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统计基因组学实验室
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实验室概述

国内外学术刊物编委

Heredity（英国遗传学会会刊、数量遗传学经典期刊）、Scientific Reports、BMC Genetics、Canadian Journal of Plant Science、作物学报和南京农业大学学报（自然科学版）

 

软件包

1、多位点随机SNP效应混合线性模型关联分析方法软件包 mrMLM v2.1 (2017-02-09更新)

     https://cran.r-project.org/web/packages/mrMLM/index.html（包括GWAS四种方法和连锁分析GCIM方法）

2、植物数量性状主基因+多基因混合遗传的分离分析方法 R 软件包 SEA.R（联系方式：soyzhang@mail.hzau.edu.cn）

3、偏分离群体连锁遗传图矫正软件包DistortedMap

     http://www.nature.com/hdy/journal/v112/n5/suppinfo/hdy2013127s1.html

4、NCII遗传交配设计QTL上位性检测windows界面软件包（可用于优异亲本和杂交组合的筛选）

     http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121034

 

代表性论著（#：同等贡献；*：通讯作者）

  1. Zhang Jin#, Feng Jian-Ying#, Ni Yuan-Li, Wen Yang-Jun, Niu Yuan, Tamba Cox Lwaka,Yue Chao, Song Qijian, Zhang Yuan-Ming*. pLARmEB: Integration of least angle regression with empirical Bayes for multi-locus genome-wide association studies. Heredity, online
  2. Wen Yang-Jun, Zhang Hanwen, Ni Yuan-Li, Huang Bo, Zhang Jin, Feng Jian-Ying, Wang Shi-Bo, Jim M. Dunwell, Zhang Yuan-Ming*, Wu Rongling*. Methodological implementation of mixed linear models in multi-locus genome-wide association studies. Briefings in Bioinformatics, online, (IF: 8.399)
  3. Tamba Cox Lwaka, Ni Yuan-Li, Zhang Yuan-Ming*. Iterative sure independence screening EM-Bayesian LASSO algorithm for multi-locus genome-wide association studies. PLoS Computational Biology 2017,13(1): e1005357
  4. Zhang Yuan-Ming*, Zhang Yinghao, Guo Mingyue. Epigenetic game theory and its application in plants. Physics of Life Reviews 2017, 20: 158-160 (IF: 8.615)
  5. Wang Shi-Bo, Wen Yang-Jun, Ren Wen-Long, Ni Yuan-Li, Zhang Jin,Feng Jian-Ying, Zhang Yuan-Ming. Mapping small-effect and linked quantitative trait loci for complex traits in backcross or DH populations via a multi-locus GWAS methodology. Scientific Reports 2016, 6: 29951
  6. Li Zhang,Shi-Bo Wang,Qi-Gang Li,Jian Song,Yu-Qi Hao,Ling Zhou, Huan-Quan Zheng,Jim M Dunwelland Yuan-Ming Zhang*. An integrated bioinformatics analysis reveals divergent evolutionary pattern of oil biosynthesis in high- and low-oil plants. PLoS ONE, 11(5): e0154882 (一个预测的油份相关转录因子已被分子生物学实验证实，见Plant Physiology)
  7. Zhou Ling#, Luo Longhai#, Zuo Jian-Fang, Yang Linfeng, Zhang Li, Guang Xuanmin, Niu Yuan, Jian Jianbo, Geng Qing-Chun, Liang Liping, Song Qijian, Jim M Dunwell, Wu Zhenzhen, Wen Jia, Liu Yu-Qin, Zhang Yuan-Ming*. 2016. Identification and validation of candidate genes associated with domesticated and improved traits in soybean. The Plant Genome 9,doi:10.3835/plantgenome2015.09.0090
  8. Wang Shi-Bo, Feng Jian-Ying, Ren Wen-Long, Huang Bo, Zhou Ling, Wen Yang-Jun, Zhang Jin,Jim M. Dunwell, Xu Shizhong*, Zhang Yuan-Ming*. 2016.Improving power and accuracy of genome-wide association studies via a multi-locus mixed linear model methodology. Scientific Reports 6: 19444
  9. Wen Jia, Zhao Xinwang, Wu Guorong, Xiang Dan, Liu Qing, Bu Su-Hong, Yi Can, Song Qijian,Jim M. Dunwell, Tu Jinxing, Zhang Tianzhen, Zhang Yuan-Ming*. 2015. Genetic dissection of heterosis using epistatic association mapping in a partial NCII mating design. Scientific Reports 5: 18376
  10. Zhou Ling#, Wang Shi-Bo#, Jian Jianbo#, Geng Qing-Chun, Wen Jia, Song Qijian, Wu Zhenzhen, Li Guang-Jun, Liu Yu-Qin, Jim M. Dunwell, Zhang Jin, Feng Jian-Ying Feng, Niu Yuan, Zhang Li, Ren Wen-Long, Zhang Yuan-Ming*. 2015. Identification of domestication-related loci associated with flowering time and seed size in soybean with the RAD-seq genotyping method. Scientific Reports 5: 9350
  11. Bu Su-Hong#, Zhao Xinwang#, Yi Can, Wen Jia, Tu Jinxing, Yuan-Ming Zhang*. Interacted QTL mapping in partial NCII design provides evidences for breeding by design. PLoS ONE 10(3):e0121034
  12. Li Meng, Liu Xiaolei, Peter Bradbury, Yu Jianming, Zhang Yuan-Ming*, Rory J Todhunter, Edward S Buckler, Zhang Zhiwu*. 2014. Enrichment of statistical power for genome-wide association studies. BMC Biology 12:73 (IF: 7.98)
  13. Xie Shang-Qian, Feng Jian-Ying, Zhang Y-M*. 2014. Linkage group correction using epistatic distorted markers in F2 and backcross populations. Heredity 112: 479-488
  14. Li Qi-Gang, Zhang Li, Li Chun, Zhang Y-M*. 2013. Comparative genomics suggests that an ancestral polyploidy event leads to enhanced root nodule symbiosis in the Papilionoideae. Molecular Biology and Evolution 30(12): 2602-2611 (IF: 14.308)(一个预测的大豆固氮基因已经被分子生物学实验证实，见PLoS Genetics)
  15. Niu Yuan, Xu Yu, Liu Xiao-Feng, Yang Sheng-Xian, Wei Shi-Ping, Xie Fang-Teng, Zhang Y-M*. 2013. Association mapping for seed size and shape traits in soybean cultivars. Molecular Breeding 31(4): 785-794
  16. Xie Shang-Qian, Jia Wen, Zhang Y-M*. 2013. Multi-QTL mapping for quantitative traits using epistatic distorted markers. PLoS ONE 8(7): e68510
  17. Feng J-Y, Zhang J, Zhang W-J, Wang S-B, Han S-F, Zhang Y-M*. 2013. An efficient hierarchical generalized linear mixed model for mapping QTL of ordinal traits in crop cultivars. PLoS ONE 8(4): e59541
  18. Li C, Li Q-G, Jim M. Dunwell, Zhang Y-M*. 2012. Divergent evolutionary pattern of starch biosynthetic pathway genes in grasses and dicots. Molecular Biology and Evolution 29(10): 3227- 3236 (2012 IF: 10.353)
  19. Li C, Li M, Jim M. Dunwell, Zhang Y-M*. 2012. Gene duplication and accelerated evolutionary rate contribute to the higher ability of protein synthesis in dicots. BMC Evolutionary Biology 12: 15
  20. Li C, Zhang Y-M*. 2011. Molecular evolution of glycinin and β-conglycinin gene families in soybean (Glycine max L. Merr.). Heredity 106: 633-641
  21. Xu Y, Li H-N, Li G, Wang X, Cheng L, Zhang Y-M*. 2011. Mapping quantitative trait loci for seed size traits in soybean (Glycine max L. Merr.). Theor Appl Genet, 122: 581-594
  22. He X-H, Qin H, Hu Z, Zhang T, Zhang Y-M*. 2011. Mapping of epistatic quantitative trait loci in four-way crosses. Theor Appl Genet 122: 33-48
  23. Lü H-Y, Liu X-F, Wei S-P, Zhang Y-M*. 2011. Epistatic association mapping in homozygous crop cultivars. PLoS ONE 6(3): e17773
  24. He X-H, Zhang Y-M*. 2011. A complete solution for dissecting pure main and epistatic effects of QTL in triple testcross design. PLoS ONE 6(9): e24575
  25. Zhang Y-M*, Gai JY. 2009. Methodologies for segregation analysis and QTL mapping in plant.The third International Conference on Quantitative Genetics. Genetica 136: 311-318
  26. He X-H, Zhang Y-M*. 2008. Mapping epistatic quantitative trait loci underlying endosperm traits using all markers on the entire genome in random hybridization design. Heredity 101: 39-47
  27. Zhu C, Wang C, Zhang Y-M*. 2007. Modeling segregation distortion for viability selection I. Reconstruction of linkage maps with distorted markers. Theor Appl Genet 114: 295-305
  28. Zhang Y-M*. 2006. Advances on methods for mapping QTL in plants. China Sci Bull 51: 2223-2231
  29. Zhang Y-M, Mao Y, Xie C, Smith H, Luo L, Xu S*. 2005. Mapping quantitative trait loci using naturally occurring genetic variance among commercial inbred lines of maize (Zea mays L.). Genetics 169: 2267-2275
  30. Wang H, Zhang Y-M, Li X, Masinde GL, Mohan S, Baylink DJ, Xu S*. 2005. Bayesian shrinkage estimation of quantitative trait loci parameters. Genetics 170: 465-480 (Comment: Nat Rev Genet 2006, 7: 229-237)
  31. Zhang Y-M, Xu S*. 2005. A penalized maximum likelihood method for estimating epistatic effects of QTL. Heredity 95: 96-104
  32. Luo L, Zhang Y-M, Xu S*. 2005. A quantitative genetics model for viability selection. Heredity 94: 347-355 (Editor Comment: Heredity 2005 94: 273-274)
  33. Xu C, Zhang Y-M, Xu S*. 2005. An EM algorithm for mapping quantitative resistance loci. Heredity 94: 119-128
  34. Zhang Y-M, Xu S*. 2005. Advanced statistical methods for detecting multiple quantitative trait loci. Recent Research Developments in Genetics and Breeding 2:1-23 (Invited Review)
  35. Zhang Y-M, Xu S*. 2004. Mapping quantitative trait loci in F2 incorporating phenotypes of F3 progeny. Genetics 166: 1981-1993
  36. Zhang Y-M*, Gai JY, Yang Y-H. 2003. The EIM algorithm in the joint segregation analysis of quantitative traits. Genetics Research 81: 157-163
  37. 李广军，李河南，程利国，章元明。大豆叶绿素含量动态表达的QTL 分析。作物学报 2010，36(2): 242-248
  38. 汪霞，徐宇，李广军，李河南，艮文全，章元明。大豆百粒重QTL 定位。作物学报 2010，36(10): 1674-1682
  39. 汪霞，徐宇，李广军，李河南，章元明。大豆株高QTL 定位及Meta 分析. 南京农业大学学报 2011, 34(3): 13-19
  40. 章元明. 植物数量遗传学的建立、发展与展望. 南京农业大学学报 2012, 35(5): 19-24
  41. 曹锡文，刘兵，章元明. 植物数量性状分离分析Windows 软件包SEA 的研制。南京农业大学学报 2013, 36(6): 1-6
  42. 闫宁，谢尚潜，耿青春，徐宇，李广军，刘兵，汪霞，李其刚，章元明。利用Bayes 分层广义线性模型剖析大豆籽粒性状的遗传基础。作物学报 2013，39(2): 258-268
  43. 牛远，谢芳腾，布素红，谢尚潜，韩世凤，耿青春，刘兵，章元明。大豆粒形性状QTL 的精细定位。作物学报 2013，39(4): 609-616
  44. 章元明主编。生物统计学（生物技术专业用，十二五规划教材）。农业出版社（待出版）
  45. 盖钧镒、章元明、王建康。植物数量性状遗传体系。科学出版社，2003
  46. 徐辰武、章元明主编。生物统计与试验设计。高等教育出版社,2015年8月出版
  47. Zhang Y-M*. 2012. F2 designs for QTL analysis. In: Scott A. Rifkin (ed.), Quantitative Trait Loci (QTL): Methods and Protocols. Methods in Molecular Biology 871: 17-29. DOI 10.1007/978- 1-61779-785-9_2.Springer Science + Business Media, LLC
  48. 谢庄、章元明主编。水产试验统计学。中国农业科技出版社，1998
  49. 盖钧镒主编，章元明统稿。试验统计方法。农业出版社，2000