JIA-2018-09

Journal of Integrative Agriculture 2018, 17(9): 1972–1978 RESEARCH ARTICLE Available online at www.sciencedirect.com ScienceDirect A simple way to visualize detailed phylogenetic tree of huge genome-wide 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 Abstract 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 genetic distance (Jiao et al . 2012), pedigree background (Liu et al . 2003; Lorenz and Hoegemeyer 2013), and domestication history (Matsuoka et al . 2002), which will facilitate hybrid cross planning, inbred line development, heterosis research, and protection of line varieties (Pejic et al . 1998; Mohammadi and Prasanna 2003). The process of constructing a phylogenetic tree of maize inbred lines requires a genome-wide molecular marker. Currently, the most extensive way to evaluate genome-scale information is DNA markers, which are developed from enzyme- based markers as well as PCR-based markers and single nucleotide polymorphism (SNP) markers (Schlötterer 2004). ASNP is the variation of one single base in the DNA sequence, but commonly, an alternative of two potential bases occurs at a specific sequence position (Vignal et al . 2002). Its widespread distribution in crop plants, such as maize (Gore et al . 2009; Chia et al . 2012), rice (Feltus et al . 2004; McNally et al . 2009; Alexandrov et al . 2015), wheat (Cavanagh et al . 2013; Choulet et al . 2014), and soybean Received 15 September, 2017 Accepted 21 December, 2017 YANG Hai-long, E-mail: hailong7519@163.com ; LIU Chang- lin, E-mail: liuchanglin@cass.cn ; XIE Chuan-xiao, E-mail: xiechuanxiao@caas.cn © 2018 CAAS. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http:// creativecommons.org/licenses/by-nc-nd/4.0/) doi: 10.1016/S2095-3119(18)62023-4 1. Introduction Maize improvement is highly dependent on the success of a crop breeding program that is supported by access to abundant genetic diversity (Hoisington et al . 1999). One very common way to assess genetic diversity is to construct a phylogenetic tree of maize inbred lines. A phylogenetic tree of maize inbred lines can provide information about