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成果及论文

近5年发表论文

- 数量遗传学

1. Li. W., Z. Wang, S. Luo, J. Wu and L. Zhou et al., 2022 Genome-Wide Association Analysis and Genetic Parameters for Feed Efficiency and Related Traits in Yorkshire and Duroc Pigs. Animals 12: 1902.

2. Xue Y, Liu S, Li W, Mao R, Zhuo Y, Xing W, Liu J, Wang C, Zhou L, Lei M, Liu J. (2022). Genome-Wide Association Study Reveals Additive and Non-Additive Effects on Growth Traits in Duroc Pigs. Genes 13 (8):1454.（共同通讯）, IF=4.474

3. Zhang Y, Zhuo Y, Ning C, Zhou L, Liu JF. (2022). Estimate of inbreeding depression on growth and reproductive traits in a Large White pig population. G3 ():1. （共同通讯）, IF=3.545

4. Yang W, Liu Z, Zhao Q, Du H, Yu J, Wang H, Liu X, Liu H, Jing X, Yang H, Shi G, Zhou L, Liu J. Population Genetic Structure and Selection Signature Analysis of Beijing Black Pig. Front Genet. 2022 Mar 24;13:860669. doi: 10.3389/fgene.2022.860669.

5. Hu Z, Li Y, Du H, Ren J, Zheng X, Wei K, Jian-Feng Liu. Transcriptome analysis reveals modulation of the STAT family in PEDV-infected IPEC-J2 cells. BMC Genomics. 2020;21(1):891. （通讯）

6. Yang W, Wu J, Yu J, Zheng X, Kang H, Wang Z, Zhang S, Zhou L, Liu J. A genome-wide association study reveals additive and dominance effects on growth and fatness traits in large white pigs. Anim Genet. 2021 Oct;52(5):749-753. doi: 10.1111/age.13131. Epub 2021 Aug 17. PMID: 34403536. 3.058

7. Ye Wang, Chenguang Diao, Huimin Kang, Wenjie Hao, Raphael Mrode, Junhai Chen, Jianfeng Liu1*, Lei Zhou1* A random regression model based on a single-step method for improving the genomic prediction accuracy of residual feed intake in pigs. Frontiers in Genetics

8. Zhou, L. , Wang, Y. , Yu, J. , Yang, H. , & Liu, J. . (2019). Improving genomic prediction for two yorkshire populations with a limited size using the single‐step method. Animal Genetics, 50(4). （通讯）

9. Kang, H, Ning, C, Zhou, L, Zhang, S, Lin, Q, and Liu J.F. (2018). Short communication: Single-step genomic evaluation of milk production traits using multiple-trait random regression model in Chinese Holsteins. J. Dairy Sci. 101(12), 11143-11149. （通讯）

10.Kang, H, Ning, C, Zhou, L, Zhang, S, Yang, N, and Liu J.F. (2018). PIBLUP: High-Performance Software for Large-Scale Genetic Evaluation of Animals and Plants. Front. Genet. 9, 226. （通讯）

11.Zhao P., Yu Y, Feng W, Du H, Yu J, Kang H., Zheng X., Wang Z., L George, W Catherine, Liu J.F.(2018). Evidence of evolutionary history and selective sweep in the genome of meishan pig reveals its genetic and phenotypic characterization.GigaScience 7, 1–12.（通讯）

12.Zhou L, Raphael Mrode, Zhang S., Zhang Q., Li B., Liu J.F. (2017). Factors affecting GEBV accuracy with single-step Bayesian models. Heredity 120, 100-109. （通讯）

13.Kang H., Lei Z. & Liu J.F. (2017). Statistical considerations for genomic selection. Front. Agr. Sci. Eng. 4, 268-278. （通讯）

14.余健,杨文静,王晔,周磊,王楚端,刘剑锋.多个场联合遗传评估提高基因组选择准确性[J/OL].中国畜牧杂志:1-8[2021-09-29].https://doi.org/10.19556/j.0258-7033.20210616-10.

15.周磊,王晔,毛瑞涵,李佳芮,刘剑锋.国外生猪育种体系简析及对我国生猪育种的几点思考[J/OL].中国畜牧杂志:1-11[2020 1215]

16.王俊健，王晓凤，李伟宁，余健，胡蒸蒸，陈少康，李爽，郑美丽，郭峰，郑瑞峰，刘剑锋. 北京地区生长育肥猪采食、排泄及生长性状间的典型相关分析[J]，中国畜牧杂志，2019.

17.周磊,杨华威,赵祖凯,杨红杰,刘剑锋.基因组选择在我国种猪育种中应用的探讨[J].中国畜牧杂志,2018,54(03):4-8.

18.杨文静,王晔,闫青霞,麻柱,刘剑锋,张胜利.应用随机回归模型对北京地区荷斯坦牛产奶性状的遗传分析[J].中国畜牧杂志,2021,57(06):141-145.DOI:10.19556/j.0258-7033.20200706-07.

- 生物信息学

1.  Wang D, Yang L, Ning C, Liu JF, Zhao X. Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs. BMC Genomics. 2021 Oct 12;22(1):736. doi: 10.1186/s12864-021-08030-1. PMID: 34641784; PMCID: PMC8507312.

2.  Du H, Zheng X, Zhao Q, Hu Z, Wang H, Zhou L, Liu JF. Analysis of Structural Variants Reveal Novel Selective Regions in the Genome of Meishan Pigs by Whole Genome Sequencing. Front Genet. 2021 Feb 4;12:550676. doi: 10.3389/fgene.2021.550676.

3.  Heng Du,Chenguang Diao,Pengju Zhao, Lei Zhou, Jian-Feng Liu. Integrated hybrid de novo assembly technologies to obtain high-quality pig genome using short and long reads, Briefings in Bioinformatics, 2021 Sep 2;22(5): bbaa399. doi: 10.1093/bib/bbaa399

4.  Wen Feng, Pengju Zhao,Xianrui Zheng,Zhengzheng Hu and Jianfeng Liu, Profiling Novel Alternative Splicing within Multiple Tissues Provides Useful Insights into Porcine Genome Annotation, Genes 2020, 11(12), 1405; https://doi.org/10.3390/genes11121405 （通讯）

5.  Yu J, Zhao P, Zheng X, Zhou L, Wang C, Liu JF*. Genome-Wide Detection of Selection Signatures in Duroc Revealed Candidate Genes Relating to Growth and Meat Quality. G3 (GENES, GENOMES, GENETICS). 2020 Oct 5;10(10):3765-3773. doi: 10.1534/g3.120.401628. （通讯）

6.  Zhao P., Zheng X., Yu Y, Hou Z., Diao C., Wang H., Kang H., Ning C., Li J., Feng W., Wang W., Liu G., Li B., Smith J., Chamba Y., and Liu J.F. (2018) Mining Unknown Porcine Protein Isoforms by Tissue-Based Map of Proteome Enhances the Pig Genome Annotation. Genomics Proteomics Bioinformatics. doi: 10.1101/391466（通讯）

7.  Ning C., Wang D., Zhou L., Wei J., Liu Y., Kang H., Zhang S., Zhou X., Xu S., Liu J.F. (2019). Efficient Multivariate Analysis Algorithms for Longitudinal Genome-wide Association Studies. Bioinformatics,btz304. （通讯）

8.  Chen M., Su G., Fu J., Wang A, Liu J.F, Lund, M, Guldbrandtsen B. (2019). Introgression of Chinese haplotypes contributed to the improvement of Danish Duroc pigs. Evol. Appl. 12, 292-300. (共同通讯）

9.  Chen M, Wang J, Wang Y, Wu Y, Fu J and Liu J.F. (2018). Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle. BMC Genet. 19, 31.（共同通讯）

10. Ning C, Wang D, Zheng X., Zhang Q, Zhang S., Raphael Mrode2 and Liu J.F. (2018). Eigen decomposition expediteslongitudinal genome‑wide association studies or milk production traits in Chinese Holstein.Genet. Sel. Evol. 50, 12. （通讯）

11. Ning C., Wang D, Kang H., Mrode R., Zhou L., Xu SZ. and Liu J.F., (2018). A rapid epistatic mixed-model association analysis by linear retransformations of genomic estimated values. Bioinformatics 34, 1817-1825.（通讯）

12. Wang H., Wang, J., Ning, C, Zheng X., Fu J., Wang A., Zhang, Q & Liu J.F. (2017). Genome-wide DNA methylation and transcriptome analyses reveal genes involved in immune responses of pig peripheral blood mononuclear cells to poly I:C. Sci. Rep. 7, 9709.（通讯）

13. Ning C., Kang H., Zhou L., Wang D , Wang H., Wang A., Fu J., Zhang S.L &Liu J.F. (2017). Performance Gains in Genome-Wide Association Studies for Longitudinal Traits via Modeling Time-varied effects. Sci. Rep. 7, 590.（通讯）

14. Feng X., Jiang J., Padhi, A, Ning, C , Fu J., Wang A., Mrode, R & Liu J.F(2017) Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals. Bmc Genet. 18, 293.（通讯）

15. Tan Z., Yang T., Wang Y., Xing K., Zhang F., Zhao X., Ao H., Chen S., Liu J. F. & Wang C.D. (2017). Metagenomic Analysis of Cecal Microbiome Identified Microbiota and Functional Capacities Associated with Feed Efficiency in Landrace Finishing Pigs. Front. Microbiol. 8, 1546.（通讯）

16. Wang D, Ning C, Liu JF, Zhang Q, Jiang L. Short communication: Replication of genome-wide association studies for milk production traits in Chinese Holstein by an efficient rotated linear mixed model. J Dairy Sci. 2019 Mar;102(3):2378-2383. doi: 10.3168/jds.2018-15298. Epub 2019 Jan 11. PMID: 30639022.

17. 黄千千,赵琦琪,张美琳,卢诗雨,于睿,杜梓桓,刘振,罗生浩,王红卫,石国华,刘先策,刘海,周磊,刘剑锋.北京黑猪氟烷敏感基因的检测与分析[J/OL].中国畜牧杂志:1-8[2021-11-11].

18. 李伟宁,刘刚,周荣,唐中林,刘剑锋,孙飞舟.MGISEQ-2000、HiSeq 2000与NovaSeq 6000平台全基因组重测序数据的比较分析[J/OL].中国畜牧杂志:1-13[2021-11-11].https://doi.org/10.19556/j.0258-7033.20210414-01.

19. 张蕾,杨华威,周磊,赵祖凯,王晔,傅金銮,刘剑锋.猪主要遗传缺陷候选基因的研究进展[J].猪业科学,2018,35(08):116-119.

20. 徐新明,哈妮克孜·吐拉甫,刘剑锋,石刚,付雪峰,于丽娟,拉扎特·艾尼瓦尔,狄江.中国美利奴羊(新疆型)羊毛长度与产毛量的全基因组关联分析[J].西北农林科技大学学报(自然科学版),2022,50(08):1-7.DOI:10.13207/j.cnki.jnwafu.2022.08.001.

21. 李亚星,成功,赵云博,王申元,吴凯峰,成立新,刘剑锋,周欢敏,李光鹏,昝林森,佟彬.秦川牛ANGPTL3基因g.-38T>C和g.509A>G的遗传多样性及其与生长和胴体性状的关联性分析[J].农业生物技术学报,2020,28(09):1543-1553.

22. 范一萍,王晓梅,贾启涛,李成勃,梁小娟,曹春伟,周磊,陶聪,赵建国,刘剑锋,王彦芳.猪PRLR和FSHβ基因多态性检测及其与繁殖性状的关联分析[J].中国畜牧兽医,2019,46(03):774-781.DOI:10.16431/j.cnki.1671-7236.2019.03.016.

23. 郭晓红,李萌,高鹏飞,曹果清,成志敏,张宁芳,乐宝玉,刘剑锋,刘小军,李步高.猪MYNN基因可变剪接体的克隆及表达特性研究[J].畜牧兽医学报,2018,49(03):477-487.

- 分子遗传学

1. Jin Y, Yuan X, Zhao W, Li H, Zhao G, Liu J. The SLC27A1 Gene and Its Enriched PPAR Pathway Are Involved in the Regulation of Flavor Compound Hexanal Content in Chinese Native Chickens. Genes (Basel). 2022 Jan 22;13(2):192. doi: 10.3390/genes13020192.

2. Xianrui Zheng† , Pengju Zhao† , Kaijie Yang† , Chao Ning , Haifei Wang , Lei Zhou and Jianfeng Liu* . CNV analysis of Meishan pig by nextgeneration sequencing and effects of AHR gene CNV on pig reproductive traits. (2020) 11:42. （通讯）

3. Zheng X, Jiang L, Ning C, Hu Z, Zhou L, Yu Y, Zhang S. and Liu J.F. (2019) A novel mutation in the promoter region of RPL8 regulates milk fat traits in dairy cattle by binding transcription factor Pax6. Biochim Biophys Acta Mol Cell Biol Lipids 1864, 158528. （通讯）

4. Wang D., Xiang H., Ning C., Liu C., Liu J.F., Zhao X.B. (2019). Mitochondrial DNA enrichment reduced NUMT contamination in porcine NGS analyses. Briefings Bioinf., bbz060.（共同通讯）

5. Feng W, Zhou L, Wang H, Hu Z, Wang X, Fu J,Wang A, Liu J.F. (2018). Functional analysis of DNA methylation of the PACSIN1 promoter in pig peripheral blood mononuclear cells. J. Cell Biochem. 120, 10118-10127.（通讯）

6. Zheng X.,Ning C., Zhao P.,Feng W., Jin Y., Zhou L.,Yu Y.* and Liu J.F. (2018). Integrated analysis of lncRNAs and mRNA expression profiles reveals the potential role of lncRNAs in different bovine lactation stage. J. Dairy Sci. 101(12), 11061-11073. （通讯）

7. Zhao P., Zheng X., Feng W, Wang H., Kang H., Ning C, Du H, Yu Y, Li B., Zhao Y., Liu J.F. (2017). Profiling Long Non-coding RNA of Multi-tissue Transcriptome enhances Porcine Non-coding Genome Annotation. Epigenomics 10, 301-320.（通讯）

8. Zheng X., Ning C., Dong Y., Zhao P., Li J., Fan Z., Li J., Yu Y., Mrode R. & Liu J.F. (2017). Quantitative proteome analysis of bovine mammary gland reveals protein dynamic changes involved in peak and late lactation stages. Biochem. Biophys. Res. Commun. 494, 292-297.（通讯）

9. Guo XH, Zhang Q, Li M, Gao PF, Cao GQ, Cheng ZM, Zhang NF, Yu Le B, Liu JF, Liu XJ, Li BG. Novel alternatively spliced isoforms of MEF2A and their mRNA expression patterns in pigs. J Genet. 2018 Sep;97(4):977-985. PMID: 30262710.

10.Wang D, Ning C, Liu JF, Zhao X. Relationship between mitochondrial DNA haplogroup and litter size in the pig. Reprod Fertil Dev. 2020 Feb;32(3):267-273. doi: 10.1071/RD19035. PMID: 31578166.

11.Pengju Zhao, Heng Du, Lin Jiang, Xianrui Zheng, Wen Feng, Chenguang Diao, Lei Zhou, George E Liu, Hao Zhang, Yangzom Chamba, Qin Zhang, Bugao Li, Jian-Feng Liu, (2020) PRE-1 Revealed Previous Unknown Introgression Events in Eurasian Boars during the Middle Pleistocene, Genome Biology and Evolution, evaa142 （通讯）

12.Pengju Zhao, Heng Du, Lin Jiang, Xianrui Zheng, Wen Feng, Chenguang Diao, Lei Zhou, George E Liu, Hao Zhang, Yangzom Chamba, Qin Zhang, Bugao Li, Jian-Feng Liu, (2020) PRE-1 Revealed Previous Unknown Introgression Events in Eurasian Boars during the Middle Pleistocene, Genome Biology and Evolution, evaa142 （通讯）


软件

  1. 基于高通量测序数据的可变基因组组装软件V1.0 （2022SR0120585）
  2. 基于混合组装的自动化基因组组装软件V1.0 （2021SRBJ1148)
  3. 种猪群体测定和种用价值评定虚拟仿真实验系统V1.0 （2021SRBJ1012）
  4. 有效群体大小估计软件V1.0 （2020SRBJ0566）
  5. 猪育种目标性状经济加权值计算软件V1.0 （2018SRBJ0418）
  6. 基因组关系矩阵构建软件V1.0 （2017SRBJ0971）
  7. 基于个体基因组估计值的全基因组上位效应检验软件V1.0 （2017SRBJ0975）
  8. 基于预条件共轭梯度法间接求解混合模型方程组软件V1.0 （2017SRBJO784）
  9. 基于贝叶斯前相关模型的多性状基因组选择计算软件V1.0 （2014SRBJ0480）
  10. 贝叶斯A+基因组选择计算软件V1.0 （2013SRBJ0546）
  11. 多性状贝叶斯Cπ基因组选择计算软件V1.0 （2014SRBJ0006）
  12. 贝叶斯B+基因组选择计算软件V1.0 （2013SRBJ0547）
  13. 多性状贝叶斯A基因组选择计算软件V1.0 (2013SRBJ0824)
  14. 贝叶斯Lasso基因组选择计算软件V1.0 （2013SRBJ0778）
  15. 贝叶斯Cπ+基因组选择计算软件V1.0 (2013SRBJ0777)


发明专利

  1. 猪全基因组50K SNP芯片及应用, 发明专利，申请号: KHP179810156.8；刘剑锋，冯文，杜恒，赵鹏举

  2. 一种与猪乳头内陷相关的SNP标记及其应用，发明专利，授权公告号:CN 110438236 B，刘剑锋，张蕾，郑先瑞，周磊，傅金銮 (专利号： ZL201910486051.2) 专利申请日：2019年6月5日，授权公告日：2020年12月4日

  3. 一种估计基因组育种值的方法及装置，发明专利，授权号：CN107563147B；刘剑锋，康慧敏，宁超，张胜利，2019-12-20，ZL201710651753.2

  4. 一种母猪综合繁殖力的评价方法及其在猪育种中的应用，发明专利，申请号：201811223761.8，授权公告号：CN109479812B，赵祖凯，杨华威，刘剑锋，周磊，杜房房，曾新斌，方铎，王晔

  5. 一种与猪产仔数相关的CNV标记及其应用，发明专利，授权公告号:CN 104846080 B；刘剑锋，杨凯捷，郑先瑞，王海飞  （专利号：ZL201510191179.8）

  6. 一种与中国荷斯坦奶牛产奶性状及体细胞评分相关的SNP标记及其应用，授权公开号：CN103045727B，发明专利，专利号码：201210480570.6；刘剑锋，王海飞，赵红梅，张勤，张胜利


著作

  1. 《动物重要经济性状基因的分离与应用》 2012.2.1 中国农业大学出版社，张勤主编，张沅 刘剑锋 副主编 （12.6万字/59万字）。

  2. 《数量遗传学》，主编，中国农业大学本科重点教材，2012 年，农大出版社。

  3. Xiong DH, Liu JF, Guo YF, Guo Y, Yang TL, et al. (2008) Quantitative trait loci mapping. Methods Mol Biol 455: 203-235, Human Press.

  4. 《现代养猪实用百科全书》，中国农业出版社，2004，苏振环主编，刘剑锋副主编。