Foxtail millet (Setaria italica) is an important C₄ model crop; however, due to its high-density planting and high stature, lodging at the filling stage resulted in a serious reduction in yield and quality. Therefore, it is imperative to identify and deploy the genes controlling foxtail millet plant height. In this study, we used a semi-dwarf line 263A and an elite high-stalk breeding variety, Chuang 29 to construct an F₂ population to identify dwarf genes. We performed transcriptome analysis (RNA-seq) using internode tissues sampled at three jointing stages of 263A and Chuang 29, as well as bulk segregant analysis (BSA) on their F₂ population. A total of 8918 differentially expressed genes (DEGs) were obtained from RNA-seq analysis, and GO analysis showed that DEGs were enriched in functions such as "gibberellin metabolic process" and "oxidoreductase activity", which have previously been shown to be associated with plant height. A total 593 mutated genes were screened by BSA-seq method. One hundred and seventy-six out of the 593 mutated genes showed differential expression levels between the two parental lines, and seven genes not only showed differential expression in two or three internode tissues but also showed high genomic variation in coding regions, which indicated they play a crucial role in plant height determination. Among them, we found a gibberellin biosynthesis related GA20 oxidase gene (Seita.5G404900), which had a single-base deletion at the third exon, leading to the frameshift mutation at 263A. Cleaved amplified polymorphic sequence assay and association analysis proved the single-base deletion in Seita.5G404900 co-segregated with dwarf phenotype in two independent F₂ populations planted in entirely different environments. Taken together, the candidate genes identified in this study will help to elucidate the genetic basis of foxtail millet plant height, and the molecular marker will be useful for marker-assisted dwarf breeding.

The diploid wild goat grass Aegilops tauschii (Ae. tauschii, 2n = 14; DD), as the D-sub genome of common wheat, provides rich germplasm resources for many aspects of wheat breeding. Abscisic acid (ABA) is an essential phytohormone that plays a pivotal role in plant adaptation to abiotic stresses. However, the gene regulation network of Ae. tauschii in response to ABA stress remains unclear. Here, we conducted a time-course strand-specific RNA-sequencing study to globally profile the transcriptome that responded to ABA treatment in Ae. tauschii. We identified 4818 differentially expressed transcription units/genes with time-point-specific induction/repression patterns. Using functional annotation, one-to-one ortholog and comparative transcriptome profiling analyses, we identified 319 ABA-responsive Ae. tauschii orthologs that were also induced/repressed under ABA treatment in hexaploid wheat. On the quantitative trait loci (QTL) used in wheat marker-assisted breeding, we found that the ABA-responsive expression patterns of eight Ae. tauschii orthologs were associated with drought stress tolerance, flowering process and/or grain quality. Of them, the ABA-responsive gene encoding sucrose:sucrose 1-fructosyltransferase in fructan and glucose metabolism pathways showed the most significant association with wheat drought tolerance. The characterization of ABA early-responsive genes in this study provides valuable information for exploring the molecular functions of the regulatory genes and will assist in wheat breeding.