Transcriptome profiling based on Illumina- and SMRT-based RNA-seq reveals circadian regulation of key pathways in flower bud development in walnut

Flower bud development is a defining feature of walnut, which contributes to the kernel yield, yield stability, fruit quality and commodity value. However, little is known about the mechanism of the flower bud development in walnut. Here, the stages of walnut female flower bud development were divided into five period (P01-05) by using histological observation. They were further studied through PacBio Iso-Seq and RNA-seq analysis. Accordingly, we obtained 52,875 full-length transcripts, where 4,579 were new transcripts, 3,065 were novel genes, 1,437 were consensus lncRNAs and 20,813 were alternatively spliced isoforms. These transcripts greatly improved the current genome annotation and enhanced our understanding of the walnut transcriptome. Next, RNA sequencing of female flower buds at five periods revealed that circadian rhythm-plant was commonly enriched along with the flower bud developmental gradient. A total of 14 differentially expressed genes (DEGs) were identified, and six of them were confirmed by real-time quantitative analysis. Additionally, six and two differentially expressed clock genes were detected to be regulated by AS events and lncRNAs, respectively. All these detected plant circadian genes form a complex interconnected network to regulate the flower bud development. Thus, investigation of key genes associated with the circadian clock could clarify the process of flower bud development in walnut.

Developmental Dynamics of Gilbertiodendron dewevrei (Fabaceae) Drive Forest Structure and Biomass in the Eastern Congo Basin

Patterns of structural change associated with monodominant tropical forest complexes have remained enigmatic for decades. Here, we extend previous efforts in presenting a longitudinal, local-scale analysis of forest dynamics in central Africa. Using four 10-ha census plots measured across three time periods (959,312 stems ≥1 cm DBH), we analyzed changes in a number of biometrical attributes for four distinct forest types capturing the developmental gradient from mixed species forest to Gilbertiodendron dewevrei-dominated forest. We modeled above-ground biomass (AGB), basal area (BA), and stem density across all species, and diameter at breast height (DBH), recruitment, and mortality for Gilbertiodendron dewevrei. We hypothesized that trends in these attributes are consistent with a slow spread of Gilbertiodendron dewevrei into adjacent mixed species forest. We identified statistically significant increases in AGB and BA across sites and positive, though nonsignificant, increases in AGB and BA for most forest types. DBH and relative recruitment increased significantly for Gilbertiodendron dewevrei stems, while relative mortality did not. When looking from mixed species to transitional to monodominant forest types, we found a statistically significant pattern of developmental aggradation and net expansion of monodominant forest. We do not attribute this to atmospheric forcing but to a combination of (a) landscape-scale recovery or response to widespread disturbance (primarily historical fires), (b) Gilbertiodendron dewevrei’s ectomycorrhizal association, and (c) Gilbertiodendron dewevrei’s exceptional stress tolerance traits.

Cellular and transcriptomic analyses reveal two-staged chloroplast biogenesis underpinning photosynthesis build-up in the wheat leaf

Background The developmental gradient in monocot leaves has been exploited to uncover leaf developmental gene expression programs and chloroplast biogenesis processes. However, the relationship between the two is barely understood, which limits the value of transcriptome data to understand the process of chloroplast development. Results Taking advantage of the developmental gradient in the bread wheat leaf, we provide a simultaneous quantitative analysis for the development of mesophyll cells and of chloroplasts as a cellular compartment. This allows us to generate the first biologically-informed gene expression map of this leaf, with the entire developmental gradient from meristematic to fully differentiated cells captured. We show that the first phase of plastid development begins with organelle proliferation, which extends well beyond cell proliferation, and continues with the establishment and then the build-up of the plastid genetic machinery. The second phase is marked by the development of photosynthetic chloroplasts which occupy the available cellular space. Using a network reconstruction algorithm, we predict that known chloroplast gene expression regulators are differentially involved across those developmental stages. Conclusions Our analysis generates both the first wheat leaf transcriptional map and one of the most comprehensive descriptions to date of the developmental history of chloroplasts in higher plants. It reveals functionally distinct plastid and chloroplast development stages, identifies processes occurring in each of them, and highlights our very limited knowledge of the earliest drivers of plastid biogenesis, while providing a basis for their future identification.

Investigation of Salt Tolerance Mechanisms Across a Root Developmental Gradient in Almond Rootstocks

The intensive use of groundwater in agriculture under the current climate conditions leads to acceleration of soil salinization. Given that almond is a salt-sensitive crop, selection of salt-tolerant rootstocks can help maintain productivity under salinity stress. Selection for tolerant rootstocks at an early growth stage can reduce the investment of time and resources. However, salinity-sensitive markers and salinity tolerance mechanisms of almond species to assist this selection process are largely unknown. We established a microscopy-based approach to investigate mechanisms of stress tolerance in and identified cellular, root anatomical, and molecular traits associated with rootstocks exhibiting salt tolerance. We characterized three almond rootstocks: Empyrean-1 (E1), Controller-5 (C5), and Krymsk-86 (K86). Based on cellular and molecular evidence, our results show that E1 has a higher capacity for salt exclusion by a combination of upregulating ion transporter expression and enhanced deposition of suberin and lignin in the root apoplastic barriers, exodermis, and endodermis, in response to salt stress. Expression analyses revealed differential regulation of cation transporters, stress signaling, and biopolymer synthesis genes in the different rootstocks. This foundational study reveals the mechanisms of salinity tolerance in almond rootstocks from cellular and structural perspectives across a root developmental gradient and provides insights for future screens targeting stress response.

Barley’s Second Spring as a Model Organism for Chloroplast Research

Barley (Hordeum vulgare) has been widely used as a model crop for studying molecular and physiological processes such as chloroplast development and photosynthesis. During the second half of the 20th century, mutants such as albostrians led to the discovery of the nuclear-encoded, plastid-localized RNA polymerase and the retrograde (chloroplast-to-nucleus) signalling communication pathway, while chlorina-f2 and xantha mutants helped to shed light on the chlorophyll biosynthetic pathway, on the light-harvesting proteins and on the organization of the photosynthetic apparatus. However, during the last 30 years, a large fraction of chloroplast research has switched to the more “user-friendly” model species Arabidopsis thaliana, the first plant species whose genome was sequenced and published at the end of 2000. Despite its many advantages, Arabidopsis has some important limitations compared to barley, including the lack of a real canopy and the absence of the proplastid-to-chloroplast developmental gradient across the leaf blade. These features, together with the availability of large collections of natural genetic diversity and mutant populations for barley, a complete genome assembly and protocols for genetic transformation and gene editing, have relaunched barley as an ideal model species for chloroplast research. In this review, we provide an update on the genomics tools now available for barley, and review the biotechnological strategies reported to increase photosynthesis efficiency in model species, which deserve to be validated in barley.

NAC transcription factors in autopolyploid Saccharum spontaneum: genome-wide identification, expression pattern and a ‘Dry’ orthologous gene

Background: The NAC acronym originates from these three genes (NAM, ATA1/2 and CUC2), and were proved to participate in plant development, sugar accumulation and stress tolerance. However, little information is available regarding these genes in sugarcane. The newly published sugarcane genome provided an opportunity to identify the SsNAC transcription factors. Results: In this study, a total of 151 NAC genes including 327 alleles were identified in the autopolyploid S. spontaneum genome and were distributed unevenly on eight chromosomes with the majority located on Chr 5(54, 16.51%), Chr 1(51, 15.60%) and Chr 2(51, 15.60%). 71.6%(234) and 12.53%(41) of SsNAC genes were mainly derived from segmental duplication and tandem duplication. Phylogeny analysis of NAC TF proteins by comparing NAC between sugarcane and Arabidopsis thaliana suggested that the NAC family can be divided into 15 subgroups with one subgroup unclassified. RNA-seq data analysis revealed that 82 SsNAC were expressed in 15 segments of the developmental gradient of the leaf and 74 SsNAC were presented in 12 different developmental stages, respectively. Remarkably, SsNAC genes of the ATAF subgroup presented the highest expression levels among the subgroups, and seven of eight SsNAC genes from the ATAF subgroup excluding SsNAC30 were present at much higher expression levels in the developmental gradient of the leaf than those in different developmental tissues types, indicating that the ATAF subgroup may have significant roles and participate in leaf growth and development and photosynthesis. Importantly, the NAC1 subgroup SsNAC91 gene, being orthologous to Sobic.006G147400 ( Dry gene ), displayed significantly higher expression levels in premature and mature stems of the low sucrose and low water content species S. spontaneum as opposed to the orthologous gene in the high sugar and high water content species S. officinarum . This suggests that the SsNAC91 gene may also play important roles in cellulose biosynthesis and water transport in sugarcane as it does in sorghum. Conclusions: This study provided the basis for the comprehensive genomic study of the SsNAC gene family and thus established a good foundation for the functional analyses of SsNAC genes which can be utilized to breed new varieties of sugarcane.

Constructing functional cuticles: analysis of relationships between cuticle lipid composition, ultrastructure and water barrier function in developing adult maize leaves

Background and Aims Prior work has examined cuticle function, composition and ultrastructure in many plant species, but much remains to be learned about how these features are related. This study aims to elucidate relationships between these features via analysis of cuticle development in adult maize (Zea mays L.) leaves, while also providing the most comprehensive investigation to date of the composition and ultrastructure of adult leaf cuticles in this important crop plant. Methods We examined water permeability, wax and cutin composition via gas chromatography, and ultrastructure via transmission electron microscopy, along the developmental gradient of partially expanded adult maize leaves, and analysed the relationships between these features. Key Results The water barrier property of the adult maize leaf cuticle is acquired at the cessation of cell expansion. Wax types and chain lengths accumulate asynchronously over the course of development, while overall wax load does not vary. Cutin begins to accumulate prior to establishment of the water barrier and continues thereafter. Ultrastructurally, pavement cell cuticles consist of an epicuticular layer, and a thin cuticle proper that acquires an inner, osmiophilic layer during development. Conclusions Cuticular waxes of the adult maize leaf are dominated by alkanes and alkyl esters. Unexpectedly, these are localized mainly in the epicuticular layer. Establishment of the water barrier during development coincides with a switch from alkanes to esters as the major wax type, and the emergence of an osmiophilic (likely cutin-rich) layer of the cuticle proper. Thus, alkyl esters and the deposition of the cutin polyester are implicated as key components of the water barrier property of adult maize leaf cuticles.

Changes in lipid composition and ultrastructure associated with functional maturation of the cuticle during adult maize leaf development

Although extensive prior work has characterized cuticle composition, function, ultrastructure and development in many plant species, much remains to be learned about how these features are interrelated. Moreover, very little is known about the adult maize leaf cuticle in spite of its significance for agronomically important traits in this major crop. We analyzed cuticle composition, ultrastructure, and permeability along the developmental gradient of partially expanded adult maize leaves to probe the relationships between these features. The water barrier property is acquired at the cessation of cell expansion. Wax types and chain lengths accumulate asynchronously along the developmental gradient, while overall wax load does not vary. Cutin begins to accumulate prior to establishment of the water barrier and continues thereafter. Ultrastructurally, pavement cell cuticles consist of an epicuticular layer, a thin cuticle proper that acquires an inner, osmiophilic layer during development, and no cuticular layer. Cuticular waxes of the adult maize leaf are dominated by alkanes and wax esters localized mainly in the epicuticular layer. Establishment of the water barrier coincides with a switch from alkanes to esters as the major wax type, and the emergence of an osmiophilic (likely cutin-rich) layer of the cuticle proper.Higlight statementChemical, ultrastructural and functional analysis of cuticle development in partially expanded adult maize leaves revealed important roles for wax esters and an osmiophilic, likely cutin-rich, layer in protection from dehydration.