A simple way to visualize detailed phylogenetic tree of huge genome-wide SNP data constructed by SNPhylo

作者：Yang Hai-long^*; Dong Le; Wang Hui; Liu Chang-lin; Liu Fang; Xie Chuan-xiao

来源：Journal of Integrative Agriculture, 2018, 17(9): 1972-1978.

DOI：10.1016/S2095-3119(18)62023-4

• phylogenetic tree
• SNP
• genetic diversity

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.

• 出版日期2018-9
• 单位中国农业科学院