GENOME ASSEMBLIES AND TRANSCRIPTOMIC ANALYSIS OF THE MAIZE MODEL LINE GASPE FLINT 1.1.1 PROVIDE INSIGHTS INTO THE GENETIC CONTROL OF FLOWERING TIME

Maize (Zea mays L.) is an important crop species with extensive genetic diversity and adapted to a wide range of environments. We assembled a high-quality genome of Gaspe Flint 1.1.1 (GF111), a super-early small stature maize model inbred line, using the PacBio long-read sequencing platform. BUSCO evaluation revealed that the assembly covered 96.6% (Single copy: 88.7%, Duplicated: 7.9%) of the orthologs from the embryophyta gene set, indicating a good coverage of the coding space. To support gene annotation and downstream transcriptomic analysis, Illumina RNA-seq was utilized across 22 distinct tissues of GF111 generating approximately 490 Gb of transcriptomic reads. Based on transcriptome evidence and orthologous protein information, a custom ab initio gene prediction model was trained. We then integrated transcriptomic, proteomic, and ab initio evidence through the MAKER pipeline to produce a comprehensive and high-confidence gene structure annotation. Additionally, transposable elements within the genome assemblies was annotated through the EDTA pipeline, constructing a comprehensive genome annotation. Further, we investigated several flowering-time-related genes, including ZmCCT, ZmRap2.7 and Vgt1, ZCN8, and others, in GF111 maize line. Comparative analysis with the NAM parent B73 line revealed six SNPs in the ZmCCT gene, which result in two amino acid missense mutations in the encoded protein, potentially contributing to the early-flowering phenotype of GF111. Moreover, transposable element annotations confirmed the presence of a MITE transposon insertion in Vgt1, consistent with previous studies showing the MITE insertion associated with early flowering. In contrast, no allelic difference was observed in ZCN8 between GF111 and B73. A more extensive comparison of GF111 flowering time allelic set up is in preparation. Additionally, differential expression analysis based on transcriptome quantification uncovered expression differences in flowering-time genes, providing further insights into the genetic basis of the early-flowering trait observed in GF111.