Candidate Gene Association Analysis of Maize Transcription Factors in Flowering Time

Maize growth period traits, including flowering time, are the ones of most important in maize breeding. The advancement of heading date, silking time, and the pollen shed can ensure maize kernels fully dehydrated and thus suited to machinery harvesting. Moreover, the saved time can also leave for wheat sowing under the Maize-Wheat farming mode in Huang-Huai-Hai area. Transcription factors are important up-stream trans-action factors of gene expression regulation, which play roles in transcriptional activation or inhibition on target genes by binding to and driving their promoters. It is of great significance to analyze the regulatory effects of transcription factors on maize flowering time at the whole genome scale, it is also emergence to obtain the maize transcription factor haplotypes which associated with earlier flowering and higher yield. The haplotypes, or the haplotype combinations, will be served as excellent germplasm resources for maize breeding.

In this study, candidate gene association analysis was performed to analyze maize flowering time related transcription factors and significant SNPs. DAP-seq was carried out to obtain the binding sites and down-stream genes of the key transcription factors. Followed by GO analysis on the down-stream genes to explore the transcription factor dependent gene expression regulatory network.

There are 75, 75, and 128 significant SNPs detected in combinations of the traits Silking time and Heading date, the traits Silking time and Pollen shed, and the traits Heading date and Pollen shed, respectively. Altogether, there are 58 significant SNPs associated with all three flowering time traits. These results suggest that the three traits of flowering time may be regulated by the same transcription factors. Flowering time associated transcription factor genes that containing 3 or more significant SNPs were selected for DAP-seq to capture the key motifs and down-stream genes. Down-stream genes bound by flowering time associated transcription factors are significantly enriched in transcription factor activity, DNA binding, RNA binding, organonitrogen compound metabolic process, reproduction-related developmental processes, etc. Different transcription factors have co-regulated downstream genes related to flowering time. The key regulatory transcription factors for flowering time traits are ARF, MYB and NAC. Through haplotype analysis, the optimal TF haplotype combination that shows earlier flowering and no negative impact on yield was selected.

In this research, through candidate gene association and DAP-seq, the regulatory network of transcription factors on the flowering time related agronomic traits were established at the whole genome scale. The optimal haplotype combination of transcription factors that not only advances the flowering time, but also has no negative impact on yield was selected for further use in maize breeding.