المؤلفون: Guang-ming XIANG, Xiu-ling ZHANG, Chang-jiang XU, Zi-yao FAN, Kui XU, Nan WANG, Yue WANG, Jing-jing CHE, Song-song XU, Yu-lian MU, Kui LI, Zhi-guo LIU

المصدر: Journal of Integrative Agriculture, Vol 22, Iss 1, Pp 202-213 (2023)

مصطلحات موضوعية: COL1A1 gene, safe harbor, knock-in, CRISPR/Cas9, pig, Agriculture (General), S1-972

الوصف: Efficient and stable expression of foreign genes in cells and transgenic animals is important for gain-of-function studies and the establishment of bioreactors. Safe harbor loci in the animal genome enable consistent overexpression of foreign genes, without side effects. However, relatively few safe harbor loci are available in pigs, a fact which has impeded the development of multi-transgenic pig research. We report a strategy for efficient transgene knock-in in the endogenous collagen type I alpha 1 chain (COL1A1) gene using the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system. After the knock-in of a 2A peptide-green fluorescence protein (2A-GFP) transgene in the last codon of COL1A1 in multiple porcine cells, including porcine kidney epithelial (PK15), porcine embryonic fibroblast (PEF) and porcine intestinal epithelial (IPI-2I) cells, quantitative PCR (qPCR), Western blotting, RNA-seq and CCK8 assay were performed to assess the safety of COL1A1 locus. The qPCR results showed that the GFP knock-in had no effect (P=0.29, P=0.66 and P=0.20 for PK15, PEF and IPI-2I cells, respectively) on the mRNA expression of COL1A1 gene. Similarly, no significant differences (P=0.64, P=0.48 and P=0.80 for PK15, PEF and IPI-2I cells, respectively) were found between the GFP knock-in and wild type cells by Western blotting. RNA-seq results revealed that the transcriptome of GFP knock-in PEF cells had a significant positive correlation (P

وصف الملف: electronic resource

العلاقة: http://www.sciencedirect.com/science/article/pii/S2095311922001836Test; https://doaj.org/toc/2095-3119Test

الوصول الحر: https://doaj.org/article/730aff45c1ec4bbf9587039fddc1b488Test

المؤلفون: Xiu-Ling Zhang, Yan-Rong Zhou, Song-Song Xu, Si Xu, Yu-Jian Xiong, Kui Xu, Chang-Jiang Xu, Jing-Jing Che, Lei Huang, Zhi-Guo Liu, Bing-Yuan Wang, Yu-Lian Mu, Shao-Bo Xiao, Kui Li

المصدر: Microbiology Spectrum, Vol 11, Iss 1 (2023)

مصطلحات موضوعية: 16S rRNA, iron absorption, gut microbiota, piglet, carboxylic acids, Microbiology, QR1-502

الوصف: ABSTRACT The gut microbiota is known to play a role in regulating host metabolism, yet the mechanisms underlying this regulation are not well elucidated. Our study aimed to characterize the differences in gut microbiota compositions and their roles in iron absorption between wild-type (WT) and CD163/pAPN double-gene-knockout (DKO) weaned piglets. A total of 58 samples along the entire digestive tract were analyzed for microbial community using 16S rRNA gene sequencing. The colonic microbiota and their metabolites were determined by metagenomic sequencing and untargeted liquid chromatography-mass spectrometry (LC-MS), respectively. Our results showed that no alterations in microbial community structure and composition were observed between DKO and WT weaned piglets, with the exception of colonic microbiota. Interestingly, the DKO piglets had selectively increased the relative abundance of the Leeia genus belonging to the Neisseriaceae family and decreased the Ruminococcaceae_UCG_014 genus abundance. Functional capacity analysis showed that organic acid metabolism was enriched in the colon in DKO piglets. In addition, the DKO piglets showed increased iron levels in important tissues compared with WT piglets without any pathological changes. Pearson’s correlation coefficient indicated that the specific bacteria such as Leeia and Ruminococcaceae_UCG_014 genus played a key role in host iron absorption. Moreover, the iron levels had significantly (P

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2165-0497Test

الوصول الحر: https://doaj.org/article/4adab337a3a84548a9c36f8ecdabdd23Test

المؤلفون: Song-Song Xu, Nan Wang, Lei Huang, Xiu-Ling Zhang, Shu-Tang Feng, Sha-Sha Liu, Yue Wang, Zhi-Guo Liu, Bing-Yuan Wang, Tian-Wen Wu, Yu-Lian Mu, Shao-Hua Hou, Kui Li

المصدر: Microbiology Spectrum, Vol 10, Iss 4 (2022)

مصطلحات موضوعية: obesity, mucosa-associated microbiota, 16S rRNA gene sequencing, transcriptome, Inflammatory responses, Microbiology, QR1-502

الوصف: ABSTRACT Several studies have suggested a role for gut mucosa-associated microbiota in the development of obesity, but the mechanisms involved are poorly defined. Here, the impact of the gut mucosa-associated microbiota on obesity and related metabolic disorders was evaluated in a metabolic syndrome (MetS) porcine model. Body composition was determined among male Wuzhishan minipigs consuming a high-energy diet (HED) and compared to that of those consuming a normal diet (ND), and gut segments (duodenum, jejunum, ileum, cecum, colon, and rectum) were sampled for paired analysis of mucosa-associated microbiota and transcriptome signatures with 16S rRNA gene and RNA sequencing, respectively. Our data indicated that long-term HED feeding significantly increased body weight and visceral fat deposition and aggravated metabolic disorders. Specially, HED feeding induced mucosa-associated microbiota dysbiosis and selectively increased the abundance of the families Enterobacteriaceae, Moraxellaceae, and Lachnospiraceae in the upper intestine. The association analysis indicated that specific bacteria play key roles in adiposity, e.g., Lactobacillus johnsonii in the duodenum, Actinobacillus indolicus in the jejunum, Acinetobacter johnsonii in the ileum, Clostridium butyricum in the cecum, Haemophilus parasuis in the colon, and bacterium NLAEzlP808, Halomonas taeheungii, and Shewanella sp. JNUH029 in the rectum. Transcriptome data further revealed intestinal lipid metabolism and immune dysfunction in the MetS individuals, which may be associated with obesity and related metabolic disorders. Our results indicated that gut mucosa-associated microbiota dysbiosis has the potential to exacerbate obesity, partially through modulating systemic inflammatory responses. IMPORTANCE Obesity is a major risk factor for metabolic syndrome, which is the most common cause of death worldwide, especially in developed countries. The link between obesity and gut mucosa-associated microbiota is unclear due to challenges associated with the collection of intestinal samples from humans. The current report provides the first insight into obesity-microbiome-gut immunity connections in a metabolic syndrome (MetS) porcine model. The present results show that dysbiosis of mucosal microbiota along the entire digestive tract play a critical role in the proinflammatory response in the host-microbial metabolism axis, resulting in obesity and related metabolic disorders in the MetS model.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2165-0497Test

الوصول الحر: https://doaj.org/article/22882543fe204ecca0e87bb782e8af87Test

المؤلفون: Song-Song Xu, Xiu-Ling Zhang, Sha-Sha Liu, Shu-Tang Feng, Guang-Ming Xiang, Chang-Jiang Xu, Zi-Yao Fan, Kui Xu, Nan Wang, Yue Wang, Jing-Jing Che, Zhi-Guo Liu, Yu-Lian Mu, Kui Li

المصدر: Frontiers in Nutrition, Vol 9 (2022)

مصطلحات موضوعية: atherothrombosis, metagenome, metatranscriptome, metabolome, transcriptome, inflammatory response, Nutrition. Foods and food supply, TX341-641

الوصف: BackgroundThe diet-induced gut microbiota dysbiosis has been suggested as a major risk factor for atherothrombosis, however, the detailed mechanism linking these conditions is yet to be fully understood.MethodsWe established a long-term excessive-energy diet-induced metabolic syndrome (MetS) inbred Wuzhishan minipig model, which is characterized by its genetic stability, small size, and human-like physiology. The metabolic parameters, atherosclerotic lesions, gut microbiome, and host transcriptome were analyzed. Metabolomics profiling revealed a linkage between gut microbiota and atherothrombosis.ResultsWe showed that white atheromatous plaque was clearly visible on abdominal aorta in the MetS model. Furthermore, using metagenome and metatranscriptome sequencing, we discovered that the long-term excessive energy intake altered the local intestinal microbiota composition and transcriptional profile, which was most dramatically illustrated by the reduced abundance of SCFAs-producing bacteria including Bacteroides, Lachnospiraceae, and Ruminococcaceae in the MetS model. Liver and abdominal aorta transcriptomes in the MetS model indicate that the diet-induced gut microbiota dysbiosis activated host chronic inflammatory responses and significantly upregulated the expression of genes related to arachidonic acid-dependent signaling pathways. Notably, metabolomics profiling further revealed an intimate linkage between arachidonic acid metabolism and atherothrombosis in the host-gut microbial metabolism axis.ConclusionsThese findings provide new insights into the relationship between atherothrombosis and regulation of gut microbiota via host metabolomes and will be of potential value for the treatment of cardiovascular diseases in MetS.

وصف الملف: electronic resource

العلاقة: https://www.frontiersin.org/articles/10.3389/fnut.2022.807118/fullTest; https://doaj.org/toc/2296-861XTest

الوصول الحر: https://doaj.org/article/caf3e88e049047bd970f5f7c2650c36dTest

المؤلفون: Song-Song Xu, Lei Gao, Min Shen, Fenghua Lyu

المصدر: Frontiers in Genetics, Vol 12 (2021)

مصطلحات موضوعية: artificial selection, genome-wide SNPs, sheep, phenotypic traits, genetic improvement, Genetics, QH426-470

الوصف: Sheep (Ovis aries) is one of the important livestock with diverse phenotypic traits. However, little is known about the molecular mechanism of diverse phenotypic traits in domestic sheep. Using the genome-wide high-density SNP data (600K) in 253 samples from 13 populations, we conducted the tests of selective sweeps (i.e., pairwise FST and XP-CLR) associated with several important phenotypic traits (e.g., tail types, horn morphology, prolificacy, coat pigmentation, ear size, milk production, meat production, body size and wool fineness). We identified strong selective signatures in previously reported (e.g., T, RXFP2, BMPR1B, TYRP1, MSRB3, TF, CEBPA, GPR21 and HOXC8) and novel genes associated with the traits, such as CERS6, BTG1, RYR3, SLC6A4, NNAT and OGT for fat deposition in the tails, FOXO4 for fertility, PTCH1 and EMX2 for ear size, and RMI1 and SCD5 for body size. Further gene annotation analysis showed that these genes were identified to be the most probable genes accounting for the diverse phenotypic traits. Our results provide novel insights into the genetic mechanisms underlying the traits and also new genetic markers for genetic improvement in sheep and other livestock.

وصف الملف: electronic resource

العلاقة: https://www.frontiersin.org/articles/10.3389/fgene.2021.738879/fullTest; https://doaj.org/toc/1664-8021Test

الوصول الحر: https://doaj.org/article/57c0e54cf1b648dfab8009fe643dbaa3Test

المؤلفون: Xin Li, Ji Yang, Min Shen, Xing-Long Xie, Guang-Jian Liu, Ya-Xi Xu, Feng-Hua Lv, Hua Yang, Yong-Lin Yang, Chang-Bin Liu, Ping Zhou, Peng-Cheng Wan, Yun-Sheng Zhang, Lei Gao, Jing-Quan Yang, Wen-Hui Pi, Yan-Ling Ren, Zhi-Qiang Shen, Feng Wang, Juan Deng, Song-Song Xu, Hosein Salehian-Dehkordi, Eer Hehua, Ali Esmailizadeh, Mostafa Dehghani-Qanatqestani, Ondřej Štěpánek, Christina Weimann, Georg Erhardt, Agraw Amane, Joram M. Mwacharo, Jian-Lin Han, Olivier Hanotte, Johannes A. Lenstra, Juha Kantanen, David W. Coltman, James W. Kijas, Michael W. Bruford, Kathiravan Periasamy, Xin-Hua Wang, Meng-Hua Li

المصدر: Nature Communications, Vol 11, Iss 1, Pp 1-16 (2020)

مصطلحات موضوعية: Science

الوصف: Genetic resources for livestock are valuable for understanding their demography and past selection, and may inform future breeding programs and agricultural improvement. Here, the authors present deep resequencing of 248 wild and domestic sheep, with associated data and analysis.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2041-1723Test

الوصول الحر: https://doaj.org/article/fdf336f0140d420598f46b242245391bTest

المؤلفون: Hosein Salehian-Dehkordi, Ya-Xi Xu, Song-Song Xu, Xin Li, Ling-Yun Luo, Ya-Jing Liu, Dong-Feng Wang, Yin-Hong Cao, Min Shen, Lei Gao, Ze-Hui Chen, Joseph T. Glessner, Johannes A. Lenstra, Ali Esmailizadeh, Meng-Hua Li, Feng-Hua Lv

المصدر: Frontiers in Genetics, Vol 12 (2021)

مصطلحات موضوعية: sheep, GWAS, CNVs, selection, genetic adaptation, Genetics, QH426-470

الوصف: Copy number variations (CNVs) are a major source of structural variation in mammalian genomes. Here, we characterized the genome-wide CNV in 2059 sheep from 67 populations all over the world using the Ovine Infinium HD (600K) SNP BeadChip. We tested their associations with distinct phenotypic traits by conducting multiple independent genome-wide tests. In total, we detected 7547 unique CNVs and 18,152 CNV events in 1217 non-redundant CNV regions (CNVRs), covering 245 Mb (∼10%) of the whole sheep genome. We identified seven CNVRs with frequencies correlating to geographical origins and 107 CNVRs overlapping 53 known quantitative trait loci (QTLs). Gene ontology and pathway enrichment analyses of CNV-overlapping genes revealed their common involvement in energy metabolism, endocrine regulation, nervous system development, cell proliferation, immune, and reproduction. For the phenotypic traits, we detected significantly associated (adjusted P < 0.05) CNVRs harboring functional candidate genes, such as SBNO2 for polycerate; PPP1R11 and GABBR1 for tail weight; AKT1 for supernumerary nipple; CSRP1, WNT7B, HMX1, and FGFR3 for ear size; and NOS3 and FILIP1 in Wadi sheep; SNRPD3, KHDRBS2, and SDCCAG3 in Hu sheep; NOS3, BMP1, and SLC19A1 in Icelandic; CDK2 in Finnsheep; MICA in Romanov; and REEP4 in Texel sheep for litter size. These CNVs and associated genes are important markers for molecular breeding of sheep and other livestock species.

وصف الملف: electronic resource

العلاقة: https://www.frontiersin.org/articles/10.3389/fgene.2021.670582/fullTest; https://doaj.org/toc/1664-8021Test

الوصول الحر: https://doaj.org/article/f08e58ced8ec433abc63d55f421ff13dTest

المؤلفون: Song-Song XU, Meng-Hua LI

المصدر: Frontiers of Agricultural Science and Engineering, Vol 4, Iss 3, Pp 279-288 (2017)

مصطلحات موضوعية: sheep, high-throughput screening, productive traits, genome-wide studies, Agriculture (General), S1-972

الوصف: Sheep are one of the most economically important domesticated animals for human society. However, genetic improvements for the key traits associated with meat, growth, milk, wool, reproduction, horns and tails progress slowly using conventional crossbreeding methods. With the development and utilization of high-throughput screening technologies over the last decade, a list of functional genes and genetic variants associated with these traits has been identified. This review covers recent genome-wide studies on sheep productive traits using high-throughput screening technologies, including those based on single-nucleotide polymorphisms and copy number variants at the whole-genome level (e.g., genome-wide association studies), transcriptome and DNA methylation sequences. Additionally, comprehensive information on functional genes and genetic variants associated with economically important traits in sheep is provided.

وصف الملف: electronic resource

العلاقة: http://academic.hep.com.cn/fase/fileup/2095-7505/PDF/1489648107766-1592023924.pdfTest; https://doaj.org/toc/2095-7505Test

الوصول الحر: https://doaj.org/article/3ad5d24021a84be69bda56e9fcf23390Test

المؤلفون: Song-Song Xu, Lei Gao, Xing-Long Xie, Yan-Ling Ren, Zhi-Qiang Shen, Feng Wang, Min Shen, Emma Eyϸórsdóttir, Jón H. Hallsson, Tatyana Kiseleva, Juha Kantanen, Meng-Hua Li

المصدر: Frontiers in Genetics, Vol 9 (2018)

مصطلحات موضوعية: sheep, prolificacy, genome-wide association study, biological pathways, regulation, Genetics, QH426-470

الوصف: Reproduction is an important trait in sheep breeding as well as in other livestock. However, despite its importance the genetic mechanisms of litter size in domestic sheep (Ovis aries) are still poorly understood. To explore genetic mechanisms underlying the variation in litter size, we conducted multiple independent genome-wide association studies in five sheep breeds of high prolificacy (Wadi, Hu, Icelandic, Finnsheep, and Romanov) and one low prolificacy (Texel) using the Ovine Infinium HD BeadChip, respectively. We identified different sets of candidate genes associated with litter size in different breeds: BMPR1B, FBN1, and MMP2 in Wadi; GRIA2, SMAD1, and CTNNB1 in Hu; NCOA1 in Icelandic; INHBB, NF1, FLT1, PTGS2, and PLCB3 in Finnsheep; ESR2 in Romanov and ESR1, GHR, ETS1, MMP15, FLI1, and SPP1 in Texel. Further annotation of genes and bioinformatics analyses revealed that different biological pathways could be involved in the variation in litter size of females: hormone secretion (FSH and LH) in Wadi and Hu, placenta and embryonic lethality in Icelandic, folliculogenesis and LH signaling in Finnsheep, ovulation and preovulatory follicle maturation in Romanov, and estrogen and follicular growth in Texel. Taken together, our results provide new insights into the genetic mechanisms underlying the prolificacy trait in sheep and other mammals, suggesting targets for selection where the aim is to increase prolificacy in breeding projects.

وصف الملف: electronic resource

العلاقة: http://journal.frontiersin.org/article/10.3389/fgene.2018.00118/fullTest; https://doaj.org/toc/1664-8021Test

الوصول الحر: https://doaj.org/article/ac157aefcf2a4ba695a9f81c0968e83eTest

المؤلفون: Guang-Wei Ma, Yan-Kai Chu, Wen-Jian Zhang, Fei-Yue Qin, Song-Song Xu, Hua Yang, En-Guang Rong, Zhi-Qiang Du, Shou-Zhi Wang, Hui Li, Ning Wang

المصدر: PLoS ONE, Vol 12, Iss 4, p e0174868 (2017)

مصطلحات موضوعية: Medicine, Science

الوصف: Follistatin (FST) is involved in hair follicle morphogenesis. However, its effects on hair traits are not clear. This study was designed to investigate the effects of FST gene single nucleotide polymorphisms (SNP) on wool quality traits in Chinese Merino sheep (Junken Type). We performed gene expression analysis, SNP detection, and association analysis of FST gene with sheep wool quality traits. The real-time RT-PCR analysis showed that FST gene was differentially expressed in adult skin between Chinese Merino sheep (Junken Type) and Suffolk sheep. Immunostaining showed that FST was localized in inner root sheath (IRS) and matrix of hair follicle (HF) in both SF and Suffolk sheep. Sequencing analysis identified a total of seven SNPs (termed SNPs 1-7) in the FST gene in Chinese Merino sheep (Junken Type). Association analysis showed that SNP2 (Chr 16. 25,633,662 G>A) was significantly associated with average wool fiber diameter, wool fineness SD, and wool crimp (P < 0.05). SNP4 (Chr 16. 25,633,569 C>T) was significantly associated with wool fineness SD and CV of fiber diameter (P < 0.05). Similarly, the haplotypes derived from these seven identified SNPs were also significantly associated with average wool fiber diameter, wool fineness SD, CV of fiber diameter, and wool crimp (P < 0.05). Our results suggest that FST influences wool quality traits and its SNPs 2 and 4 might be useful markers for marker-assisted selection and sheep breeding.

وصف الملف: electronic resource

العلاقة: http://europepmc.org/articles/PMC5383234?pdf=renderTest; https://doaj.org/toc/1932-6203Test

الوصول الحر: https://doaj.org/article/5fbff37a2a4646afb675031aa60ca975Test