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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

Effect of the C.–1388 A>G polymorphism in chicken heat shock transcription factor 3 gene on heat tolerance

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Journal of Integrative Agriculture 2015年第9期14卷 1808-1815页

作者： zhang Wen-wu KONG Li-na zhang De-xiang JI Cong-liang zhang xi-quan LUO Qing-bin College of Animal Science South China Agricultural University Key Laboary of Chicken Genetics Breeding and ReproductionMinistry of Agriculture/South China Agricultural University Guangdong Enterprise Laboary of Healthy Animal Husbandry and Environment Control South China Agricultural University Guangdong Wens Food Group Limited Company

Heat stress is one of the main factors that inlfuence poultry production. Heat shock proteins (HSPs) are known to affect heat tolerance. The formation of HSPs is regulated by heat shock transcription factor 3 (HSF3) in chicken. A DNA pool was established for identifying single nucleotide polymorphisms (SNPs) of the chicken HSF3, and 13 SNPs were detected. The bioinformatic analysis showed that 8 SNPs had the capacity to alter the transcription activity of HSF3. The dual luciferase report gene assay showed that there was a signiifcant difference (PG (S1) and C.–1 388 A>G (S4) sites at the 5′-untranslated region (UTR) of chicken HSF3. The elec-trophoretic mobility shift assay showed that the S4 site was a transcription binding factor. The analysis of the association of the S1 and S4 sites with heat tolerance index revealed that the S4 site was signiifcantly correlated with the CD3+T cel , corticosterone, and T3 levels in Lingshan chickens and with the heterophil/lymphocyte value in White Recessive Rock. These results showed that the S4 site at the 5′ UTR of chicken HSF3 might have an impact on heat tolerance in summer and could be used as a potential marker for the selection of chicken with heat tolerance in the future.

关键词： chicken heat shock factor 3 dual luciferase report gene heat tolerance

The Effects of Different Sex-Linked Dwarf Variations on Chinese Native Chickens

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Journal of Integrative Agriculture 2012年第9期11卷 1500-1508页

作者： OUYANG Jian-hua xiE Liang NIE Qing-hua ZENG Hua PENG Zhi-jun zhang De-xiang zhang xi-quan Department of Animal Science College of Animal Science and Technology Jiangxi Agricultural University Nanchang 330045 P.R. China Department of Animal Genetics Breeding and Reproduction College of Animal Science South China Agricultural University Guangzhou 510642 P.R.China Guangdong Wens Foodstuff Company Ltd. Guangdong 527439 P.R.China Institute of Animal Science & Veterinary Hainan Academy of Agricultural Sciences Haikou 571100 P.R.China

Variants in chicken growth hormone receptor （GHR） gene lead to sex-linked dwarf （SLD） chickens, but effects of different variants are distinct. In this study, 11 SLD chicken breeds or strains including 3 Chinese native breeds and 8 breeding strains were studied in order to investigate the effects of different sex-linked dwarf variations on growth performance. The results showed that there were three reasons which could lead to dwarfism in the 11 breeds or strains. Firstly, an about 1.7 kb deletion of growth hormone receptor （GHR） gene leads to dwarfism in Jiangxi dwarf chicken, strains GF24, GF26, N308, N309, and N310. Secondly, a T354C mutation in exon 5 of the GHR gene leads to dwarfism in strains N301 and N305. Thirdly, an unknown variant leads to dwarfism in Guizhou Yellow Dwarf chicken and Yixing Bantam chicken. In addition, all individuals of N303 had the 1.7 kb deletion of the GHR gene, and additionally, some of them also carried the T354C mutation. As far as the performance of individuals were compared among T354C homozygote, deletion homozygote, and heterozygote carrying both T354C and deletion, it was found that the T354C＇s impacts on body weight of Chinese chickens were maximum, the body weight of chickens with homozygote T354C was 92.12% of those with heterozygote, and the difference of the body weight between deletion homozygote and heterozygote was not significant. There was no significant difference of shank length among three genotypes.

关键词： SLD chicken GHR dwarf allele phenotypic effect

Effect of HSPB9 on Apoptosis of DF-1 Cells

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Biomedical and Environmental Sciences 2019年第2期32卷 107-120页

作者： XU Yong Jie HU Mei Ling ZHOU Liang Hui WANG Qi zhang xi quan LUO Qing Bin Department of Animal Genetics Breeding and Reproduction College of Animal Science/Key Laboratory of Chicken Genetics Breeding and Reproduction Ministry of Agriculture South China Agricultural University

Objective Our aim was to explore whether heat stress protein(HSP) 9 preferentially expresses under heat stress and affects the expression of other heat stress proteins as well as to explore the effect of HSPB9 overexpression and knockdown on apoptosis in DF-1. Methods We used gene cloning to construct an overexpression vector of the target gene, and synthesized the target gene interference fragment to transfect the chicken fibroblast cell line. Gene and protein expression, as well as apoptosis, were detected by RT-qPCR, Western blot, and flow cytometry. Results Chicken DF-1 cells showed an early state of apoptosis in the early stages of HSPB9 overexpression. In the later stages, as HSPB9 expression increased, the cells showed inhibition of apoptosis. When the cells were under heat stress, HSPB9 expression was much higher and earlier than the expression of HSPB1 and HSPA2. In addition, high expression of HSPB9 had a negative effect on HSPB1 and HSPA2 expression. This negative feedback decreased the percentage of early stages of apoptotic cells and promoted cell survival. Conclusion HSPB9 expression, although rapid, is detrimental to cell survival early during its overexpression. In heat stress, HSPB9 overexpression, while inhibiting the expression of HSPA2 and HSPB1, is beneficial to cell survival.

关键词： Heat stress HSPB9 HSPB1 HSPA2 Apoptosis

Identification of SNPs and Their Effects on Swine Growth and Carcass Traits for Porcine IGFBP-3 Gene

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Agricultural Sciences in China 2008年第5期7卷 630-635页

作者： LIU De-wu zhang Hao WU Zhen-fang LI Jia-qi YANG Guan-fu zhang xi-quan College of Animal Science South China Agricultural University Guangzhou 510642 P.R.China

The insulin-like growth factor binding protein-3 （IGFBP-3） was known as a key factor that regulates the effect of insulin- like growth factors （IGF-1 and IGF-2） on pig growth and development. We first identified 38 single nucleotide polymorphisms （SNPs） from a fragment of the IGFBP-3 gene spanning 1 823 bp using the denaturing high-performance liquid chromatography （DHPLC） method and confirmed them by direct sequencing. Among these SNPs, 36 located in introns and the remaining 2 in the 3 prime untranslated region （3UTR）. In addition, 16 PCR-RFLP polymorphisms were identified within these SNPs. Three SNPs were then selected to genotype 272 F2 individuals with PCR-RFLP method and the association of polymorphism with growth and carcass traits were analyzed. The results showed that no significant associations were observed between polymorphisms of A265G and A952G and traits. However, the A2670G significantly related with live body length, loin muscle area, and skin and fat percentage （P〈0.05）; highly significantly associated with weight of carcass lean and lean percentage （P〈 0.01）.

关键词： pig IGFBP-3 gene single nucleotide polymorphism (SNP) denaturing high-performance liquid chromatography(DHPLC) performance

An efficient and rapid method to detect and verify natural antisense transcripts of animal genes

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Journal of Integrative Agriculture 2016年第9期15卷 2070-2076页

作者： zhang Li ZHAO Rui xiAO Mei LIN Shu-dai LI Bi-xiao QIU Feng-fang MA Jing-e zhang De-xiang NIE Qing-hua AN Li-long zhang xi-quan Agricultural College Guangdong Ocean University Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/Key Lab of Chicken Genetics Breeding and Reproduction Ministry of Agriculture/South China Agricultural University

High-throughput sequencing has identified a large number of sense-antisense transcriptional pairs, which indicates that these genes were transcribed from both directions. Recent reports have demonstrated that many antisense RNAs, especially lnc RNA（long non-coding RNA）, can interact with the sense RNA by forming an RNA duplex. Many methods, such as RNA-sequencing, Northern blotting, RNase protection assays and strand-specific PCR, can be used to detect the antisense transcript and gene transcriptional orientation. However, the applications of these methods have been constrained, to some extent, because of the high cost, difficult operation or inaccuracy, especially regarding the analysis of substantial amounts of data. Thus, we developed an easy method to detect and validate these complicated RNAs. We primarily took advantage of the strand specificity of RT-PCR and the single-strand specificity of S1 endonuclease to analyze sense and antisense transcripts. Four known genes, including mouse β-actin and Tsix（xist antisense RNA）, chicken LXN（latexin） and GFM1（Gelongation factor, mitochondrial 1）, were used to establish the method. These four genes were well studied and transcribed from positive strand, negative strand or both strands of DNA, respectively, which represented all possible cases. The results indicated that the method can easily distinguish sense, antisense and sense-antisense transcriptional pairs. In addition, it can be used to verify the results of high-throughput sequencing, as well as to analyze the regulatory mechanisms between RNAs. This method can improve the accuracy of detection and can be mainly used in analyzing single gene and was low cost.

关键词： natural antisense transcripts transcription orientation detection method RNA sequencing long non-coding RNA

Incorporating genomic annotation into single-step genomic prediction with imputed whole-genome sequence data

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Journal of Integrative Agriculture 2022年第4期21卷 1126-1136页

作者： TENG Jin-yan YE Shao-pan GAO Ning CHEN Zi-tao DIAO Shu-qi LI xiu-jin YUAN xiao-long zhang Hao LI Jia-qi zhang xi-quan zhang Zhe Guangdong Laboratory of Lingnan Modern Agriculture/Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding College of Animal ScienceSouth China Agricultural UniversityGuangzhou 510642P.R.China State Key Laboratory of Biocontrol School of Life SciencesSun Yat-sen UniversityGuangzhou 510006P.R.China Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding College of Animal Sciences and TechnologyZhongkai University of Agriculture and EngineeringGuangzhou 510225P.R.China

Single-step genomic best linear unbiased prediction(ss GBLUP) is now intensively investigated and widely used in livestock breeding due to its beneficial feature of combining information from both genotyped and ungenotyped individuals in the single model. With the increasing accessibility of whole-genome sequence(WGS) data at the population level, more attention is being paid to the usage of WGS data in ss GBLUP. The predictive ability of ss GBLUP using WGS data might be improved by incorporating biological knowledge from public databases. Thus, we extended ss GBLUP, incorporated genomic annotation information into the model, and evaluated them using a yellow-feathered chicken population as the examples. The chicken population consisted of 1 338 birds with 23 traits, where imputed WGS data including 5 127 612 single nucleotide polymorphisms(SNPs) are available for 895 birds. Considering different combinations of annotation information and models, original ss GBLUP, haplotype-based ss GHBLUP, and four extended ss GBLUP incorporating genomic annotation models were evaluated. Based on the genomic annotation(GRCg6a) of chickens, 3 155 524 and 94 837 SNPs were mapped to genic and exonic regions, respectively. Extended ss GBLUP using genic/exonic SNPs outperformed other models with respect to predictive ability in 15 out of 23 traits, and their advantages ranged from 2.5 to 6.1% compared with original ss GBLUP. In addition, to further enhance the performance of genomic prediction with imputed WGS data, we investigated the genotyping strategies of reference population on ss GBLUP in the chicken population. Comparing two strategies of individual selection for genotyping in the reference population, the strategy of evenly selection by family(SBF) performed slightly better than random selection in most situations. Overall, we extended genomic prediction models that can comprehensively utilize WGS data and genomic annotation information in the framework of ss GBLUP, and valida

关键词： genomic selection prior information sequencing data genotype imputation haplotype

Characterization of MicroRNA^＊ Species in Peking Duck Skin

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Journal of Integrative Agriculture 2013年第9期12卷 1614-1619页

作者： zhang Li xiE xiu-juan JIA Shan-gang xiAO Mei LIN Shu-dai AN Li-long LUO Wen JIA xin-zheng NIE Qing-hua zhang xi-quan Agricultural College Guangdong Ocean University Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding South China Agricultural University Beijing Institute of Genomics Chinese Academy of Sciences

A substantial fraction of miRNA^＊ species are conserved in animals and can repress activities of target genes. This study aims to investigate the miRNA^＊ species in duck skin by using Solexa sequencing. We obtained a total of 96 miRNA^＊ species in two skin small RNA libraries and identified 56 miRNA/miRNA^＊（miR/miR^＊） pairs. Nucleotide bias of miRNA^＊ indicated that the priority was C〉A〉U〉G for the first nucleotide and U〉C〉A〉G for the last nucleotide. Comparison analyses showed that 3＇-U accounted for a higher proportion in the 56 miR/miR＊ pairs. Among the top 20 expressed miRNA^＊ species, 17 were shared by two libraries and most of the miRNA^＊ species were highly conservative, especially in the ＂seed region＂, miR-199a^＊ were expressed highly in our samples, which was also previously shown abundant in mouse hair follicle. Furthermore, four miRNA^＊ species were predicted to target their genes in signal pathways of feather follicle development and feather morphogenesis despite very low levels.

关键词： Peking duck miRNA star species (miRNA&^*) skin nucleotide bias

A bare-metal stents treatment of arterial injuries at the joint levels

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Chinese Medical Journal 2020年第21期133卷 2625-2627页

作者： Shuai Li Zhen Yang Min Li Jian-Zhong Zhu xi-quan zhang Postgraduate Department Shandong First Medical UniversityTaianShandong 271016China Department of Nuclear Medicine PLA 960th HospitalJinanShandong 250031China Department of Medical Imaging The Second Affiliated Hospital of Shandong First Medical UniversityTaianShandong 271000China Department of Interventional Vascular PLA 960th HospitalZiboShandong 255300China

Reports indicate that peripheral arterial injuries are especially challenging as they are associated with a high risk of limb *** diagnosis and intervention is required to provide limb salvage and can be *** endovascular techniques and tools continue to evolve,open repair has been not the only option in the management of traumatic vascular ***,minimally invasive percutaneous endovascular therapies offer an attractive treatment *** salvage in acute traumatic vascular lesions may be improved because of the endovascular therapies to perform diagnostic evaluation and therapeutic intervention nearly simultaneously.

关键词： arterial diagnosis treatment