Transcriptome analysis of sweet potato responses to potassium deficiency

Anthocyanin biosynthesis, quality, and yield in purple sweet potatoes: responses to different potassium fertilizer

Purple sweet potato (PSP) (Ipomoea batatas (L.) Lam) is a nutrient-rich "K-favoring" crop. The reasonable application of potassium is an important means of improving the quality and yield of PSP. We designed four different forms of potassium fertilizer treatments: K2SO4, KCl, KH2PO4, and K2HPO4, and used qRT-PCR and HPLC techniques to explore their differences in anthocyanin synthesis, accumulation, quality, and yield in PSP tubers. Our findings indicate that potassium fertilizer treatment enhances the expression of structural genes such as CHI (chalcone--flavonone isomerase), F3H (naringenin,2-oxogluturate 3-dioxygenase-like), F3‧H (flavonoid 3'-monooxygenase), ANS (leucoanthocyanidin dioxygenase-like), DFR (dihydroflavonol 4-reductase-like), and CHS (chalcone synthase), which encode key enzymes of the anthocyanin metabolism pathway. This is achieved by stimulating the high levels of expression of the transcription factor MYB, which controls anthocyanin accumulation. Consequently, this leads to increased activities of key anthocyanin biosynthetic enzymes Phenylalanine ammonia lyase (PAL, EC 4.3.1.5), chalcone isomerase (CHI, EC 5.5.1.6), dihydroflavonol 4-reductase (DFR, EC 1.1.1.219), and UDP-galactose flavonoid 3-O-galactosyltransferase (UFGT, EC 2.4.1.234), thereby promoting the synthesis and accumulation of anthocyanins within PSP tubers. This ultimately improves tuber quality and yield. Analysis conducted through hierarchical clustering heat map, principal component analysis (PCA), and comprehensive evaluation revealed that PSP exhibits varying sensitivities to different forms of potassium fertilizer, with KCl treatment significantly enhancing anthocyanin production efficiency. Our results will provide a theoretical basis and data support for the rational selection of potassium fertilizer types for actual PSP production.

Genome-wide analysis of PHT gene family and their role in LP and salt stress in sweet potato

Phosphate transporters (PHTs), which are essential for phosphate (Pi) uptake, translocation, and utilization, play crucial roles in regulating plant growth and development. Despite extensive characterization of PHTs in many plant species, their function in sweet potato remains unclear. Here, we conducted a genome-wide investigation, and identified 27 PHTs in cultivated hexaploid sweet potato (Ipomoea batatas L.), which are divided into five clusters (IbPHT1-IbPHT5). Phylogenetic analysis and collinearity analysis showed that sweet potato shares a closer homological evolutionary relationship with dicotyledonous (Arabidopsis) species compared with the monocotyledonous (rice). Promoter analysis revealed that the MYB (myeloblastosis) cis-element is the most abundant among all cis-elements found in the promoters of IbPHTs. RNA-seq analysis in different tissues and under low phosphate (LP) stress revealed that IbPHT1;3, IbPHT1;4, IbPHT1;5 and IbPHT3;3 were the most highly expressed genes in sweet potato. IbPHT1; 5, which located on plasma membrane, was functionally characterized and involved in Pi uptake and transport in transgenic Arabidopsis and yeast. Besides, the Pi uptake and transcriptome analysis assay showed that salt stress inhibits Pi uptake and expression of most members in PHT1 subfamily (at least 50%). This suggested that PHTs may play crucial roles in salt stress response in sweet potato. This study provides new insights for understanding the function of IbPHTs, which are candidate for improving phosphorus use efficiency and abiotic stress tolerance in cultivated sweet potato.

A comprehensive overview of omics-based approaches to enhance biotic and abiotic stress tolerance in sweet potato

Biotic and abiotic stresses negatively affect the yield and overall plant developmental process, thus causing substantial losses in global sweet potato production. To cope with stresses, sweet potato has evolved numerous strategies to tackle ever-changing surroundings and biological and environmental conditions. The invention of modern sequencing technology and the latest data processing and analysis instruments has paved the way to integrate biological information from different approaches and helps to understand plant system biology more precisely. The advancement in omics technologies has accumulated and provided a great source of information at all levels (genome, transcript, protein, and metabolite) under stressful conditions. These latest molecular tools facilitate us to understand better the plant's responses to stress signaling and help to process/integrate the biological information encoded within the biological system of plants. This review briefly addresses utilizing the latest omics strategies for deciphering the adaptive mechanisms for sweet potatoes' biotic and abiotic stress tolerance via functional genomics, transcriptomics, proteomics, and metabolomics. This information also provides a powerful reference to understand the complex, well-coordinated stress signaling genetic regulatory networks and better comprehend the plant phenotypic responses at the cellular/molecular level under various environmental stimuli, thus accelerating the design of stress-resilient sweet potato via the latest genetic engineering approaches.

Transcriptome and Metabolome Analyses Reflect the Molecular Mechanism of Drought Tolerance in Sweet Potato

Sweet potato (Ipomoea batatas (L.) Lam.) is one of the most widely cultivated crops in the world, with outstanding stress tolerance, but drought stress can lead to a significant decrease in its yield. To reveal the response mechanism of sweet potato to drought stress, an integrated physiological, transcriptome and metabolome investigations were conducted in the leaves of two sweet potato varieties, drought-tolerant zhenghong23 (Z23) and a more sensitive variety, jinong432 (J432). The results for the physiological indexes of drought showed that the peroxidase (POD) and superoxide dismutase (SOD) activities of Z23 were 3.68 and 1.21 times higher than those of J432 under severe drought, while Z23 had a higher antioxidant capacity. Transcriptome and metabolome analysis showed the importance of the amino acid metabolism, respiratory metabolism, and antioxidant systems in drought tolerance. In Z23, amino acids such as asparagine participated in energy production during drought by providing substrates for the citrate cycle (TCA cycle) and glycolysis (EMP). A stronger respiratory metabolism ability could better maintain the energy supply level under drought stress. Drought stress also activated the expression of the genes encoding to antioxidant enzymes and the biosynthesis of flavonoids such as rutin, resulting in improved tolerance to drought. This study provides new insights into the molecular mechanisms of drought tolerance in sweet potato.

Genome-wide identification of potassium channels in maize showed evolutionary patterns and variable functional responses to abiotic stresses

Potassium (K) channels are essential components of plant biology, mediating not only K ion (K+) homeostasis but also regulating several physiological processes and stress tolerance. In the current investigation, we identified 27 K+ channels in maize and deciphered the evolution and divergence pattern with four monocots and five dicot species. Chromosomal localization and expansion of K+ channel genes showed uneven distribution and were independent of genome size. The dispersed duplication is the major force in expanding K+ channels in the target genomes. The mean Ka/Ks ratio of <0.5 in paralogs and orthologs indicates horizontal and vertical expansions of K+ channel genes under strong purifying selection. The one-to-one K+ channel orthologs were prominent among the closely related species, with higher synteny between maize and the rest of the monocots. Comprehensive K+ channels promoter analysis revealed various cis-regulatory elements mediating stress tolerance with the predominance of MYB and STRE binding sites. The regulatory network showed AP2-EREBP TFs, miR164 and miR399 are prominent regulatory elements of K+ channels. The qRT-PCR analysis of K+ channels and regulatory miRNAs showed significant expressions in response to drought and waterlogging stresses. The present study expanded the knowledge on K+ channels in maize and will serve as a basis for an in-depth functional analysis.

Genome-wide systematic characterization of the NRT2 gene family and its expression profile in wheat (Triticum aestivum L.) during plant growth and in response to nitrate deficiency

BACKGROUND

Wheat (Triticum aestivum L.) is a major cereal crop that is grown worldwide, and it is highly dependent on sufficient N supply. The molecular mechanisms associated with nitrate uptake and assimilation are still poorly understood in wheat. In plants, NRT2 family proteins play a crucial role in NO₃^- acquisition and translocation under nitrate limited conditions. However, the biological functions of these genes in wheat are still unclear, especially their roles in NO₃^- uptake and assimilation.

RESULTS

In this study, a comprehensive analysis of wheat TaNRT2 genes was conducted using bioinformatics and molecular biology methods, and 49 TaNRT2 genes were identified. A phylogenetic analysis clustered the TaNRT2 genes into three clades. The genes that clustered on the same phylogenetic branch had similar gene structures and nitrate assimilation functions. The identified genes were further mapped onto the 13 wheat chromosomes, and the results showed that a large duplication event had occurred on chromosome 6. To explore the TaNRT2 gene expression profiles in wheat, we performed transcriptome sequencing after low nitrate treatment for three days. Transcriptome analysis revealed the expression levels of all TaNRT2 genes in shoots and roots, and based on the expression profiles, three highly expressed genes (TaNRT2-6A.2, TaNRT2-6A.6, and TaNRT2-6B.4) were selected for qPCR analysis in two different wheat cultivars ('Mianmai367' and 'Nanmai660') under nitrate-limited and normal conditions. All three genes were upregulated under nitrate-limited conditions and highly expressed in the high nitrogen use efficiency (NUE) wheat 'Mianmai367' under low nitrate conditions.

CONCLUSION

We systematically identified 49 NRT2 genes in wheat and analysed the transcript levels of all TaNRT2s under nitrate deficient conditions and over the whole growth period. The results suggest that these genes play important roles in nitrate absorption, distribution, and accumulation. This study provides valuable information and key candidate genes for further studies on the function of TaNRT2s in wheat.

Morphophysiological and transcriptome analysis reveal that reprogramming of metabolism, phytohormones and root development pathways governs the potassium (K+) deficiency response in two contrasting chickpea cultivars

Potassium (K⁺) is an essential macronutrient for plant growth and development. K⁺ deficiency hampers important plant processes, such as enzyme activation, protein synthesis, photosynthesis and stomata movement. Molecular mechanism of K⁺ deficiency tolerance has been partly understood in model plants Arabidopsis, but its knowledge in legume crop chickpea is missing. Here, morphophysiological analysis revealed that among five high yielding desi chickpea cultivars, PUSA362 shows stunted plant growth, reduced primary root growth and low K⁺ content under K⁺ deficiency. In contrast, PUSA372 had negligible effect on these parameters suggesting that PUSA362 is K⁺ deficiency sensitive and PUSA372 is a K⁺ deficiency tolerant chickpea cultivar. RNA-seq based transcriptome analysis under K⁺ deficiency revealed a total of 820 differential expressed genes (DEG's) in PUSA362 and 682 DEGs in PUSA372. These DEGs belongs to different functional categories, such as plant metabolism, signal transduction components, transcription factors, ion/nutrient transporters, phytohormone biosynthesis and signalling, and root growth and development. RNA-seq expression of randomly selected 16 DEGs was validated by RT-qPCR. Out of 16 genes, 13 showed expression pattern similar to RNA-seq expression, that verified the RNA-seq expression data. Total 258 and 159 genes were exclusively up-regulated, and 386 and 347 genes were down-regulated, respectively in PUSA362 and PUSA372. 14 DEGs showed contrasting expression pattern as they were up-regulated in PUSA362 and down-regulated in PUSA372. These include somatic embryogenesis receptor-like kinase 1, thaumatin-like protein, ferric reduction oxidase 2 and transcription factor bHLH93. Nine genes which were down-regulated in PUSA362 found to be up-regulated in PUSA372, including glutathione S-transferase like, putative calmodulin-like 19, high affinity nitrate transporter 2.4 and ERF17-like protein. Some important carbohydrate metabolism related genes, like fructose-1,6-bisphosphatase and sucrose synthase, and root growth related Expansin gene were exclusively down-regulated, while an ethylene biosynthesis gene 1-aminocyclopropane-1-carboxylate oxidase 1 (ACO1) was up-regulated in PUSA362. Interplay of these and several other genes related to hormones (auxin, cytokinin, GA etc.), signal transduction components (like CBLs and CIPKs), ion transporters and transcription factors might underlie the contrasting response of two chickpea cultivars to K⁺ deficiency. In future, some of these key genes will be utilized in genetic engineering and breeding programs for developing chickpea cultivars with improved K⁺ use efficiency (KUE) and K⁺ deficiency tolerance traits.