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1976 YANG Hai-long et al. Journal of Integrative Agriculture 2018, 17(9): 1972–1978 in our study, the last two steps just need one tree format file for the process of adjusting branches in MEGA and plotting groups in Adobe Illustrator, which seems much easier, more efficient, and faster than the methods discussed above. 5. Conclusion Thus, our method provides an alternative way to better analyze and present genetic diversity among maize inbred lines, which should speed up the identification and clustering of germplasm resources as well as further breeding and association analysis. Acknowledgements This work was financially supported by the National Natural Science Foundation of China (31361140364), the National Major Project for Developing New GM Crops, Ministry of Agriculture, China (2016ZX080009-001), and the Agricultural Science and Technology Innovation Program (ASTIP) of Chinese Academy of Agricultural Sciences to Xie Chuanxiao. Appendices associated with this paper can be available on http:// www.ChinaAgriSci.com/V2/En/appendix.htm References Alexandrov N, Tai S, Wang W, Mansueto L, Palis K, Fuentes R R, Ulat V J, Chebotarov D, Zhang G, Li Z. 2015. SNP-Seek database of SNPs derived from 3000 rice genomes. Nucleic Acids Research , 43 , D1023–D1027. Barrett J C. 2009. Haploview: Visualization and analysis of SNP genotype data. Cold Spring Harbor Protocols , 10 , pdb. ip71. Barrett J C, Fry B, Maller J, Daly M J. 2005. Haploview: Analysis and visualization of LD and haplotype maps. Bioinformatics , 21 , 263–265. Campbell N R, Harmon S A, Narum S R. 2015. Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing. Molecular Ecology Resources , 15 , 855–867. Cavanagh C R, Chao S, Wang S, Huang B E, Stephen S, Kiani S, Forrest K, Saintenac C, Brown-Guedira G L, Akhunova A. 2013. Genome- wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proceedings of the National Academy of Sciences of the United States of America , 110 , 8057–8062. Chia J M, Song C, Bradbury P J, Costich D, de Leon N, Doebley J, Elshire R J, Gaut B, Geller L, Glaubitz J C, Gore M, Guill K E, Holland J, Hufford M B, Lai J S, Li M, Liu X, Lu Y L, McCombie R, Nelson R, et al . 2012. Maize HapMap2 identifies extant variation from a genome in flux. Nature Genetics , 44 , 803–807. Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A, Paux E. 2014. Structural and functional partitioning of bread wheat chromosome 3B. Science , 345 , 1249721. Cook J P, McMullen M D, Holland J B, Tian F, Bradbury P, Ross-Ibarra J, Buckler E S, Flint-Garcia S A. 2012. Genetic architecture of maize Table 1 List of the main genetic diversity analysis software programs 1) Software Data 2) Platform LD MAF Steps before analysis Analysis method Subsequent analysis accessibility Missing data detectability Low coverage detectability SNPhylo SNP (VCF, hapmap, GDS) Linux, MacOS X √ √ ≤1 Principal component analysis (PCA), relatedness analysis, multiple alignment, maximum likelihood method and others MEGA, Newick utility, PhyML, etc. √ √ PowerMarker SSR, SNP, RFLP, etc. Windows √ √ >3 F -statistics and population differentiation test FigTree, MEGA, TreeView, etc. √ × Structure SNP, STR, etc. Linux, MacOS X, Windows √ √ >3 Bayesian clustering model CLUMPP, distruct, CLUMPAK, etc. √ × PLINK SNP (hapmap) Linux, MacOS X, Windows √ √ ≥1 Complete-linkage hierarchical clustering and multidimensional scaling (MDS) gPLINK, Haploview, qqman, etc. √ √ 1) LD, linkage disequilibrium; MAF, minor allele frequency. 2) SNP, single nucleotide polymorphism; VCF, variant call format; GDS, genomic data structure; SSR, simple sequence repeat; RFLP, restriction fragment length polymorphism; STR, microsatellite short tandem repeat.