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Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis

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Journal of animal Science and Biotechnology 2024年第1期15卷 88-107页

作者： Guangliang Gao Hongmei Zhang Jiangping Ni Xianzhi Zhao Keshan Zhang Jian Wang Xiangdong Kong Qigui Wang chongqing academy of animal Science Rongchang DistrictChongqing 402460China Livestock and Poultry Multi‑Omics Key Laboratory of Ministry of Agriculture and Rural Affairs College of Animal Science and TechnologySichuan Agricultural UniversityChengdu 611130China chongqing Engineering Research Center of Goose Genetic Improvement Rongchang DistrictChongqing 402460China Department of Cardiovascular Ultrasound and Non‑Invasive Cardiology Sichuan Academy of Medical Sciences and Sichuan Provincial People’s HospitalUniversity of Electronic Science and Technology of ChinaChengdu611731China Ultrasound in Cardiac Electrophysiology and Biomechanics Key Laboratory of Sichuan Province University of Electronic Science and Technology of ChinaChengdu611731China JiguangGene Biotechnology Co. Ltd.Nanjing210032China Jiangsu Agri-animal Vocational College Taizhou225300China Poultry Science Institute Chongqing Academy of Animal ScienceNo.51 Changzhou AvenueRongchang DistrictChongqing 402460P.R.China

Background Domestic goose breeds are descended from either the Swan goose(Anser cygnoides)or the Greylag goose(Anser anser),exhibiting variations in body size,reproductive performance,egg production,feather color,and other phenotypic *** a pan-genome facilitates a thorough identification of genetic variations,thereby deepening our comprehension of the molecular mechanisms underlying genetic diversity and phenotypic *** To comprehensively facilitate population genomic and pan-genomic analyses in geese,we embarked on the task of 659 geese whole genome resequencing data and compiling a database of 155 RNA-seq *** constructing the pan-genome for geese,we generated non-reference contigs totaling 612 Mb,unveiling a collection of 2,813 novel genes and pinpointing 15,567 core genes,1,324 softcore genes,2,734 shell genes,and 878 cloud genes in goose ***,we detected an 81.97 Mb genomic region showing signs of genome selection,encompassing the TGFBR2 gene correlated with variations in body weight among ***-wide association studies utilizing single nucleotide polymorphisms(SNPs)and presence-absence variation revealed significant genomic associations with various goose meat quality,reproductive,and body composition *** instance,a gene encoding the SVEP1 protein was linked to carcass oblique length,and a distinct gene-CDS haplotype of the SVEP1 gene exhibited an association with carcass oblique ***,the pan-genome analysis revealed enrichment of variable genes in the“hair follicle maturation”Gene Ontology term,potentially linked to the selection of feather-related traits in geese.A gene presence-absence variation analysis suggested a reduced frequency of genes associated with“regulation of heart contraction”in domesticated geese compared to their wild *** study provided novel insights into gene expression features and functions by integrating gene expression patterns across multiple orga

关键词： Gene-CDS haplotype Goose GWAS Pan-genome Presence-absence variation Selection signal

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Herpetrione, a New Type of PPARα Ligand as a Therapeutic Strategy Against Nonalcoholic Steatohepatitis

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Research 2024年第3期2023卷 513-527页

作者： Lang Linghu Wei Zong Yixuan Liao Qianyu Chen Fancheng Meng Guowei Wang Zhihua Liao Xiaozhong Lan Min Chen Key Laboratory of Luminescence Analysis and Molecular Sensing(Southwest University) Ministry of EducationCollege of Pharmaceutical SciencesSouthwest UniversityChongqing 400715China Scholof Pharmacy Zunyi Medical UniversityZunyi 563000China School of Life Sciences Integrative Science Center of Germplasm Creation in Western China(chongqing)Science City and Southwest University TAAHC SWU Medicinal Plant Joint R&D CentreSouthwest UniversityChongqing 400715China TAAHC-SWU Medicinal Plant R&D Center Tibet Agricultural and Animal Husbandry UniversityNyingchiTibet 860000China.

Non-alcoholic fatty liver disease, especially nonalcoholic steatohepatitis (NASH), is a leading cause of cirrhosis and liver cancer worldwide;nevertheless, there are no Food and Drug Administration-approved drugs for treating NASH until now. Peroxisome proliferator-activated receptor alpha (PPARα) is an interesting therapeutic target for treating metabolic disorders in the clinic, including NASH. Herpetrione, a natural lignan compound isolated from Tibetan medicine Herpetospermum caudigerum, exerts various hepatoprotective effects, but its efficacy and molecular mechanism in treating NASH have not yet been elucidated. Here, we discovered that herpetrione lessened lipid accumulation and inflammation in hepatocytes stimulated with oleic acid and lipopolysaccharide, and effectively alleviated NASH caused by a high-fat diet or methionine-choline-deficient diet by regulating glucolipid metabolism, insulin resistance, and inflammation. Mechanistically, RNA-sequencing analyses further showed that herpetrione activated PPAR signaling, which was validated by protein expression. Furthermore, the analysis of molecular interactions illustrated that herpetrione bound directly to the PPARα protein, with binding sites extending to the Arm III domain. PPARα deficiency also abrogated the protective effects of herpetrione against NASH, suggesting that herpetrione protects against hepatic steatosis and inflammation by activation of PPARα signaling, thereby alleviating NASH. Our findings shed light on the efficacy of a natural product for treating NASH, as well as the broader prospects for NASH treatment by targeting PPARα.

关键词： PPARα protective metabolism

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NAD^(+) and its possible role in gut microbiota:Insights on the mechanisms by which gut microbes influence host metabolism

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animal Nutrition 2022年第3期10卷 360-371页

作者： Zhongxiang Ren Yetong Xu Tiejun Li Weizhong Sun Zhiru Tang Yongsheng Wang Kaifeng Zhou Jigang Li Qi Ding Kaiyang Liang Liuting Wu Yulong Yin Zhihong Sun Laboratory for Bio-feed and Molecular Nutrition College of Animal Science and TechnologySouthwest UniversityChongqing 400715China Institute of Subtropical Agriculture Chinese Academy of SciencesChangsha 410125China Nutrition&Health Research Institute COFCOBeijing 102209China Shandong Provincial animal husbandry General Station Jinan 250002China chongqing academy of animal Sciences Chongqing 500153China

Nicotinamide adenine dinucleotide(NAD^(+))is an enzyme cofactor,co-substrate,and redox factor in all living cells and is necessary for maintaining cell *** has been shown that appropriate supplementation of NAD^(+)precursors or inhibition of NAD^(+)-depleting enzymes can promote mitochondrial oxidative phosphorylation and improve host energy utilization *** addition,increasing evidence indicates that the gut microbiota plays a pivotal role in host ***,there should be a close correlation among NAD^(+),gut microbiota,and host metabolism;however,the information is *** this review,we summarize the metabolic process of NAD^(+)and its impact on host metabolism,the link between gut microbiota and host metabolism,as well as the potential effects of NAD^(+)on microbial metabolism,providing a new perspective on the interaction between gut microbiota and host metabolism.

关键词： NAD^(+) Gut microbiota Host metabolism Metabolic diseases

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Functions of Mulberry in the Development of Ecological animal husbandry and Development Ideas

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animal husbandry and Feed Science 2017年第6期9卷 370-372页

作者： Zeng Xiu Wang Jieping Zhou Chan Lv Jinfeng Wang Haiyan Gu Shanlin Xiong Dingkui chongqing academy of animal husbandry

Ecological animal husbandry is an animal husbandry industry system integrating ecological benefit, economic benefit and social benefit. Breeding cycle is one of the main patterns of ecological animal husbandry development, but breeding cycle does not form a relatively closed cycle of endogenous resources. In recent years, forage value and ecological value of mulberry have made some progresses in different research areas and angles, but the thought and practice of both forage and ecological value of mulberry has not been systematically interpreted and researched. Based on the short board of animal husbandry development and the advan- tage of mulberry, animal husbandry and mulberry were complemented and fused, and relatively closed planting and raising ecological recycling pattern with mulberry as the axis was raised. Phased scientific research and production test data were obtained, and the problems and development suggestions were put forward in the following aspects ： selection of mulberry varieties with both forage and ecological value, cost control of mulberry with both forage and ecological value, quality and safety control system of forage mulberry, orientation of feeding value of forage mulberry.

关键词： Mulberry Ecological animal husbandry Protein feed resources Energy conservation and emission reduction Quality and safety of agricultural products Forage value Ecological value

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Investigation of mitochondrial DNA genetic diversity and phylogeny of goats worldwide

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Journal of Integrative Agriculture 2022年第6期21卷 1830-1837页

作者： GUO Yi GONG Ying HE Yong-meng YANG Bai-gao ZHANG Wei-yi CHEN Bo-er HUANG Yong-fu ZHAO Yong-ju ZHANG Dan-ping MA Yue-hui CHU Ming-xing E Guang-xin College of animal Science and Technology Southwest UniversityChongqing 400715P.R.China chongqing Agriculture and Rural Affairs Committee of Tongnan Chongqing 402660P.R.China Dazhou animal husbandry Technology Extension Station Dazhou 635299P.R.China Institute of animal Sciences Chinese Academy of Agricultural SciencesBeijing 100193P.R.China

Genetic diversity,population structure,and population expansion of goats worldwide(4165 individuals from 196 breeds)were analyzed using published mitochondrial DNA(mtDNA)D_loop hypervariable region *** showed that 2409 haplotypes and 301 polymorphic sites were present within the 401-bp length D_loop region,the nucleotide diversity(Pi)was 0.03471,and the haplotype diversity(Hd)was *** analysis revealed that 98.92%of haplotypes were divided into six obvious clusters,consistent with the classification of the known mitochondrial haplogroups of *** A accounted for the largest proportion(86%).Interestingly,two unknown divisions(Unknown I and Unknown II)were discovered from goats in Southwest China,suggesting that Southwest China has unique maternal *** of molecular variance(AMOVA)and the average number of pairwise differences between populations(PiXY)indicated that geographical variation was small but *** tests(Tajima’s D and Fu’s FS tests)and mismatch distribution showed that haplogroups B,C,and G had expansion *** addition,the phylogenetic relationship between domestic and wild goats suggested that Capra aegagrus is the most likely wild ancestor and may have participated in the domestication of ancestral populations of A,B,C,and F haplogroups.A meta-analysis on the mtDNA sequences of goats from international databases was conducted to analyze goats’genetic diversity,population structure,and matrilineal system evolution *** results may help further understand the domestication history and gene flow of goats worldwide.

关键词： mitochondrial DNA genetic diversity population structure population expansion phylogeny

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Epigenome-wide DNA methylation analysis reveals differentially methylation patterns in skeletal muscle between Chinese Chenghua and Qingyu pigs

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Journal of Integrative Agriculture 2022年第6期21卷 1731-1739页

作者： WANG Kai WU Ping-xian WANG Shu-jie JI Xiang CHEN Dong JIANG An-an XIAO Wei-hang JIANG Yan-zhi ZHU Li ZENG Yang-shuang XU Xu QIU Xiao-tian LI Ming-zhou LI Xue-wei TANG Guo-qing Farm animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province Sichuan Agricultural UniversityChengdu 611130P.R.China College of Life Science Sichuan Agricultural UniversityYa’an 625014P.R.China Sichuan animal husbandry Station Chengdu 610041P.R.China National animal husbandry Service Beijing 100125P.R.China chongqing academy of animal Science Chongqing 402460P.R.China

Chenghua(CH)pig and Qingyu(QY)pig are typical Chinese native fatty *** pig is mainly distributed in Chengdu Plain,while QY pig is widely distributed throughout the mountain areas around the Sichuan *** are significant differences in their phenotypic traits,including body image,growth performance,and meat *** study compared several meat quality traits of CH and QY pigs and conducted a genome-wide DNA methylation analysis using reduced representation bisulfite sequencing(RRBS).It was observed that the pH at 45 min(pH_(45min),P=5.22e-13),lightness at 45 min(L^(*)_(45min),P=4.85e-5),and lightness at 24 h(L^(*)_(24h),P=3.57e-5)of CH pigs were higher than those of QY *** detected 10699 differentially methylated cytosines(DMCs)and 2760 differentially methylated genes(DMGs)associated with these *** analysis showed that these DMGs were mainly enriched in the AMPK signaling pathway,Type II diabetes mellitus,Insulin signaling pathway,mTOR signaling pathway,and Insulin ***,15 DMGs were associated with fat metabolism(ACACA,CAB39,CRADD,CRTC2,FASN,and GCK),muscle development(HK2,IKBKB,MTOR,PIK3CD,PPARGC1A,and RPTOR),or meat quality traits(PCK1,PRKAG2,and SLC2A4).The findings may help to understand further the epigenetic regulation mechanisms of meat quality traits in pigs and provide new basic data for the study of local pigs.

关键词： DNA methylation reduced representation bisulfite sequencing(RRBS) Chenghua pig Qingyu pig

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Studies on Cloning and Transformation of CBF1 Gene of Maize Grass

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animal husbandry and Feed Science 2013年第4期5卷 189-191,197页

作者： XIANG Bai-ju LI Cheng-jun ZHANG Jian LUO Yi JIANG An chongqing academy of animal husbandry Sciences

[Objective]It is revealed whether the similar maize transcriptional activator in CBF1 gene is regulatory cold resistance gene to lay the foundation for breeding new transgenic Forage Maize Varieties with high cold resistance ability.[Methods]In the present paper,the transcriptional factor gene CBF1 was Successfully cloned by PCR from the leaves of *** sequence was preliminarily analyzed and plant expression vector was *** with agrobacterium-mediated transgene technique,CBF1 gene was introduced into maize SAUMZ1.[Results]PCR assay revealed that the CBF1 gene was integrated in the maize grass SAUMZ1 *** different low temperature treatment,the relative electrolyte leakage percentage of transgenic plant was lower than Control.[Conclusion] The results showed that the cold-resistance of maize grass SAUMZ1 enhanced after transforming CBF1 gene.

关键词： CBF1 gene Transcriptional factor Cold resistance Transform Maize SAUMZ1

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Effects of Heat Stress on Microbial Numbers in Rumen Fluid of Dairy Cows

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animal husbandry and Feed Science 2013年第4期5卷 179-184,188页

作者： DU Rui-ping WEN Ya-li YAO Yan-chu JIANG Shan GAO Min animal Nutrition Institute of Agriculture and animal husbandry academy of Inner Mongolia animal Nutrition Institute of chongqing academy of animal Sciences

[Objective]This experiment was conducted to investigate the effects of heat stress on microbial numbers in rumen fluid of dairy cows during different lactating periods by real-time PCR.[Methods]A 2 ×3 crossover design was used and eighteen healthy Chinese Holstein cows were *** cows were allocated into three periods based on their parity,average days in milk,and milk yield：early lactation（postpartum 15 to 100 days）,mid-lactation（postpartum 112 to 175 days）and late lactation（postpartum 200 to 230 days）,and six cows in each period.A self-control trial between heat stress period and non-heat stress period was used based on temperature and humidity index（THI）measurement on site.[Results]The results showed as follows：compared with non-heat stress period,heat stress significantly increased the microbial numbers in early lactation,the Ruminococcus flavefaciens number in different lactation and Bacteroides succinogenes number in early and mid-lactation（P 〈0.01）.The total bacteria and Ruminococcus albus numbers in mid-and late lactation and Bacteroides succinogenes number in late lactation were decreased significantly by heat stress（P 〈0.01）.There were strong correlation between THI and the numbers of total bacteria（P 〈0.01）,anaerobic fungi（P 〈0.05）,Ruminococcus albus（P 〈0.01）and Ruminococcus flavefaciens（P 〈0.05）in rumen fluid of dairy cows in early lactation,but the correlation between THI and these indexes in mid-and late lactation were poor.[Conclusion]It is indicated that the rumen microbial numbers in early lactation are more sensitive to heat stress.

关键词： Heat stress Dairy cows Rumen Microbial numbers

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Genome-wide Analysis of Long Non-coding RNAs at Early Stage of Skin Pigmentation in Goats(Capra hircus)

Genome-wide Analysis of Long Non-coding RNAs at Early Stage ...

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第七届中国畜牧科技论坛

作者： Ren hangxing Wang gaofu Chen lei Jiang jing Liu liangjia Li nianfu Zhao jinhong Sun xiaoyan Zhou peng chongqing academy of animal Sciences chongqing Engineering Research Center for Goats Youyang animal husbandry Bureau

(Background) Long noncoding RNAs(IncRNAs) play roles in almost all biological processes;however,their function and profile in skin development and pigmentation is less *** addition,because IncRNAs are species-specific,their function in goats has not been established.(Result) We systematically identified IncRNAs in 100-day-old fetal skin by deep RNA-sequencing using the Youzhou dark goat(dark skin) and Yudong white goat(white skin) as a model of skin pigmentation.A total of 841,895,634 clean reads were obtained from six libraries(samples).We identified 1,336 specific IncRNAs in fetal skin that belonged to three subtypes,including 999 intergenic IncRNAs(lincRNAs),218 anti-sense IncRNAs,and 119 intronic *** results demonstrated significant differences in gene architecture and expression among the three IncRNA subtypes,particularly in terms of density and position bias of transpose elements near the transcription start *** also investigated the impact of IncRNAs on its target genes in cis and trans,indicating that these IncRNAs have a strict tissue specificity and functional conservation during skin development and pigmentation.(Conclusion) The present study provides a resource for IncRNA studies in diseases involved in pigmentation and skin *** expands our knowledge about IncRNA biology as well as contributes to the annotation of the goat genome.

关键词： skin IncRNA goat pigmentation transcriptome

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Transcriptome Analysis Revealing the Genetic Difference in Fetal Skin Pigmentation in Goats(Capra hircus)

Transcriptome Analysis Revealing the Genetic Difference in F...

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第七届中国畜牧科技论坛

作者： Ren hangxing Wang gaofu Chen lei Jiang jing Liu liangjia Li nianfu Zhao jinhong Li jie Zhou peng chongqing academy of animal Sciences chongqing Engineering Research Center for Goats Youyang animal husbandry Bureau

(Background) Although many genes have been found to be associated with skin pigmentation,the characteristics of global gene expression is still not well understood at early stage of skin pigmentation in *** we reported a rare natural group of goat(Youzhou dark skin goat) featuring the dark skin of body including the visible mucous membranes,which may be an exclusive kind of mammalian species with this special phenotype so *** two goat groups with different skin colors as the models,we investigated the global gene expression in the fetal skin at gestation of 100 days in goats by deep RNA-sequencing method.(Results) With a computational pipeline,we identified 1616 novel transcripts with certain protein coding potential but differing from the catalog of IncRNA in goat *** to their annotation,these novel transcripts were classified into two distinct groups,especially large differences observed in TEs density and position bias near TSS in their gene ***,we identified a large amount of alternative splicing(AS) events in the present ***,there were AS events in the differentially expressed(DE) genes between the two groups of goat with different skin colors,such as ASIP,TYRP1,DCT,and RAB27 A,which are well-known genes associated with *** functional enrichment analysis of the DE genes demonstrated that 7 terms relative to(hyper) pigmentation and one KEGG pathway associated with melanogenesis were most overrepresented in our *** addition,ASIP and TYRP1 were also significantly enriched in a kind of OMIMISEASE in *** findings above provide the considerable evidence underlying a diversity of dermal colors in goats at global level of gene expression.(Conclusion) There are obvious differences in the characteristics of fetal skin transcriptome between hyperpigmented and normal skin of *** findings can not only contribute to elucidate the mystery of skin pigmentation at early stage of de

关键词： skin pigmentation transcriptome goat

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