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Journal of Integrative Agriculture  2018, Vol. 17 Issue (09): 1972-1978    DOI: 10.1016/S2095-3119(18)62023-4
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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
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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: 14 August 2018
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.

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