## 3 Results
### Gene Ontology Enrichment Analysis of Differentially Expressed Genes and Transcripts  
Consensus sequences of drought-responsive genes and transcripts were subjected to Blast2 Go to identify gene functions. GO enrichment analysis was performed on the Blast results to investigate biological functions. The results of GO Slim enrichment analyses were divided into two categories: drought-related genes and flowering-time-related genes. The results reveal a strong enrichment of functions involved in the response to stress and response to abiotic stress (GO: 006950 and GO: 009628) (Figure 2 and Table S3). In addition, functions such as response to external stimulus (GO: 009605) that might contribute to drought tolerance were observed in the biological process category. GO terms for the response to stress were also observed in the molecular function category. The gene expression pattern of maize under drought stress has been reported to differ according to the tissue and development stage [19; 22; 23; 62]. We identified genes in Ki11 that are also involved in the drought response in B73. For example, the drought-responsive genes GRMZMZG031033, GRMZMZG366532, GRMZMZG031033, GRMZMZG059799, GRMZMZG126812, GRMZMZG122816, AC208204_3_FG006, and GRMZMZG154628, which have been reported as hub genes in B73 under drought stress, were also observed in Ki11 [19]. Moreover, in contigs, we detected orthologous genes that have been reported as drought-responsive genes in B73 (GRMZMZSG833699, GRMZMZG059799, GRMZMZG079440, and GRMZMZG059799). In addition, several contigs (orthologs of GRMZMZG063340, GRMZMZG133802, and GRMZMZG132093) and genes (GRMZM5G858784, GRMZMZG56884600, and GRMZMZG159724) reported to be directly or indirectly involved in drought stress from genome-wide association results were identified as drought-responsive genes. Blast analysis characterized these genes as involved in the response to stress (GO: 0006950) and response to stimulus (GO: 0009628). Figure 2: Enrichment analysis of drought-responsive genes and transcripts of Ki11. Significantly overrepresented GO terms were determined using the BiNGO app in Cytoscape. The size of a node is proportional to the number of GO categories. The node colors represent the significance of enrichment. Furthermore, the expression profiles of 66 genes involved in flowering time were annotated with GO terms for reproduction (GO: 0000003). The flowering-time-related genes include _ZCN_, _FLOWERING LOCUS T, MADS-box_, and _CONSTANS_. We also found genes that were not associated with GO terms for reproduction but could affect flowering time. Of the drought-responsive genes, four genes and five contigs were also DEGs with potential effects on flowering time. These genes were obtained by comparing candidate genes involved in flowering time in maize with the genes of other plants, including cloned and homologous flowering-time genes [27] (Table S2). Three genes (GRMZM2G018627, GRMZM2G126018, and GRMZM2G348863) involved in the response to drought stress may have roles analogous to those of chlorophyll a-b binding protein (_CAB_), _SQUAMOSA PROMOTER BINDING LIKE PROTEIN (SPL)_ 17, and flowering-promoting factor 1 (_FPFI_), respectively. One gene (GRMZM2G546097, homolog of GRMZM2G126018) and five contigs (contig854, homolog of GRMZM2G018627; contig4549, homolog of GRMZM2G431157; contig477 and contig312, homolog of GRMZM2G142718; contig6971, homolog of GRMZM2G373928; and contig7875, homolog of GRMZM2G013478) that were identified as responsive to drought are expected to play roles analogous to those of CAB, _DNA-binding one zinc finger (Dof)_, and _Heading date 3a (Hd3a)_. In addition, we detected DEGs that were previously reported as drought-responsive genes in B73 under short-day and drought conditions [30]. By comparing the two datasets, we identified genes (GRMZM2G094990, GRMZM2G13501, GRMZM2G012717, and GRMZM2G120619) and contigs (two homologs of GRMZM2G142718) that are responsive to drought and potentially change flowering time.