De novo analysis of transcriptome reveals genes associated with leaf abscission in sugarcane (Saccharum officinarum L.)

Novel mutation in patients with microcephalic osteodysplastic primordial dwarfism type II (MOPD II)

A rare type of autosomal recessive skeletal disorder, known as microcephalic osteodysplastic primordial dwarfism (MOPD) type II, causes a wide range of clinical abnormalities, including skeletal dysplasia, microcephaly, abnormal skin pigmentation, insulin resistance, typical facial features, and severe tooth deformities. Given the diverse manifestations of MOPD disorders and the overlapping clinical characteristics among primordial dwarfism (PD) subtypes, mutation analysis is crucial for accurate diagnosis and confirmation of MOPD II. In this study, whole-exome sequencing (WES) and GAP-PCR were employed to identify relevant genetic variants in three patients suspected of having MOPD. The clinical characteristics of three Iranian patients exhibiting hallmark features of MOPD were assessed. All patients were the offspring of consanguineous marriages and were referred from various provinces of Iran. WES was performed, and the identified variants were prioritized according to the standard filtration criteria. In the next step, Sanger sequencing was conducted to validate the candidate variants identified through WES in patients and their parents. Finally, GAP-PCR was implemented to resolve conflicting results between WES and Sanger sequencing for one of the patients. Analysis of three distinct cases revealed a novel homozygous copy number variation (CNV) in Case 3, consisting of a 490 bp deletion harboring exon 19 in the PCNT gene. Additionally, a nonsense homozygous variant in the PCNT gene (c.2812 C > T, p.Gln 938*) was found in Cases 1 and 2. This pathogenic variant has been previously documented in the literature. Reporting a novel deletion in the PCNT gene improves genetic testing services, including PND and pre-implantation genetic diagnosis (PGD) for MOPD II.

Fine mapping of leaf delayed virescence gene dv4 in Triticum aestivum

Wheat (Triticum aestivum L.) is one of the most important crops worldwide, and its yield affects national food security. Wheat leaves are key photosynthetic organs where carbohydrates are synthesized for grain yield. Leaf colour mutants are ideal germplasm resources for molecular genetic studies of wheat chloroplast development, chlorophyll synthesis and photosynthesis. We obtained a wheat mutant delayed virescence 4 (dv4) from cultivar Guomai 301. The leaves of mutant dv4 were pale yellow at the seedling stage, golden yellow at the turning green stage, and they started to turn green at the jointing stage. Genetic analysis demonstrated that the yellow-leaf phenotype was controlled by a single recessive gene named as dv4. Gene dv4 was fine mapped in a 1.46 Mb region on chromosome 7DS by SSR and dCAPS marker assays. Three putative candidate genes were identified in this region. Because no leaf colour genes have been reported on wheat chromosome arm 7DS previously, dv4 is a novel leaf colour gene. The result facilitates map-based cloning of dv4 and provides information for the construction of a high-photosynthetic efficiency ideotype for improving wheat yield.

Genomic loci associated with leaf abscission contribute to machine picking and environmental adaptability in upland cotton (Gossypium hirsutum L.)

INTRODUCTION

Defoliation by applying defoliants before machine picking is an important agricultural practice that enhances harvesting efficiency and leads to increased raw cotton purity. However, the fundamental characteristics of leaf abscission and the underlying genetic basis in cotton are not clearly understood.

OBJECTIVES

In this study, we aimed to (1) reveal the phenotypic variations in cotton leaf abscission, (2) discover the whole-genome differentiation sweeps and genetic loci related to defoliation, (3) identify and verify the functions of key candidate genes associated with defoliation, and (4) explore the relationship between haplotype frequency of loci and environmental adaptability.

METHODS

Four defoliation-related traits of 383 re-sequenced Gossypium hirsutum accessions were investigated in four environments. The genome-wide association study (GWAS), linkage disequilibrium (LD) interval genotyping and functional identification were conducted. Finally, the haplotype variation related to environmental adaptability and defoliation traits was revealed.

RESULTS

Our findings revealed the fundamental phenotypic variations of defoliation traits in cotton. We showed that defoliant significantly increased the defoliation rate without incurring yield and fiber quality penalties. The strong correlations between defoliation traits and growth period traits were observed. A genome-wide association study of defoliation traits identified 174 significant SNPs. Two loci (RDR7 on A02 and RDR13 on A13) that significantly associated with the relative defoliation rate were described, and key candidate genes GhLRR and GhCYCD3;1, encoding a leucine-rich repeat (LRR) family protein and D3-type cell cyclin 1 protein respectively, were functional verified by expression pattern analysis and gene silencing. We found that combining of two favorable haplotypes (HapRDR7 and HapRDR13) improved sensitivity to defoliant. The favorable haplotype frequency generally increased in high latitudes in China, enabling adaptation to the local environment.

CONCLUSION

Our findings lay an important foundation for the potentially broad application of leveraging key genetic loci in breeding machine-pickable cotton.

Developing new sugarcane varieties suitable for mechanized production in China: principles, strategies and prospects

The sugar industry, which relates to people's livelihood, is strategic and fundamental in the development of agricultural economy. In China, sugar derived from sugarcane accounts for approximately 85% of total sugar production. Mechanization is the "flower" of sugarcane industry. As the saying goes "when there are blooming flowers, there will be sweet honey." However, due to limitations in land resources, technology, equipment, organization, and management, mechanization throughout the sugarcane production process has not yet brought about the economic benefits that a mechanized system should provide and has not reached an ideal yield through the integration of agricultural machinery and agronomic practice. This paper briefly describes how to initiate the mechanization of Chinese sugarcane production to promote the sound, healthy, and rapid development of the sugarcane industry, and how to ultimately achieve the transformation of sugarcane breeding in China and the modernization of the sugarcane industry from three perspectives, namely, requirements of mechanized production for sugarcane varieties, breeding strategies for selecting new sugarcane varieties suitable for mechanized production, and screening for sugarcane varieties that are suitable for mechanization and diversification in variety distribution or arrangement in China. We also highlight the current challenges surrounding this topic and look forward to its bright prospects.

Genome-Wide Identification, Characterization, and Expression Analysis of the NAC Gene Family in Litchi chinensis

NAC proteins play an essential role in the growth and development of litchi, especially during reproductive development. However, a comprehensive analysis of the litchi NAC gene family is currently absent. Based on information from the litchi genome, we found that the 112 NAC genes of litchi show an uneven distribution on the chromosomes. Phylogenetic and conserved structural domain analyses indicated that different types of variability were exhibited in the family of litchi NACs (LcNACs). Gene covariance analysis showed that the LcNACs showed better similarity in the same genus than with Arabidopsis. We further investigated the differential expression patterns of LcNACs in buds and rudimentary leaves of litchi. qRT-PCR results implied that they were involved in the process. Profiling of LcNAC promoter elements in litchi showed that they were extensively involved in light response, phytohormone regulation, abiotic stress response, and plant growth and development processes. This study provides new insights into the identification, structural characterization, tissue-specific expression analysis, and promoter response elements of LcNACs. It reveals the characteristics of the LcNACs and lays the foundation for the subsequent understanding of its biological functions and molecular regulatory mechanisms.

Transcriptomic and Proteomic Landscape of Sugarcane Response to Biotic and Abiotic Stressors

Sugarcane, a C₄ plant, provides most of the world's sugar, and a substantial amount of renewable bioenergy, due to its unique sugar-accumulating and feedstock properties. Brazil, India, China, and Thailand are the four largest sugarcane producers worldwide, and the crop has the potential to be grown in arid and semi-arid regions if its stress tolerance can be improved. Modern sugarcane cultivars which exhibit a greater extent of polyploidy and agronomically important traits, such as high sugar concentration, biomass production, and stress tolerance, are regulated by complex mechanisms. Molecular techniques have revolutionized our understanding of the interactions between genes, proteins, and metabolites, and have aided in the identification of the key regulators of diverse traits. This review discusses various molecular techniques for dissecting the mechanisms underlying the sugarcane response to biotic and abiotic stresses. The comprehensive characterization of sugarcane's response to various stresses will provide targets and resources for sugarcane crop improvement.

Transcriptomic and metabolomic analyses reveal molecular mechanisms associated with the natural abscission of blue honeysuckle (Lonicera caerulea L.) ripe fruits

Blue honeysuckle (Lonicera caerulea L.) is rich in phenolic compounds and has an extremely high nutritional value. Fruit abscission in the ripe period significantly impacts production and economic benefits. However, the mechanism associated with the abscission of blue honeysuckle fruit remains largely unknown. The easy-abscission cultivar 'HSY' and the hard-abscission cultivar 'Berel' were selected as plant materials. Anatomical changes of the 'HSY' fruit abscission zone (FAZ) during the abscission mainly included cell expansion, detachment, and collapse. Active changes in cell wall-degrading enzyme activity between 39 days postanthesis (DPA) and 55 DPA in 'HSY' FAZ, but not in 'Berel', suggest a critical role for cell-wall-degrading enzymes in regulating abscission. Transcriptome and metabolome analyses revealed that the genes and metabolites responding to abscission mainly act on pathways such as plant hormone signal transduction, starch and sucrose metabolism, pentose and glucuronate interconversions, and phenylpropanoid biosynthesis. The regulatory pathways of fruit abscission are mainly summarized into two parts: phytohormone synthesis and signal transduction, FAZ cell wall metabolism. In this study, 46 key genes related to plant hormone response, 45 key genes involved in FAZ cell wall metabolism, and 73 transcription factors were screened. Quantitative real-time PCR (qRT-PCR) assessed the expression pattern of 12 selected candidate genes, demonstrating the accuracy of the transcriptome data and elucidating the expression patterns of key candidate genes during growth and development. This study will provide an essential resource for understanding the molecular regulatory mechanism of fruit abscission in the blue honeysuckle.

Transgene-Free Genome Editing for Biotic and Abiotic Stress Resistance in Sugarcane: Prospects and Challenges

Sugarcane (Saccharum spp.) is one of the most valuable food and industrial crops. Its production is constrained due to major biotic (fungi, bacteria, viruses and insect pests) and abiotic (drought, salt, cold/heat, water logging and heavy metals) stresses. The ever-increasing demand for sugar and biofuel and the rise of new pest and disease variants call for the use of innovative technologies to speed up the sugarcane genetic improvement process. Developing new cultivars through conventional breeding techniques requires much time and resources. The advent of CRISPR/Cas genome editing technology enables the creation of new cultivars with improved resistance/tolerance to various biotic and abiotic stresses. The presence of genome editing cassette inside the genome of genome-edited plants hinders commercial exploitation due to regulatory issues. However, this limitation can be overcome by using transgene-free genome editing techniques. Transgene-free genome editing approaches, such as delivery of the RNPs through biolistics or protoplast fusion, virus-induced genome editing (VIGE), transient expression of CRISPR/Cas reagents through Agrobacterium-mediated transformation and other approaches, are discussed. A well-established PCR-based assay and advanced screening systems such as visual marker system and Transgene killer CRISPR system (TKC) rapidly identify transgene-free genome edits. These advancements in CRISPR/Cas technology speed up the creation of genome-edited climate-smart cultivars that combat various biotic and abiotic stresses and produce good yields under ever-changing conditions.

Grapevine VaRPP13 protein enhances oomycetes resistance by activating SA signal pathway

Expression of the VaRPP13 in Arabidopsis and tobacco enhanced resistance to oomycete pathogens, and this enhancement is closely related to the activation of salicylic acid (SA) signaling pathway. Resistance (R) genes, which usually contain a nucleotide-binding site and a leucine-rich repeat (NBS-LRR) domain, play crucial roles in disease resistance. In this study, we cloned a CC-NBS-LRR gene VaRPP13 from Vitis amurensis 'Shuang Hong' grapevine, and investigated its function on disease resistance. VaRPP13 expression was induced by Plasmopara viticola, an oomycetes pathogen causing downy mildew disease in grapevine. Heterologous expression VaRPP13 could also enhance resistance to Hyaloperonospora arabidopsidis in Arabidopsis thaliana and Phytophthora capsici in Nicotiana benthamiana, both oomycete pathogens. Further study indicated that VaRPP13 could enhance the expression of genes in SA signal pathway, while exogenous SA could also induce the expression of VaRPP13. In conclusion, our studies demonstrated that VaRPP13 contributes to a broad-spectrum resistance to oomycetes via activating SA signaling pathway.

Impact of Agroclimatic Variables on Proteogenomics in Sugar Cane (Saccharum spp.) Plant Productivity

Sugar cane (Saccharum spp. hybrids) is a major crop for sugar and renewable bioenergy worldwide, grown in arid and semiarid regions. China, the world's fourth-largest sugar producer after Brazil, India, and the European Union, all share ∼80% of the global production, and the remaining ∼20% of sugar comes from sugar beets, mostly grown in the temperate regions of the Northern Hemisphere, also used as a raw material in production of bioethanol for renewable energy. In view of carboxylation strategies, sugar cane qualifies as one of the best C4 crop. It has dual CO2 concentrating mechanisms located in its unique Krantz anatomy, having dimorphic chloroplasts located in mesophylls and bundle sheath cells for integrated operation of C4 and C3 carbon fixation cycles, regulated by enzymes to upgrade/sustain an ability for improved carbon assimilation to acquire an optimum carbon economy by producing enhanced plant biomass along with sugar yield under elevated temperature and strong irradiance with improved water-use efficiency. These superior intrinsic physiological carbon metabolisms encouraged us to reveal and recollect the facts for moving ahead with the molecular approaches to reveal the expression of proteogenomics linked with plant productivity under abiotic stress during its cultivation in specific agrizones globally.

Modern Biotechnologies: Innovative and Sustainable Approaches for the Improvement of Sugarcane Tolerance to Environmental Stresses

Sugarcane (Saccharum spp.) is one of the most important industrial cash crops, contributing to the world sugar industry and biofuel production. It has been cultivated and improved from prehistoric times through natural selection and conventional breeding and, more recently, using the modern tools of genetic engineering and biotechnology. However, the heterogenicity, complex poly-aneuploid genome and susceptibility of sugarcane to different biotic and abiotic stresses represent impediments that require us to pay greater attention to the improvement of the sugarcane crop. Compared to traditional breeding, recent advances in breeding technologies (molecular marker-assisted breeding, sugarcane transformation, genome-editing and multiple omics technologies) can potentially improve sugarcane, especially against environmental stressors. This article will focus on efficient modern breeding technologies, which provide crucial clues for the engineering of sugarcane cultivars resistant to environmental stresses.

Single-Molecule Long-Read Sequencing of Purslane (Portulaca oleracea) and Differential Gene Expression Related with Biosynthesis of Unsaturated Fatty Acids

This study aimed to obtain the full-length transcriptome of purslane (Portulaca oleracea); assorted plant samples were used for single-molecule real-time (SMRT) sequencing. Based on SMRT, functional annotation of transcripts, transcript factors (TFs) analysis, simple sequence repeat analysis and long non-coding RNAs (LncRNAs) prediction were accomplished. Total 15.33-GB reads were produced; with 9,350,222 subreads and the average length of subreads, 1640 bp was counted. With 99.99% accuracy, after clustering, 132,536 transcripts and 78,559 genes were detected. All unique SMART transcripts were annotated in seven functional databases. 4180 TFs (including transcript regulators) and 7289 LncRNAs were predicted. The results of RNA-seq were confirmed with qRT–PCR analysis. Illumina sequencing of leaves and roots of two purslane genotypes was carried out. Amounts of differential expression genes and related KEGG pathways were found. The expression profiles of related genes in the biosynthesis of unsaturated fatty acids pathway in leaves and roots of two genotypes of purslane were analyzed. Differential expression of genes in this pathway built the foundation of ω-3 fatty acid accumulation in different organs and genotypes of purslane. The aforementioned results provide sequence information and may be a valuable resource for whole-genome sequencing of purslane in the future.

Functional characterization of PETIOLULE-LIKE PULVINUS (PLP) gene in abscission zone development in Medicago truncatula and its application to genetic improvement of alfalfa

Alfalfa (Medicago sativa L.) is one of the most important forage crops throughout the world. Maximizing leaf retention during the haymaking process is critical for achieving superior hay quality and maintaining biomass yield. Leaf abscission process affects leaf retention. Previous studies have largely focused on the molecular mechanisms of floral organ, pedicel and seed abscission but scarcely touched on leaf and petiole abscission. This study focuses on leaf and petiole abscission in the model legume Medicago truncatula and its closely related commercial species alfalfa. By analysing the petiolule-like pulvinus (plp) mutant in M. truncatula at phenotypic level (breakstrength and shaking assays), microscopic level (scanning electron microscopy and cross-sectional analyses) and molecular level (expression level and expression pattern analyses), we discovered that the loss of function of PLP leads to an absence of abscission zone (AZ) formation and PLP plays an important role in leaflet and petiole AZ differentiation. Microarray analysis indicated that PLP affects abscission process through modulating genes involved in hormonal homeostasis, cell wall remodelling and degradation. Detailed analyses led us to propose a functional model of PLP in regulating leaflet and petiole abscission. Furthermore, we cloned the PLP gene (MsPLP) from alfalfa and produced RNAi transgenic alfalfa plants to down-regulate the endogenous MsPLP. Down-regulation of MsPLP results in altered pulvinus structure with increased leaflet breakstrength, thus offering a new approach to decrease leaf loss during alfalfa haymaking process.

The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns

The protein kinase (PK) superfamily is one of the largest superfamilies in plants and the core regulator of cellular signaling. Despite this substantial importance, the kinomes of sugarcane and sorghum have not been profiled. Here, we identified and profiled the complete kinomes of the polyploid Saccharum spontaneum (Ssp) and Sorghum bicolor (Sbi), a close diploid relative. The Sbi kinome was composed of 1,210 PKs; for Ssp, we identified 2,919 PKs when disregarding duplications and allelic copies, and these were related to 1,345 representative gene models. The Ssp and Sbi PKs were grouped into 20 groups and 120 subfamilies and exhibited high compositional similarities and evolutionary divergences. By utilizing the collinearity between the species, this study offers insights into Sbi and Ssp speciation, PK differentiation and selection. We assessed the PK subfamily expression profiles via RNA-Seq and identified significant similarities between Sbi and Ssp. Moreover, coexpression networks allowed inference of a core structure of kinase interactions with specific key elements. This study provides the first categorization of the allelic specificity of a kinome and offers a wide reservoir of molecular and genetic information, thereby enhancing the understanding of Sbi and Ssp PK evolutionary history.

Evaluation of Cotton (Gossypium hirsutum L.) Leaf Abscission Sensitivity Triggered by Thidiazuron through Membership Function Value

Chemical defoliation is an essential agricultural practice in cotton production for mechanic harvesting. Thidiazuron (TDZ) is the active ingredient of the chemical defoliant used on cotton. So far, few studies havefocused on the method of identifying the sensitivity of cotton cultivars to TDZ. Therefore, a greenhouse soil culture experiment was performed by using two widely cultivatedupland cotton cultivars CRI 49 and CRI 12 treated with seven different concentrations (0, 100, 200, 300, 400, 500, and 1000 mg L⁻¹) of TDZ at the seedling stage to establish a screening system. Principal component analysis and the membership function value (MFV) method was used to analyze the physiological and phenotypic characters, including abscission rate, amino acids content, net photosynthetic rate (Pn), etc. Finally, we developed a mathematical evaluation model, selected 100 mg L⁻¹ TDZ as the optimal concentration and identified reliable characters net photosynthetic rate (Pn), stomatal conductance (Gs), and transpiration rate (Tr) to evaluate cotton leaf abscission sensitivity. These results also confirmed that CRI 12 was more sensitive to TDZ than CRI 49. This is the first time using a mathematical evaluation method to evaluate the cotton leaf abscission sensitivity triggered by TDZ at the seedling stage and the results were also confirmed in the field experiment. Furthermore, it will be valuable that MFV method is applied to stress sensitivity evaluation in other crop species under stress environment.

Amino Acid and Carbohydrate Metabolism Are Coordinated to Maintain Energetic Balance during Drought in Sugarcane

The ability to expand crop plantations without irrigation is a major goal to increase agriculture sustainability. To achieve this end, we need to understand the mechanisms that govern plant growth responses under drought conditions. In this study, we combined physiological, transcriptomic, and genomic data to provide a comprehensive picture of drought and recovery responses in the leaves and roots of sugarcane. Transcriptomic profiling using oligoarrays and RNA-seq identified 2898 (out of 21,902) and 46,062 (out of 373,869) transcripts as differentially expressed, respectively. Co-expression analysis revealed modules enriched in photosynthesis, small molecule metabolism, alpha-amino acid metabolism, trehalose biosynthesis, serine family amino acid metabolism, and carbohydrate transport. Together, our findings reveal that carbohydrate metabolism is coordinated with the degradation of amino acids to provide carbon skeletons to the tricarboxylic acid cycle. This coordination may help to maintain energetic balance during drought stress adaptation, facilitating recovery after the stress is alleviated. Our results shed light on candidate regulatory elements and pave the way to biotechnology strategies towards the development of drought-tolerant sugarcane plants.

Molecular Mechanisms Underlying Sugarcane Response to Aluminum Stress by RNA-Seq

Some metals are beneficial to plants and contribute to critical physiological processes. Some metals, however, are not. The presence of aluminum ions (Al³⁺) can be very toxic, especially in acidic soils. Considerable parts of the world's arable land are acidic in nature; mechanistically elucidating a plant's response to aluminum stress is critical to mitigating this stress and improving the quality of plants. To identify the genes involved in sugarcane response to aluminum stress, we generated 372 million paired-end RNA sequencing reads from the roots of CTC-2 and RB855453, which are two contrasting cultivars. Data normalization resulted in 162,161 contigs (contiguous sequences) and 97,335 genes from a de novo transcriptome assembly (trinity genes). A total of 4858 and 1307 differently expressed genes (DEGs) for treatment versus control were identified for the CTC-2 and RB855453 cultivars, respectively. The DEGs were annotated into 34 functional categories. The majority of the genes were upregulated in the CTC-2 (tolerant cultivar) and downregulated in RB855453 (sensitive cultivar). Here, we present the first root transcriptome of sugarcane under aluminum stress. The results and conclusions of this study are a crucial launch pad for future genetic and genomic studies of sugarcane. The transcriptome analysis shows that sugarcane tolerance to aluminum may be explained by an efficient detoxification mechanism combined with lateral root formation and activation of redox enzymes. We also present a hypothetical model for aluminum tolerance in the CTC-2 cultivar.

Petal abscission in fragrant roses is associated with large scale differential regulation of the abscission zone transcriptome

Flowers of fragrant roses such as Rosa bourboniana are ethylene-sensitive and undergo rapid petal abscission while hybrid roses show reduced ethylene sensitivity and delayed abscission. To understand the molecular mechanism underlying these differences, a comparative transcriptome of petal abscission zones (AZ) of 0 h and 8 h ethylene-treated flowers from R. bourboniana was performed. Differential regulation of 3700 genes (1518 up, 2182 down) representing 8.5% of the AZ transcriptome was observed between 0 and 8 h ethylene-treated R. bourboniana petal AZ. Abscission was associated with large scale up-regulation of the ethylene pathway but prominent suppression of the JA, auxin and light-regulated pathways. Regulatory genes encoding kinases/phosphatases/F-box proteins and transcription factors formed the major group undergoing differential regulation besides genes for transporters, wall modification, defense and phenylpropanoid pathways. Further comparisons with ethylene-treated petals of R. bourboniana and 8 h ethylene-treated AZ (R. hybrida) identified a core set of 255 genes uniquely regulated by ethylene in R. bourboniana AZ. Almost 23% of these encoded regulatory proteins largely conserved with Arabidopsis AZ components. Most of these were up-regulated while an entire set of photosystem genes was prominently down-regulated. The studies provide important information on regulation of petal abscission in roses.

Transcriptome Profiling Provides Molecular Insights into Auxin-Induced Adventitious Root Formation in Sugarcane (Saccharum spp. Interspecific Hybrids) Microshoots

Adventitious root (AR) formation was enhanced following the treatment of sugarcane microshoots with indole-3-butyric acid (IBA) and 1-naphthalene acetic acid (NAA) combined, suggesting that auxin is a positive regulator of sugarcane microshoot AR formation. The transcriptome profile identified 1737 and 1268 differentially expressed genes (DEGs) in the basal tissues (5 mm) of sugarcane microshoots treated with IBA+NAA compared to nontreated control on the 3rd and 7th days post-auxin or water treatment (days post-treatment—dpt), respectively. To understand the molecular changes, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed. This analysis showed that DEGs associated with the pathways were associated with plant hormone signaling, flavonoid and phenylpropanoid biosyntheses, cell cycle, and cell wall modification, and transcription factors could be involved in sugarcane microshoot AR formation. Furthermore, qRT–PCR analysis was used to validate the expression patterns of nine genes associated with root formation and growth, and the results were consistent with the RNA-seq results. Finally, a hypothetical hormonal regulatory working model of sugarcane microshoot AR formation is proposed. Our results provide valuable insights into the molecular processes associated with auxin-induced AR formation in sugarcane.

Comparative transcriptomics of an arctic foundation species, tussock cottongrass (Eriophorum vaginatum), during an extreme heat event

Tussock cottongrass (Eriophorum vaginatum) is a foundation species for much of the arctic moist acidic tundra, which is currently experiencing extreme effects of climate change. The Arctic is facing higher summer temperatures and extreme weather events are becoming more common. We used Illumina RNA-Seq to analyse cDNA libraries for differential expression of genes from leaves of ecologically well-characterized ecotypes of tussock cottongrass found along a latitudinal gradient in the Alaskan Arctic and transplanted into a common garden. Plant sampling was performed on a typical summer day and during an extreme heat event. We obtained a de novo assembly that contained 423,353 unigenes. There were 363 unigenes up-regulated and 1,117 down-regulated among all ecotypes examined during the extreme heat event. Of these, 26 HSP unigenes had >log2-fold up-regulation. Several TFs associated with heat stress in previous studies were identified that had >log2-fold up- or down-regulation during the extreme heat event (e.g., DREB, NAC). There was consistent variation in DEGs among ecotypes, but not specifically related to whether plants originated from taiga or tundra ecosystems. As the climate changes it is essential to determine ecotypic diversity at the genomic level, especially for widespread species that impact ecosystem function.

High-throughput sequencing reveals genes associated with high-temperature stress tolerance in sugarcane

Sugarcane (Saccharum spp.) is a major sugar crop grown in tropical and sub-tropical areas throughout the world which is vulnerable to high temperature stress due to climate change. In this present study, we have generated a transcriptome profile of sugarcane variety Co 99004 exposed to high-temperature stress (47 ^°C). The Illumina Nexseq2500 platform yielded a total of 39.28 and 13.44 million reads, corresponding to 3.9 and 1.3 gigabase pair (Gb) of the processed reads for control and high-temperature-stressed samples, respectively. Initially, the reads were de novo assembled into 118,017 unigenes with an average length of 780 bp. The longest sequence in the assembly was 21 kb. Further, these transcripts were BLASTed against GO, KEGG and COG databases to identify the novel genes/transcripts expressed due to elevated temperature conditions. The different expression analysis showed 1137 transcripts which were up-regulated during heat temperature stress when compared to control conditions. Analysis of relative gene expression showed phytepsin, ferredoxin-dependent glutamate synthase, and stress protein DDR-48 threefold increased expression during heat stress. These findings reveal novel targets for subsequent research on the genomics genetic manipulation and molecular mechanism of elevated stress tolerance in sugarcane.

Genomic resources for energy cane breeding in the post genomics era

Sugarcane is one of the most sustainable energy crops among cultivated crops presenting the highest tonnage of cultivated plants. Its high productivity of sugar, bioethanol and bioelectricity make it a promising green alternative to petroleum. Furthermore, the myriad of products that can be derived from sugarcane biomass has been driving breeding programs towards varieties with a higher yield of fiber and a more vigorous and sustainable performance: the energy cane. Here we provide an overview of the energy cane including plant description, breeding efforts, types, and end-uses. In addition, we describe recently published genomic resources for the development of this crop, discuss current knowledge of cell wall metabolism, bioinformatic tools and databases available for the community.

Transcriptome analysis of the effect of GA3 in sugarcane culm

Our earlier studies have indicated that GA₃, being a growth hormone, increases internodal length, in turn increasing sink strength and improving sucrose accumulation in sugarcane. In this study, transcriptomic level analysis was carried out on internodal samples of a high sugar accumulating variety (CoLk 94184) of sugarcane, to determine the effect of exogenous application of GA₃ vis a vis functional analysis of differentially expressing transcripts. Overall, a total of 201,184 transcripts were identified, with median contig length of 450 bp and N50 length of 1029 bp. Analyzing the data from control and GA₃-treated canes, at 0.01 significance, a total of 1516 differentially expressing transcripts were identified in bottom internodes and 1589 in top internodes. A KEGG (enrichment) analysis grouped the transcripts into 153 plant-related functional categories. From among these, the transcripts which were functionally relevant to sugar metabolism and photosynthesis were sieved out. Starch and sucrose metabolizing genes showed maximum fold change of 5.0 and 3.0 among top and bottom internodal samples. A homology match using Blastx analysis tool yielded 65 transcripts/differentially expressed genes (DEGs) which were found to share homology with C₄ plants like Saccharum, Sorghum and Zea mays. Differentially expressing transcripts from both top and bottom internodes were validated by qRT-PCR, indicating their importance in such study. Results also enriched sugarcane transcriptome resources useful for omics study in genus Saccharum and family Poaceae.

Sugarcane Omics: An Update on the Current Status of Research and Crop Improvement

Sugarcane is an important crop from Poaceae family, contributing about 80% of the total world's sucrose with an annual value of around US$150 billion. In addition, sugarcane is utilized as a raw material for the production of bioethanol, which is an alternate source of renewable energy. Moving towards sugarcane omics, a remarkable success has been achieved in gene transfer from a wide variety of plant and non-plant sources to sugarcane, with the accessibility of efficient transformation systems, selectable marker genes, and genetic engineering gears. Genetic engineering techniques make possible to clone and characterize useful genes and also to improve commercially important traits in elite sugarcane clones that subsequently lead to the development of an ideal cultivar. Sugarcane is a complex polyploidy crop, and hence no single technique has been found to be the best for the confirmation of polygenic and phenotypic characteristics. To better understand the application of basic omics in sugarcane regarding agronomic characters and industrial quality traits as well as responses to diverse biotic and abiotic stresses, it is important to explore the physiology, genome structure, functional integrity, and collinearity of sugarcane with other more or less similar crops/plants. Genetic improvements in this crop are hampered by its complex genome, low fertility ratio, longer production cycle, and susceptibility to several biotic and abiotic stresses. Biotechnology interventions are expected to pave the way for addressing these obstacles and improving sugarcane crop. Thus, this review article highlights up to date information with respect to how advanced data of omics (genomics, transcriptomic, proteomics and metabolomics) can be employed to improve sugarcane crops.

Leaf Transcriptome Assembly of Protium copal (Burseraceae) and Annotation of Terpene Biosynthetic Genes

Plants in the Burseraceae are globally recognized for producing resins and essential oils with medicinal properties and have economic value. In addition, most of the aromatic and non-aromatic components of Burseraceae resins are derived from a variety of terpene and terpenoid chemicals. Although terpene genes have been identified in model plant crops (e.g., Citrus, Arabidopsis), very few genomic resources are available for non-model groups, including the highly diverse Burseraceae family. Here we report the assembly of a leaf transcriptome of Protium copal, an aromatic tree that has a large distribution in Central America, describe the functional annotation of putative terpene biosynthetic genes and compare terpene biosynthetic genes found in P. copal with those identified in other Burseraceae taxa. The genomic resources of Protium copal can be used to generate novel sequencing markers for population genetics and comparative phylogenetic studies, and to investigate the diversity and evolution of terpene genes in the Burseraceae.

Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing

Background

Sugarcane is an important global food crop and energy resource. To facilitate the sugarcane improvement program, genome and gene information are important for studying traits at the molecular level. Most currently available transcriptome data for sugarcane were generated using second-generation sequencing platforms, which provide short reads. The de novo assembled transcripts from these data are limited in length, and hence may be incomplete and inaccurate, especially for long RNAs.

Methods

We generated a transcriptome dataset of leaf tissue from a commercial Thai sugarcane cultivar Khon Kaen 3 (KK3) using PacBio RS II single-molecule long-read sequencing by the Iso-Seq method. Short-read RNA-Seq data were generated from the same RNA sample using the Ion Proton platform for reducing base calling errors.

Results

A total of 119,339 error-corrected transcripts were generated with the N50 length of 3,611 bp, which is on average longer than any previously reported sugarcane transcriptome dataset. 110,253 sequences (92.4%) contain an open reading frame (ORF) of at least 300 bp long with ORF N50 of 1,416 bp. The mean lengths of 5′ and 3′ untranslated regions in 73,795 sequences with complete ORFs are 1,249 and 1,187 bp, respectively. 4,774 transcripts are putatively novel full-length transcripts which do not match with a previous Iso-Seq study of sugarcane. We annotated the functions of 68,962 putative full-length transcripts with at least 90% coverage when compared with homologous protein coding sequences in other plants.

Discussion

The new catalog of transcripts will be useful for genome annotation, identification of splicing variants, SNP identification, and other research pertaining to the sugarcane improvement program. The putatively novel transcripts suggest unique features of KK3, although more data from different tissues and stages of development are needed to establish a reference transcriptome of this cultivar.

The Challenge of Analyzing the Sugarcane Genome

Reference genome sequences have become key platforms for genetics and breeding of the major crop species. Sugarcane is probably the largest crop produced in the world (in weight of crop harvested) but lacks a reference genome sequence. Sugarcane has one of the most complex genomes in crop plants due to the extreme level of polyploidy. The genome of modern sugarcane hybrids includes sub-genomes from two progenitors Saccharum officinarum and S. spontaneum with some chromosomes resulting from recombination between these sub-genomes. Advancing DNA sequencing technologies and strategies for genome assembly are making the sugarcane genome more tractable. Advances in long read sequencing have allowed the generation of a more complete set of sugarcane gene transcripts. This is supporting transcript profiling in genetic research. The progenitor genomes are being sequenced. A monoploid coverage of the hybrid genome has been obtained by sequencing BAC clones that cover the gene space of the closely related sorghum genome. The complete polyploid genome is now being sequenced and assembled. The emerging genome will allow comparison of related genomes and increase understanding of the functioning of this polyploidy system. Sugarcane breeding for traditional sugar and new energy and biomaterial uses will be enhanced by the availability of these genomic resources.

De novo assembly and characterizing of the culm-derived meta-transcriptome from the polyploid sugarcane genome based on coding transcripts

Sugarcane biomass has been used for sugar, bioenergy and biomaterial production. The majority of the sugarcane biomass comes from the culm, which makes it important to understand the genetic control of biomass production in this part of the plant. A meta-transcriptome of the culm was obtained in an earlier study by using about one billion paired-end (150 bp) reads of deep RNA sequencing of samples from 20 diverse sugarcane genotypes and combining de novo assemblies from different assemblers and different settings. Although many genes could be recovered, this resulted in a large combined assembly which created the need for clustering to reduce transcript redundancy while maintaining gene content. Here, we present a comprehensive analysis of the effect of different assembly settings and clustering methods on de novo assembly, annotation and transcript profiling focusing especially on the coding transcripts from the highly polyploid sugarcane genome. The new coding sequence-based transcript clustering resulted in a better representation of transcripts compared to the earlier approach, having 121,987 contigs, which included 78,052 main and 43,935 alternative transcripts. About 73%, 67%, 61% and 10% of the transcriptome was annotated against the NCBI NR protein database, GO terms, orthologous groups and KEGG orthologies, respectively. Using this set for a differential gene expression analysis between the young and mature sugarcane culm tissues, a total of 822 transcripts were found to be differentially expressed, including key transcripts involved in sugar/fiber accumulation in sugarcane. In the context of the lack of a whole genome sequence for sugarcane, the availability of a well annotated culm-derived meta-transcriptome through deep sequencing provides useful information on coding genes specific to the sugarcane culm and will certainly contribute to understanding the process of carbon partitioning, and biomass accumulation in the sugarcane culm.

Transcriptomic characterization and potential marker development of contrasting sugarcane cultivars

Sugarcane (Saccharum officinarum L.) is an important crop for sugar production and bioenergy worldwide. In this study, we performed transcriptome sequencing for six contrasting sugarcane genotypes involved in leaf abscission, tolerance to pokkah boeng disease and drought stress. More than 465 million high-quality reads were generated, which were de novo assembled into 93,115 unigenes. Based on a similarity search, 43,526 (46.74%) unigenes were annotated against at least one of the public databases. Functional classification analyses showed that these unigenes are involved in a wide range of metabolic pathways. Comparative transcriptome analysis revealed that many unigenes involved in response to abscisic acid and ethylene were up-regulated in the easy leaf abscission genotype, and unigenes associated with response to jasmonic acid and salicylic acid were up-regulated in response to the pokkah boeng disease in the tolerance genotype. Moreover, unigenes related to peroxidase, antioxidant activity and signal transduction were up-regulated in response to drought stress in the tolerant genotype. Finally, we identified a number of putative markers, including 8,630 simple sequence repeats (SSRs) and 442,152 single-nucleotide polymorphisms (SNPs). Our data will be important resources for future gene discovery, molecular marker development, and genome studies in sugarcane.

The Tomato Hybrid Proline-rich Protein regulates the abscission zone competence to respond to ethylene signals

The Tomato Hybrid Proline-rich Protein (THyPRP) gene was specifically expressed in the tomato (Solanum lycopersicum) flower abscission zone (FAZ), and its stable antisense silencing under the control of an abscission zone (AZ)-specific promoter, Tomato Abscission Polygalacturonase4, significantly inhibited tomato pedicel abscission following flower removal. For understanding the THyPRP role in regulating pedicel abscission, a transcriptomic analysis of the FAZ of THyPRP-silenced plants was performed, using a newly developed AZ-specific tomato microarray chip. Decreased expression of THyPRP in the silenced plants was already observed before abscission induction, resulting in FAZ-specific altered gene expression of transcription factors, epigenetic modifiers, post-translational regulators, and transporters. Our data demonstrate that the effect of THyPRP silencing on pedicel abscission was not mediated by its effect on auxin balance, but by decreased ethylene biosynthesis and response. Additionally, THyPRP silencing revealed new players, which were demonstrated for the first time to be involved in regulating pedicel abscission processes. These include: gibberellin perception, Ca²⁺-Calmodulin signaling, Serpins and Small Ubiquitin-related Modifier proteins involved in post-translational modifications, Synthaxin and SNARE-like proteins, which participate in exocytosis, a process necessary for cell separation. These changes, occurring in the silenced plants early after flower removal, inhibited and/or delayed the acquisition of the competence of the FAZ cells to respond to ethylene signaling. Our results suggest that THyPRP acts as a master regulator of flower abscission in tomato, predominantly by playing a role in the regulation of the FAZ cell competence to respond to ethylene signals.

Transcriptional profiling of sugarcane leaves and roots under progressive osmotic stress reveals a regulated coordination of gene expression in a spatiotemporal manner

Sugarcane is one of the most important crops worldwide and is a key plant for the global production of sucrose. Sugarcane cultivation is severely affected by drought stress and it is considered as the major limiting factor for their productivity. In recent years, this plant has been subjected to intensive research focused on improving its resilience against water scarcity; particularly the molecular mechanisms in response to drought stress have become an underlying issue for its improvement. To better understand water stress and the molecular mechanisms we performed a de novo transcriptomic assembly of sugarcane (var. Mex 69-290). A total of 16 libraries were sequenced in a 2x100 bp configuration on a HiSeq-Illumina platform. A total of 536 and 750 genes were differentially up-regulated along with the stress treatments for leave and root tissues respectively, while 1093 and 531 genes were differentially down-regulated in leaves and roots respectively. Gene Ontology functional analysis showed that genes related to response of water deprivation, heat, abscisic acid, and flavonoid biosynthesis were enriched during stress treatment in our study. The reliability of the observed expression patterns was confirmed by RT-qPCR. Additionally, several physiological parameters of sugarcane were significantly affected due to stress imposition. The results of this study may help identify useful target genes and provide tissue-specific data set of genes that are differentially expressed in response to osmotic stress, as well as a complete analysis of the main groups is significantly enriched under this condition. This study provides a useful benchmark for improving drought tolerance in sugarcane and other economically important grass species.

Genome-wide identification of leaf abscission associated microRNAs in sugarcane (Saccharum officinarum L.)

Background

Sugarcane (Saccharum officinarum L.) is an economically important crop, mainly due to the production of sugar and biofuel (Azevedo RA, Carvalho RF, Cia MC, & Gratão PL, Trop Plant Biol 4:42-51, 2011). Grown mainly in tropical and subtropical countries, sugarcane is a highly polyploid plant with up to ten copies of each chromosome, which increases the difficulties of genome assembly and genetic, physiologic and biochemical analyses. The increasing demands of sugar and the increasing cost of sugarcane harvest require sugarcane varieties which can shed their leaves during the maturity time, so it is important to study the mechanism of leaf abscission in sugarcane.

Results

To improve the understanding of miRNA roles in sugarcane leaf abscission, we reported the genome-wide characterization of miRNAs and their putative targets in sugarcane using deep sequencing for six small RNA libraries. In total, 93 conserved miRNAs and 454 novel miRNAs were identified in sugarcane using previously reported transcriptome as reference. Among them, 25 up-regulated and 13 down-regulated miRNAs were identified in leaf abscission sugarcane plants (LASP) compared to leaf packaging sugarcane plants (LPSP). Target prediction revealed several miRNA-mRNA modules including miR156-SPL, miR319-TPR2, miR396-GRF and miR408-LAC3 might be involved in the sugarcane leaf abscission. KEGG pathway enrichment analysis showed differentially expressed miRNAs may regulate pathways like “plant hormone signal transduction” and “plant-pathogen interaction”, which is consistent with previous transcriptome study. In addition, we identified 96 variant miRNAs with 135 single nucleotide polymorphisms (SNPs). The expression of sugarcane miRNAs and variant miRNAs were confirmed by qRT-PCR. We identified a possible poaceae specific miRNA called miR5384 for the first time in sugarcane.

Conclusions

We not only reported miR5384, a possible poaceae specific miRNA, for the first time in sugarcane but also presented some miRNA-mRNA modules including miR156-SPL, miR319-TPR2, miR396-GRF and miR408-LAC in sugarcane. These modules might be involved in the regulation of sugarcane leaf abscission during the maturity time. All of these findings may lay ground work for future application of sugarcane breeding program and benefit research studies of sugarcane miRNAs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-4053-3) contains supplementary material, which is available to authorized users.

De novo assembly, functional annotation, and analysis of the giant reed (Arundo donax L.) leaf transcriptome provide tools for the development of a biofuel feedstock

BACKGROUND

Arundo donax has attracted renewed interest as a potential candidate energy crop for use in biomass-to-liquid fuel conversion processes and biorefineries. This is due to its high productivity, adaptability to marginal land conditions, and suitability for biofuel and biomaterial production. Despite its importance, the genomic resources currently available for supporting the improvement of this species are still limited.

RESULTS

We used RNA sequencing (RNA-Seq) to de novo assemble and characterize the A. donax leaf transcriptome. The sequencing generated 1249 million clean reads that were assembled using single-k-mer and multi-k-mer approaches into 62,596 unique sequences (unitranscripts) with an N50 of 1134 bp. TransDecoder and Trinotate software suites were used to obtain putative coding sequences and annotate them by mapping to UniProtKB/Swiss-Prot and UniRef90 databases, searching for known transcripts, proteins, protein domains, and signal peptides. Furthermore, the unitranscripts were annotated by mapping them to the NCBI non-redundant, GO and KEGG pathway databases using Blast2GO. The transcriptome was also characterized by BLAST searches to investigate homologous transcripts of key genes involved in important metabolic pathways, such as lignin, cellulose, purine, and thiamine biosynthesis and carbon fixation. Moreover, a set of homologous transcripts of key genes involved in stomatal development and of genes coding for stress-associated proteins (SAPs) were identified. Additionally, 8364 simple sequence repeat (SSR) markers were identified and surveyed. SSRs appeared more abundant in non-coding regions (63.18%) than in coding regions (36.82%). This SSR dataset represents the first marker catalogue of A. donax. 53 SSRs (PolySSRs) were then predicted to be polymorphic between ecotype-specific assemblies, suggesting genetic variability in the studied ecotypes.

CONCLUSIONS

This study provides the first publicly available leaf transcriptome for the A. donax bioenergy crop. The functional annotation and characterization of the transcriptome will be highly useful for providing insight into the molecular mechanisms underlying its extreme adaptability. The identification of homologous transcripts involved in key metabolic pathways offers a platform for directing future efforts in genetic improvement of this species. Finally, the identified SSRs will facilitate the harnessing of untapped genetic diversity. This transcriptome should be of value to ongoing functional genomics and genetic studies in this crop of paramount economic importance.