Identification of the Q Gene Playing a Role in Spike Morphology Variation in Wheat Mutants and Its Regulatory Network

The wheat AP2 family gene Q controls domestication traits, including spike morphology and threshability, which are critical for the widespread cultivation and yield improvement of wheat. Although many studies have investigated the molecular mechanisms of the Q gene, its direct target genes, especially those controlling spike morphology, are not clear, and its regulatory pathways are not well established. In this study, we conducted gene mapping of a wheat speltoid spike mutant and found that a new allele of the Q gene with protein truncation played a role in spike morphology variation in the mutant. Dynamic expression levels of the Q gene throughout the spike development process suggested that the transcript abundances of the mutant were decreased at the W6 and W7 scales compared to those of the WT. We identified several mutation sites on the Q gene and showed that mutations in different domains resulted in distinct phenotypes. In addition, we found that the Q gene produced three transcripts via alternative splicing and that they exhibited differential expression patterns in nodes, internodes, flag leaves, and spikes. Finally, we identified several target genes directly downstream of Q, including TaGRF1-2D and TaMGD-6B, and proposed a possible regulatory network. This study uncovered the target genes of Q, and the results can help to clarify the mechanism of wheat spike morphology and thereby improve wheat grain yield.

Multi-locus genome-wide association mapping for spike-related traits in bread wheat (Triticum aestivum L.)

Background Bread wheat (Triticum aestivum L.) is one of the most important cereal food crops for the global population. Spike-layer uniformity (the consistency of the spike distribution in the vertical space)-related traits (SLURTs) are quantitative and have been shown to directly affect yield potential by modifying the plant architecture. Therefore, these parameters are important breeding targets for wheat improvement. The present study is the first genome-wide association study (GWAS) targeting SLURTs in wheat. In this study, a set of 225 diverse spring wheat accessions were used for multi-locus GWAS to evaluate SLURTs, including the number of spikes per plant (NSPP), spike length (SL), number of spikelets per spike (NSPS), grain weight per spike (GWPS), lowest tiller height (LTH), spike-layer thickness (SLT), spike-layer number (SLN) and spike-layer uniformity (SLU). Results In total, 136 significant marker trait associations (MTAs) were identified when the analysis was both performed individually and combined for two environments. Twenty-nine MTAs were detected in environment one, 48 MTAs were discovered in environment two and 59 MTAs were detected using combined data from the two environments. Altogether, 15 significant MTAs were found for five traits in one of the two environments, and four significant MTAs were detected for the two traits, LTH and SLU, in both environments i.e. E1, E2 and also in combined data from the two environments. In total, 279 candidate genes (CGs) were identified, including Chaperone DnaJ, ABC transporter-like, AP2/ERF, SWEET sugar transporter, as well as genes that have previously been associated with wheat spike development, seed development and grain yield. Conclusions The MTAs detected through multi-locus GWAS will be useful for improving SLURTs and thus yield in wheat production through marker-assisted and genomic selection.

Genome-wide profiling of long noncoding RNAs involved in wheat spike development

Background Long noncoding RNAs (lncRNAs) have been shown to play important roles in the regulation of plant growth and development. Recent transcriptomic analyses have revealed the gene expression profiling in wheat spike development, however, the possible regulatory roles of lncRNAs in wheat spike morphogenesis remain largely unclear. Results Here, we analyzed the genome-wide profiling of lncRNAs during wheat spike development at six stages, and identified a total of 8,889 expressed lncRNAs, among which 2,753 were differentially expressed lncRNAs (DE lncRNAs) at various developmental stages. Three hundred fifteen differentially expressed cis- and trans-regulatory lncRNA-mRNA pairs comprised of 205 lncRNAs and 279 genes were predicted, which were found to be mainly involved in the stress responses, transcriptional and enzymatic regulations. Moreover, the 145 DE lncRNAs were predicted as putative precursors or target mimics of miRNAs. Finally, we identified the important lncRNAs that participate in spike development by potentially targeting stress response genes, TF genes or miRNAs. Conclusions This study outlines an overall view of lncRNAs and their possible regulatory networks during wheat spike development, which also provides an alternative resource for genetic manipulation of wheat spike architecture and thus yield.

Interactions between two QTLs for time to anthesis on spike development and fertility in wheat

Earliness per se (Eps) genes are reported to be important in fine-tuning flowering time in wheat independently of photoperiod (Ppd) and vernalisation (Vrn). Unlike Ppd and Vrn genes, Eps have relatively small effects and their physiological effect along with chromosomal position are not well defined. We evaluated eight lines derived from crossing two vernalisation insensitive lines, Paragon and Baj (late and early flowering respectively), to study the detailed effects of two newly identified QTLs, Eps-7D and Eps-2B and their interactions under field conditions. The effect of both QTLs was minor and was affected by the allelic status of the other. While the magnitude of effect of these QTLs on anthesis was similar, they are associated with very different profiles of pre-anthesis development which also depends on their interaction. Eps-7D affected both duration before and after terminal spikelet while not affecting final leaf number (FLN) so Eps-7D-early had a faster rate of leaf appearance. Eps-2B acted more specifically in the early reproductive phase and slightly altered FLN without affecting the leaf appearance rate. Both QTLs affected the spike fertility by altering the rate of floret development and mortality. The effect of Eps-2B was very small but consistent in that -late allele tended to produce more fertile florets.

Pleiotropic function of the SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE gene TaSPL14 in wheat plant architecture

Main conclusion The function of SQUAMOSA PROMOTER-BINDING PROTEIN-BOX gene TaSPL14 in wheat is similar to that of OsSPL14 in rice in regulating plant height, panicle length, spikelet number, and thousand-grain weight of wheat, but differs during tiller development. TaSPL14 may regulate spike development via ethylene-response gene EIN3-LIKE 1 (TaEIL1), ETHYLENE-RESPONSIVE TRANSCRIPTION FACTOR 2.11 (TaRAP2.11), and ETHYLENE-RESPONSIVE TRANSCRIPTION FACTOR 1 (TaERF1), but not DENSE AND ERECT PANICLE 1 (TaDEP1) in wheat. Abstract The SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE gene OsSPL14 from rice is considered to be a major determinant of ideal plant architecture consisting of few unproductive tillers, more grains per spike, and high resistance of stems to lodging. However, the function of its orthologous gene, TaSPL14, in wheat is unknown. Here, we reported the functional similarities and differences between TaSPL14 and OsSPL14. Similar to OsSPL14 knock-outs in rice, wheat TaSPL14 knock-out plants exhibited decreased plant height, panicle length, spikelet number, and thousand-grain weight. In contrast to OsSPL14, however, TaSPL14 did not affect tiller number. Transcriptome analysis revealed that the expression of genes related to ethylene response was significantly decreased in young spikes of TaSPL14 knock-out lines as compared with wild type. TaSPL14 directly binds to the promoters of the ethylene-response genes TaEIL1, TaRAP2.11, and TaERF1, and promotes their expression, suggesting that TaSPL14 might regulate wheat spike development via the ethylene-response pathway. The elucidation of TaSPL14 will contribute to understanding of the molecular mechanisms that underlie wheat plant architecture.

Interactions Between SQUAMOSA and SVP MADS-box Proteins Regulate Meristem Transitions During Wheat Spike Development

ABSTRACTA better understanding of spike development can contribute to improving wheat productivity. MADS-box genes VRN1 and FUL2 (SQUAMOSA-clade) play critical and redundant roles in wheat spike and spikelet development, where they act as repressors of MADS-box genes of the SHORT VEGETATIVE PHASE (SVP) clade (VRT2, SVP1 and SVP3). Here, we show that wheat vrt2 svp1 mutants are late flowering, have shorter stems, increased number of spikelets per spike and unusual axillary inflorescences in nodes of the elongating stem. Constitutive expression of VRT2 resulted in leafy glumes and lemmas, reversion of basal spikelets to spikes, and down-regulation of MADS-genes involved in floral development. Moreover, constitutive expression of VRT2 enhanced spikelet defects of ful2, whereas vrt2 reduced vegetative characteristics in the spikelets of vrn1 ful2 mutants heterozygous for VRN-A1. These SVP-SQUAMOSA genetic interactions were paralleled by physical interactions among their encoded proteins. SVP proteins were able to reduce SQUAMOSA-SEPALLATA interactions in yeast-three-hybrid experiments. We propose that SQUAMOSA-SVP complexes act during the early reproductive phase to promote heading, formation of the terminal spikelet, and stem elongation, but that down-regulation of SVP genes is then necessary for the formation of SQUAMOSA-SEPALLATA complexes that are required for normal spikelet and floral development.

RING-Type E3 Ubiqitin Ligase Barley Genes (HvYrg1–2) Control Characteristics of Both Vegetative Organs and Seeds as Yield Components

Previously, studies on RING-type E3 ubiquitin ligases in cereals were preferentially focused on GW2 genes primarily controlling seed parameters in rice and wheat. Here we report cloning two HvYrg genes from barley that share significant homology with rice GW2 gene. In antisense genotypes efficiency of gene silencing varied between genes and transgenic lines: ASHvYrg1: 30–50% and ASHvYrg2: 20–27%. Reduced activity of both genes altered shoot system with increasing number of side shoots. Changes in leaf width, weight, or plant weight and height reached significant levels in some transgenic lines. Lowering expression of the two barley HvYrg genes caused opposite responses in spike development. Plants with ASHvYrg1 gene construct showed earlier heading time and prolonged grain-filling period, while plants from ASHvYrg2 genotype flowered in delay. Digital imaging of root development revealed that down-regulation of HvYrg1 gene variant stimulated root growth, while ASHvYrg2 plants developed reduced root system. Comparison of seed parameters indicated an increase in thousand grain weight accompanied with longer and wider seed morphology. In summary we conclude that in contrast to inhibition of GW2 genes in rice and wheat plants, down-regulation of the barely HvYrg genes caused substantial changes in vegetative organs in addition to alteration of seed parameters.

Interactions between two QTLs for time to anthesis on spike development and fertility in wheat

Earliness per se (Eps) genes are reported to be important in fine-tuning flowering time in wheat independently of photoperiod (Ppd) and vernalisation (Vrn). Unlike Ppd and Vrn genes, Eps have relatively small effects and their physiological effect along with chromosomal position are not well defined. We evaluated eight lines derived from crossing Paragon and Baj (late and early flowering respectively), vernalisation insensitive, to study the detailed effects of two newly identified QTLs, Eps-7D and Eps-2B and their interactions under field conditions. The effect of both QTLs were minor but their effect was modulated by the allelic status of the other. While the magnitude of effect of these QTLs on anthesis was similar, they are associated with very different profiles of pre-anthesis development which also depends on their interaction. Eps-7D affected both duration before and after terminal spikelet while not affecting final leaf number (FLN) so Eps-7D-early had a faster rate of leaf appearance. Eps-2B acted more specifically in the early reproductive phase and slightly altered FLN without affecting the leaf appearance rate. Both Eps-7D and 2B affected the spike fertility by altering the rate of floret development and mortality. The effect of the latter was very small but consistent in that the -late allele tended to produced more fertile florets.