Phylogenetic analysis of the Si7PPO gene in foxtail millet, Setaria italica, provides further evidence for multiple origins of the negative phenol color reaction phenotype

• Published in: Genes & Genetic Systems 2020/08/01, Vol.95(4), pp.191-199
• Main Authors: Fukunaga, Kenji, Nur, Meili Zakiyah, Inoue, Takahiko, Taketa, Shin, Ichitani, Katsuyuki
• Format: Article
• Language: English
• Subjects: Catechol Oxidase - genetics; Color; crop evolution; domestication; Evolution; foxtail millet; Genetic diversity; Insertion; Millet; Nucleotide sequence; Phenols; Phenotype; Phenotypes; Phylogenetics; Phylogeny; Plant Proteins - genetics; polyphenol oxidase; Setaria italica; Setaria Plant - classification; Setaria Plant - genetics; Stop codon
• ISSN: 1341-7568; 1880-5779
• DOI: 10.1266/ggs.20-00011

To elucidate the diversity and evolution of the Si7PPO gene that controls phenol color reaction (Phr) in foxtail millet, Setaria italica, we analyzed sequence polymorphisms of the Si7PPO gene in 39 accessions consisting of foxtail millet landraces (32 accessions) and their wild ancestor ssp. viridis (seven accessions) collected from various regions in Europe and Asia. The accessions included wild type (positive Phr) and three different types of loss-of-function phenotype (negative Phr), “stop codon type”, “TE1-insertion type” and “6-bp duplication type”, found in our previous study. We constructed a phylogenetic tree of the gene and found that accessions with positive Phr showed higher genetic diversity at the nucleotide sequence level. We also found that the three different loss-of-function types formed different clusters, suggesting that landraces with negative Phr have multiple origins from three different lineages including both landrace and ssp. viridis accessions with positive Phr.