Please wait a minute...
Journal of Integrative Agriculture  2018, Vol. 17 Issue (09): 1972-1978    DOI: 10.1016/S2095-3119(18)62023-4
Crop Science Advanced Online Publication | Current Issue | Archive | Adv Search |
A simple way to visualize detailed phylogenetic tree of huge genomewide SNP data constructed by SNPhylo
YANG Hai-long, DONG Le, WANG Hui, LIU Chang-lin, LIU Fang, XIE Chuan-xiao
National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
Download:  PDF (10046KB) ( )  
Export:  BibTeX | EndNote (RIS)      

Phylogenetic trees based on genome-wide single nucleotide polymorphisms (SNPs) among diverse inbreds could provide valuable and intuitive information for breeding and germplasm management in crops.  As a result of sequencing technology developments, a huge amount of whole genome SNP data have become available and affordable for breeders.  However, it is a challenge to perform quick and reliable plotting based on the huge amount of SNP data.  To meet this goal, a visualization pipeline was developed and demonstrated based on publicly available SNP data from the current important maize inbred lines, including temperate, tropical, sweetcorn, and popcorn.  The detailed phylogenetic tree plotted by our pipeline revealed the authentic genetic diversity of these inbreds, which was consistent with several previous reports and indicated that this straightforward pipeline is reliable and could potentially speed up advances in crop breeding.
Keywords:  phylogenetic tree        SNP        genetic diversity  
Received: 15 September 2017   Accepted:
Fund: 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.
About author:  YANG Hai-long, E-mail:; LIU Chang-lin, E-mail:; XIE Chuan-xiao, E-mail:

Cite this article: 

YANG Hai-long, DONG Le, WANG Hui, LIU Chang-lin, LIU Fang, XIE Chuan-xiao. 2018. A simple way to visualize detailed phylogenetic tree of huge genomewide SNP data constructed by SNPhylo. Journal of Integrative Agriculture, 17(09): 1972-1978.

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 kernel composition in the nested association mapping and inbred association panels. Plant Physiology, 158, 824–834.
Cornelis S, Gansemans Y, Deleye L, Deforce D, Van Nieuwerburgh F. 2017. Forensic SNP genotyping using nanopore MinION sequencing. Scientific Reports, 7, 41759.
Davey J W, Hohenlohe P A, Etter P D, Boone J Q, Catchen J M, and Blaxter M L. 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics, 12, 499–510.
Earl D A. 2012. STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4, 359–361.
Feltus F A, Wan J, Schulze S R, Estill J C, Jiang N, Paterson A H. 2004. An SNP resource for rice genetics and breeding based on subspecies Indica and Japonica genome alignments. Genome Research, 14, 1812–1819.
Flint-Garcia S A, Thuillet A C, Yu J, Pressoir G, Romero S M, Mitchell S E, Doebley J, Kresovich S, Goodman M M, Buckler E S. 2005. Maize association population: A high-resolution platform for quantitative trait locus dissection. The Plant Journal, 44, 1054–1064.
Gore M A, Chia J-M, Elshire R J, Sun Q, Ersoz E S, Hurwitz B L, Peiffer J A, McMullen M D, Grills G S, Ross-Ibarra J. 2009. A first-generation haplotype map of maize. Science, 326, 1115–1117.
He J, Zhao X, Laroche A, Lu Z X, Liu H, Li Z. 2014. Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Frontiers in Plant Science, 5, 484.
Hoisington D, Khairallah M, Reeves T, Ribaut J M, Skovmand B, Taba S, Warburton M. 1999. Plant genetic resources: What can they contribute toward increased crop productivity. Proceedings of the National Academy of Sciences of the United States of America, 96, 5937–5943.
Jakobsson M, Rosenberg N A. 2007. CLUMPP: A cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics, 23, 1801–1806.
Jiao Y, Zhao H, Ren L, Song W, Zeng B, Guo J, Wang B, Liu Z, Chen J, Li W. 2012. Genome-wide genetic changes during modern breeding of maize. Nature Genetics, 44, 812–815.
Kopelman N M, Mayzel J, Jakobsson M, Rosenberg N A, Mayrose I. 2015. Clumpak: A program for identifying clustering modes and packaging population structure inferences across K. Molecular Ecology Resources, 15, 1179–1191.
LaFramboise T. 2009. Single nucleotide polymorphism arrays: A decade of biological, computational and technological advances. Nucleic Acids Research, 37, 4181–4193.
Lam H M, Xu X, Liu X, Chen W, Yang G, Wong F L, Li M W, He W, Qin N, Wang B, Li J, Jian M, Wang J, Shao G, Wang J, Sun S S, Zhang G. 2010. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nature Genetics, 42, 1053–1059.
Larkin M A, Blackshields G, Brown N P, Chenna R, McGettigan P A, McWilliam H, Valentin F, Wallace I M, Wilm A, Lopez R, Thompson J D, Gibson T J, Higgins D G. 2007. Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947–2948.
Lee T H, Guo H, Wang X, Kim C, Paterson A H. 2014. SNPhylo: A pipeline to construct a phylogenetic tree from huge SNP data. BMC Genomics, 15, 162.
Li Y H, Zhou G, Ma J, Jiang W, Jin L G, Zhang Z, Guo Y, Zhang J, Sui Y, Zheng L, Zhang S S, Zuo Q, Shi X H, Li Y F, Zhang W K, Hu Y, Kong G, Hong H L, Tan B, Song J, et al. 2014. De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nature Biotechnology, 32, 1045–1052.
Liu K, Goodman M, Muse S, Smith J S, Buckler E, Doebley J. 2003. Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics, 165, 2117–2128.
Liu K, Muse S V. 2005. PowerMarker: An integrated analysis environment for genetic marker analysis. Bioinformatics, 21, 2128–2129.
Lorenz A, Hoegemeyer T. 2013. The phylogenetic relationships of US maize germplasm. Nature Genetics, 45, 844–845.
Matsuoka Y, Vigouroux Y, Goodman M M, Sanchez J, Buckler E, Doebley J. 2002. A single domestication for maize shown by multilocus microsatellite genotyping. Proceedings of the National Academy of Sciences of the United States of America, 99, 6080–6084.
McNally K L, Childs K L, Bohnert R, Davidson R M, Zhao K, Ulat V J, Zeller G, Clark R M, Hoen D R, Bureau T E. 2009. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proceedings of the National Academy of Sciences of the United States of America, 106, 12273–12278.
Mohammadi S, Prasanna B. 2003. Analysis of genetic diversity in crop plants-salient statistical tools and considerations. Crop Science, 43, 1235–1248.
Nielsen R, Paul J S, Albrechtsen A, Song Y S. 2011. Genotype and SNP calling from next-generation sequencing data. Nature Reviews Genetics, 12, 443–451.
Peakall R, Smouse P E. 2006. GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Resources, 6, 288–295.
Pejic I, Ajmone-Marsan P, Morgante M, Kozumplick V, Castiglioni P, Taramino G, Motto M. 1998. Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs, and AFLPs. Theoretical and Applied Genetics, 97, 1248–1255.
Porras-Hurtado L, Ruiz Y, Santos C, Phillips C, Carracedo A, Lareu M V. 2013. An overview of STRUCTURE: Applications, parameter settings, and supporting software. Frontiers in Genetics, 4, 98.
Pritchard J K, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics, 155, 945–959.
Pritchard J K, Wen X, and Falush D. 2009. Documentation for structure software: Version 2.3. Department of Human Genetics, University of Chicago, Chicago, USA.
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira M A, Bender D, Maller J, Sklar P, de Bakker P I, Daly M J, Sham P C. 2007. PLINK: A tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics, 81, 559–575.
Ragoussis J. 2009. Genotyping technologies for genetic research. Annual Review of Genomics and Human Genetics, 10, 117–133.
Rosenberg N A. 2004. DISTRUCT: A program for the graphical display of population structure. Molecular Ecology Resources, 4, 137–138.
Schlötterer C. 2004. The evolution of molecular markers-just a matter of fashion? Nature Reviews Genetics, 5, 63–69.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30, 2725–2729.
Thomson M J. 2014. High-throughput SNP genotyping to accelerate crop improvement. Plant Breeding and Biotechnology, 2, 195–212.
Vignal A, Milan D, SanCristobal M, Eggen A. 2002. A review on SNP and other types of molecular markers and their use in animal genetics. Genetics Selection Evolution, 34, 275–306.
Wang D, Sun Y, Stang P, Berlin J A, Wilcox M A, Li Q. 2009. Comparison of methods for correcting population stratification in a genome-wide association study of rheumatoid arthritis: Principal-component analysis versus multidimensional scaling. BMC Proceedings, 3(Suppl. 7), S109.
Weirather J L, de Cesare M, Wang Y, Piazza P, Sebastiano V, Wang X J, Buck D, Au K F. 2017. Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis. F1000Research, 6, 100.
[1] ZHANG Ying, CAO Yu-fen, HUO Hong-liang, XU Jia-yu, TIAN Lu-ming, DONG Xing-guang, QI Dan, LIU Chao. An assessment of the genetic diversity of pear (Pyrus L.) germplasm resources based on the fruit phenotypic traits[J]. >Journal of Integrative Agriculture, 2022, 21(8): 2275-2290.
[2] GUO Yi, GONG Ying, HE Yong-meng, YANG Bai-gao, ZHANG Wei-yi, CHEN Bo-er, HUANG Yong-fu, ZHAO Yong-ju, ZHANG Dan-ping, MA Yue-hui, CHU Ming-xing, E Guang-xin. Investigation of Mitochondrial DNA genetic diversity and phylogeny of goats worldwide[J]. >Journal of Integrative Agriculture, 2022, 21(6): 1830-1837.
[3] XU Xin, YE Jun-hua, YANG Ying-ying, LI Ruo-si, LI Zhen, WANG Shan, SUN Yan-fei, ZHANG Meng-chen, XU Qun, FENG Yue, WEI Xing-hua, YANG Yao-long. Genetic diversity analysis and GWAS reveal the adaptive loci of milling and appearance quality of japonica (oryza sativa L.) in Northeast China[J]. >Journal of Integrative Agriculture, 2022, 21(6): 1539-1550.
[4] YANG Zhen, ZHANG Lan, ZHAO Jin-fa, ZHANG Xing-kai, WANG Ying, LI Tai-sheng, ZHANG Wei, ZHOU Yan. New geographic distribution and molecular diversity of Citrus chlorotic dwarf-associated virus in China[J]. >Journal of Integrative Agriculture, 2022, 21(1): 293-298.
[5] SUN Jing-xuan, LI Qian, TAN Xiao-ling, FAN Jia, ZHANG Yong, QIN Yao-guo, Frédéric FRANCIS, CHEN Ju-lian. Population genetic structure of Sitobion miscanthi in China[J]. >Journal of Integrative Agriculture, 2022, 21(1): 178-187.
[6] QU Cheng, WANG Ran, CHE Wu-nan, LI Feng-qi, ZHAO Hai-peng, WEI Yi-yun, LUO Chen, XUE Ming. Identification and tissue distribution of odorant binding protein genes in Harmonia axyridis (Coleoptera: Coccinellidae)[J]. >Journal of Integrative Agriculture, 2021, 20(8): 2204-2213.
[7] LIU Na, CHENG Fang-yun, GUO Xin, ZHONG Yuan. Development and application of microsatellite markers within transcription factors in flare tree peony (Paeonia rockii) based on next-generation and single-molecule long-read RNA-seq[J]. >Journal of Integrative Agriculture, 2021, 20(7): 1832-1848.
[8] YAN Zhi-yong, ZHAO Mei-sheng, MA Hua-yu, LIU Ling-zhi, YANG Guang-ling, GENG Chao, TIAN Yan-ping, LI Xiang-dong. Biological and molecular characterization of tomato brown rugose fruit virus and development of quadruplex RT-PCR detection[J]. >Journal of Integrative Agriculture, 2021, 20(7): 1871-1879.
[9] YANG Meng-jiao, WANG Cai-rong, Muhammad Adeel HASSAN, WU Yu-ying, XIA Xian-chun, SHI Shu-bing, XIAO Yong-gui, HE Zhong-hu. QTL mapping of seedling biomass and root traits under different nitrogen conditions in bread wheat (Triticum aestivum L.)[J]. >Journal of Integrative Agriculture, 2021, 20(5): 1180-1192.
[10] DIAO Shu-qi, XU Zhi-ting, YE Shao-pan, HUANG Shu-wen, TENG Jin-yan, YUAN Xiao-long, CHEN Zan-mou, ZHANG Hao, LI Jia-qi, ZHANG Zhe. Exploring the genetic features and signatures of selection in South China indigenous pigs[J]. >Journal of Integrative Agriculture, 2021, 20(5): 1359-1371.
[11] HU Fu-chu, CHEN Zhe, WANG Xiang-he, WANG Jia-bao, FAN Hong-yan, QIN Yong-hua, ZHAO Jietang, HU Gui-bing. Construction of high-density SNP genetic maps and QTL mapping for dwarf-related traits in Litchi chinensis Sonn[J]. >Journal of Integrative Agriculture, 2021, 20(11): 2900-2913.
[12] REN Yun, CHEN Dan, LI Wen-jie, TAO Luo, YUAN Guo-qiang, CAO Ye, LI Xue-mei, DENG Qi-ming, WANG Shi-quan, ZHENG Ai-ping, ZHU Jun, LIU Huai-nian, WANG Ling-xia, LI Ping, LI Shuang-cheng . Genome-wide pedigree analysis of elite rice Shuhui 527 reveals key regions for breeding[J]. >Journal of Integrative Agriculture, 2021, 20(1): 35-45.
[13] CUI Hong-ying, ZHAO Zhang-wu. Structure and function of neuropeptide F in insects[J]. >Journal of Integrative Agriculture, 2020, 19(6): 1429-1438.
[14] NAN Jiu-hong, YIN Li-lin, TANG Zhen-shuang, CHEN Jian-hai, ZHANG Jie, WANG Hai-yan, DU Xiao-yong, LIU Xiang-dong . Genetic parameter estimation and genome-wide association study (GWAS) of red blood cell count at three stages in a Duroc×Erhualian pig population[J]. >Journal of Integrative Agriculture, 2020, 19(3): 793-799.
[15] May Oo kHINE, brozenká MICHAELA, LIU Yan, Jiban kumar kUNDU, WANG Xi-feng. Molecular diversity of barley yellow dwarf virus-PAV from China and the Czech Republic[J]. >Journal of Integrative Agriculture, 2020, 19(11): 2736-2745.
No Suggested Reading articles found!