A molecular framework for grain number determination in barley

Flowering plants with indeterminate inflorescences often produce more floral structures than they require. We found that floral primordia initiations in barley (Hordeum vulgare L.) are molecularly decoupled from their maturation into grains. While initiation is dominated by flowering-time genes, floral growth is specified by light signaling, chloroplast, and vascular developmental programs orchestrated by barley CCT MOTIF FAMILY 4 (HvCMF4), which is expressed in the inflorescence vasculature. Consequently, mutations in HvCMF4 increase primordia death and pollination failure, mainly through reducing rachis greening and limiting plastidial energy supply to developing heterotrophic floral tissues. We propose that HvCMF4 is a sensory factor for light that acts in connection with the vascular-localized circadian clock to coordinate floral initiation and survival. Notably, stacking beneficial alleles for both primordia number and survival provides positive implications on grain production. Our findings provide insights into the molecular underpinnings of grain number determination in cereal crops.

[1]  B. Carver,et al.  TaCol-B5 modifies spike architecture and enhances grain yield in wheat , 2022, Science.

[2]  A. Fernie,et al.  Convergent selection of a WD40 protein that enhances grain yield in maize and rice , 2022, Science.

[3]  T. Schnurbusch,et al.  Evolution of inflorescence branch modifications in cereal crops. , 2022, Current opinion in plant biology.

[4]  OUP accepted manuscript , 2022, Molecular Biology And Evolution.

[5]  E. López-Juez,et al.  Chloroplast development in green plant tissues: the interplay between light, hormone, and transcriptional regulation. , 2021, The New phytologist.

[6]  A. Junker,et al.  Mutation of the ALBOSTRIANS Ohnologous Gene HvCMF3 Impairs Chloroplast Development and Thylakoid Architecture in Barley , 2021, Frontiers in Plant Science.

[7]  T. Schnurbusch,et al.  Strategies of grain number determination differentiate barley row-types. , 2021, Journal of experimental botany.

[8]  T. Schnurbusch,et al.  ‘Spikelet stop’ determines the maximum yield potential stage in barley , 2021, Journal of experimental botany.

[9]  E. López-Juez,et al.  Cellular and transcriptomic analyses reveal two-staged chloroplast biogenesis underpinning photosynthesis build-up in the wheat leaf , 2021, Genome biology.

[10]  M. Hannah,et al.  Chronoculture, harnessing the circadian clock to improve crop yield and sustainability , 2021, Science.

[11]  T. Schnurbusch,et al.  Transcriptional landscapes of floral meristems in barley , 2021, Science Advances.

[12]  M. Korff,et al.  Supplementary Information for INTERMEDIUM-M encodes an HvAP2L-H5 ortholog and is required for inflorescence indeterminacy and spikelet determinacy in barley , 2021 .

[13]  OUP accepted manuscript , 2021, Journal Of Experimental Botany.

[14]  P. Langridge,et al.  The barley pan-genome reveals the hidden legacy of mutation breeding , 2020, Nature.

[15]  Heather M Meyer In search of function: nuclear bodies and their possible roles as plant environmental sensors. , 2020, Current opinion in plant biology.

[16]  T. Ischebeck,et al.  Ties between Stress and Lipid Droplets Pre-date Seeds. , 2020, Trends in plant science.

[17]  Sylvestre Marillonnet,et al.  Synthetic DNA Assembly Using Golden Gate Cloning and the Hierarchical Modular Cloning Pipeline , 2020, Current protocols in molecular biology.

[18]  E. Truernit,et al.  A Reservoir of Pluripotent Phloem Cells Safeguards the Linear Developmental Trajectory of Protophloem Sieve Elements , 2020, Current Biology.

[19]  I. Haferkamp,et al.  Identification of Chloroplast Envelope Proteins with Critical Importance for Cold Acclimation1[OPEN] , 2019, Plant Physiology.

[20]  T. Schnurbusch,et al.  Of floral fortune: tinkering with the grain yield potential of cereal crops. , 2020, The New phytologist.

[21]  Robert J. Schmitz,et al.  The prevalence, evolution and chromatin signatures of plant regulatory elements , 2019, Nature Plants.

[22]  M. Lercher,et al.  Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees , 2019, Nucleic Acids Res..

[23]  K. Mayer,et al.  TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools , 2019, Genome Biology.

[24]  A. Himmelbach,et al.  Leaf Variegation and Impaired Chloroplast Development Caused by a Truncated CCT Domain Gene in albostrians Barley[OPEN] , 2019, Plant Cell.

[25]  R. Simon,et al.  CENTRORADIALIS Interacts with FLOWERING LOCUS T-Like Genes to Control Floret Development and Grain Number1[OPEN] , 2019, Plant Physiology.

[26]  Alireza Hadj Khodabakhshi,et al.  Metascape provides a biologist-oriented resource for the analysis of systems-level datasets , 2019, Nature Communications.

[27]  T. Schnurbusch,et al.  Unleashing floret fertility in wheat through the mutation of a homeobox gene , 2019, Proceedings of the National Academy of Sciences.

[28]  S. Kelly,et al.  OrthoFinder: phylogenetic orthology inference for comparative genomics , 2019, Genome Biology.

[29]  Matthias Lange,et al.  Genebank genomics highlights the diversity of a global barley collection , 2018, Nature Genetics.

[30]  R. Dolferus,et al.  Anther Morphological Development and Stage Determination in Triticum aestivum , 2018, Front. Plant Sci..

[31]  James C. W. Locke,et al.  Phytochromes function as thermosensors in Arabidopsis , 2016, Science.

[32]  M. von Korff,et al.  The Genetic Control of Reproductive Development under High Ambient Temperature1[OPEN] , 2016, Plant Physiology.

[33]  Roland Eils,et al.  Complex heatmaps reveal patterns and correlations in multidimensional genomic data , 2016, Bioinform..

[34]  T. Kleine,et al.  Retrograde signaling: Organelles go networking. , 2016, Biochimica et biophysica acta.

[35]  Lior Pachter,et al.  Near-optimal probabilistic RNA-seq quantification , 2016, Nature Biotechnology.

[36]  Ari Pekka Mähönen,et al.  Plant vascular development: from early specification to differentiation , 2015, Nature Reviews Molecular Cell Biology.

[37]  Steven Maere,et al.  A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants1[OPEN] , 2015, Plant Physiology.

[38]  A. Pankin,et al.  Global Transcriptome Profiling of Developing Leaf and Shoot Apices Reveals Distinct Genetic and Environmental Control of Floral Transition and Inflorescence Development in Barley[OPEN] , 2015, The Plant Cell.

[39]  Dawn H. Nagel,et al.  Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis , 2015, Proceedings of the National Academy of Sciences.

[40]  S. Friedel,et al.  The low molecular weight fraction of compounds released from immature wheat pistils supports barley pollen embryogenesis , 2015, Front. Plant Sci..

[41]  Luyan Zhang,et al.  QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations , 2015 .

[42]  T. Hatanaka,et al.  CO2-Responsive CONSTANS, CONSTANS-Like, and Time of Chlorophyll a/b Binding Protein Expression1 Protein Is a Positive Regulator of Starch Synthesis in Vegetative Organs of Rice1[OPEN] , 2015, Plant Physiology.

[43]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[44]  S. Kay,et al.  Tissue-specific clocks in Arabidopsis show asymmetric coupling , 2014, Nature.

[45]  B. Kilian,et al.  Mapping-by-Sequencing Identifies HvPHYTOCHROME C as a Candidate Gene for the early maturity 5 Locus Modulating the Circadian Clock and Photoperiodic Flowering in Barley , 2014, Genetics.

[46]  B. Trevaskis,et al.  EARLY FLOWERING3 Regulates Flowering in Spring Barley by Mediating Gibberellin Production and FLOWERING LOCUS T Expression[C][W] , 2014, Plant Cell.

[47]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[48]  J. Franco-Zorrilla,et al.  DNA-binding specificities of plant transcription factors and their potential to define target genes , 2014, Proceedings of the National Academy of Sciences.

[49]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[50]  B. Drosse,et al.  HvLUX1 is a candidate gene underlying the early maturity 10 locus in barley: phylogeny, diversity, and interactions with the circadian clock and photoperiodic pathways , 2013, The New phytologist.

[51]  J. Sheen,et al.  Glucose–TOR signalling reprograms the transcriptome and activates meristems , 2013, Nature.

[52]  Paul D. Shaw,et al.  Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley , 2012, Nature Genetics.

[53]  S. Taudien,et al.  Genome Dynamics Explain the Evolution of Flowering Time CCT Domain Gene Families in the Poaceae , 2012, PloS one.

[54]  Eunkyoo Oh,et al.  Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses , 2012, Nature Cell Biology.

[55]  Johannes E. Schindelin,et al.  Fiji: an open-source platform for biological-image analysis , 2012, Nature Methods.

[56]  Katja E. Jaeger,et al.  PHYTOCHROME INTERACTING FACTOR4 controls the thermosensory activation of flowering , 2012, Nature.

[57]  Thomas Altmann,et al.  Dynamic ¹³C/¹ H NMR imaging uncovers sugar allocation in the living seed. , 2011, Plant biotechnology journal.

[58]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[59]  Daniel Koenig,et al.  WOX4 Promotes Procambial Development1[W][OA] , 2009, Plant Physiology.

[60]  H. Piepho,et al.  Population structure and phenotypic variation of a spring barley world collection set up for association studies , 2009 .

[61]  Peng Wang,et al.  GLK Transcription Factors Coordinate Expression of the Photosynthetic Apparatus in Arabidopsis[W][OA] , 2009, The Plant Cell Online.

[62]  H. Rolletschek,et al.  Molecular physiology of adventitious root formation in Petunia hybrida cuttings: involvement of wound response and primary metabolism. , 2009, The New phytologist.

[63]  Lei Wang,et al.  Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice , 2008, Nature Genetics.

[64]  J. Kumlehn,et al.  Efficient generation of transgenic barley: the way forward to modulate plant-microbe interactions. , 2008, Journal of plant physiology.

[65]  S. Kay,et al.  PRR3 Is a Vascular Regulator of TOC1 Stability in the Arabidopsis Circadian Clock[W][OA] , 2007, The Plant Cell Online.

[66]  Xing Wang Deng,et al.  Light-regulated transcriptional networks in higher plants , 2007, Nature Reviews Genetics.

[67]  Hongyu Zhao,et al.  Analysis of Transcription Factor HY5 Genomic Binding Sites Revealed Its Hierarchical Role in Light Regulation of Development[W] , 2007, The Plant Cell Online.

[68]  P. Hayes,et al.  Validation of the VRN-H2/VRN-H1 epistatic model in barley reveals that intron length variation in VRN-H1 may account for a continuum of vernalization sensitivity , 2007, Molecular Genetics and Genomics.

[69]  D. Laurie,et al.  The Pseudo-Response Regulator Ppd-H1 Provides Adaptation to Photoperiod in Barley , 2005, Science.

[70]  Anthony Hall,et al.  Plant Circadian Clocks Increase Photosynthesis, Growth, Survival, and Competitive Advantage , 2005, Science.

[71]  Shelley Hepworth,et al.  CONSTANS acts in the phloem to regulate a systemic signal that induces photoperiodic flowering of Arabidopsis , 2004, Development.

[72]  P. Wall,et al.  A Quantitative Scale of Spike Initial and Pistil Development in Barley and Wheat , 1983 .

[73]  W. R. Stern,et al.  The Vascular System in the Rachis of a Wheat Ear , 1981 .

[74]  E. Kirby,et al.  The Vascular Anatomy of the Barley Spikelet , 1975 .