Genome-Wide Characterization and Haplotypic Variation Analysis of the Gene Family in Foxtail Millet ().

The indeterminate domain proteins (IDD proteins) play essential roles in the growth and development of various plant tissues and organs across different developmental stages, but members of this gene family have not yet been characterized in foxtail millet (). To have a comprehensive understanding of the gene family in foxtail millet, we performed a genome-wide characterization and haplotypic variation analysis of the gene family in foxtail millet. In this study, sixteen genes were identified across the reference genome of Yugu1, a foxtail millet cultivar. Phylogenetic analysis revealed that the () proteins were clustered into four groups together with IDD proteins from (dicot) and (monocot). Conserved protein motif and gene structure analyses revealed that the closely clustered genes were highly conserved within each subgroup. Furthermore, chromosomal location analysis showed that the genes were unevenly distributed on nine chromosomes of foxtail millet and shared collinear relationships with genes of other grass species. Transcriptional analysis revealed that the genes differed greatly in their expression patterns, and paralogous genes shared similar expression patterns. In addition, superior haplotypes for two genes ( and ) were identified to correlate with traits of early heading date, and high thousand seed weight and molecular markers were designed for and to distinguish different haplotypes for breeding. Taken together, the results of this study provide useful information for further functional investigation of genes, and the superior haplotypes of and will be particularly beneficial for improving heading date and yield of foxtail millet in breeding programs.