Revisiting the origin and identity specification of the spikelet: A structural innovation in grasses (Poaceae)

CLAVATA signalling shapes barley inflorescence by controlling activity and determinacy of shoot meristem and rachilla

The large variety of inflorescence architectures evolved in grasses depends on shape, longevity and determinacy of meristems directing growth of the main and lateral axes. The CLAVATA pathway is known to regulate meristem size and inflorescence architecture in grasses. However, how individual meristem activities are determined and integrated to generate specific inflorescences is not yet understood. We found that activity of distinct meristems in the barley inflorescence is controlled by a signalling pathway comprising the receptor-like kinase Hordeum vulgare CLAVATA1 (HvCLV1) and the secreted CLAVATA3/EMBRYO-SURROUNDING REGION RELATED (CLE)-family peptide FON2-LIKE CLE PROTEIN1 (HvFCP1). HvFCP1 and HvCLV1 interact to promote spikelet formation, but restrict inflorescence meristem and rachilla proliferation. Hvfcp1 or Hvclv1 mutants generate additional rows of spikelets and supernumerary florets from extended rachilla activity. HvFCP1/HvCLV1 signalling coordinates meristem activity through regulation of trehalose-6-phosphate levels. Our discoveries outline a path to engineer inflorescence architecture via specific regulation of distinct meristem activities.

Historic rewiring of grass flowering time pathways and implications for crop improvement under climate change

Grasses are fundamental to human survival, providing a large percentage of our calories, fuel, and fodder for livestock, and an enormous global carbon sink. A particularly important part of the grass plant is the grain-producing inflorescence that develops in response to both internal and external signals that converge at the shoot tip to influence meristem behavior. Abiotic signals that trigger reproductive development vary across the grass family, mostly due to the unique ecological and phylogenetic histories of each clade. The time it takes a grass to flower has implications for its ability to escape harsh environments, while also indirectly affecting abiotic stress tolerance, inflorescence architecture, and grain yield. Here, we synthesize recent insights into the evolution of grass flowering time in response to past climate change, particularly focusing on genetic convergence in underlying traits. We then discuss how and why the rewiring of a shared ancestral flowering pathway affects grass yields, and outline ways in which researchers are using this and other information to breed higher yielding, climate-proof cereal crops.

The role of Ancestral MicroRNAs in grass inflorescence development

Plant inflorescences are complex, highly diverse structures whose morphology is determined in meristems that form during reproductive development. Inflorescence structure influences flower formation, and consequently grain number, and yield in crops. Correct inflorescence and flower development require tight control of gene expression via complex interplay between regulatory networks. MicroRNAs (miRNAs) have emerged as fundamental modulators of gene expression at the transcriptional and/or post-transcriptional level in plant inflorescence development. First discovered more than three decades ago, miRNAs have proved to be revolutionary in advancing our mechanistic understanding of gene expression. This review highlights current knowledge of downstream target genes and pathways of some highly conserved miRNAs that regulate the maintenance, identity, and activity of inflorescence and floral meristems in economically and agriculturally important grass species, including rice (Oryza sativa), maize (Zea mays), barley (Hordeum vulgare), and wheat (Triticum aestivum). Furthermore, we summarize emerging regulatory networks of miRNAs and their targets to suggest new avenues and strategies for application of miRNAs as a tool to enhance crop yield and performance.

The diversification of the shoot branching system: A quantitative and comparative perspective in meristem determinacy

Reiterative shoot branching largely defines important yield components of crops and is essentially controlled by programs that direct the initiation, dormancy release, and differentiation of meristems in the axils of leaves. Here, we focus on meristem determinacy, defining the number of reiterations that shape the shoot architectures and exhibit enormous diversity in a wide range of species. The meristem determinacy per se is hierarchically complex and context-dependent for the successively emerged meristems, representing a crucial mechanism in shaping the complexity of the shoot branching. In addition, we have highlighted that two key components of axillary meristem developmental programs may have been co-opted in controlling flower/ear number of an axillary inflorescence in legumes/maize, hinting at the diversification of axillary-meristem-patterning programs in different lineages. This begs the question how axillary meristem patterning programs may have diversified during plant evolution and hence helped shape the rich variation in shoot branching systems.

OsMADS6-OsMADS32 and REP1 control palea cellular heterogeneity and morphogenesis in rice

Precise regulation of cell proliferation and differentiation is vital for organ morphology. Rice palea, serving as sepal, comprises two distinct regions: the marginal region (MRP) and body of palea (BOP), housing heterogeneous cell populations, which makes it an ideal system for studying organ morphogenesis. We report that the transcription factor (TF) REP1 promotes epidermal cell proliferation and differentiation in the BOP, resulting in hard silicified protrusion cells, by regulating the cyclin-dependent kinase gene, OsCDKB1;1. Conversely, TFs OsMADS6 and OsMADS32 are expressed exclusively in the MRP, where they limit cell division rates by inhibiting OsCDKB2;1 expression and promote endoreduplication, yielding elongated epidermal cells. Furthermore, reciprocal inhibition between the OsMADS6-OsMADS32 complex and REP1 fine-tunes the balance between cell division and differentiation during palea morphogenesis. We further show the functional conservation of these organ identity genes in heterogeneous cell growth in Arabidopsis, emphasizing a critical framework for controlling cellular heterogeneity in organ morphogenesis.

The ldp1 Mutation Affects the Expression of Auxin-Related Genes and Enhances SAM Size in Rice

Panicle type is one of the important factors affecting rice (Oryza sativa L.) yield, and the identification of regulatory genes in panicle development can provide significant insights into the molecular network involved. This study identified a large and dense panicle 1 (ldp1) mutant produced from the Wuyunjing 7 (WYJ7) genotype, which displayed significant relative increases in panicle length, number of primary and secondary branches, number of grains per panicle, grain width, and grain yield per plant. Scanning electron microscopy results showed that the shoot apical meristem (SAM) of ldp1 was relatively larger at the bract stage (BM), with a significantly increased number of primary (PBM) and secondary branch (SBM) meristematic centers, indicating that the ldp1 mutation affects early stages in SAM development Comparative RNA-Seq analysis of meristem tissues from WYJ7 and ldp1 at the BM, PBM, and SBM developmental stages indicated that the number of differentially expressed genes (DEGs) were highest (1407) during the BM stage. Weighted gene coexpression network analysis (WGCNA) revealed that genes in one module (turquoise) are associated with the ldp1 phenotype and highly expressed during the BM stage, suggesting their roles in the identity transition and branch differentiation stages of rice inflorescences. Hub genes involved in auxin synthesis and transport pathways, such as OsAUX1, OsAUX4, and OsSAUR25, were identified. Moreover, GO and KEGG analysis of the DEGs in the turquoise module and the 1407 DEGs in the BM stage revealed that a majority of genes involved in tryptophan metabolism and auxin signaling pathway were differentially expressed between WYJ and ldp1. The genetic analysis indicated that the ldp1 phenotype is controlled by a recessive monogene (LDP1), which was mapped to a region between 16.9 and 18.1 Mb on chromosome seven. This study suggests that the ldp1 mutation may affect the expression of key genes in auxin synthesis and signal transduction, enhance the size of SAM, and thus affect panicle development. This study provides insights into the molecular regulatory network underlying rice panicle morphogenesis and lays an important foundation for further understanding the function and molecular mechanism of LDP1 during panicle development.

Identification and map-based cloning of long glume mutant gene lgm1 in barley

The spikes of gramineous plants are composed of specialized units called spikelets. Two bracts at the spikelet bases are known as glumes. The spikelet glumes in barley are degenerated into threadlike structures. Here, we report a long glume mutant, lgm1, similar in appearance to a lemma with a long awn at the apex. Map-based cloning showed that the mutant lgm1 allele has an approximate 1.27 Mb deletion of in chromosome 2H. The deleted segment contains five putative high-confidence genes, among which HORVU.MOREX.r3.2HG0170820 encodes a C2H2 zinc finger protein, an ortholog of rice NSG1/LRG1 and an important candidate for the Lgm1 allele. Line GA01 with a long glume and short awn was obtained in progenies of crosses involving the lgm1 mutant. Interestingly, lsg1, a mutant with long glumes on lateral spikelets, was obtained in the progenies of the lgm1 mutant. The long glume variant increased the weight of kernels in the lateral spikelets and increased kernel uniformity across the entire spike, greatly improving the potential of six-rowed barley for malting.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01448-x.

Form follows function in Triticeae inflorescences

Grass inflorescences produce grains, which are directly connected to our food. In grass crops, yields are mainly affected by grain number and weight; thus, understanding inflorescence shape is crucially important for cereal crop breeding. In the last two decades, several key genes controlling inflorescence shape have been elucidated, thanks to the availability of rich genetic resources and powerful genomics tools. In this review, we focus on the inflorescence architecture of Triticeae species, including the major cereal crops wheat and barley. We summarize recent advances in our understanding of the genetic basis of spike branching, and spikelet and floret development in the Triticeae. Considering our changing climate and its impacts on cereal crop yields, we also discuss the future orientation of research.

Genetic control of morphological traits useful for improving sorghum

Global climate change and global warming, coupled with the growing population, have raised concerns about sustainable food supply and bioenergy demand. Sorghum [Sorghum bicolor (L.) Moench] ranks fifth among cereals produced worldwide; it is a C₄ crop with a higher stress tolerance than other major cereals and has a wide range of uses, such as grains, forage, and biomass. Therefore, sorghum has attracted attention as a promising crop for achieving sustainable development goals (SDGs). In addition, sorghum is a suitable genetic model for C₄ grasses because of its high morphological diversity and relatively small genome size compared to other C₄ grasses. Although sorghum breeding and genetic studies have lagged compared to other crops such as rice and maize, recent advances in research have identified several genes and many quantitative trait loci (QTLs) that control important agronomic traits in sorghum. This review outlines traits and genetic information with a focus on morphogenetic aspects that may be useful in sorghum breeding for grain and biomass utilization.

Plastid phylogenomics and morphological character evolution of Chloridoideae (Poaceae)

Chloridoideae is one of the largest subfamilies of Poaceae, containing many species of great economic and ecological value; however, phylogenetic relationships among the subtribes and genera of Cynodonteae are controversial. In the present study, we combined 111 plastomes representing all five tribes, including 25 newly sequenced plastomes that are mostly from Cynodonteae. Phylogenetic analyses supported the five monophyletic tribes of Chloridoideae, including Centropodieae, Triraphideae, Eragrostideae, Zoysieae and Cynodonteae. Simultaneously, nine monophyletic lineages were revealed in Cynodonteae: supersubtribe Boutelouodinae, subtribes Tripogoninae, Aeluropodinae, Eleusininae, Dactylocteniinae, supersubtribe Gouiniodinae, Cleistogenes and Orinus, and subtribe Triodiinae. Within the tribe of Cynodonteae, the basal lineage is supersubtribe Boutelouodinae and Tripogoninae is sister to the remaining lineages. The clade formed of Aeluropodinae and Eleusininae is sister to the clade composed of Dactylocteniinae, supersubtribe Gouiniodinae, Cleistogenes and Orinus, and subtribe Triodiinae. The clade comprising Dactylocteniinae and supersubtribe Gouiniodinae is sister to the clade comprising Cleistogenes, Orinus, and Triodiinae. Acrachne is a genus within Eleusininae but not within Dactylocteniinae. Molecular evidence determined that Diplachne is not clustered with Leptochloa, which indicated that Diplachne should not be combined into Leptochloa. Cleistogenes is sister to a clade composed of Orinus and Triodia, whereas the recently proposed subtribe Orininae was not supported. Cynodonteae was estimated to have experienced rapid divergence within a short period, which could be a major obstacle in resolving its phylogenetic relationships. Ancestral state reconstructions of morphological characters showed that the most recent common ancestor (MRCA) of Chloridoideae has a panicle, multiple florets in each spikelet, the peaked type of stomatal subsidiary cells, and a saddle-shaped phytoliths, while the ancestral morphological characters of Cynodonteae are the panicle, peaked type of stomatal subsidiary cells, sharp-cap cell typed and equal-base-cell microhair, and square-shaped phytoliths. Overall, plastome phylogenomics provides new insights into the phylogenetic relationships and morphological character evolution of Chloridoideae.