2018 1 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, 1 Feb 2017, DOI: 10.1093/bib/bbw145 2 Wen-Long Ren#, Yang-Jun Wen#, Jim M. Dunwell, Yuan-Ming Zhang*. pKWmEB: integration of Kruskal-Wallis test with empirical Bayes under polygenic background control for multi-locus genome-wide association study. Heredity, online 2017 3 Li Wen-Ting#, Zhang Meng-Meng#, Li Qi-Gang#, Tang Hui, Zhang Li-Fan, Wang Ke-Jun, Zhu Mu-Zhen, Lu Yun-Feng, Bao Hai-Gang, Zhang Yuan-Ming*, Li Qiu-Yan*, Wu Ke-Liang*, Wu Chang-Xin. Whole-genome resequencing reveals candidate mutations for pig prolificacy. Proceedings of the Royal Society Biological Sciences 2017, 284(1869): 20172437. DOI: 10.1098/rspb.2017.2437. 4 Zhang Jin#, Feng Jian-Ying Feng#, Ni Yuan-Li, Wen Yang-Jun Wen, 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 2017, 118(6): 517-524 (Featured Article) 5 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 6 Zhang Yuan-Ming*, Zhang Yinghao, Guo Mingyue. Epigenetic game theory and its application in plants. Physics of Life Reviews 2017, 20: 158-160 2016
7 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 8 Yan-Da Zeng, Jun-Ling Sun, Su-Hong Bu, Kang-Sheng Deng, Tao Tao, Yuan-Ming Zhang, Tian-Zhen Zhang, Xiong-Ming Du* & Bao-Liang Zhou*. EcoTILLING revealed SNPs in GhSus genes that are associated with fiber- and seed-related traits in upland cotton. Scientific Reports 2016, 6: 29250
9 Li Zhang, Shi-Bo Wang, Qi-Gang Li, Jian Song, Yu-Qi Hao, Ling Zhou, Huan-Quan Zheng, Jim M Dunwell, Yuan-Ming Zhang*. 2016. An integrated bioinformatics analysis reveals divergent evolutionary pattern of oil biosynthesis in high- and low-oil plants. PLoS ONE, 11(5): e0154882 10 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. 11 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 2015 12 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*. Genetic dissection of heterosis using epistatic association mapping in a partial NCII mating design. Scientific Reports 2015, 5: 18376 13 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 14 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. 15 Li Lanzhi, He Xiaohong, Zhang Hongyan, Wang Zhiming, Sun Congwei, Mou Tongmin, Li Xinqi, Zhang Yuanming, Hu Zhongli*. 20015. Genomewide mapping reveals a combination of different genetic effects causing the genetic basis of heterosis in two elite rice hybrids. Journal of Genetics 94(2): 261-270
2014 16 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 17 Xie S-Q, Feng J-Y, Zhang Y-M*. 2014. Linkage group correction using epistatic distorted markers in F2 and backcross populations. Heredity 112: 479-488 18 Zhang W-J, Niu Y, Bu S-H, Li M, Feng J-Y, Zhang J, Yang S-X, Medrine Mmyi Odinga, Wei S-P, Liu X-F, Zhang Y-M*. 2014. Epistatic association mapping for alkaline and salinity tolerance traits in the soybean germination stage. PLoS ONE 9(1): e84750 19 Xie F-T, Niu Y, Zhang J, Bu S-H, Zhang H-Z, Geng Q-C, Feng J-Y, Zhang Y-M*. 2014. Fine mapping of quantitative trait loci for seed size traits in soybean. Molecular Breeding 34(4): 2165-2179
2013 20 Li Qi-Gang, Zhang Li, Li Chun, Jim M. Dunwell, 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 (2013 IF: 14.308) 21 Li Q-G, Zhang Y-M*. 2013. The origin and functional transition of P34. Heredity 110(3): 259-266 22 Wen Jia, Can Van Toan, Zhang Y-M*. 2013. Multi-QTL mapping for quantitative traits using distorted markers. Molecular Breeding 31(2): 395-404 23 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 24 Xie Shang-Qian, Jia Wen, Zhang Y-M*. 2013. Multi-QTL mapping for quantitative traits using epistatic distorted markers. PLoS ONE 8(7): e68510 25 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 26 Zhang T*, Qian N, Zhu X, Chen H, Wang S, Mei H, Zhang Y. 2013. Variations and transmission of QTL alleles for yield and fiber qualities in upland cotton cultivars developed in China. PLoS ONE 8(2): e57220
2012 27 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) 28 Zhang J, Yue C, Zhang Y-M*. 2012. Bias correction for estimated QTL effects using the penalized maximum likelihood method. Heredity 108: 396-402 29 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 30 He Xiao-Hong, Hu Zhongli, Zhang Y-M*. 2012. Genome-wide mapping of QTL associated with heterosis in the RIL-based NCIII design. Chin Sci Bull 57(21): 2655-2665 31 Liu R, Wang B, Guo W, Qin Y, Wang L, Zhang Y, Zhang T*. 2012. Quantitative trait loci mapping for yield and its components by using two immortalized populations of a heterotic hybrid in Gossypium hirsutum L. Molecular Breeding 29(2): 297-311 32 Jiangbo Zhou, Yuan-Ming Zhang, Haiyan Lü, Aiqing You, Lili Zhu, Guangcun He*. 2012. Transmission of important chromosomal regions under selection revealed in rice pedigree breeding programs. Molecular Breeding 30(2): 717-729 33 Chen X, Guo W, Liu B, Zhang Y, Song X, Zhang L, Zhang T*. 2012. Molecular mechanisms of fiber differential development between G. barbadense and G. hirsutum revealed by genetical genomics. PLoS ONE 7(1): e30056 34 Guo H-L, Li Y, Xuan J-P, Liu J-X*, Zhang Y-M, Zheng Yi-Qi. 2012. Association of molecular markers with cold tolerance and green period in Zoysiagrass (Zoysia Willd.). Breeding Science 62: 320-327 2011 35 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 36 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 37 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 38 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 39 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 40 Kuang F-L, Wang X, Zhou L, Zhang Y-M*. 2011. Linkage graph analysis: A linkage-group-based QTL synthesis analysis approach. China Sci Bull 56: 1092-1099 41 Zhu X, Ai N, Zhang Y, Guo W, Zhang T-Z*. 2011. Relationships between differential gene expression and heterosis in cotton hybrids developed from the foundation parent CRI-12 and its pedigree-derived lines. Plant Science 180: 221-227 2010 42 Dou BD*, Hou BW, Wang F, Yang JB, Ni ZF, Sun QX, Zhang Y-M*. 2010. Further mapping of quantitative trait loci for female sterility in wheat. Genetics Research 92(1): 63-70 43 Liu G, Li M, Wen J, Du Y, Zhang Y-M*. 2010. Functional mapping of quantitative trait loci associated with rice tillering. Molecular Genetics and Genomics 284: 263-271 44 Li G-J, LI H-N, Cheng L-G, Zhang Y-M*. 2010. QTL Analysis for Dynamic Expression of Chlorophyll Content in Soybean (Glycine max L. Merr.). Acta Agronomica Sinica 36(2): 242-248 2009 45 Lü H-Y, Li M, Yao L-L, Li G-J, Lin F, Zhang Y-M*. 2009. Multi-loci in silico mapping in inbred lines. Heredity 103: 346-354 46 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 2008 47 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 48 Zhang Y-M*, Lü H-Y, Yao L-L. 2008. Multiple quantitative trait loci Haseman-Elston regression using all markers on the entire genome. Theor Appl Genet 117: 683-690 49 Zhu C, Zhang Y-M*, Guo Z. 2008. Mapping quantitative trait loci for binary trait in the F2:3 design. Journal of Genetics 87(3): 201-207 50 Qin H, Guo W, Zhang Y-M, Zhang TZ*. 2008. QTL mapping of yield and fiber traits based on a four-way cross population in Gossypium hirsutum L. Theor Appl Genet 117: 883-894 2007 51 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 52 Zhu C, Zhang Y-M*. 2007. An EM algorithm for mapping segregation distortion loci. BMC Genetics 8: 82 53 Zhu C, Huang J, Zhang Y-M*. 2007. Mapping binary trait loci in the F2:3 design. Journal of Heredity 98: 337-344 54 Geng J, Zhu C, Zhang X, Cheng Y, Zhang Y-M*, Hou X*. 2007. A genetic linkage map of nonheading chinese cabbage. Journal of American Society for Horticultural Science 132: 816-823 55 Zhu C, Wang F, Wang J，Li G，Zhang H*, Zhang Y-M*. 2007. Reconstruction of linkage maps in the segregation populations of backcross, double haploid and recombinant inbred line. Chin Sci Bull 52: 1648-1653 56 Wang X, Hu Z, Wang W, Li Y, Zhang Y-M, Xu C*. 2007. A mixture model approach to the mapping of QTL controlling endosperm traits with bulked samples Status. Genetica 132: 59-70 2006 57 Zhang Y-M*. 2006. Advances on methods for mapping QTL in plants. China Sci Bull 51: 2223-2231 58 Zhang Y-M*. 2006. Shrinkage estimation method for mapping multiple quantitative trait loci. Acta Genetica Sinica 33(10): 861-869 59 Xue Y, Wan J*, Jiang L, Wang C, Liu L, Zhang Y-M, Zhai H. 2006. Identification of quantitative trait loci associated with aluminum tolerance in rice (Oryza Sativa L.). Euphytica 150: 37-45 2005 60 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 61 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) 62 Zhang Y-M, Xu S*. 2005. A penalized maximum likelihood method for estimating epistatic effects of QTL. Heredity 95: 96-104 63 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) (Featured Article) 64 Xu C, Zhang Y-M, Xu S*. 2005. An EM algorithm for mapping quantitative resistance loci. Heredity 94: 119-128 65 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) 66 Hansen C, Yi N, Zhang Y-M, Xu S, Gavora J, Cheng HH*. 2005. Identification of QTL for production traits in chickens. Animal Biotechnology 16: 67-79 2004 67 Zhang Y-M, Xu S*. 2004. Mapping quantitative trait loci in F2 incorporating phenotypes of F3 progeny. Genetics 166: 1981-1993 2003 68 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 69 Tao A, Zeng H, Zhang Y-M，Xie G-S, Qin F-L, Zheng Y-L, Zhang D-P*. 2003. Genetic analysis of the low critical sterility temperature point in photoperiod-thermo sensitive genic male sterile rice. Acta Genetica Sinica 30(1): 40-48
2009年以来的主要中文学术论文（*：通讯作者；#：同等贡献）
1 程利国, 李广军, 刘玉芹, 李河南，章元明. 大豆对大豆花叶病毒Sa 株系抗扩展特性的遗传分析. 南京农业大学学报, 2009, 32(4): 13-17 2 李河南，汪霞，李广军，程利国，何小红，张国政，章元明。大豆粒形的主基因+多基因混合遗传。大豆科学 2009，28(1): 16-20 3 李广军，李河南，程利国，章元明。大豆对豆卷叶螟抗性的QTL定位。中国油料作物学报 2009，31(3): 365-3693 4 匡峰磊, 汪霞, 周玲, 章元明。关联图分析: 一种基于连锁图的QTL 综合分析方法。科学通报 2010，55(29): 2828-2836 5 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 6 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 7 魏世平，刘晓芬，杨胜先，吕海燕，牛远，章元明。中国栽培大豆群体结构不同分类方法的比较. 南京农业大学学报 2011, 34(2):13-17 8 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 9 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 10 牛远，徐宇，李广军，王云清，刘晓芬，李河南，魏世平，章元明。大豆籽粒大小和粒形的驯化研究。大豆科学 2012，31(4): 522-528 11 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 12 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 13 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
专著与教材 1、章元明主编。生物统计学（生物技术专业用，农业部十二五规划教材）。农业出版社，2017 2、章元明著。数量性状分离分析与R软件。金琅学术出版社，2017 3、宁海龙主编。金益、章元明主审。试验设计与统计分析（第二版）。中国农业出版社，2016 4、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 5、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 6、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 7、盖钧镒主编，章元明统稿。试验统计方法。农业出版社，2000 8、谢庄、章元明主编。水产试验统计学。中国农业科技出版社，1998
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