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| 1 | A new insight into cattle's maternal origin in six Asian countries显示文摘The domestication of cattle fuelled the development of agricultural society in the history of human being.The evolution and genetic relationship of cattle can be elucidated by investigating the variation of mitochondrial DNA(mtDNA) D-loop sequence.In this study,we built a cattle phylogeny with a pool of 856 individual D-loop sequences,of which 264 Chinese cattle D-loop sequences were obtained in this study(141 ones were first analyzed,and 123 were first submitted) and the rest sequences of cattle from six Asian countries(Japan,Korea,Mongolia,Nepal,India and China) were retrieved from GenBank.Our results indicated that cattle from six Asian countries fell into three clades,Bos taurus(taurine),Bos indicus(zebu) and yak.Four main haplogroups T1A,T2,T3(including T3A and T3B) and T5 were found in taurine,and two haplogroups I1 and I2 in zebu.Furthermore,we found that I1 and I2 haplogroups were separated by four variable sites rather than five ones and four haplogroups or sub-haplogroups of T1A,T3A,T3B and T5 were found for the first time in these Asian cattle.These data brought us a new insight into cattle's genetic structure in these six Asian countries.The geographical distribution of haplogroups was also outlined to provide systematic information on cattle genetic resources. | Shangang Jia Yan Zhou Chuzhao Lei Ru Yao Zhiying Zhang Xingtang Fang Hong Chen | 2010 | Journal of Genetics and Genomics2010，37，3： | 8 |
| 2 | Genomic analyses reveal distinct genetic architectures and selective pressures in Chinese donkeys显示文摘Donkey(Equus asinus)is an important livestock animal in China because of its draft and medicinal value.After a long period of natural and artificial selection,the variety and phenotype of donkeys have become abundant.We clarified the genetic and demographic characteristics of Chinese domestic donkeys and the selection pressures by analyzing 78 whole genomes from 12 breeds.According to population structure,most Chinese domestic donkeys showed a dominant ancestral type.However,the Chinese donkeys still represented a significant geographical distribution trend.In the selective sweep,gene annotation,functional enrichment,and differential expression analyses between large and small donkey groups,we identified selective signals,including NCAPG and LCORL,which are related to rapid growth and large body size.Our findings elucidate the evolutionary history and formation of different donkey breeds and provide theoretical insights into the genetic mechanism underlying breed characteristics and molecular breeding programs of donkey clades. | Jiafei Shen Jie Yu Xuelei Da Mei Li Gang Wang Ningbo Chen Hong Chen Chuzhao Lei Ruihua Dang | 2021 | Journal of Genetics and Genomics2021，48，8： | 2 |
| 3 | An atlas of CNV maps in cattle, goat and sheep显示文摘Copy number variation(CNV)is the most prevalent type of genetic structural variation that has been recognized as an important source of phenotypic variation in humans,animals and plants.However,the mechanisms underlying the evolution of CNVs and their function in natural or artificial selection remain unknown.Here,we generated CNV region(CNVR)datasets which were diverged or shared among cattle,goat,and sheep,including 886 individuals from 171 diverse populations.Using 9 environmental factors for genome-wide association study(GWAS),we identified a series of candidate CNVRs,including genes relating to immunity,tick resistance,multi-drug resistance,and muscle development.The number of CNVRs shared between species is significantly higher than expected(P<0.00001),and these CNVRs may be more persist than the single nucleotide polymorphisms(SNPs)shared between species.We also identified genomic regions under long-term balancing selection and uncovered the potential diversity of the selected CNVRs close to the important functional genes.This study provides the evidence that balancing selection might be more common in mammals than previously considered,and might play an important role in the daily activities of these ruminant species. | Yongzhen Huang Yunjia Li Xihong Wang Jiantao Yu Yudong Cai Zhuqing Zheng Ran Li Shunjin Zhang Ningbo Chen Hojjat Asadollahpour Nanaei Quratulain Hanif Qiuming Chen Weiwei Fu Chao Li Xiukai Cao Guangxian Zhou Shudong Liu Sangang He Wenrong Li Yulin Chen Hong Chen Chuzhao Lei Mingjun Liu Yu Jiang | 2021 | Science China(Life Sciences)2021，64，10： | 2 |
| 4 | Effects of SNPs and alternative splicing within HGF gene on its expression patterns in Qinchuan cattle显示文摘Background: Identification of genetic variants, including SNPs(Single Nucleotide Polymorphisms), CNVs(Copy Number Variations) and alternative splicing, within functional genes has received increasing attention in animal science research. HGF(Hepatocyte Growth Factor) is a very important growth factor that works as a mitogen or a morphogen during tissue growth, development and regeneration. However, to date, the functions of genetic variants within the bovine HGF gene, particularly their effects on m RNA expression, have not been determined well.Results: The present study aimed to perform association analysis between genetic variants and m RNA expression for the bovine HGF gene in Qinchuan cattle using various strategies, including PCR-RFLP(Restriction Fragment Length Polymorphism), q PCR(Quantitative Real-time quantitative PCR), TA cloning, DNA sequencing and bioinformatics analysis. A total of five SNPs were identified and only SV1 locus significantly affected HGF m RNA expression in fetal skeletal muscle(P < 0.05). Heterozygous genotype individuals showed significantly higher HGF expression(P < 0.05), which was significantly greater in the 'CTCCAGGGTT' combined genotype than that in the'CCCCGGGGTT' combined genotype(P < 0.05). In addition, two alternative splicing variations, HGF-W and HGF-M,were identified, which resulted from alternative 3′ splice sites of exon 5, and HGF-W showed higher m RNA levels than HGF-M in all tissues.Conclusion: In summary, genetic variations within the HGF gene affected m RNA expression. These findings provide new insight into the molecular characteristics and functions of bovine HGF. | Hanfang Cai Yang Zhou Wenchao Jia Bowen Zhang Xianyong Lan Chuzhao Lei Xintang Fang Hong Chen | 2016 | Journal of Animal Science and Biotechnology2016，7，2： | 1 |
| 5 | A TaqI PCR-RFLP Detecting a Novel SNP in Exon?2 of the Bovine POU1F1 Gene显示文摘 | Chuanying Pan Xianyong Lan Hong Chen Yikun Guo Jianhong Shu Chuzhao Lei Xinzhuang Wang | 2008 | Biochemical Genetics (-)2008，，7： | 1 |
| 6 | mtDNA diversity and genetic lineages of eighteen cattle breeds from Bos taurus and Bos indicus in China显示文摘 | Xin Cai Hong Chen Chuzhao Lei | 2007 | Genetica2007，131，： | 1 |
| 7 | Genetic variation in eight Chinese cattle breeds based on the analysis of microsatellite markers显示文摘 | Weibin Sun Hong Chen Chuzhao Lei | | 0，，： | 1 |
| 8 | circSVIL regulates bovine myoblast development by inhibiting STAT1 phosphorylation显示文摘Circular RNAs(circRNAs),a novel class of non-coding RNAs with a loop structure,have recently been shown to participate in various pathophysiological processes.However,the precise role of circRNAs in myoblasts remains unclear.In this report,circSVIL was screened and identified from our previous sequencing analysis;we then performed gain-and loss-of-function experiments on bovine myoblasts by CCK8,EdU,flow cytometry,qRT-PCR,and Western blotting.The results indicate that circSVIL facilitates bovine myoblast proliferation and inhibits cell apoptosis.Using mechanism assays such as bioinformatics prediction,RNA immunoprecipitation(RIP),and cytoplasmic separation,we demonstrate that circSVIL could interact with STAT1 and inhibit STAT1 phosphorylation,thereby restraining STAT1’s nuclear translocation and affecting its downstream signal cascade.Our results may elucidate a new regulatory pathway for bovine skeletal muscle development. | Binglin Yue Haiyan Yang Jiyao Wu Jian Wang Wenxiu Ru Jie Cheng Yongzheng Huang Xianyong Lan Chuzhao Lei Hong Chen | 2022 | Science China(Life Sciences)2022，65，2： | 1 |
| 9 | Dynamic chromatin architectures provide insights into the genetics of cattle myogenesis显示文摘Background Sharply increased beef consumption is propelling the genetic improvement projects of beef cattle in China.Three-dimensional genome structure is confirmed to be an important layer of transcription regulation.Although genome-wide interaction data of several livestock species have already been produced,the genome structure states and its regulatory rules in cattle muscle are still limited.Results Here we present the first 3D genome data in Longissimus dorsi muscle of fetal and adult cattle(Bos taurus).We showed that compartments,topologically associating domains(TADs),and loop undergo re-organization and the structure dynamics were consistent with transcriptomic divergence during muscle development.Furthermore,we annotated cis-regulatory elements in cattle genome during myogenesis and demonstrated the enrichments of promoter and enhancer in selection sweeps.We further validated the regulatory function of one HMGA2 intronic enhancer near a strong sweep region on primary bovine myoblast proliferation.Conclusions Our data provide key insights of the regulatory function of high order chromatin structure and cattle myogenic biology,which will benefit the progress of genetic improvement of beef cattle. | Jie Cheng Xiukai Cao Xiaogang Wang Jian Wang Binglin Yue Wei Sun Yongzhen Huang Xianyong Lan Gang Ren Chuzhao Lei Hong Chen | 2023 | Journal of Animal Science and Biotechnology2023，14，4： | 0 |
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