Systematic mining and functional analysis of factors regulating wheat spike development for breeding selection

Abstract Spike architecture largely affects grain number embraced, which is an important trait to optimize during wheat breeding process. In this study, we incorporated multi-omic data and investigated the genetic regulation of wheat spike development. We generated transcriptome and epigenome profiles of shoot apex at eight developmental stages and observed that chromatin accessibility and H3K27me3 abundance coordinated with transcriptome alteration for flowering transition. A core transcriptional regulatory network (TRN) that drove the formation of the wheat spike was constructed. Integration of the TRN and genome-wide association analysis (GWAS) led to the identification of 227 transcription factors (TFs) with both known (42) and unknown (185) functions. Multi-layer regulatory module among TaSPL6, TaMADS34 and TaMADS15 identified by TRN was validated experimentally. Of the 85 novel TFs with homozygous mutant lines in TILLING library, 38 showed altered spike architecture or flowering time, including bHLH, MYB, and WRKY. Furthermore, we demonstrated that TaMYB4-A regulates fertile spikelet number likely via regulating hormones homeostasis and signaling, and is downstream of, and repressed by WFZP. The elite allele of TaMYB4-A, with a C-SNP at the WFZP binding site, was selected for balancing spikelet number and fertility during breeding process in China. Collectively, our findings provide high-confidence novel regulators and an efficient strategy for studying the genetic basis of wheat spike development for practical breeding applications.