Semi-dwarfism and lodging tolerance in tef (Eragrostis tef) is linked to a mutation in the α-Tubulin 1 gene

Highlight The semi-dwarf and lodging-tolerant kegne mutant linked to defects in microtubule orientation has the potential to enhance the productivity of an African orphan crop tef (Eragrostis tef).

Alignment: The protein sequences were aligned using Mafft v6.903b (Katoh et al., 2005;Larkin et al., 2007;Thompson et al., 1994) with the default parameters. If one sequence had an insertion of greater than 20 bases pairs not present in any other sequences, this insertion was trimmed from the sequence.
Tree: PhyML (Guindon et al., 2005) was used to obtain a maximum likelihood tree using the default parameters. Branch support was inferred using the Shimodaira-Hasegawa-like (SH) aLRT provided by PhyML. The phylogenetic tree was visualized using FigTree v1.3.1 (Rambaut).

Analysis:
The CoGeBlast tool of the CoGe website was used to find the scaffolds in Eragrostis tef (coge id: id38364) and Oryza sativa japonica (coge id: id3) closest to the kegne mutant. These genomic segments were analyzed with GEvo at the same website. The analysis can be reproduced at: http://www.genomevolution.org/r/dljt.
Supplementary Fig. 7. Phylogenetic tree of α-Tubulin protein sequences from diverse plant species. The coding sequences for various species were obtained from Phytozome, NCBI, the tef genome (http://www.tef-research.org) and IRGSP as described in the methods. Tef sequences are shown in blue while Arabidopsis sequences are shown in red. The maximum likelihood tree was inferred using PhyML with the default parameters. The scale bar reflects evolutionary distance, measured in units of substitution per site. Branch support was inferred using the Shimodaira-Hasegawa-like (SH) aLRT provided by PhyML. The tree was rooted with a β-Tubulin from Arabidopsis (not shown).
Supplementary Fig. 8. Comparison of orthologous syntenic genomic regions between tef and rice. The genes in the tef genome (Cannarozzi et al., 2014) closest to the TUA1 gene were identified on scaffold867 and scaffold868. This region on these two scaffolds is was compared to the orthologous region on the rice genome. All genes within 50 kbp upstream and downstream were investigated. None of the eight genes in the region had any reported effect on plant stature. The eight genes in close proximity to the TUA1 gene in the tef and rice genomes are briefly described below.   ******::****:**:************:*:** ** :***********::** **** * tid1 mutation in rice kegne mutation in tef Supplementary Table 1. Yield and yield components of 312 WT and kegne plants grown in a tray of 0.128 m 2 under equal day conditions. 100-seed weight was calculated as average from 10 x 100 seeds. One standard deviation is given in parentheses. Yield per hectare was extrapolated from the harvest obtained from the tray.