Inflorescences of the tribe Triticeae, which includes wheat (Triticum sp. L.) and barley (Hordeum vulgare L.) are characterized by sessile spikelets directly borne on the main axis, thus forming a branchless spike. ‘Compositum-Barley’ and tetraploid ‘Miracle-Wheat’ (T. turgidum convar. compositum (L.f.) Filat.) display noncanonical spike-branching in which spikelets are replaced by lateral branch-like structures resembling small-sized secondary spikes. As a result of this branch formation ‘Miracle-Wheat’ produces significantly more grains per spike, leading to higher spike yield. In this study, we first isolated the gene underlying spike-branching in ‘Compositum-Barley,’ i.e., compositum 2 (com2). Moreover, we found that COM2 is orthologous to the branched headt (bht) locus regulating spike branching in tetraploid ‘Miracle-Wheat.’ Both genes possess orthologs with similar functions in maize BRANCHED SILKLESS 1 (BD1) and rice FRIZZY PANICLE/BRANCHED FLORETLESS 1 (FZP/BFL1) encoding AP2/ERF transcription factors. Sequence analysis of the bht locus in a collection of mutant and wild-type tetraploid wheat accessions revealed that a single amino acid substitution in the DNA-binding domain gave rise to the domestication of ‘Miracle-Wheat.’ mRNA in situ hybridization, microarray experiments, and independent qRT-PCR validation analyses revealed that the branch repression pathway in barley is governed through the spike architecture gene Six-rowed spike 4 regulating COM2 expression, while HvIDS1 (barley ortholog of maize INDETERMINATE SPIKELET 1) is a putative downstream target of COM2. These findings presented here provide new insights into the genetic basis of spike architecture in Triticeae, and have disclosed new targets for genetic manipulations aiming at boosting wheat’s yield potential.

Grasses have varying inflorescence shapes; however, little is known about the genetic mechanisms specifying such shapes among tribes. Here, we identify the grass-specific TCP transcription factor COMPOSITUM 1 (COM1) expressing in inflorescence meristematic boundaries of different grasses. COM1 specifies branch-inhibition in barley (Triticeae) versus branch-formation in non-Triticeae grasses. Analyses of cell size, cell walls and transcripts reveal barley COM1 regulates cell growth, thereby affecting cell wall properties and signaling specifically in meristematic boundaries to establish identity of adjacent meristems. COM1 acts upstream of the boundary gene Liguleless1 and confers meristem identity partially independent of the COM2 pathway. Furthermore, COM1 is subject to purifying natural selection, thereby contributing to specification of the spike inflorescence shape. This meristem identity pathway has conceptual implications for both inflorescence evolution and molecular breeding in Triticeae.

Key message Modifying morphometric inflorescence traits is important for increasing grain yield in wheat . Mapping revealed nine QTL, including new QTL and a new allele for the q locus, controlling wheat spike morphometric traits . Abstract To identify loci controlling spike morphometric traits, namely spike length (SL), internode length (IL), node number per spike (NPS), and node density (ND), we studied 146 Recombinant Inbred Lines of tetraploid wheat ( Triticum turgidum L.) derived from standard spike and spike-branching mutant parents. Phenotypic analyses of spike morphometric traits showed low genetic coefficients of variation, resulting in high heritabilities. The phenotypic correlation between NPS with growing degree days (GDD) suggested the importance of GDD in the determination of node number in wheat. The major effect QTL for GDD or heading date was mapped to chromosome 7BS carrying the flowering time gene, Vrn3 - B1 . Mapping also identified nine QTL controlling spike morphometric traits. Most of these loci controlled more than a single trait, suggesting a close genetic interrelationship among spike morphometric traits. For example, this study identified a new QTL, QND . ipk - 4AL , controlling ND (up to 17.6% of the phenotypic variance), IL (up to 11% of the phenotypic variance), and SL (up to 20.8% of the phenotypic variance). Similarly, the major effect QTL for IL was mapped to the q locus. Sequencing of the Q / q gene further revealed a new q allele, q del - 5A , in spike-branching accessions possessing a six base pair deletion close to the miR172 target site. The identification of q del - 5A suggested that the spike-branching tetraploid wheats are double mutants for the spikelet meristem (SM) identity gene, i.e., branched head t ( TtBH t ), and the q gene, which is believed to be involved in the SM indeterminacy complex in wheat. Electronic supplementary material The online version of this article (10.1007/s00122-019-03305-4) contains supplementary material, which is available to authorized users.

Organ development in plants predominantly occurs postembryonically through combinatorial activity of meristems; therefore, meristem and organ fate are intimately connected. Inflorescence morphogenesis in grasses (Poaceae) is complex and relies on a specialized floral meristem, called spikelet meristem, that gives rise to all other floral organs and ultimately the grain. The fate of the spikelet determines reproductive success and contributes toward yield-related traits in cereal crops. Here, we examined the transcriptional landscapes of floral meristems in the temperate crop barley (Hordeum vulgare L.) using RNA-seq of laser capture microdissected tissues from immature, developing floral structures. Our unbiased, high-resolution approach revealed fundamental regulatory networks, previously unknown pathways, and key regulators of barley floral fate and will equally be indispensable for comparative transcriptional studies of grass meristems.

Key message Genetic modification of spike architecture is essential for improving wheat yield. Newly identified loci for the ‘Miracle wheat’ phenotype on chromosomes 1AS and 2BS have significant effects on spike traits. Abstract The wheat (Triticum ssp.) inflorescence, also known as a spike, forms an unbranched inflorescence in which the inflorescence meristem generates axillary spikelet meristems (SMs) destined to become sessile spikelets. Previously, we identified the putatively causative mutation in the branched headt (bht) gene (TtBH-A1) of tetraploid wheat (T. turgidum convar. compositum (L.f.) Filat.) responsible for the loss of SM identity, converting the non-branching spike to a branched wheat spike. In the current study, we performed whole-genome quantitative trait loci (QTL) analysis using 146 recombinant inbred lines (RILs) derived from a cross between spike-branching wheat (‘Miracle wheat’) and an elite durum wheat cultivar showing broad phenotypic variation for spike architecture. Besides the previously found gene at the bht-A1 locus on the short arm of chromosome 2A, we also mapped two new modifier QTL for spike-branching on the short arm of chromosome 1A, termed bht-A2, and 2BS. Using biparental mapping population and GWAS in 302 diverse accessions, the 2BS locus was highly associated with coding sequence variation found at the homoeo-allele of TtBH-B1 (bht-B1). Thus, RILs that combined both bht-A1 and bht-B1 alleles showed additive genetic effects leading to increased penetrance and expressivity of the supernumerary spikelet and/or mini-spike formation.

41Grasses have varying inflorescence shapes; however, little is known about the genetic mechanis ms 42 specifying such shapes among tribes. We identified the grass-specific TCP transcription factor 43 COMPOSITUM 1 (COM1) expressed in inflorescence meristematic boundaries of differe nt 44 grasses. COM1 specifies branch-inhibition in Triticeae (barley) versus branch-formation in non- 45 Triticeae grasses. Analyses of cell size, cell walls and transcripts revealed barley COM1 regulates 46 cell growth, affecting cell wall properties and signaling specifically in meristematic boundaries to 47 establish identity of adjacent meristems. COM1 acts upstream of the boundary gene Liguleless1 48 and confers meristem identity independent of the COM2 pathway. Furthermore, COM1 is subject 49 to purifying natural selection, thereby contributing to specification of the spike inflorescence shape. 50 This meristem identity module has conceptual implications for both inflorescence evolution and 51 molecular breeding in Triticeae. 52 53 54 55 56 57 58 59 60 61 4 Main Text: 62 63The grass family (Poaceae), one of the largest angiosperm families, has evolved a striking diversity 64 of inflorescence morphologies bearing complex structures such as branches and specialized 65 spikelets 1 . These structural features are key for sorting the grass family into tribes 1 . Current grass 66 inflorescences are proposed to originate from a primitive ancestral shape exhibiting "a relative ly 67 small panicle-like branching system made up of primary and secondary paracladia (branches), each 68 one standing single at the nodes" 2 ( Fig. 1A). This ancestral panicle-like inflorescence is also 69 known as a compound spike [3][4][5] . Several independent or combined diversification processes 70 throughout the evolutionary history of the grass family have resulted in the broad diversity of 71 today's grass inflorescences 2,3,6 . Some tribes, e.g. Oryzeae (rice) and Andropogoneae (maize and 72 sorghum), still display ancestral and complex compound shapes, keeping true-lateral long primary 73 and secondary branches. Other grasses, such as Brachypodium distachyon, show lower 74 inflorescence complexity with branch length and number reduced to lateral, small pedicels ending 75 in only one multi-floretted spikelet ( Fig. 1A-C). Inflorescences within the tribe Triticeae, e.g. 76 barley (Hordeum vulgare L.), probably evolved from the ancestral compound spike into the typical 77 unbranched spike (Fig. 1D). The spike displays the least-complex inflorescence shape due to the 78 sessile nature of spikelets and reduction in rachis internodes 2,7 . Architectural variation is often 79 manifested through subtle modifications of transcriptional programs during critical transitio na l 80 windows of inflorescence meristem (IM) maturation 7,8 or functional divergence of key 81 transcriptional regulators and/or other genes 9,10 . Identification of key genetic determinants is 82 crucial for better understanding and explaining both the origin of grass inflores...

Vascular plants segment their body axis with iterative nodes of lateral branches and internodes. Appropriate node initiation and internode elongation are fundamental to plant fitness and crop yield formation; but how they are spatiotemporally coordinated remains elusive. We show that in barley (Hordeum vulgare L.), selections under domestication have extended the apical meristematic phase to promote node initiation, but constrained subsequent internode elongation. In both vegetative and reproductive axes, internode elongation displays a dynamic proximal - distal gradient, and among subpopulations of domesticated barleys at the global range, node initiation and proximal internode elongation are associated with latitudinal and longitudinal gradients, respectively. Genetic and functional analysis suggest that, in addition to their converging roles in node initiation, flowering time genes are repurposed to specify the dynamic internode elongation. Our study provides an integrated view of barley node initiation and internode elongation, and suggests that plant architecture has to be recognized as dynamic phytomeric units in the context of crop evolution.