Hormone-mediated growth dynamics of the barley pericarp as revealed by magnetic resonance imaging and transcript profiling

Comparative Transcriptome Analysis Reveals Key Functions of MiMYB Gene Family in Macadamia Nut Pericarp Formation

Macadamia nuts are one of the most important economic food items in the world. Pericarp thickness and flavonoid composition are the key quality traits of Macadamia nuts, but the underlying mechanism of pericarp formation is still unknown. In this study, three varieties with significantly different pericarp thicknesses, namely, A38, Guire No.1, and HAES 900, at the same stage of maturity, were used for transcriptome analysis, and the results showed that there were significant differences in their gene expression profile. A total of 3837 new genes were discovered, of which 1532 were functionally annotated. The GO, COG, and KEGG analysis showed that the main categories in which there were significant differences were flavonoid biosynthesis, phenylpropanoid biosynthesis, and the cutin, suberine, and wax biosynthesis pathways. Furthermore, 63 MiMYB transcription factors were identified, and 56 R2R3-MYB transcription factors were clustered into different subgroups compared with those in Arabidopsis R2R3-MYB. Among them, the S4, S6, and S7 subgroups were involved in flavonoid biosynthesis and pericarp formation. A total of 14 MiMYBs' gene expression were verified by RT-qPCR analysis. These results provide fundamental knowledge of the pericarp formation regulatory mechanism in macadamia nuts.

Temporal and spatial transcriptional regulation of phytohormone metabolism during seed development in barley (Hordeum vulgare L.)

Plant hormones play important roles in seed development; however, transcriptional regulation of their metabolism and levels of the respective bioactive forms during barley seed development is poorly understood. To this end, this study performed a comprehensive analysis of changes in the expression patterns phytohormone metabolism genes and levels of the respective bioactive forms in the embryo and endosperm tissues. Our study showed the presence of elevated levels of abscisic acid (ABA), bioactive forms of gibberellins (GAs), jasmonate (JA) and cytokinins (CKs), auxin and salicylic acid (SA) in the endosperm and embryo tissues at early stage of seed filling (SF). The levels of all hormones in both tissues, except that of ABA, decreased to low levels during SF. In contrast, embryonic ABA level increased during SF and peaked at physiological maturity (PM) while the endospermic ABA was maintained at a similar level observed during SF. Although its level decreased high amount of ABA was still present in the embryo during post-PM. We detected low levels of ABA in the endosperm and all the other hormones in both tissues during post-PM phase except the relatively higher levels of jasmonoyl-isoleucine and SA detected at late stage of post-PM. Our data also showed that spatiotemporal changes in the levels of plant hormones during barley seed development are mediated by the expression of specific genes involved in their respective metabolic pathways. These results indicate that seed development in barley is mediated by spatiotemporal modulation in the metabolism and levels of plant hormones.

Integrative analysis of transcriptome and miRNAome reveals molecular mechanisms regulating pericarp thickness in sweet corn during kernel development

Pericarp thickness affects the edible quality of sweet corn (Zea mays L. saccharata Sturt.). Therefore, breeding varieties with a thin pericarp is important for the quality breeding of sweet corn. However, the molecular mechanisms underlying the pericarp development remain largely unclear. We performed an integrative analysis of mRNA and miRNA sequencing to elucidate the genetic mechanism regulating pericarp thickness during kernel development (at 15 days, 19 days, and 23 days after pollination) of two sweet corn inbred lines with different pericarp thicknesses (M03, with a thinner pericarp and M08, with a thicker pericarp). A total of 2,443 and 1,409 differentially expressed genes (DEGs) were identified in M03 and M08, respectively. Our results indicate that phytohormone-mediated programmed cell death (PCD) may play a critical role in determining pericarp thickness in sweet corn. Auxin (AUX), gibberellin (GA), and brassinosteroid (BR) signal transduction may indirectly mediate PCD to regulate pericarp thickness in M03 (the thin pericarp variety). In contrast, abscisic acid (ABA), cytokinin (CK), and ethylene (ETH) signaling may be the key regulators of pericarp PCD in M08 (the thick pericarp variety). Furthermore, 110 differentially expressed microRNAs (DEMIs) and 478 differentially expressed target genes were identified. miRNA164-, miRNA167-, and miRNA156-mediated miRNA-mRNA pairs may participate in regulating pericarp thickness. The expression results of DEGs were validated by quantitative real-time PCR. These findings provide insights into the molecular mechanisms regulating pericarp thickness and propose the objective of breeding sweet corn varieties with a thin pericarp.

The da1 mutation in wheat increases grain size under ambient and elevated CO2 but not grain yield due to trade-off between grain size and grain number

Grain size is potentially yield determining in wheat, controlled by the ubiquitin pathway and negatively regulated by ubiquitin receptor DA1. We analyzed whether increased thousand grain weight in wheat da1 mutant is translated into higher grain yield and whether additional carbon provided by elevated (e)CO₂ can be better used by the da1, displaying higher grain sink strength and size. Yield-related, biomass, grain quality traits, and grain dimensions were analyzed by two-factorial mixed-model analysis, regarding genotype and eCO₂. da1 increased grain size but reduced spikes and grains per plant, grains per spike, and spikelets per spike, independent of eCO₂ treatment, leaving total grain yield unchanged. eCO₂ increased yield and grain number additively and independently of da1 but did not overcome the trade-off between grain size and number observed for da1. eCO₂ but not da1 impaired grain quality, strongly decreasing concentrations of several macroelement and microelement. In conclusion, intrinsic stimulation of grain sink strength and grain size, achieved by da1, is not benefitting total yield unless trade-offs between grain size and numbers can be overcome. The results reveal interactions of yield components in da1-wheat under ambient and eCO₂, thereby uncovering limitations enhancing wheat yield potential.

Esmraldi: efficient methods for the fusion of mass spectrometry and magnetic resonance images

Background

Mass spectrometry imaging (MSI) is a family of acquisition techniques producing images of the distribution of molecules in a sample, without any prior tagging of the molecules. This makes it a very interesting technique for exploratory research. However, the images are difficult to analyze because the enclosed data has high dimensionality, and their content does not necessarily reflect the shape of the object of interest. Conversely, magnetic resonance imaging (MRI) scans reflect the anatomy of the tissue. MRI also provides complementary information to MSI, such as the content and distribution of water.

Results

We propose a new workflow to merge the information from 2D MALDI–MSI and MRI images. Our workflow can be applied to large MSI datasets in a limited amount of time. Moreover, the workflow is fully automated and based on deterministic methods which ensures the reproducibility of the results. Our methods were evaluated and compared with state-of-the-art methods. Results show that the images are combined precisely and in a time-efficient manner.

Conclusion

Our workflow reveals molecules which co-localize with water in biological images. It can be applied on any MSI and MRI datasets which satisfy a few conditions: same regions of the shape enclosed in the images and similar intensity distributions.

Trehalose 6-phosphate promotes seed filling by activating auxin biosynthesis

Plants undergo several developmental transitions during their life cycle. One of these, the differentiation of the young embryo from a meristem-like structure into a highly specialized storage organ, is believed to be controlled by local connections between sugars and hormonal response systems. However, we know little about the regulatory networks underpinning the sugar-hormone interactions in developing seeds. By modulating the trehalose 6-phosphate (T6P) content in growing embryos of garden pea (Pisum sativum), we investigate here the role of this signaling sugar during the seed-filling process. Seeds deficient in T6P are compromised in size and starch production, resembling the wrinkled seeds studied by Gregor Mendel. We show also that T6P exerts these effects by stimulating the biosynthesis of the pivotal plant hormone, auxin. We found that T6P promotes the expression of the auxin biosynthesis gene TRYPTOPHAN AMINOTRANSFERASE RELATED2 (TAR2), and the resulting effect on auxin concentrations is required to mediate the T6P-induced activation of storage processes. Our results suggest that auxin acts downstream of T6P to facilitate seed filling, thereby providing a salient example of how a metabolic signal governs the hormonal control of an integral phase transition in a crop plant.

Allelic variation in rice Fertilization Independent Endosperm 1 contributes to grain width under high night temperature stress

A higher minimum (night-time) temperature is considered a greater limiting factor for reduced rice yield than a similar increase in maximum (daytime) temperature. While the physiological impact of high night temperature (HNT) has been studied, the genetic and molecular basis of HNT stress response remains unexplored. We examined the phenotypic variation for mature grain size (length and width) in a diverse set of rice accessions under HNT stress. Genome-wide association analysis identified several HNT-specific loci regulating grain size as well as loci that are common for optimal and HNT stress conditions. A novel locus contributing to grain width under HNT conditions colocalized with Fie1, a component of the FIS-PRC2 complex. Our results suggest that the allelic difference controlling grain width under HNT is a result of differential transcript-level response of Fie1 in grains developing under HNT stress. We present evidence to support the role of Fie1 in grain size regulation by testing overexpression (OE) and knockout mutants under heat stress. The OE mutants were either unaltered or had a positive impact on mature grain size under HNT, while the knockouts exhibited significant grain size reduction under these conditions.

Whole Genome Scan Reveals Molecular Signatures of Divergence and Selection Related to Important Traits in Durum Wheat Germplasm

The first breeding program in the world for durum wheat was conceived in Italy in the early 1900s. Over the decades, pressure exerted by natural and artificial selection could have progressively reduced the genetic diversity of the durum wheat germplasm. In the present study, a large panel of Italian durum wheat accessions that includes landraces, old and modern cultivars was subjected to genotyping using the Illumina iSelect 15K wheat SNP array. The aim was to assess the impact that selection has in shaping Italian durum wheat genetic diversity and to exploit the patterns of genetic diversity between populations to identify molecular signatures of divergence and selection. Relatively small differences in genetic diversity have been observed among accessions, which have been selected and cultivated in Italy over the past 150 years. Indeed, directional selection combined with that operated by farmers/breeders resulted in the increase of linkage disequilibrium (LD) and in changes of the allelic frequencies in DNA regions that control important agronomic traits. Results from this study also show that major well-known genes and/or QTLs affecting plant height (RHT), earliness (VRN, PPD) and grain quality (GLU, PSY, PSD, LYC, PPO, LOX3) co-localized with outlier SNP loci. Interestingly, many of these SNPs fall in genomic regions where genes involved in nitrogen metabolism are. This finding highlights the key role these genes have played in the transition from landraces to modern cultivars. Finally, our study remarks on the need to fully exploit the genetic diversity of Italian landraces by intense pre-breeding activities aimed at introducing a new source of adaptability and resistance in the genetic background of modern cultivars, to contrast the effect of climate change. The list of divergent loci and loci under selection associated with useful agronomic traits represents an invaluable resource to detect new allelic variants for target genes and for guiding new genomic selection programs in durum wheat.

Inferring vascular architecture of the wheat spikelet based on resource allocation in the branched headt (bht-A1) near isogenic lines

Substantial genetic and physiological efforts were made to understand the causal factors of floral abortion and grain filling problem in wheat. However, the vascular architecture during wheat spikelet development is surprisingly under-researched. We used the branched headt near-isogenic lines, FL-bht-A1-NILs, to visualise the dynamics of spikelet fertility and dry matter accumulation in spikelets sharing the same rachis node (henceforth Primary Spikelet, PSt, and Secondary Spikelet, SSt). The experiment was conducted after grouping FL-bht-A1-NILs into two groups, where tillers were consistently removed from one group. Our results show differential spikelet fertility and dry matter accumulation between the PSt and SSt, but also showed a concomitant improvement after de-tillering. This suggests a tight regulation of assimilate supply and dry matter accumulation in wheat spikelets. Since PSt and SSt share the same rachis node, the main vascular bundle in the rachis/rachilla is expected to bifurcate to connect each spikelet/floret to the vascular system. We postulate that the vascular structure in the wheat spikelet might even follow Murray's law, where the wide conduits assigned at the base of the spikelet feed the narrower conduits of the distal florets. We discuss our results based on the two modalities of the vascular network systems in plants.

The search for candidate genes associated with natural variation of grain Zn accumulation in barley

Combating hidden hunger through molecular breeding of nutritionally enriched crops requires a better understanding of micronutrient accumulation. We studied natural variation in grain micronutrient accumulation in barley (Hordeum vulgare L.) and searched for candidate genes by assessing marker-trait associations (MTAs) and by analyzing transcriptional differences between low and high zinc (Zn) accumulating cultivars during grain filling. A collection of 180 barley lines was grown in three different environments. Our results show a pronounced variation in Zn accumulation, which was under strong genotype influence across different environments. Genome-wide association mapping revealed 13 shared MTAs. Across three environments, the most significantly associated marker was on chromosome 2H at 82.8 cM and in close vicinity to two yellow stripe like (YSL) genes. A subset of two pairs of lines with contrasting Zn accumulation was chosen for detailed analysis. Whole ears and flag leaves were analyzed 15 days after pollination to detect transcriptional differences associated with elevated Zn concentrations in the grain. A putative α-amylase/trypsin inhibitor CMb precursor was decidedly higher expressed in high Zn cultivars in whole ears in all comparisons. Additionally, a gene similar to barley metal tolerance protein 5 (MTP5) was found to be a potential candidate gene.

Translating auxin responses into ovules, seeds and yield: Insight from Arabidopsis and the cereals

Grain production in cereal crops depends on the stable formation of male and female gametes in the flower. In most angiosperms, the female gamete is produced from a germline located deep within the ovary, protected by several layers of maternal tissue, including the ovary wall, ovule integuments and nucellus. In the field, germline formation and floret fertility are major determinants of yield potential, contributing to traits such as seed number, weight and size. As such, stimuli affecting the timing and duration of reproductive phases, as well as the viability, size and number of cells within reproductive organs can significantly impact yield. One key stimulant is the phytohormone auxin, which influences growth and morphogenesis of female tissues during gynoecium development, gametophyte formation, and endosperm cellularization. In this review we consider the role of the auxin signaling pathway during ovule and seed development, first in the context of Arabidopsis and then in the cereals. We summarize the gene families involved and highlight distinct expression patterns that suggest a range of roles in reproductive cell specification and fate. This is discussed in terms of seed production and how targeted modification of different tissues might facilitate improvements.

A reductionist approach to dissecting grain weight and yield in wheat

Grain yield is a highly polygenic trait that is influenced by the environment and integrates events throughout the life cycle of a plant. In wheat, the major grain yield components often present compensatory effects among them, which alongside the polyploid nature of wheat, makes their genetic and physiological study challenging. We propose a reductionist and systematic approach as an initial step to understand the gene networks regulating each individual yield component. Here, we focus on grain weight and discuss the importance of examining individual sub-components, not only to help in their genetic dissection, but also to inform our mechanistic understanding of how they interrelate. This knowledge should allow the development of novel combinations, across homoeologs and between complementary modes of action, thereby advancing towards a more integrated strategy for yield improvement. We argue that this will break barriers in terms of phenotypic variation, enhance our understanding of the physiology of yield, and potentially deliver improved on-farm yield.

Grain number and grain yield distribution along the spike remain stable despite breeding for high yield in winter wheat

Two winter wheat (Triticum aestivum L.) populations, i.e. 180 genetic resources and 210 elite varieties, were compared in a field trial to analyse how grain number and grain yield distribution along the spike changed during the breeding process and how this associates to yield-related traits. Elites showed in average 38% more yield compared to resources. This breeding improvement mainly derived from an increase in grains and yield per spike in addition to grains and yield per spikelet. These increments corresponded to 19, 23, 21 and 25%, respectively. Not much gain in thousand grain weight (4%) was observed in elites as compared to resources. The number of spikelets per spike was not, or even negatively, correlated with most traits, except of grains per spike, which suggests that this trait was not favoured during breeding. The grain number and grain yield distributions along the spike (GDAS and GYDAS) were measured and compared by using a novel mathematical tool. GDAS and GYDAS measure the deviation of a spike of interest from the architecture of a model spike with even grain and yield distribution along all spikelets, respectively. Both traits were positively correlated. Elites showed in average only a 1% improvement in GDAS and GYDAS values compared to resources. This comparison revealed that breeding increased grain number and yield uniformly along the spike without changing relative yield input of individual spikelets, thereby, maintaining the general spike architecture.

Down-regulation of the sucrose transporters HvSUT1 and HvSUT2 affects sucrose homeostasis along its delivery path in barley grains

Sucrose transport and partitioning are crucial for seed filling. While many plasma-membrane-localised sucrose transporters (SUT1 family members) have been analysed in seeds, the functions of vacuolar SUT2 members are still obscure. In barley grains, expression of HvSUT1 and HvSUT2 overlap temporally and spatially, suggesting concerted functions to regulate sucrose homeostasis. Using HvSUT2-RNAi plants, we found that grains were also deficient in HvSUT1 expression and seemingly sucrose-limited during mid-to-late grain filling. Transgenic endosperms accumulated less starch and dry weight, although overall sucrose and hexose contents were higher. Comprehensive transcript and metabolite profiling revealed that genes related to glycolysis, the tricarboxylic acid cycle, starch and amino acid synthesis, grain maturation, and abscisic acid signalling were down-regulated together with most glycolytic intermediates and amino acids. Sucrose was increased along the sucrose delivery route in the nucellar projection, the endosperm transfer cells, and the starchy endosperm, indicating that suppressed transporter activity diminished sucrose efflux from vacuoles, which generated sugar deficiency in the cytoplasm. Thus, endosperm vacuoles may buffer sucrose concentrations to regulate homeostasis at grain filling. Transcriptional changes revealed that limited endosperm sucrose initiated sugar starvation responses, such as sugar recycling from starch, hemicelluloses and celluloses together with vacuolar protein degradation, thereby supporting formation of nucleotide sugars. Barley endosperm cells can thus suppress certain pathways to retrieve resources to maintain essential cell functions.