cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17059745
title: Molecular and phylogenetic analysis of MHC class I exons 7–8 in a variety of cattle and buffalo breeds

description: The present study was conducted on the MHC class I (BoLA-A/BuLA-A) gene in Sahiwal, Jersey, Hariana, and Tharparkar breeds of cattle and Murrah, Mehsana, and Bhadawari breeds of buffalo to study the polymorphism. Exons 7–8 of the MHC class I gene was first characterized for polymorphism study in buffalo and the results reveal that this gene has a higher level of nucleotide changes than the cattle. Genes were investigated for polymorphisms in 285 animals of cattle and buffalo breeds. Molecular characterization of the MHC class I (BoLa-A/Bula-A) gene reveals a higher degree of polymorphism at the nucleotide level in cattle and buffalo. Results revealed this region has a higher level of polymorphisms in buffalo as campared to the cattle. <i>Alu</i>l restriction patterns were monomorphic except for three different patterns but it was able to illustrate the differences in buffalo and cattle. SSCP analysis of exons 7–8 showed remarkable differences in cattle and buffalo. Sequence analysis revealed more closeness of Murrah breed with crossbred and indigenous cattle than Holstein Friesian. Exon 8 had more deletion and stop codon as compared to exon 7. The investigation confirmed that MHC class I BoLa-A/Bula-A exons 7–8 is highly polymorphic in buffalo as compared to cattle.
DOI: 10.6084/m9.figshare.17059745.v1
title: Molecular and phylogenetic analysis of MHC class I exons 7–8 in a variety of cattle and buffalo breeds

description: The present study was conducted on the MHC class I (BoLA-A/BuLA-A) gene in Sahiwal, Jersey, Hariana, and Tharparkar breeds of cattle and Murrah, Mehsana, and Bhadawari breeds of buffalo to study the polymorphism. Exons 7–8 of the MHC class I gene was first characterized for polymorphism study in buffalo and the results reveal that this gene has a higher level of nucleotide changes than the cattle. Genes were investigated for polymorphisms in 285 animals of cattle and buffalo breeds. Molecular characterization of the MHC class I (BoLa-A/Bula-A) gene reveals a higher degree of polymorphism at the nucleotide level in cattle and buffalo. Results revealed this region has a higher level of polymorphisms in buffalo as campared to the cattle. <i>Alu</i>l restriction patterns were monomorphic except for three different patterns but it was able to illustrate the differences in buffalo and cattle. SSCP analysis of exons 7–8 showed remarkable differences in cattle and buffalo. Sequence analysis revealed more closeness of Murrah breed with crossbred and indigenous cattle than Holstein Friesian. Exon 8 had more deletion and stop codon as compared to exon 7. The investigation confirmed that MHC class I BoLa-A/Bula-A exons 7–8 is highly polymorphic in buffalo as compared to cattle.
DOI: 10.6084/m9.figshare.17703162
title: Identification of genes related to growth traits from transcriptome profiles of duck breast muscle tissue

description: The growth and development of duck skeletal muscle is an important economic trait that is genetically regulated. The internal mechanism underlying the regulation of skeletal muscle growth and development in ducks remains unclear. The purpose of this study was to identify candidate genes related to the growth of duck skeletal muscle. RNA-sequencing technology was used to compare the transcriptome of duck breast muscles in an F<sub>2</sub> population with the high breast muscle rate (HB) and the low breast muscle rate (LB). A total of 14,522 genes were confirmed to be expressed in the breast muscle, and 173 differentially expressed genes (DEGs) were identified between the HB and LB groups. Functional analysis showed that these DEGs were mainly involved in biological processes and pathways of fat metabolism and muscle growth, especially the <i>FABP3</i> and <i>MYL4</i> involved in the PPAR signaling pathway and cardiac muscle contraction pathway. These findings deepened our understanding of the molecular mechanisms involved in muscle growth in ducks and provided a theoretical basis for improving duck production and breeding of ducks.
DOI: 10.6084/m9.figshare.17703162.v1
title: Identification of genes related to growth traits from transcriptome profiles of duck breast muscle tissue

description: The growth and development of duck skeletal muscle is an important economic trait that is genetically regulated. The internal mechanism underlying the regulation of skeletal muscle growth and development in ducks remains unclear. The purpose of this study was to identify candidate genes related to the growth of duck skeletal muscle. RNA-sequencing technology was used to compare the transcriptome of duck breast muscles in an F<sub>2</sub> population with the high breast muscle rate (HB) and the low breast muscle rate (LB). A total of 14,522 genes were confirmed to be expressed in the breast muscle, and 173 differentially expressed genes (DEGs) were identified between the HB and LB groups. Functional analysis showed that these DEGs were mainly involved in biological processes and pathways of fat metabolism and muscle growth, especially the <i>FABP3</i> and <i>MYL4</i> involved in the PPAR signaling pathway and cardiac muscle contraction pathway. These findings deepened our understanding of the molecular mechanisms involved in muscle growth in ducks and provided a theoretical basis for improving duck production and breeding of ducks.
DOI: 10.6084/m9.figshare.19083335
title: Developmental changes of nutrient digestion in young lambs are influenced by weaning and associated with intestinal microbiota

description: Understanding the effects of weaning on the changes of digestive function could help to design efficient intervention strategies for promoting the development of the lamb during the early stages of life. In this study, 24 lambs were divided into two groups (control group, lambs were not weaned; and weaning group, lambs were weaned at 21 days of age). The growth, nutrient digestion, gastrointestinal enzyme activity, plasma biochemical indicators, and intestinal microbiota at 7–49 days were determined, as well as the impact of early weaning. The nutrient digestion changed rapidly with age, especially at 14–28 days (<i>p</i> &lt; 0.05). Weaning reduced the dry matter (DM), crude protein (CP), and ether extract (EE) intake and digestion, but increased the starch, neutral detergent fiber (NDF), and acid detergent fiber (ADF) intake and digestion (<i>p</i> &lt; 0.05). Weaning did not affect the overall jejunal microbiota (<i>p</i> &gt; 0.05), but affected the relative abundance of certain bacteria taxa (<i>p</i> &lt; 0.05). Lactic acid-producing bacteria, such as <i>Olsenella</i>, <i>Bacillus</i>, <i>Sharpea</i>, and <i>Bifidobacterium</i> are closely related to CP or EE digestion and growth performance (<i>p</i> &lt; 0.05). In summary, we delineated the pattern of nutrient digestion and intestinal microbiota development in young lambs, and the impact of early weaning.
DOI: 10.6084/m9.figshare.19166280
title: Selection signatures of Qinchuan cattle based on whole-genome sequences

description: Qinchuan cattle has gradually improved in body shape and growth rate in the long-term breeding process from the draft cattle to beef cattle. As the head of the five local yellow cattle in China, the Qinchuan cattle has been designated as a specialized beef cattle breed. We investigated the selection signatures using whole genome sequencing data in Qinchuan cattle. Based on <i>F</i>st, we detected hundreds of candidate genes under selection across Qinchuan, Red Angus, and Japanese Black cattle. Through protein-protein interaction analysis and functional annotation of candidate genes, the results revealed that <i>KMT2E</i>, <i>LTBP1</i> and <i>NIPBL</i> were related to brain size, body characteristics, and limb development, respectively, suggesting that these potential genes may affect the growth and development traits in Qinchuan cattle. <i>ARIH2</i>, <i>DACT1</i> and <i>DNM2</i>, <i>et al.</i> are related to meat quality. Meanwhile, <i>TBXA2R</i> can be used as a gene associated with reproductive function, and <i>USH2A</i> affect coat color. This provided a glimpse into the formation of breeds and molecular genetic breeding. Our findings will promote genome-assisted breeding to improve animal production and health.
DOI: 10.6084/m9.figshare.19235675
title: Transcriptome identification and characterization of long non-coding RNAs in the ovary of hens at four stages

description: Long non-coding RNAs (lncRNAs) play important roles in transcriptional and post-transcriptional regulation. LncRNAs, which are defined as non-coding RNAs more than 200 bp in length, are involved in key biological processes, such as cell proliferation and differentiation, epigenetic regulation, and gene transcriptional translation. Recent studies have shown that lncRNAs also play major regulatory roles in the reproduction of mammals. However, knowledge of the roles of lncRNAs in the chicken ovary lacking. In this study, we performed RNA-seq analyses of ovarian tissue from Hy-Line brown laying hens at four physiological stages [15, 20, 30, and 68 weeks of age (W)]. We identified 657 lncRNA transcripts that were differentially expressed during ovarian development, the number of down-regulated lncRNAs was higher than the number of up-regulated lncRNAs during development. We predicted the cis and trans target genes of the DE lncRNAs and constructed a lncRNA-mRNA interaction network, which indicated that the DE genes (DEGs) and the target genes of the DE lncRNAs are mainly involved in signaling pathways associated with ovarian development, including oocyte meiosis, calcium signaling pathways, ECM-receptor interactions, and ribosome and focal adhesion. Overall, we found that twelve lncRNAs were strongly involved in ovarian development: LNC_013443, LNC_001029, LNC_005713, LNC_016762, ENSGALT00000101857, LNC_003913, LNC_013692, LNC_012219, LNC_004140, ENSGALT00000096941, LNC_009356, and ENSGALT00000098716. In summary, our study utilized RNA-seq analysis of hen ovaries to explore key lncRNAs involved in ovarian development and function. Furthermore, the comprehensive analysis identified the target genes of these lncRNAs providing a better understanding of the mechanisms underlying ovarian development in hens and a theoretical basis for further research.
DOI: 10.6084/m9.figshare.19235675.v1
title: Transcriptome identification and characterization of long non-coding RNAs in the ovary of hens at four stages

description: Long non-coding RNAs (lncRNAs) play important roles in transcriptional and post-transcriptional regulation. LncRNAs, which are defined as non-coding RNAs more than 200 bp in length, are involved in key biological processes, such as cell proliferation and differentiation, epigenetic regulation, and gene transcriptional translation. Recent studies have shown that lncRNAs also play major regulatory roles in the reproduction of mammals. However, knowledge of the roles of lncRNAs in the chicken ovary lacking. In this study, we performed RNA-seq analyses of ovarian tissue from Hy-Line brown laying hens at four physiological stages [15, 20, 30, and 68 weeks of age (W)]. We identified 657 lncRNA transcripts that were differentially expressed during ovarian development, the number of down-regulated lncRNAs was higher than the number of up-regulated lncRNAs during development. We predicted the cis and trans target genes of the DE lncRNAs and constructed a lncRNA-mRNA interaction network, which indicated that the DE genes (DEGs) and the target genes of the DE lncRNAs are mainly involved in signaling pathways associated with ovarian development, including oocyte meiosis, calcium signaling pathways, ECM-receptor interactions, and ribosome and focal adhesion. Overall, we found that twelve lncRNAs were strongly involved in ovarian development: LNC_013443, LNC_001029, LNC_005713, LNC_016762, ENSGALT00000101857, LNC_003913, LNC_013692, LNC_012219, LNC_004140, ENSGALT00000096941, LNC_009356, and ENSGALT00000098716. In summary, our study utilized RNA-seq analysis of hen ovaries to explore key lncRNAs involved in ovarian development and function. Furthermore, the comprehensive analysis identified the target genes of these lncRNAs providing a better understanding of the mechanisms underlying ovarian development in hens and a theoretical basis for further research.
DOI: 10.6084/m9.figshare.17704983
title: Genome-wide identification and analysis of TMT-based proteomes in longissimus dorsi tissue from Kazakh cattle and Xinjiang brown cattle

description: With the gradual completion of the human genome project, proteomes have gained extremely important value in the fields of human disease and biological process research. In our previous research, we performed transcriptomic analyses of longissimus dorsi tissue from Kazakh cattle and Xinjiang brown cattle and conducted in-depth studies on the muscles of both species through epigenetics. However, it is unclear whether differentially expressed proteins in Kazakh cattle and Xinjiang brown cattle regulate muscle production and development. In this study, a proteomic analysis was performed on Xinjiang brown cattle and Kazakh cattle by using TMT markers, HPLC classification, LC/MS and bioinformatics analysis. A total of 13,078 peptides were identified, including 11,258 unique peptides. We identified a total of 1874 proteins, among which 1565 were quantifiable. Compared to Kazakh cattle, Xinjiang brown cattle exhibited 75 upregulated proteins and 44 downregulated proteins. These differentially expressed proteins were enriched for the functions of adrenergic signaling in cardiomyocytes, fatty acid degradation and glutathione metabolism. In our research, we found differentially expressed proteins in longissimus dorsi tissue between Kazakh cattle and Xinjiang brown cattle. We predict that these proteins regulate muscle production and development through select enriched signaling pathways. This study provides novel insights into the roles of proteomes in cattle genetics and breeding.
DOI: 10.6084/m9.figshare.17704983.v2
title: Genome-wide identification and analysis of TMT-based proteomes in longissimus dorsi tissue from Kazakh cattle and Xinjiang brown cattle

description: With the gradual completion of the human genome project, proteomes have gained extremely important value in the fields of human disease and biological process research. In our previous research, we performed transcriptomic analyses of longissimus dorsi tissue from Kazakh cattle and Xinjiang brown cattle and conducted in-depth studies on the muscles of both species through epigenetics. However, it is unclear whether differentially expressed proteins in Kazakh cattle and Xinjiang brown cattle regulate muscle production and development. In this study, a proteomic analysis was performed on Xinjiang brown cattle and Kazakh cattle by using TMT markers, HPLC classification, LC/MS and bioinformatics analysis. A total of 13,078 peptides were identified, including 11,258 unique peptides. We identified a total of 1874 proteins, among which 1565 were quantifiable. Compared to Kazakh cattle, Xinjiang brown cattle exhibited 75 upregulated proteins and 44 downregulated proteins. These differentially expressed proteins were enriched for the functions of adrenergic signaling in cardiomyocytes, fatty acid degradation and glutathione metabolism. In our research, we found differentially expressed proteins in longissimus dorsi tissue between Kazakh cattle and Xinjiang brown cattle. We predict that these proteins regulate muscle production and development through select enriched signaling pathways. This study provides novel insights into the roles of proteomes in cattle genetics and breeding.
DOI: 10.6084/m9.figshare.19134709
title: Comparative transcriptomics analysis of testicular miRNA from indicine and taurine cattle

description: Numerous studies have shown that several microRNAs (miRNAs) are specifically expressed in testis, play an essential role in regulating testicular spermatogenesis. Hainan and Mongolian cattle are two representative Chinese native cattle breeds representing <i>Bos indicus</i> (indicine cattle) and <i>Bos taurus</i> (taurine cattle), respectively, which are distributed in hot Hainan and cold Inner Mongolia province. To study the functional differences of miRNA in spermatogenesis between indicine and taurine cattle, six mature testes samples from indicine cattle (<i>n</i> = 3) and taurine cattle (<i>n</i> = 3) were collected, respectively. We detected miRNA expression using small RNA sequencing technology following bioinformatic analysis. A total of 578 known miRNAs and 132 novel miRNAs were detected in the six libraries. Among the 710 miRNAs, 564 miRNAs were expressed in both indicine and taurine cattle, 73 miRNAs were found solely in indicine cattle and 73 miRNAs were found solely in taurine cattle. After further analysis, among the miRNAs were identified in both indicine and taurine cattle, 184 miRNAs were differentially expressed (|log2 fold change| ≥ 1 and corrected <i>p</i>-value &lt;0.05). Among the miRNAs that were only expressed in indicine cattle, 10 miRNAs were differentially expressed, whereas, among the miRNAs that were only expressed in taurine cattle, six miRNAs were differentially expressed. The enrichment analysis result showed that predicted target genes of a total of 200 differentially expressed miRNAs were enriched on some testicular spermatogenesis-related Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, especially mitogen-activated protein kinase (MAPK) signaling pathway. These findings identify miRNAs as key factors to regulate spermatogenesis in both indicine and taurine cattle, which may also be helpful for improving cattle reproductive performance in future studies.
DOI: 10.6084/m9.figshare.19134709.v1
title: Comparative transcriptomics analysis of testicular miRNA from indicine and taurine cattle

description: Numerous studies have shown that several microRNAs (miRNAs) are specifically expressed in testis, play an essential role in regulating testicular spermatogenesis. Hainan and Mongolian cattle are two representative Chinese native cattle breeds representing <i>Bos indicus</i> (indicine cattle) and <i>Bos taurus</i> (taurine cattle), respectively, which are distributed in hot Hainan and cold Inner Mongolia province. To study the functional differences of miRNA in spermatogenesis between indicine and taurine cattle, six mature testes samples from indicine cattle (<i>n</i> = 3) and taurine cattle (<i>n</i> = 3) were collected, respectively. We detected miRNA expression using small RNA sequencing technology following bioinformatic analysis. A total of 578 known miRNAs and 132 novel miRNAs were detected in the six libraries. Among the 710 miRNAs, 564 miRNAs were expressed in both indicine and taurine cattle, 73 miRNAs were found solely in indicine cattle and 73 miRNAs were found solely in taurine cattle. After further analysis, among the miRNAs were identified in both indicine and taurine cattle, 184 miRNAs were differentially expressed (|log2 fold change| ≥ 1 and corrected <i>p</i>-value &lt;0.05). Among the miRNAs that were only expressed in indicine cattle, 10 miRNAs were differentially expressed, whereas, among the miRNAs that were only expressed in taurine cattle, six miRNAs were differentially expressed. The enrichment analysis result showed that predicted target genes of a total of 200 differentially expressed miRNAs were enriched on some testicular spermatogenesis-related Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, especially mitogen-activated protein kinase (MAPK) signaling pathway. These findings identify miRNAs as key factors to regulate spermatogenesis in both indicine and taurine cattle, which may also be helpful for improving cattle reproductive performance in future studies.
DOI: 10.6084/m9.figshare.17161230
title: Transcriptomic analysis reveals that non-forage or forage fiber source promotes rumen development through different metabolic processes in lambs

description: Dietary fiber supplementation can stimulate rumen development in lambs during the pre-weaning period. However, it is unclear whether different sources of fiber have varying effects on rumen development. This study aimed to investigate the molecular mechanism of rumen morphological and functional development based on non-forage or forage as a starter dietary fiber source. Twenty-four male Hu lambs with similar body weights (BW, 3.67 ± 0.08 kg) were selected and divided into two groups that received diets supplemented with either alfalfa hay (AH) or soybean hull (SH). At the age of 70 days, six lambs were slaughtered from each treatment group for rumen fermentation and morphological analyses. Three samples of the rumen tissue from the ventral sac were collected for transcriptomic analysis. The results identified 633 differentially expressed genes (DEGs), of which 210 were upregulated and 423 were downregulated in the SH group compared with those in the AH group. The upregulated DEGs were most enriched in the immune function and proteolysis pathways, whereas the downregulated DEGs were mainly involved in cell proliferation, apoptosis, and differentiation pathways. These findings indicated that non-forage as a starter dietary fiber source improved immune function and enhanced nitrogen utilization, whereas forage facilitated rumen morphological development.
DOI: 10.6084/m9.figshare.17161230.v1
title: Transcriptomic analysis reveals that non-forage or forage fiber source promotes rumen development through different metabolic processes in lambs

description: Dietary fiber supplementation can stimulate rumen development in lambs during the pre-weaning period. However, it is unclear whether different sources of fiber have varying effects on rumen development. This study aimed to investigate the molecular mechanism of rumen morphological and functional development based on non-forage or forage as a starter dietary fiber source. Twenty-four male Hu lambs with similar body weights (BW, 3.67 ± 0.08 kg) were selected and divided into two groups that received diets supplemented with either alfalfa hay (AH) or soybean hull (SH). At the age of 70 days, six lambs were slaughtered from each treatment group for rumen fermentation and morphological analyses. Three samples of the rumen tissue from the ventral sac were collected for transcriptomic analysis. The results identified 633 differentially expressed genes (DEGs), of which 210 were upregulated and 423 were downregulated in the SH group compared with those in the AH group. The upregulated DEGs were most enriched in the immune function and proteolysis pathways, whereas the downregulated DEGs were mainly involved in cell proliferation, apoptosis, and differentiation pathways. These findings indicated that non-forage as a starter dietary fiber source improved immune function and enhanced nitrogen utilization, whereas forage facilitated rumen morphological development.