: Thyroid transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in Small Tail Han sheep with <i>FecB<sup>++</sup></i> genotype

description: The thyroid gland is an important endocrine gland in animals, which mainly secretes thyroid hormones and acts on various organs of the body. Long-chain non-coding RNA (lncRNA) plays an important role in animal reproduction. However, there is still a lack of understanding of their expression patterns and potential roles in the thyroid of Small Tail Han (STH) sheep. In this study, RNA-seq was used to examine the transcriptome expression patterns of lncRNAs and mRNAs in the follicular phase (ww_FT) and luteal phase (ww_LT) in <i>FecB<sup>++</sup></i> genotype STH Sheep. A total of 17,217 lncRNAs and 39,112 mRNAs were identified including 96 differentially expressed lncRNAs (DELs) and 1054 differentially expressed mRNAs (DEGs). Functional analysis of genes with significant differences in expression level showed that these genes could be enriched in Ras signalling pathway, hedgehog (HH) signalling pathway, ATP-binding cassette (ABC) transporters and other signalling pathways related to animal reproduction. In addition, through correlation analysis for lncRNA–mRNA co-expression and network construction, we found that LNC_009115 and LNC_005796 trans target NIK-related kinase (<i>NRK</i>) and poly(A)-specific ribonuclease (<i>PARN</i>). LNC_007189 and LNC_002045 trans target progesterone-induced blocking factor 1 (<i>PIBF1</i>), LNC_009013 trans targets small mothers against decapentaplegic (<i>SMAD1</i>) are related to animal reproduction. These genes add new resources for elucidating the regulatory mechanisms of reproduction in sheep with different reproductive cycles of the <i>FecB<sup>++</sup></i> genotype STH sheep.
DOI: 10.6084/m9.figshare.27005062
title: The impact of genetic variants related to the fatty acid metabolic process pathway on milk production traits in Jersey cows

description: The synthesis of fatty acids plays a critical role in shaping milk production characteristics in dairy cattle. Thus, identifying effective haplotypes within the fatty acid metabolism pathway will provide novel and robust insights into the genetics of dairy cattle. This study aimed to comprehensively examine the individual and combined impacts of fundamental genes within the fatty acid metabolic process pathway in Jersey cows. A comprehensive phenotypic dataset was compiled, considering milk production traits, to summarize a cow’s productivity across three lactations. Genotyping was conducted through PCR-RFLP and Sanger sequencing, while the association between genotype and phenotype was quantified using linear mixed models. Moderate biodiversity and abundant variation suitable for haplotype analysis were observed across all examined markers. The individual effects of the <i>FABP3</i>, <i>LTF</i> and <i>ANXA9</i> genes significantly influenced both milk yield and milk fat production. Additionally, this study reveals novel two-way interactions between genes in the fatty acid metabolism pathway that directly affect milk fat properties. Notably, we identified that the GGAAGG haplotype in <i>FABP3</i>×<i>LTF</i>×<i>ANXA9</i> interaction may be a robust genetic marker concerning both milk fat yield and percentage. Consequently, the genotype combinations highlighted in this study serve as novel and efficient markers for assessing the fat content in cow’s milk.
DOI: 10.6084/m9.figshare.27005062.v1
title: The impact of genetic variants related to the fatty acid metabolic process pathway on milk production traits in Jersey cows

description: The synthesis of fatty acids plays a critical role in shaping milk production characteristics in dairy cattle. Thus, identifying effective haplotypes within the fatty acid metabolism pathway will provide novel and robust insights into the genetics of dairy cattle. This study aimed to comprehensively examine the individual and combined impacts of fundamental genes within the fatty acid metabolic process pathway in Jersey cows. A comprehensive phenotypic dataset was compiled, considering milk production traits, to summarize a cow’s productivity across three lactations. Genotyping was conducted through PCR-RFLP and Sanger sequencing, while the association between genotype and phenotype was quantified using linear mixed models. Moderate biodiversity and abundant variation suitable for haplotype analysis were observed across all examined markers. The individual effects of the <i>FABP3</i>, <i>LTF</i> and <i>ANXA9</i> genes significantly influenced both milk yield and milk fat production. Additionally, this study reveals novel two-way interactions between genes in the fatty acid metabolism pathway that directly affect milk fat properties. Notably, we identified that the GGAAGG haplotype in <i>FABP3</i>×<i>LTF</i>×<i>ANXA9</i> interaction may be a robust genetic marker concerning both milk fat yield and percentage. Consequently, the genotype combinations highlighted in this study serve as novel and efficient markers for assessing the fat content in cow’s milk.
DOI: 10.6084/m9.figshare.26598676
title: Discover QTLs for the level of blood components in Shaoxing duck using GWAS and haplotype sharing analysis

description: Blood composition is indicative of health-related traits such as immunity and metabolism. The use of molecular genetics to investigate alterations in these attributes in laying ducks is a novel approach. Our objective was to employ genome − wide association studies (GWAS) and haplotype − sharing analysis to identify genomic regions and potential genes associated with 11 blood components in Shaoxing ducks. Our findings revealed 35 SNPs and 1 SNP associated with low-density lipoprotein cholesterol (LDL) and globulin (GLB), respectively. We identified 36 putative candidate genes for the LDL trait in close proximity to major QTLs and key loci. Based on their biochemical and physiological properties, <i>TRA2A</i>, <i>NPY</i>, <i>ARHGEF26</i>, <i>DHX36</i>, and <i>AADAC</i> are the strongest putative candidate genes. Through linkage disequilibrium analysis and haplotype sharing analysis, we identified three haplotypes and one haplotype, respectively, that were significantly linked with LDL and GLB. These haplotypes could be selected as potential candidate haplotypes for molecular breeding of Shaoxing ducks. Additionally, we utilized a bootstrap test to verify the reliability of GWAS with small experimental samples. The test can be accessed at https://github.com/xuwenwu24/Bootstrap-test.
DOI: 10.6084/m9.figshare.26598676.v1
title: Discover QTLs for the level of blood components in Shaoxing duck using GWAS and haplotype sharing analysis

description: Blood composition is indicative of health-related traits such as immunity and metabolism. The use of molecular genetics to investigate alterations in these attributes in laying ducks is a novel approach. Our objective was to employ genome − wide association studies (GWAS) and haplotype − sharing analysis to identify genomic regions and potential genes associated with 11 blood components in Shaoxing ducks. Our findings revealed 35 SNPs and 1 SNP associated with low-density lipoprotein cholesterol (LDL) and globulin (GLB), respectively. We identified 36 putative candidate genes for the LDL trait in close proximity to major QTLs and key loci. Based on their biochemical and physiological properties, <i>TRA2A</i>, <i>NPY</i>, <i>ARHGEF26</i>, <i>DHX36</i>, and <i>AADAC</i> are the strongest putative candidate genes. Through linkage disequilibrium analysis and haplotype sharing analysis, we identified three haplotypes and one haplotype, respectively, that were significantly linked with LDL and GLB. These haplotypes could be selected as potential candidate haplotypes for molecular breeding of Shaoxing ducks. Additionally, we utilized a bootstrap test to verify the reliability of GWAS with small experimental samples. The test can be accessed at https://github.com/xuwenwu24/Bootstrap-test.
DOI: 10.6084/m9.figshare.26831566
title: Spatial distribution of maternal factors in pig mature oocytes

description: It is known that asymmetrical maternal transcripts play an important role in the cell fate of the early embryo, but few studies are available in mammal oocytes especially in pig. To investigate the spatial factors in pig oocytes, the oriented bisection was established for collecting karyoplasts (NSOs) and cytoplasts (SSOs) with more than 95% efficiency. Subsequently, RNA-Seq and LC-MS/MS analysis were performed on NSOs and SSOs. Although no differentially expressed genes (DEGs) could be detected between NSOs and SSOs, 89 of the differentially expressed proteins (DEPs) were detected, that 58 proteins higher expressed but 31 proteins lower expressed in NSOs compared with SSOs. These DEPs mainly participated in the ‘cell cycle’ and ‘ribosome’ pathway, while the up-regulated DEPs were mainly GO in ‘spindle’ and ‘positive regulation of translation’, and the down-regulated DEPs were in ‘cytosolic small ribosomal subunit’ and ‘mRNA binding’. The up-regulated DEP SIRT5 which are related to the regulation of gene expression, epigenetic were further detected and revealed. A spatial asymmetry of maternal factors at the protein level was firstly detected in pig mature oocytes.