Summary: Pre‐harvest sprouting (PHS), the germination of grain before harvest, is a serious problem resulting in wheat yield and quality losses. Here, we mapped the PHS resistance gene PHS‐3D from synthetic hexaploid wheat to a 2.4 Mb presence–absence variation (PAV) region and found that its resistance effect was attributed to the pleiotropic Myb10‐D by integrated omics and functional analyses. Three haplotypes were detected in this PAV region among 262 worldwide wheat lines and 16 Aegilops tauschii, and the germination percentages of wheat lines containing Myb10‐D was approximately 40% lower than that of the other lines. Transcriptome and metabolome profiling indicated that Myb10‐D affected the transcription of genes in both the flavonoid and abscisic acid (ABA) biosynthesis pathways, which resulted in increases in flavonoids and ABA in transgenic wheat lines. Myb10‐D activates 9‐cis‐epoxycarotenoid dioxygenase (NCED) by biding the secondary wall MYB‐responsive element (SMRE) to promote ABA biosynthesis in early wheat seed development stages. We revealed that the newly discovered function of Myb10‐D confers PHS resistance by enhancing ABA biosynthesis to delay germination in wheat. The PAV harboring Myb10‐D associated with grain color and PHS will be useful for understanding and selecting white grained PHS resistant wheat cultivars.

Maize kernels are complex biological systems composed of three genetic sources, namely maternal tissues, progeny embryos, and progeny endosperms. The lack of gene expression profiles with spatial information has limited the understanding of the specific functions of each cell population, and hindered the exploration of superior genes in kernels. In our study, we conduct microscopic sectioning and spatial transcriptomics analysis during the grain filling stage of maize kernels. This enables us to visualize the expression patterns of all genes through electronical RNA in situ hybridization, and identify 11 cell populations and 332 molecular marker genes. Furthermore, we systematically elucidate the spatial storage mechanisms of the three major substances in maize kernels: starch, protein, and oil. These findings provide valuable insights into the functional genes that control agronomic traits in maize kernels.

Summary: Plant transcription factors (TFs), such as basic helix‐loop‐helix (bHLH) and AT‐rich zinc‐binding proteins (PLATZ), play critical roles in regulating the expression of developmental genes in cereals. We identified the bHLH protein TaPGS1 (T. aestivum Positive Regulator of Grain Size 1) specifically expressed in the seeds at 5–20 days post‐anthesis in wheat. TaPGS1 was ectopically overexpressed (OE) in wheat and rice, leading to increased grain weight (up to 13.81% in wheat and 18.55% in rice lines) and grain size. Carbohydrate and total protein levels also increased. Scanning electron microscopy results indicated that the starch granules in the endosperm of TaPGS1 OE wheat and rice lines were smaller and tightly embedded in a proteinaceous matrix. Furthermore, TaPGS1 was bound directly to the E‐box motif at the promoter of the PLATZ TF genes TaFl3 and OsFl3 and positively regulated their expression in wheat and rice. In rice, the OsFl3 CRISPR/Cas9 knockout lines showed reduced average thousand‐grain weight, grain width, and grain length in rice. Our results reveal that TaPGS1 functions as a valuable trait‐associated gene for improving cereal grain yield.

The PLATZ (plant AT-rich protein and zinc-binding protein) transcription factor family is a class of plant-specific zinc-dependent DNA-binding proteins. PLATZ has essential roles in seed endosperm development, as well as promoting cell proliferation duration in the earlier stages of the crops. In the present study, 62 TaPLATZ genes were identified from the wheat genome, and they were unequally distributed on 15 chromosomes. According to the phylogenetic analysis, 62 TaPLATZ genes were classified into six groups, including two groups that were unique in wheat. Members in the same groups shared similar exon-intron structures. The polyploidization, together with genome duplication of wheat, plays a crucial role in the expansion of the TaPLATZs family. Transcriptome data indicated a distinct divergence expression pattern of TaPLATZ genes that could be clustered into four modules. The TaPLATZs in Module b possessed a seed-specific expression pattern and displayed obvious high expression in the earlier development stage of seeds. Subcellular localization data of TaPLATZs suggesting that they likely perform a function as a conventional transcription factor. This study provides insight into understanding the structure divergence, evolutionary features, expression profiles, and potential function of PLATZ in wheat.

Early endosperm development in maize (Zea mays) is essential for creating a functional endosperm for filling, but its rapid and dynamic process remains largely unknown. The coenocytic stage is a particular stage with rapid nuclear division without cytokinesis. From 48-144 h after pollination (HAP), endosperm mainly undergoes four cellular processes: coenocyte, cellularization, cell proliferation, and differentiation. Although the high temporal-resolution transcriptome data within 144 HAP of maize kernel development have been investigated, due to technical limitations, the samples contained the maternal nucellus and the embryo sac; as a consequence, many endosperm-specifically-expressed genes might be over-looked. In this study, we isolated early endosperms by free hand and laser-capture microdissection (LCM) and generated high-resolution transcriptome data from 48 to 144 HAP with an interval of 24 h. Through weighted gene co-expression network analysis (WGCNA), we identified nine distinct modules of co-expressed gene sets, of which Module 7 was composed of 5,555 genes that showed the highest expression levels at the coenocytic stage. In Module 7, there were 391 genes not expressed in nucellus, and thus were named as the Coenocyte-Expressed (CE) Gene Set. These genes were involved in transcriptional regulation and auxin-activated signaling pathway. Consistent with the stage transition of early endosperm development, the co-expressed gene sets and enriched gene function modules were changed accordingly. We verified the reliability of the transcriptome data by in situ hybridization. Our work provides a valuable gene resource for early endosperm development studies in the future.

The grain-filling stage is highly sensitive to heat, impacting wheat yield and quality. This study uncovered Chuanmai104's grain spatial transcriptome atlas under heat stress, identifying over 120 specifically expressed genes crucial for cell sorting and subsequent spatial sequencing across twelve cell types. The cell differentiation trajectory of endosperm indicated high expression of genes for cell development and programmed cell death at early stages, and the subsequent expressed genes enable grains accumulate nutrients. At 15 DAP, recovery grains under heat stress showed significant gene expression changes, especially in the nucellar projection, endosperm near the scutellum, and embryo. Heat stress reduced starch and ABA synthesis gene expression, shortening grain-filling time, reducing grain weight by 28.9%, and raising germination rates from 7.9% to 52.0%. Spatial transcriptomics revealed unexpected shifts in the major expression domains for 189 genes due to heat stress, featuring three major spatial shifts: AL-SCU, ENC-PR, and EXC-NP.