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The shape of an inflorescence varies among cereals, ranging from a highly branched panicle in rice to a much more compact spike in barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.). However, little is known about the molecular basis of cereal inflorescence architecture. We profiled transcriptomes at three developmental stages of the barley main shoot apex — spikelet initiation, floral organ differentiation, and floral organ growth — and compared them with those from vegetative seedling tissue. Transcript analyses identified 3688 genes differentially transcribed between the three meristem stages, with a further 1394 genes preferentially expressed in reproductive compared with vegetative tissue. Co-expression assembly and Gene Ontology analysis classified these 4888 genes into 28 clusters, revealing distinct patterns for genes such as transcription factors, histone modification, and cell-cycle progression specific for each stage of inflorescence development. We also compared expression patterns of VRS (SIX-ROWED SPIKE) genes and auxin-, gibberellic acid- and cytokinin-associated genes between two-rowed and six-rowed barley to describe regulators of lateral spikelet fertility. Our findings reveal barley inflorescence phase-specific gene expression, identify new candidate genes that regulate barley meristem activities and flower development, and provide a new genetic resource for further dissection of the molecular mechanisms of spike development. Keywords: Inflorescence meristem, Transcriptome, Gene expression, Hormones, Barley

This work was supported by funds from the National Key Basic Research Developments Program, Ministry of Science and Technology, China (2013CB126902); National Transgenic Major Program Grant (2016ZX08009003-003-007); National Natural Science Foundation of China (31322040); China Innovative Research Team, Ministry of Education, and the Program of Introducing Talents of Discipline to Universities (111 Project, B14016); the Science and Technology Commission of Shanghai Municipality (grant no. 13JC1408200). Work in the Higgins laboratory is supported by the BBSRC.

During reproductive development, rice plants develop unique flower organs which determine the final grain yield. OsMADS1, one of SEPALLATA-like MADS-box genes, has been unraveled to play critical roles in rice floral organ identity specification and floral meristem determinacy. However, the molecular mechanisms underlying interactions of OsMADS1 with other floral homeotic genes in regulating flower development remains largely elusive. In this work, we studied the genetic interactions of OsMADS1 with B-, C-, and D-class genes along with physical interactions among their proteins. We show that the physical and genetic interactions between OsMADS1 and OsMADS3 are essential for floral meristem activity maintenance and organ identity specification; while OsMADS1 physically and genetically interacts with OsMADS58 in regulating floral meristem determinacy and suppressing spikelet meristem reversion. We provided important genetic evidence to support the neofunctionalization of two rice C-class genes (OsMADS3 and OsMADS58) during flower development. Gene expression profiling and quantitative RT-PCR analyses further revealed that OsMADS1 affects the expression of many genes involved in floral identity and hormone signaling, and chromatin immunoprecipitation (ChIP)–PCR assay further demonstrated that OsMADS17 is a direct target gene of OsMADS1. Taken together, these results reveal that OsMADS1 has diversified regulatory functions in specifying rice floral organ and meristem identity, probably through its genetic and physical interactions with different floral homeotic regulators.

Rice ( Oryza sativa ) has unique floral patterns that contribute to grain yield. However, the molecular mechanism underlying the specification of floral organ identities in rice, particularly the interaction among floral homeotic genes, remains poorly understood. Here, we show that the floral homeotic gene OsMADS16 (also called SUPERWOMAN1 , SPW1 , a B-class gene) acts together with the rice C-class genes OsMADS3 and OsMADS58 in specifying floral organ patterning. OsMADS16 and the two C-class genes have an overlapping expression pattern in the third whorl founder cells. Compared with the single mutants, both spw1-1 osmads3-4 and spw1-1 osmads58 double mutants exhibit additional whorls of glume-like organs within the flower, particularly an extra whorl of six glume-like structures formed at the position of the wild-type stamens. These ectopic glume-like structures were shown to have palea identity through cellular observation and in situ hybridization analysis using marker genes. Our results suggest that B- and C-class genes play a key role in suppressing indeterminate growth within the floral meristem, particularly whorl-3 primordia. We also hypothesize that, in contrast to previous assumptions, the specialized spikelet organ in rice, the palea, is the counterpart of the sepal in eudicots, and the lemma is homologous to the bract. SUMMARY The rice floral homeotic B-class gene OsMADS16 interacts with C-class genes in specifying floral organ patterning, particularly suppressing indeterminate growth within whorl-3 primordia. This work provides the evidence of the origin of the specialized organs, the lemma and the palea.

To understand the molecular mechanism of male reproductive development in the model crop rice, we isolated a complete male sterile mutant post-meiotic deficient anther1 (pda1) from a gamma-ray-treated rice mutant library. Genetic analysis revealed that the pda1 mutant was controlled by a recessive nucleus gene. The pda1 mutant anther seemed smaller with white appearance. Histological analysis demonstrated that the pda1 mutant anther undergoes normal early tapetum development without obvious altered meiosis. However, the pda1 mutant displayed obvious defects in postmeiotic tapetal development, abnormal degeneration occurred in the tapetal cells at stage 9 of anther development. Also we observed abnormal lipidic Ubisch bodies from the tapetal layer of the pda1 mutant, causing no obvious pollen exine formation. RT-PCR analysis indicated that the expression of genes involved in anther development including GAMYB, OsC4 and Wax-deficient anther1 (WDA1) was greatly reduced in the pda1 mutant anther. Using map-based cloning approach, the PDA1 gene was finely mapped between two markers HLF610 and HLF627 on chromosome 6 using 3,883 individuals of F(2) population. The physical distance between HLF610 and HLF627 was about 194 kb. This work suggests that PDA1 is required for post-meiotic tapetal development and pollen/microspore formation in rice.

As a complex wall system in flowering plants, the pollen outer wall mainly contains aliphatic sporopollenin; however, the mechanism for synthesizing these lipidic precursors during pollen development remains less well understood. Here, we report on the function of the rice tapetum-expressing TDR ( Tapetum Degeneration Retardation ) gene in aliphatic metabolism and its regulatory role during rice pollen development. The observations of transmission electron microscopy (TEM) and scanning electron microscopy (SEM) analyses suggested that pollen wall formation was significantly altered in the tdr mutant. The contents of aliphatic compositions of anther were greatly changed in the tdr mutant revealed by GC–MS (gas chromatography–mass spectrometry) testing, particularly less accumulated in fatty acids, primary alcohols, alkanes and alkenes, and an abnormal increase in secondary alcohols with carbon lengths from C29 to C35 in tdr . Microarray data revealed that a group of genes putatively involved in lipid transport and metabolism were significantly altered in the tdr mutant, indicating the critical role of TDR in the formation of the pollen wall. Also, a wide range of genes (236 in total—154 up-regulated and 82 down-regulated) exhibited statistically significant expressional differences between wild-type and tdr . In addition to its function in promoting tapetum PCD, TDR possibly plays crucial regulatory roles in several basic biological processes during rice pollen development.