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Building a sequence map of the pig pan-genome from multiple de novo assemblies and Hi-C data

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Science China(Life Sciences) 2020年第5期63卷 750-763页

作者： Xiaomeng Tian Ran Li Weiwei Fu Yan Li Xihong Wang Ming Li Duo Du Qianzi Tang Yudong Cai Yiming Long Yue Zhao Mingzhou Li Yu Jiang Key Laboratory of animal Genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYangling 712100China Institute of animal Genetics and Breeding College of Animal Science and TechnologySichuan Agricultural UniversityChengdu 611130China

Pigs were domesticated independently in the Near East and China,indicating that a single reference genome from one individual is unable to represent the full spectrum of divergent sequences in pigs ***,12 de novo pig assemblies from Eurasia were compared in this study to identify the missing sequences from the reference *** a result,72.5 Mb of nonredundant sequences(~3% of the genome)were found to be absent from the reference genome(Sscrofa11.1)and were defined as *** the pan-sequences,9.0 Mb were dominant in Chinese pigs,in contrast with their low frequency in European *** sequence dominant in Chinese pigs contained the complete genic region of the tazarotene-induced gene 3(TIG3)gene which is involved in fatty acid *** flanking sequences and Hi-C based methods,27.7% of the sequences could be anchored to the reference *** supplementation of these sequences could contribute to the accurate interpretation of the 3D chromatin structure.A web-based pan-genome database was further provided to serve as a primary resource for exploration of genetic diversity and promote pig breeding and biomedical research.

关键词： pan-genome pig reference genome 3D chromatin structure presence-absence variation

The phylogenetic status of typical Chinese native pigs: analyzed by Asian and European pig mitochondrial genome sequences

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Journal of animal Science and Biotechnology 2013年第2期4卷 145-151页

作者： Guanghui Yu Hai Xiang Jikun Wang Xingbo Zhao National Engineering Laboratory for animal Breeding Ministry of Agricultural Key Laboratory of Animal Genetics Breeding and Reproduction State Key Laboratory for Agribiotechnology College of Animal Science and Technology China Agricultural University

China is one of the most diverse countries, which have developed 88 indigenous pig breeds. Several studies showed that pigs were independently domesticated in multiple regions of the world. The purpose of this study was to investigate the origin and evolution of Chinese pigs using complete mitochondrial genomic sequences (mtDNA) from Asian and European domestic pigs and wild boars. Thirty primer pairs were designed to determine the mtDNA sequences of Xiang pig, Large White, Lantang, Jinhua and Pietrain. The phylogenetic status of Chinese native pigs was investigated by comparing the mtDNA sequences of complete coding regions and D-loop regions respectively amongst Asian breeds, European breeds and wild boars. The analyzed results by two cluster methods contributed to the same conclusion that all pigs were classified into two major groups, European clade and Asian clade. It revealed that Chinese pigs were only recently diverged from each other and distinctly different from European pigs. Berkshire was clustered with Asian pigs and Chinese pigs were involved in the development of Berkshire breeding. The Malaysian wild boar had distant genetic relationship with European and Asian pigs. Jinhua and Lanyu pigs had more nucleotide diversity with Chinese pigs although they all belonged to the Asian major clade. Chinese domestic pigs were clustered with wild boars in Yangtze River region and South China.

关键词： Mitochondrial DNA Origin and evolution Phylogenetic analysis Pig

The SNPs C.513A>T in the MHC B-F gene and rs15001532 in the SPOCK1 gene are associated with Salmonella pullorum disease resistance in chickens

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Journal of Integrative Agriculture 2016年第8期15卷 1856-1862页

作者： ZHANG Ze-tang GAN Jian-kang ZHANG Wen-wu ZHANG De-xiang ZHANG Xi-quan LUO Qing-bin College of animal Science South China Agricultural University Key Lab of Chicken Genetics Breeding and Reproduction Ministry of Agriculture Xinguang Agriculture & animal Husbandry Co. Ltd.

supported by the Earmarked Fund for the Modern Agroindustry Technology Research System, China （CARS-41）;the National High Technology Research and Development Program of China （2011AA100301）

关键词： MHC B-F gene SPOCK1 gene SNPs Salmonella pullorum partridge chicken

MiR-214-3p promotes proliferation and inhibits estradiol synthesis in porcine granulosa cells

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Journal of animal Science and Biotechnology 2021年第1期12卷 185-197页

作者： Shengjie Shi Xiaoge Zhou Jingjing Li Lutong Zhang Yamei Hu Yankun Li Gongshe Yang Guiyan Chu Key Laboratory of animal Genetics Breeding and Reproduction of Shaanxi ProvinceYangling 712100China Laboratory of animal Fat Deposition&Muscle Development College of Animal Science and TechnologyNorthwest A&F UniversityYangling 712100China

Background: Granulosa cells(GCs) proliferation and estradiol synthesis significantly affect follicular *** miR-214-3p expression in the ovarian tissues of high-yielding sows is higher than that in low-yielding sows,indicating that miR-214-3p may be involved in sow fertility. However, the functions and mechanisms of miR-214-3p on GCs are unclear. This study focuses on miR-214-3p in terms of the effects on GCs proliferation and estradiol ***: Our findings revealed that miR-214-3p promotes proliferation and inhibits estradiol synthesis in porcine GCs. MiR-214-3p can increase the percentage of S-phase cells, the number of EdU labeled positive cells, and cell viability. However, E2 concentration was reduced after miR-214-3p agomir treatment. We also found that miR-214-3p up-regulates the expression of cell cycle genes including cell cycle protein B(Cyclin B), cell cycle protein D(Cyclin D), cell cycle protein E(Cyclin E), and cyclin-dependent kinase 4(CDK4) at the transcription and translation levels, but down-regulates the mRNA and protein levels of cytochrome P450 family 11 subfamily A member 1(CYP11A1), cytochrome P450 family 19 subfamily A member 1(CYP19A1), and steroidogenic acute regulatory protein(StAR)(i.e., the key enzymes in estradiol synthesis). On-line prediction, bioinformatics analysis, a luciferase reporter assay, RT-qPCR, and Western blot results showed that the target genes of miR-214-3p in proliferation and estradiol synthesis are Mfn2 and NR5A1, ***: Our findings suggest that miR-214-3 p plays an important role in the functional regulation of porcine GCs and therefore may be a target gene for regulating follicular development.

关键词： Estradiol synthesis Granulosa cells MiR-214-3p Proliferation

Evaluation of heat stress effects on cellular and transcriptional adaptation of bovine granulosa cells

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Journal of animal Science and Biotechnology 2020年第2期11卷 348-366页

作者： Adnan Khan Jinhuan Dou Yachun Wang Xiaolong Jiang Muhammad Zahoor Khan Hanpeng Luo Tahir Usman Huabin Zhu Key Laboratory of animal Genetics Breedingand ReproductionMARANational Engineering Laboratory for Animal BreedingCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing 100193People’s Republic of China Embryo Biotechnology and reproduction Laboratory Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijingChina College of Veterinary Sciences and animal Husbandry Abdul Wali Khan UniversityMardan 23200Pakistan

Background:Heat stress is known to affect follicular dynamics,oocyte maturation,and fertilization by impairing steroidogenic ability and viability of bovine granulosa cell(bGCs).The present study explored the physiological and molecular response of bGCs to different heat stress intensities *** exposed the primary bGCs to heat stress(HS)at 39℃,40℃ and 41℃ along with control samples(38℃)for 2 *** evaluate the impact of heat stress on bGCs,several in vitro cellular parameters including cell apoptosis,intracellular reactive oxygen species(ROS)accumulation and HSP70 kinetics were assessed by flow cytometry,florescence microscopy and western blot,***,the ELISA was performed to confirm the 17β-estradiol(E2)and progesterone(P4)*** addition,the RNA sequencing(RNA-Seq)method was used to get the molecular based response of bGCs to different heat ***:Our findings revealed that the HS significantly decreased the cell viability,E2 and P4 levels in bGCs,whereas,increased the cellular apoptosis and ***,the RNA-Seq experiments showed that all the treatments(39℃,40℃ and 41℃)significantly regulated many differentially expressed genes(DEGs)***2L1,STAR,CYP11A1,CASP3,SOD2,HSPA13,and MAPK8IP1 and pathways associated with heat stress,apoptosis,steroidogenesis,and oxidative ***,our data demonstrated that the impact of 40°C treatment was comparatively detrimental for cell viability,apoptosis and ROS ***,a similar trend of gene expression was reported by RT-qPCR for RNA-seq ***:Our study presented a worthy strategy for the first time to characterize the cellular and transcriptomic adaptation of bGCs to heat stress(39,40 and 41°C)*** results infer that these genes and pathways reported in present study could be useful candidates/indicators for heat stress research in dairy ***,the established model of bGCs to heat stress in the current study provides an appropriate

关键词： Bovine granulosa cells Differentially expressed genes Follicles Heat stress RNA-Seq

Recent advances in immunocastration in sheep and goat and its animal welfare benefits:A review

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Journal of Integrative Agriculture 2022年第2期21卷 299-309页

作者： ZENG Fan-mei DING Yi Teketay WASSIE JING Hai-jing Sohail AHMED LIU Gui-qiong JIANG Xun-ping Key Laboratory of Agricultural animal Genetics Breeding and Reproduction of Ministry of EducationHuazhong Agricultural UniversityWuhan 430070P.R.China Laboratory of Sheep and Goat Genetics Breeding and ReproductionCollege of Animal Science and TechnologyHuazhong Agricultural UniversityWuhan 430070P.R.China

Castration of male animals is a common practice in the meat industry aimed at reducing aggressive behavior, preventing unpleasant flavor, and controlling undesirable breeding. For many years, mechanical castration and surgical castration have been practiced to sterilize the animals. However, these castration methods are not humane because of the associated risk of death, pain, and stress. Recently, immunocastration targeting the hypothalamic-pituitary-gonadal axis(HPG) axis has been reported as an animal-friendly approach that circumvents many of the concerns with conventional castration, and suggested by researches as an alternative to surgical castration. However, there is no compilation of updated information on the use of immunocastration in sheep and goats. Therefore, this review aims to summarize the developmental process from traditional surgical castration to immunocastration and to screen the process of immune targets. It also compares the respective advantages and disadvantages of traditional castration technologies and immunocastration, in particular including analyses in the characteristics, features application and welfare benefits of immunocastration in sheep and goats were also analyzed.

关键词： immunocastration reversibility safety animal welfare DNA vaccine

Calcium potentiates the effect of estradiol on PGF2α production in the bovine endometrium

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Journal of animal Science and Biotechnology 2015年第2期6卷 215-221页

作者： Claudia Maria Bertan Membrive Pauline Martins da Cunha Flávio Vieira Meirelles Mario Binelli S?o Paulo State University Department of animal reproduction School of Veterinary Medicine and Animal Science University of S?o Paulo Department of Veterinary Medicine School of Animal Sciences and Food Engineering University of S?o Paulo

Background： Estradiol （E2） is required for luteolysis in cows and its injection stimulates prostaglandin F2α （PGF2α） release. The main goal of our study was to investigate the ability of endometrial explants and cells treated with E2 and the calcium ionophore （CI） A23187 to synthesize PGF2α. Results： Treatment with E2 in vivo resulted in a 48.4% increase of PGF2α production by endometrial explants treated in vitro with A23187. Production of PGF20 was better stimulated with A23187 at concentrations of 10^-6 and 10^-5 mol/L compared with other concentrations used. The concentration of PGF2α for untreated bovine endometrial cell cultures was 33.1 pg/mL, while for cultures treated with E2, A23187, or a combination of E2 and A23187, the PGF2α concentration was 32.5, 92.4 and 145.6 pg/mL, respectively. Conclusions： Treatment with A23187 tended to stimulate PGF20 production. In the presence of E2, A23187 significantly stimulated PGF20 synthesis. It appears that A23187 potentiates the effects of E2 with respect to synthesis of endometrial PGF2α in cattle.

关键词： animal reproduction Cattle Estradiol Luteolysis PGF2α synthesis Reproductive physioloqy

Blood neutrophil extracellular traps:a novel target for the assessment of mammary health in transition dairy cows

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Journal of animal Science and Biotechnology 2023年第3期14卷 1068-1079页

作者： Luyi Jiang Huizeng Sun Fengfei Gu Jin He Fengqi Zhao Jianxin Liu Institute of Dairy Science College of Animal SciencesZhejiang UniversityHangzhouChina Ministry of Education Key Laboratory of Molecular animal Nutrition Zhejiang UniversityHangzhouChina Institute of animal Genetics and reproduction College of Animal SciencesZhejiang UniversityHangzhouChina Department of animal&Veterinary Sciences University of VermontBurlingtonUSA

Background:Mammary health is important for transition dairy cows and has been well recognized to exert decisive effects on animal ***,the factors influencing mammary health are still *** somatic cell count(DSCC)could reflect the mastitis risk since it is the percentage of neutrophils plus lymphocytes in total somatic cells and could be reflective of mammary health of dairy *** work aimed to investigate the assessment and prognosis of the health of transition cows based on blood neutrophil extracellular traps(NETs).Results:Eighty-four transition Holstein dairy cows were *** serum was sampled in all the animals at week 1 pre-and postpartum,and milk was sampled at week 1 *** on the DSCC in milk at week 1,cows with lower(7.4%±4.07%,n=15)and higher(83.3%±1.21%,n=15)DSCCs were *** DSCC cows had higher levels of red blood cell counts(P<0.05),hemoglobin(P=0.07),and hematocrit(P=0.05),higher concentrations of serum oxidative variables[reactive oxygen species(P<0.05),malondialdehyde(P<0.05),protein carbonyl(P<0.05),and 8-hydroxy-2-deoxyguanosine(P=0.07)],higher levels of serum and milk NETs(P<0.05)and blood-milk barrier indicators,including serumβ-casein(P=0.05)and milk immunoglobulin G2(P=0.09),than those of low DSCC *** addition,lower concentrations of serum nutrient metabolites(cholesterol and albumin)(P<0.05)and a lower level of serum deoxyribonuclease I(P=0.09)were observed in high DSCC cows than in low DSCC *** the assessments performed using levels of the three prepartum serum parameters(NETs,deoxyribonuclease I andβ-casein),the area under the curve(0.973)of NETs was the *** addition,the sensitivity(1.00)and specificity(0.93)were observed for the discrimination of these cows using NETs levels with a critical value of 32.2 ng/mL(P<0.05).Conclusions:The formation of NETs in blood in transition dairy cows may damage the integrity of the blood-milk barrier and thereby increase the risk for

关键词： Blood-milk barrier Differential somatic cell count Mastitis risk Neutrophil extracellular traps

GSTM3, but not IZUMO1, is a cryotolerance marker of boar sperm

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Journal of animal Science and Biotechnology 2019年第4期10卷 931-941页

作者： Marc Llavanera Ariadna Delgado-Bermúdez Beatriz Fernandez-Fuertes Sandra Recuero Yentel Mateo Sergi Bonet Isabel Barranco Marc Yeste Biotechnology of animal and Human reproduction (Techno Sperm) Unit of Cell Biology Department of Biology Institute of Food and Agricultural Technology University of Girona

Background: Cryopreservation is currently the most efficient method for long-term preservation of mammalian gametes and is extensively used in swine artificial insemination(AI) centres. However, it is well-known that cryopreservation procedures induce changes in the water phase in both intra and extracellular compartments,which alter the content and localisation of several proteins and ends up curtailing the structural integrity of functional sperm(i.e., cryoinjuries). Alterations and deficiencies of sperm-oocyte binding proteins during gamete recognition are one of the causes of reproductive failure both in vitro and in vivo. In this sense, characterisation of cryopreservation effects upon oocyte-binding proteins of sperm, such as IZUMO1 and GSTM3, is essential when assessing the impact of this technique in swine ***: Cryopreservation was found to induce changes in the localisation of IZUMO1 and GSTM3 in boar ***, the relative content of both proteins was not altered after thawing. Furthermore, whereas IZUMO1 content was found not to be related to the cryotolerance of boar sperm, GSTM3 content was observed to be higher in poor(PFE) than in good(GFE) freezability ejaculates in both pre-frozen(1.00 INT·mm^2± 0.14 INT·mm^2 vs.0.72 INT·mm^2± 0.15 INT·mm^2;P < 0.05) and post-thawed(0.96 INT·mm^2± 0.20 INT·mm^2 vs. 70 INT·mm^2± 0.19 INT·mm^2;P < 0.05) samples. Moreover, GSTM3 levels were found to be higher in those spermatozoa that exhibited low mitochondrial activity, high reactive oxygen species(ROS) production, and high membrane lipid disorder postthaw(P < 0.05).Conclusions: The difference in GSTM3 content between GFE and PFE, together with this protein having been found to be related to poor sperm quality post-thaw, suggests that it could be used as a cryotolerance marker of boar spermatozoa. Furthermore, both IZUMO1 and GSTM3 relocate during cryopreservation, which could contribute to the reduced fertilising capacity of frozen-thawed boar

关键词： Boar Cryopreservation GSTM3 IZUMO1 ROS Sperm