Sweetpotato (Ipomoea batatas (L.) Lam.) is the seventh most important crop in the world and is mainly cultivated for its underground storage root (SR). The genetic studies of this species have been hindered by a lack of high-quality reference sequence due to its complex genome structure. Diploid Ipomoea trifida is the closest relative and putative progenitor of sweetpotato, which is considered a model species for sweetpotato, including genetic, cytological, and physiological analyses. Here, we generated the chromosome-scale genome sequence of SR-forming diploid I. trifida var. Y22 with high heterozygosity (2.20%). Although the chromosome-based synteny analysis revealed that the I. trifida shared conserved karyotype with Ipomoea nil after the separation, I. trifida had a much smaller genome than I. nil due to more efficient eliminations of LTR-retrotransposons and lack of species-specific amplification bursts of LTR-RTs. A comparison with four non-SR-forming species showed that the evolution of the beta-amylase gene family may be related to SR formation. We further investigated the relationship of the key gene BMY11 (with identity 47.12% to beta-amylase 1) with this important agronomic trait by both gene expression profiling and quantitative trait locus (QTL) mapping. And combining SR morphology and structure, gene expression profiling and qPCR results, we deduced that the products of the activity of BMY11 in splitting starch granules and be recycled to synthesize larger granules, contributing to starch accumulation and SR swelling. Moreover, we found the expression pattern of BMY11, sporamin proteins and the key genes involved in carbohydrate metabolism and stele lignification were similar to that of sweetpotato during the SR development. We constructed the high-quality genome reference of the highly heterozygous I. trifida through a combined approach and this genome enables a better resolution of the genomics feature and genome evolutions of this species. Sweetpotato SR development genes can be identified in I. trifida and these genes perform similar functions and patterns, showed that the diploid I. trifida var. Y22 with typical SR could be considered an ideal model for the studies of sweetpotato SR development.

Background: As one of three essential nutrients, potassium is regarded as a main limiting factor for growth and development in plant. Sweet potato (Ipomoea batatas L.) is one of seven major food crops grown worldwide, and is both a nutrient-rich food and a bioenergy crop. It is a typical ‘K-favoring’ crop, and the level of potassium ion (K⁺) supplementation directly influences its production. However, little is known about the transcriptional changes in sweet potato genes under low-K⁺ conditions. Here, we analyzed the transcriptomic profiles of sweet potato roots in response to K⁺ deficiency to determine the effect of low-K⁺ stress on this economically important crop. Results: The roots of sweet potato seedlings with or without K⁺ treatment were harvested and used for transcriptome analyses. The results showed 559 differently expressed genes (DEGs) in low and high K⁺ groups. Among the DEGs, 336 were upregulated and 223 were downregulated. These DEGs were involved in transcriptional regulation, calcium binding, redox-signaling, biosynthesis, transport, and metabolic process. Further analysis revealed previously unknow genes involved in low-K⁺ stress, which could be investigated further to improve low K⁺ tolerance in plants. Confirmation of RNA-sequencing results using qRT-PCR displayed a high level of consistency between the two experiments. Analysis showed that many auxin-, ethylene- and jasmonic acid-related genes respond to K⁺ deficiency, suggesting that these hormones have important roles in K⁺ nutrient signaling in sweet potato. Conclusions: According to the transcriptome data of sweet potato, various DEGs showed transcriptional changes in response to low-K⁺ stress. However, the expression level of some kinases, transporters, transcription factors (TFs), hormone-related genes, and plant defense-related genes changed significantly, suggesting that they have important roles during K⁺ deficiency. Thus, this study identifies potential genes for genetic improvement of responses to low-K⁺ stress and provides valuable insight into the molecular mechanisms regulating low K⁺ tolerance in sweet potato. Further research is required to clarify the function of these DEGs under low-K⁺ stress.

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.

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.

DNA methylation, a highly conserved epigenetic modification, plays an essential role in regulating gene expression and maintaining genome stability. Aberrations in DNA methylation patterns can significantly disrupt plant developmental processes, often leading to abnormal phenotypes. These methylation states are governed by a dynamic interplay of de novo methylation, maintenance methylation, and active demethylation, mediated by a suite of specialized enzymes operating under distinct regulatory pathways. This review explores the multifaceted roles of DNA methylation in plants. We provide a comprehensive overview of methylases, demethylases, and regulatory factors, elucidating how these components interact within the broader methylation machinery. Key functions of DNA methylation, including its roles in transposon silencing, gene expression regulation, and chromatin interactions, are systematically examined. Additionally, the impact of DNA methylation on plant development is analyzed, with a focus on its involvement in responses to biotic and abiotic stressors. Finally, we discuss the potential applications of DNA methylation in crop improvement, highlighting its promise for advancing modern agricultural practices.

Potassium (K+) is an essential mineral element for plant growth and development. Members of the HAK/KUP/KT (HAK) gene family play key roles in K+ uptake and ho-meostasis. Although many of them have been extensively identified in a variety of plant species, sweet potato has not yet undergone systemic characterization. In this work, 22 potential IbHAK genes are identified based on phylogenetic analysis, and categorized into four groups (I-IV). We performed comprehensive analysis of IbHAK genes, including protein property, chromosome localization, gene structure, collinear-ity and promoter cis-element investigations for each one. Five IbHAK5 proteins (IbHAK5A-IbHAK5E) were found on the same branch as AtHAK5, OsHAK5, and ZmHAK5, suggesting that small-scale duplication events contributed to the expansion of IbHAK5s in sweet potato. IbHAK5A, a gene highly expressed in various tissues and significantly induced under low-K+ (LK) stress, was cloned and functionally charac-terized in potassium transporter deficient yeast and transgenic Arabidopsis. An AP2/EREBP family transcription factor, IbPTL1, was subsequent identified as having the ability to bind the IbHAK5A promoter and playing a role in regulating the K+ sig-naling pathway. This study provides a foundation for further functional characteriza-tion of HAK/KUP /KT transporters in sweet potato and key candidate genes for further functional analysis, which may be useful for breeding sweet potato that utilizes potas-sium more efficiently in the future.