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| 1 | Formation age and tectonic environment of the Gantaohe Group,North China Craton:Geology,geochemistry,SHRIMP zircon geochronology and Hf-Nd isotopic systematics显示文摘The Gantaohe Group is an important early Precambrian unit in the Trans-North China Orogen,North China Craton,and is mainly composed of greenschist-facies metabasalt,meta-sandstone and dolomitic marble.We report whole-rock geochemical compositions and SHRIMP zircon ages as well as LA-ICP-MS Hf-in-zircon isotopeic analyses for metabasalts from the Gantaohe Group.SHRIMP dating yielded a weighted mean 207Pb/206Pb age of 2087±16 Ma(MSWD=1.3) for magmatic zircons,but there are also abundant ca.2.5 Ga inherited zircon xenocrysts.The magmatic zircons shows a large Hf(t) variation in Hf(t) from 7.17 to +0.45,suggesting an isotopically highly heterogeneous source for the metabasalt.Chemically all samples show no distinct Zr or Hf anomalies,and some samples show no Nd or Ta anomalies in a primitive mantle-normalized trace element variation diagram,and their whole-rock Nd(t) values range from 4.0 to 0.8.We suggest that the basalt is formed by partial melting of a depleted mantle source,followed by significant crustal contamination.Field observations,the presence of abundant inherited zircon,as well as isotope and trace elements geochemistry support formation of the Gantaohe Group on top of a continental basement.These data and the regional geology lead us to conclude that the Trans-North China Orogen constituted an intracontinental rift during the Paleoproterozoic that was connected to the Eastern Block since the end of the Archean. | XIE HangQiang LIU DunYi YIN XiaoYan ZHOU HongYing YANG ChongHui DU LiLin WAN YuSheng | 2012 | Chinese Science Bulletin2012，57，36： | 16 |
| 2 | rMVP: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool for Genome-wide Association Study显示文摘Along with the develoipment of high-throughput sequencing technologies,both sample size and SNP number are increasing rapidly in genome-wide association studies(GWAS),and the associated computation is more challenging than ever.Here,we present a memory-efficient,visualization-enhanced,and parallel-accelerated R package called“r MVP”to address the need for improved GWAS computation.r MVP can 1)effectively process large GWAS data,2)rapidly evaluate population structure,3)efficiently estimate variance components by Efficient Mixed-Model Association e Xpedited(EMMAX),Factored Spectrally Transformed Linear Mixed Models(Fa ST-LMM),and Haseman-Elston(HE)regression algorithms,4)implement parallel-accelerated association tests of markers using general linear model(GLM),mixed linear model(MLM),and fixed and random model circulating probability unification(Farm CPU)methods,5)compute fast with a globally efficient design in the GWAS processes,and 6)generate various visualizations of GWASrelated information.Accelerated by block matrix multiplication strategy and multiple threads,the association test methods embedded in r MVP are significantly faster than PLINK,GEMMA,and Farm CPU_pkg.r MVP is freely available at https://github.com/xiaolei-lab/r MVP. | Lilin Yin Haohao Zhang Zhenshuang Tang Jingya Xu Dong Yin Zhiwu Zhang Xiaohui Yuan Mengjin Zhu Shuhong Zhao Xinyun Li Xiaolei Liu | 2021 | Genomics, Proteomics & Bioinformatics2021，19，4： | 12 |
| 3 | Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features显示文摘Background:A large number of pig breeds are distributed around the world,their features and characteristics vary among breeds,and they are valuable resources.Understanding the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved pig breeds.Results:In this study,we performed GWAS using a standard mixed linear model with three types of genome variants(SNP,InDel,and CNV)that were identified from public,whole-genome,sequencing data sets.We used 469 pigs of 57 breeds,and we identified and analyzed approximately 19 million SNPs,1.8 million InDels,and 18,016 CNVs.We defined six biological phenotypes by the characteristics of breed features to identify the associated genome variants and candidate genes,which included coat color,ear shape,gradient zone,body weight,body length,and body height.A total of 37 candidate genes was identified,which included 27 that were reported previously(e.g.,PLAG1 for body weight),but the other 10 were newly detected candidate genes(e.g.,ADAMTS9 for coat color).Conclusion:Our study indicated that using GWAS across a modest number of breeds with high density genome variants provided efficient mapping of complex traits. | Jingya Xu Yuhua Fu Yan Hu Lilin Yin Zhenshuang Tang Dong Yin Mengjin Zhu Mei Yu Xinyun Li Yang Zhou Shuhong Zhao Xiaolei Liu | 2021 | Journal of Animal Science and Biotechnology2021，12，2： | 1 |
| 4 | Transcriptomic basis of neutrophil ratio variation induced by poly I:C stimulation in porcine peripheral blood显示文摘Neutrophils are vital components of defense mechanisms against invading pathogens and are closely linked with the individual antiviral capacity of pigs and other mammals. Neutrophilia is a well-known clinical characteristic of viral and bacterial infections. Using Affymetrix porcine genome microarrays, we investigated the gene expression profiles associated with neutrophil variation in porcine peripheral blood before and after polyriboinosinic-polyribocytidylic acid stimulation. Transcriptomic analysis showed 796 differentially expressed genes(DEGs) in extreme response(ER) pigs and 192 DEGs in moderate response(MR) pigs. Most DEGs were related to immune responses, included MXD1, CXCR4,CREG1, My D88, CD14, TLR2, TLR4, IRF3 and IRF7.Gene ontology analysis indicated that the DEGs of both ER and MR pigs were involved in common biological processes, such as cell proliferation, growth regulation,immune response, inflammatory response and cell activation. The ER and MR groups also showed differences in DEGs involved in biological processes. DEGs involved in cell division and cell cycle were specifically found in the ER pigs, whereas DEGs involved in cell migration were specifically found in the MR pigs. The study provides a basic understanding of the molecular basis for the antiviral capacity of pigs and other mammals. | Haiyan WANG Qiaoxia ZHANG Lilin YIN Xiangdong LIU Shuhong ZHAO Mengjin ZHU Changchun LI | 2017 | Frontiers of Agricultural Science and Engineering2017，4，3： | 0 |
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