RNA-Seq and iTRAQ Reveal the Dwarfing Mechanism of Dwarf Polish Wheat (Triticum polonicum L.)

Morphological, anatomical, and transcriptomics analysis reveals the regulatory mechanisms of cassava plant height development

BACKGROUND

Cassava is one of three major potato crops and the sixth most important food crop globally. Improving yield remains a primary aim in cassava breeding. Notably, plant height significantly impacts the yield and quality of crops; however, the mechanisms underlying cassava plant height development are yet to be elucidated.

RESULTS

In this study, we investigated the mechanisms responsible for cassava plant height development using phenotypic, anatomical, and transcriptomic analyses. Phenotypic and anatomical analysis revealed that compared to the high-stem cassava cultivar, the dwarf-stem cassava cultivar exhibited a significant reduction in plant height and a notable increase in internode tissue xylem area. Meanwhile, physiological analysis demonstrated that the lignin content of dwarf cassava was significantly higher than that of high cassava. Notably, transcriptome analysis of internode tissues identified several differentially expressed genes involved in cell wall synthesis and expansion, plant hormone signal transduction, phenylpropanoid biosynthesis, and flavonoid biosynthesis between the two cassava cultivars.

CONCLUSIONS

Our findings suggest that internode tissue cell division, secondary wall lignification, and hormone-related gene expression play important roles in cassava plant height development. Ultimately, this study provides new insights into the mechanisms of plant height morphogenesis in cassava and identifies candidate regulatory genes associated with plant height that can serve as valuable genetic resources for future crop dwarfing breeding.

High-resolution genetic linkage map and height-related QTLs in an oil palm (Elaeis guineensis) family planted across multiple sites

A refined SNP array containing 92,459 probes was developed and applied for chromosome scanning, construction of a high-density genetic linkage map and QTL analysis in a selfed Nigerian oil palm family (T128). Genotyping of the T128 mapping family generated 76,447 good quality SNPs for detailed scanning of aberration and homozygosity in the individual pseudo-chromosomes. Of them, 25,364 polymorphic SNPs were used for linkage analysis resulting in an 84.4% mapping rate. A total of 21,413 SNPs were mapped into 16 linkage groups (LGs), covering a total map length of 1364.5 cM. This genetic map is 16X denser than the previous version used to establish pseudo-chromosomes of the oil palm reference genome published in 2013. The QTLs associated with height, height increment and rachis length were identified in LGs TT05, 06, 08, 15 and 16. The present QTLs as well as those published previously were tagged to the reference genome to determine their chromosomal locations. Almost all the QTLs identified in this study were either close to or co-located with those reported in other populations. Determining the QTL position on chromosomes was also helpful in mining for the underlying candidate genes. In total, 55 putative genes and transcription factors involved in the biosynthesis, conjugation and signalling of the major phytohormones, especially for gibberellins and cell wall morphogenesis were found to be present in the identified genomic QTL regions, and their potential roles in plant dwarfism are discussed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01360-2.

Integrated metabolomic and transcriptomic analyses of regulatory mechanisms associated with uniconazole-induced dwarfism in banana

BACKGROUND

Uniconazole is an effective plant growth regulator that can be used in banana cultivation to promote dwarfing and enhance lodging resistance. However, the mechanisms underlying banana dwarfing induced by uniconazole are unknown. In uniconazole-treated bananas, gibberellin (GA) was downregulated compared to the control groups. An integrative analysis of transcriptomes and metabolomes was performed on dwarf bananas induced by uniconazole and control groups. The key pathways involved in uniconazole-induced dwarfism in banana were determined according to the overlap of KEGG annotation of differentially expressed genes and (DEGs) differential abundant metabolites (DAMs).

RESULTS

Compared with the control groups, the levels of some flavonoids, tannins, and alkaloids increased, and those of most lipids, amino acids and derivatives, organic acids, nucleotides and derivatives, and terpenoids decreased in uniconazole-treated bananas. Metabolome analysis revealed the significant changes of flavonoids in uniconazole-treated bananas compared to control samples at both 15 days and 25 days post treatment. Transcriptome analysis shows that the DEGs between the treatment and control groups were related to a series of metabolic pathways, including lignin biosynthesis, phenylpropanoid metabolism, and peroxidase activity. Comprehensive analysis of the key pathways of co-enrichment of DEGs and DAMs from 15 d to 25 d after uniconazole treatment shows that flavonoid biosynthesis was upregulated.

CONCLUSIONS

In addition to the decrease in GA, the increase in tannin procyanidin B1 may contribute to dwarfing of banana plants by inhibiting the activity of GA. The increased of flavonoid biosynthesis and the change of lignin biosynthesis may lead to dwarfing phenotype of banana plants. This study expands our understanding of the mechanisms underlying uniconazole-induced banana dwarfing.

Conuping BSA-Seq and RNA-Seq Reveal the Molecular Pathway and Genes Associated with the Plant Height of Foxtail Millet (Setaria italica)

Foxtail millet (Setaria italica) plays an important role in C4 crop research and agricultural development in arid areas due to its short growth period, drought tolerance, and barren tolerance. Exploration of the dwarfing mechanism and the dwarf genes of foxtail millet can provide a reference for dwarf breeding and dwarf research of other C4 crops. In this study, genetic analysis was performed using phenotypic data, candidate genes were screened by bulk segregant analysis sequencing (BSA-Seq); differentially expressed genes and metabolic pathways in different strains of high samples were analyzed by RNA sequencing (RNA-Seq). The association analysis of BSA-Seq and RNA-Seq further narrowed the candidate range. As a result, a total of three quantitative trait loci (QTLs) and nine candidate genes related to plant height were obtained on chromosomes I and IX. Based on the functional prediction of the candidate genes, we propose a hypothetical mechanism for the formation of millet dwarfing, in which, metabolism and MAPK signaling play important roles in the formation of foxtail millet plant height.

Relationship between the Phenylpropanoid Pathway and Dwarfism of Paspalum seashore Based on RNA-Seq and iTRAQ

Seashore paspalum is a major warm-season turfgrass requiring frequent mowing. The use of dwarf cultivars with slow growth is a promising method to decrease mowing frequency. The present study was conducted to provide an in-depth understanding of the molecular mechanism of T51 dwarfing in the phenylpropane pathway and to screen the key genes related to dwarfing. For this purpose, we obtained transcriptomic information based on RNA-Seq and proteomic information based on iTRAQ for the dwarf mutant T51 of seashore paspalum. The combined results of transcriptomic and proteomic analysis were used to identify the differential expression pattern of genes at the translational and transcriptional levels. A total of 8311 DEGs were detected at the transcription level, of which 2540 were upregulated and 5771 were downregulated. Based on the transcripts, 2910 proteins were identified using iTRAQ, of which 392 (155 upregulated and 237 downregulated) were DEPs. The phenylpropane pathway was found to be significantly enriched at both the transcriptional and translational levels. Combined with the decrease in lignin content and the increase in flavonoid content in T51, we found that the dwarf phenotype of T51 is closely related to the abnormal synthesis of lignin and flavonoids in the phenylpropane pathway. CCR and HCT may be the key genes for T51 dwarf. This study provides the basis for further study on the dwarfing mechanism of seashore paspalum. The screening of key genes lays a foundation for further studies on the molecular mechanism of seashore paspalum dwarfing.

Transcriptional Cascade in the Regulation of Flowering in the Bamboo Orchid Arundina graminifolia

Flowering in orchids is the most important horticultural trait regulated by multiple mechanisms. Arundina graminifolia flowers throughout the year unlike other orchids with a narrow flowering span. However, little is known of the genetic regulation of this peculiar flowering pattern. This study identifies a number of transcription factor (TF) families in five stages of flower development and four tissue types through RNA-seq transcriptome. About 700 DEGs were annotated to the transcription factor category and classified into 35 TF families, which were involved in multiple signaling pathways. The most abundant TF family was bHLH, followed by MYB and WRKY. Some important members of the bHLH, WRKY, MYB, TCP, and MADS-box families were found to regulate the flowering genes at transcriptional levels. Particularly, the TFs WRKY34 and ERF12 possibly respond to vernalization and photoperiod signaling, MYB108, RR9, VP1, and bHLH49 regulate hormonal balance, and CCA1 may control the circadian pathway. MADS-box TFs including MADS6, 14, 16, AGL5, and SEP may be important regulators of flowering in A. graminifolia. Therefore, this study provides a theoretical basis for understanding the molecular mechanism of flowering in A. graminifolia.

Comparative transcriptomic analysis reveals the regulatory mechanism of the gibberellic acid pathway of Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) dwarf mutants

BACKGROUND

Tartary buckwheat is an important minor crop species with high nutritional and medicinal value and is widely planted worldwide. Cultivated Tartary buckwheat plants are tall and have hollow stems that lodge easily, which severely affects their yield and hinders the development of the Tartary buckwheat industry.

METHODS

Heifeng No. 1 seeds were treated with ethylmethanesulfonate (EMS) to generate a mutant library. The dwarf mutant ftdm was selected from the mutagenized population, and the agronomic characteristics giving rise to the dwarf phenotype were evaluated. Ultra-fast liquid chromatography-electrospray ionization tandem mass spectrometry (UFLC-ESI-MS/MS) was performed to determine the factors underlying the different phenotypes between the wild-type (WT) and ftdm plants. In addition, RNA sequencing (RNA-seq) was performed via the HiSeq 2000 platform, and the resulting transcriptomic data were analysed to identify differentially expressed genes (DEGs). Single-nucleotide polymorphism (SNP) variant analysis revealed possible sites associated with dwarfism. The expression levels of the potential DEGs between the WT and ftdm mutant were then measured via qRT-PCR and fragments per kilobase of transcript per million mapped reads (FPKM).

RESULT

The plant height (PH) of the ftdm mutant decreased to 42% of that of the WT, and compared with the WT, the mutant and had a higher breaking force (BF) and lower lodging index (LI). Lower GA4 and GA7 contents and higher contents of jasmonic acid (JA), salicylic acid (SA) and brassinolactone (BR) were detected in the stems of the ftdm mutant compared with the WT. Exogenous application of GAs could not revert the dwarfism of the ftdm mutant. On the basis of the transcriptomic analysis, 146 homozygous SNP loci were identified. In total, 12 DEGs with nonsynonymous mutations were ultimately identified, which were considered potential candidate genes related to the dwarf trait. When the sequences of eight genes whose expression was downregulated and four genes whose expression was upregulated were compared, SKIP14, an F-box protein whose sequence is 85% homologous to that of SLY1 in Arabidopsis, presented an amino acid change (from Ser to Asn) and was expressed at a lower level in the stems of the ftdm mutant compared with the WT. Hence, we speculated that this amino acid change in SKIP14 resulted in a disruption in GA signal transduction, indirectly decreasing the GA content and downregulating the expression of genes involved in GA biosynthesis or the GA response. Further studies are needed to determine the molecular basis underlying the dwarf phenotype of the ftdm mutant.

CONCLUSION

We report a Tartary buckwheat EMS dwarf mutant, ftdm, suitable for high-density planting and commercial farming. A significant decrease in GA4 and GA7 levels was detected in the ftdm mutant, and 12 DEGs expressed in the stems of the ftdm mutant were selected as candidates of the dwarfing gene. One nonsynonymous mutation was detected in the SKIP14 gene in the ftdm mutant, and this gene had a lower transcript level compared with that in the WT.

The semi-dwarfing gene Rht-dp from dwarf polish wheat (Triticum polonicum L.) is the "Green Revolution" gene Rht-B1b

Background

The wheat dwarfing gene increases lodging resistance, the grain number per spike and harvest index. Dwarf Polish wheat (Triticum polonicum L., 2n = 4x = 28, AABB, DPW), initially collected from Tulufan, Xinjiang, China, carries a semi-dwarfing gene Rht-dp on chromosome 4BS. However, Rht-dp and its dwarfing mechanism are unknown.

Results

Homologous cloning and mapping revealed that Rht-dp is the ‘Green Revolution’ gene Rht-B1b. A haplotype analysis in 59 tetraploid wheat accessions showed that Rht-B1b was only present in T. polonicum. Transcriptomic analysis of two pairs of near-isogenic lines (NILs) of DPW × Tall Polish wheat (Triticum polonicum L., 2n = 4x = 28, AABB, TPW) revealed 41 differentially expressed genes (DEGs) as potential dwarfism-related genes. Among them, 28 functionally annotated DEGs were classed into five sub-groups: hormone-related signalling transduction genes, transcription factor genes, cell wall structure-related genes, reactive oxygen-related genes, and nitrogen regulation-related genes.

Conclusions

These results indicated that Rht-dp is Rht-B1b, which regulates pathways related to hormones, reactive oxygen species, and nitrogen assimilation to modify the cell wall structure, and then limits cell wall loosening and inhibits cell elongation, thereby causing dwarfism in DPW.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07367-x.

Comprehensive transcriptomics, proteomics, and metabolomics analyses of the mechanisms regulating tiller production in low-tillering wheat

Tiller development in low-tillering wheat is related to several differentially expressed genes, proteins, and metabolites, as determined by an integrated omics approach combining transcriptome analysis, iTRAQ, and HPLC-MS on multiple NILs. Tillering is an important aspect of plant morphology that affects spike number, thereby contributing to the final crop yield. However, the mechanisms inhibiting tiller production in low-tillering wheat are poorly characterized. To investigate this aspect of wheat biology, two pairs of near-isogenic lines were developed, and an integrated omics approach combining transcriptome analysis, isobaric tags for relative and absolute quantification, and high-performance liquid chromatography-mass spectrometry were used to compare the free-tillering and low-tillering caused by an allele at Qltn.sicau-2D in wheat samples. Overall, 474 genes, 166 proteins, and 28 metabolites were identified as tillering-associated differentially expressed genes, proteins, and metabolites (DEGs, DEPs, and DEMs, respectively). Functional analysis indicated that the abundance of DEGs/DEPs/DEMs was related to lignin and cellulose metabolism, cell division, cell cycle processes, and glycerophospholipid metabolism; three transcription factor families, GRAS, GRF, and REV, might be related to the decrease in tillering in low-tillering wheat. These findings contribute to improve our understanding of the mechanisms responsible for the inhibition of tiller development in low-tillering wheat cultivars.

Identification of Transcription Factors Involved in the Regulation of Flowering in Adonis Amurensis Through Combined RNA-seq Transcriptomics and iTRAQ Proteomics

Temperature is one of the most important environmental factors affecting flowering in plants. Adonis amurensis, a perennial herbaceous flower that blooms in early spring in northeast China where the temperature can drop to −15 °C, is an ideal model for studying the molecular mechanisms of flowering at extremely low temperatures. This study first investigated global gene expression profiles at different developmental stages of flowering in A. amurensis by RNA-seq transcriptome and iTRAQ proteomics. Finally, 123 transcription factors (TFs) were detected in both the transcriptome and the proteome. Of these, 66 TFs belonging to 14 families may play a key role in multiple signaling pathways of flowering in A. amurensis. The TFs FAR1, PHD, and B3 may be involved in responses to light and temperature, while SCL, SWI/SNF, ARF, and ERF may be involved in the regulation of hormone balance. SPL may regulate the age pathway. Some members of the TCP, ZFP, MYB, WRKY, and bHLH families may be involved in the transcriptional regulation of flowering genes. The MADS-box TFs are the key regulators of flowering in A. amurensis. Our results provide a direction for understanding the molecular mechanisms of flowering in A. amurensis at low temperatures.

Comprehensive transcriptome profiling of soybean leaves in response to simulated acid rain

As a source of edible oil and protein, soybean is a major globally important economic crop; Improving its production has been an important objective of soybean breeding. Acid rain has been shown to influence soybean growth and productivity, with consequent adverse impacts on its production for use by human populations. In this study, RNA sequencing technology was utilized to examine changes in gene expression when soybean was exposed to simulated acid rain (SAR). We sampled soybean leaves at five time intervals (0, 6, 30, 54, 78, and 102 h), and built the cDNA library. In total, 54,175 expression genes were found, including 2016 genes with differential expression. A total of 416 genes were considered, as they were closely related to the response to SAR. Genes related to the regulation of sulfur and nitrogen metabolism, carbohydrate metabolism, photosynthesis, and reactive oxygen species were among those differentially expressed in response to SAR. In this study, we examined the response mechanisms of soybean under SAR exposure. Our findings will improve our understanding of the molecular mechanisms employed by soybean in responding to abiotic stress, and therefore provides important information in developing soybean breeding to improve tolerance to these stresses.

Transcriptomic Profiles Reveal the Interactions of Cd/Zn in Dwarf Polish Wheat (Triticum polonicum L.) Roots

Different intra- or interspecific wheat show different interactions of Cd/Zn. Normally, Zn has been/being widely utilized to reduce the Cd toxicity. In the present study, the DPW seedlings exhibited strong Cd tolerance. Zn and Cd mutually inhibited their uptake in the roots, showed antagonistic Cd/Zn interactions. However, Zn promoted the Cd transport from the roots to shoots, showed synergistic. In order to discover the interactive molecular responses, a transcriptome, including 123,300 unigenes, was constructed using RNA-Sequencing (RNA-Seq). Compared with CK, the expression of 1,269, 820, and 1,254 unigenes was significantly affected by Cd, Zn, and Cd+Zn, respectively. Only 381 unigenes were co-induced by these three treatments. Several metal transporters, such as cadmium-transporting ATPase and plant cadmium resistance 4, were specifically regulated by Cd+Zn. Other metal-related unigenes, such as ABC transporters, metal chelator, nicotianamine synthase (NAS), vacuolar iron transporters (VIT), metal-nicotianamine transporter YSL (YSL), and nitrate transporter (NRT), were regulated by Cd, but were not regulated by Cd+Zn. These results indicated that these transporters participated in the mutual inhibition of the Cd/Zn uptake in the roots, and also participated in the Cd transport, accumulation and detoxification. Meanwhile, some unigenes involved in other processes, such as oxidation-reduction, auxin metabolism, glutathione (GSH) metabolism nitrate transport, played different and important roles in the detoxification of these heavy metals.

Proteomic Profiling of the Interactions of Cd/Zn in the Roots of Dwarf Polish Wheat (Triticum polonicum L.)

Cd and Zn have been shown to interact antagonistically or synergistically in various plants. In the present study of dwarf polish wheat (DPW)roots, Cd uptake was inhibited by Zn, and Zn uptake was inhibited by Cd, suggesting that Cd and Zn interact antagonistically in this plant. A study of proteomic changes showed that Cd, Zn, and Cd+Zn stresses altered the expression of 206, 303, and 190 proteins respectively. Among these, 53 proteins were altered significantly in response to all these stresses (Cd, Zn, and Cd+Zn), whereas 58, 131, and 47 proteins were altered in response to individual stresses (Cd, Zn, and Cd+Zn, respectively). Sixty-one differentially expressed proteins (DEPs) were induced in response to both Cd and Zn stresses; 33 proteins were induced in response to both Cd and Cd+Zn stresses; and 57 proteins were induced in response to both Zn and Cd+Zn stresses. These results indicate that Cd and Zn induce differential molecular responses, which result in differing interactions of Cd/Zn. A number of proteins that mainly participate in oxidation-reduction and GSH, SAM, and sucrose metabolisms were induced in response to Cd stress, but not Cd+Zn stress. This result indicates that these proteins participate in Zn inhibition of Cd uptake and ultimately cause Zn detoxification of Cd. Meanwhile, a number of proteins that mainly participate in sucrose and organic acid metabolisms and oxidation-reduction were induced in response to Zn stress but not Cd+Zn stress. This result indicates that these proteins participate in Cd inhibition of Zn uptake and ultimately cause the Cd detoxification of Zn. Other proteins induced in response to Cd, Zn, or Cd+Zn stress, participate in ribosome biogenesis, DNA metabolism, and protein folding/modification and may also participate in the differential defense mechanisms.

De Novo Sequencing and Characterization of the Transcriptome of Dwarf Polish Wheat (Triticum polonicum L.)

Construction as well as characterization of a polish wheat transcriptome is a crucial step to study useful traits of polish wheat. In this study, a transcriptome, including 76,014 unigenes, was assembled from dwarf polish wheat (DPW) roots, stems, and leaves using the software of Trinity. Among these unigenes, 61,748 (81.23%) unigenes were functionally annotated in public databases and classified into differentially functional types. Aligning this transcriptome against draft wheat genome released by the International Wheat Genome Sequencing Consortium (IWGSC), 57,331 (75.42%) unigenes, including 26,122 AB-specific and 2,622 D-specific unigenes, were mapped on A, B, and/or D genomes. Compared with the transcriptome of T. turgidum, 56,343 unigenes were matched with 103,327 unigenes of T. turgidum. Compared with the genomes of rice and barley, 14,404 and 7,007 unigenes were matched with 14,608 genes of barley and 7,708 genes of rice, respectively. On the other hand, 2,148, 1,611, and 2,707 unigenes were expressed specifically in roots, stems, and leaves, respectively. Finally, 5,531 SSR sequences were observed from 4,531 unigenes, and 518 primer pairs were designed.