De novo transcriptome sequencing and gene expression profiling of sweet potato leaves during low temperature stress and recovery

Transcriptomic analysis reveals mechanisms for the different drought tolerance of sweet potatoes

Drought is a common environmental stress with great negative impacts on plant growth, development and geographical distribution as well as agriculture and food production. Sweet potato is characterized by starchy, fresh and pigmented tuber, and is regarded as the seventh most important food crop. However, there has been no comprehensive study of the drought tolerance mechanism of different sweet potato cultivars to date. Here, we studied the mechanism for drought response of seven sweet potato drought-tolerant cultivars using the drought coefficients, physiological indicators and transcriptome sequencing. The seven sweet potato cultivars were classified into four groups of drought tolerance performance. A large number of new genes and transcripts were identified, with an average of about 8000 new genes per sample. Alternative splicing events in sweet potato, which were dominated by first exon and last exon alternative splicing, were not conserved among different cultivars and not significantly affected by drought stress. Furthermore, different drought-tolerance mechanisms were revealed through differentially expressed gene analysis and functional annotation. Two drought-sensitive cultivars, Shangshu-9 and Xushu-22, mainly resisted drought stress by up-regulating plant signal transduction. The other drought-sensitive cultivar Jishu-26 responded to drought stress by down-regulating isoquinoline alkaloid biosynthesis and nitrogen/carbohydrate metabolism. In addition, the drought-tolerant cultivar Chaoshu-1 and drought-preferred cultivar Z15-1 only shared 9% of differentially expressed genes, as well as many opposite metabolic pathways in response to drought. They mainly regulated flavonoid and carbohydrate biosynthesis/metabolism in response to drought, while Z15-1 increased photosynthesis and carbon fixation capacity. The other drought-tolerant cultivar Xushu-18 responded to drought stress by regulating the isoquinoline alkaloid biosynthesis and nitrogen/carbohydrate metabolism. The extremely drought-tolerant cultivar Xuzi-8 was almost unaffected by drought stress and responded to drought environment only by regulating the cell wall. These findings provide important information for the selection of sweet potatoes for specific purposes.

Comparative transcriptomic and proteomic analysis reveals common molecular factors responsive to heat and drought stresses in sweetpotaoto (Ipomoea batatas)

Introduction

Crops are affected by various abiotic stresses, among which heat (HT) and drought (DR) stresses are the most common in summer. Many studies have been conducted on HT and DR, but relatively little is known about how drought and heat combination (DH) affects plants at molecular level.

Methods

Here, we investigated the responses of sweetpotato to HT, DR, and DH stresses by RNA-seq and data-independent acquisition (DIA) technologies, using controlled experiments and the quantification of both gene and protein levels in paired samples.

Results

Twelve cDNA libraries were created under HT, DR, and DH conditions and controls. We identified 536, 389, and 907 DEGs in response to HT, DR, and DH stresses, respectively. Of these, 147 genes were common and 447 were specifically associated with DH stress. Proteomic analysis identified 1609, 1168, and 1535 DEPs under HT, DR, and DH treatments, respectively, compared with the control, of which 656 were common and 358 were exclusive to DH stress. Further analysis revealed the DEGs/DEPs were associated with heat shock proteins, carbon metabolism, phenylalanine metabolism, starch and cellulose metabolism, and plant defense, amongst others. Correlation analysis identified 6465, 6607, and 6435 co-expressed genes and proteins under HT, DR, and DH stresses respectively. In addition, a combined analysis of the transcriptomic and proteomic data identified 59, 35, and 86 significantly co-expressed DEGs and DEPs under HT, DR, and DH stresses, respectively. Especially, top 5 up-regulated co-expressed DEGs and DEPs (At5g58770, C24B11.05, Os04g0679100, BACOVA_02659 and HSP70-5) and down-regulated co-expressed DEGs and DEPs (AN3, PMT2, TUBB5, FL and CYP98A3) were identified under DH stress.

Discussion

This is the first study of differential genes and proteins in sweetpotato under DH stress, and it is hoped that the findings will assist in clarifying the molecular mechanisms involved in sweetpotato resistance to heat and drought stress.

Integrative Transcriptomic and Phytohormonal Analyses Provide Insights into the Cold Injury Recovery Mechanisms of Tea Leaves

Tea plant is susceptible to low temperature, while the cold injury recovery mechanisms of tea leaves are still unclear. Windbreak has an effective and gradient range of protecting tea plants. Tea plants with increasing cold damage degree have varying recovery status accordingly, which are the ideal objects for investigating the cold injury recovery mechanisms of tea leaves. Here, we investigated the transcriptome and phytohormone profiles of tea leaves with different cold injury degrees in recovery (adjacent to the windbreak), and the levels of chlorophylls, malondialdehyde, major phytohormones as well as the activities of peroxidase (POD) and superoxide dismutase (SOD) were also measured. The results showed the content of total chlorophylls and the activity of POD in mature tea leaves gradually decreased with the distance to windbreak, while SOD showed the opposite. The major phytohormones were highly accumulated in the moderately cold-injured tea leaves. The biosynthesis of abscisic acid (ABA) was enhanced in the moderate cold damaged tea leaves, suggesting that ABA plays an important role in the cold response and resistance of tea plants. The transcriptomic result showed that the samples in different rows were well discriminated, and the pathways of plant-pathogen interaction and flavonoid biosynthesis were enriched based on KEGG analysis. WRKY, GRAS and NAC were the top classes of transcription factors differentially expressed in the different cold-injured tea leaves. Thus, windbreak is effective to protect adjacent tea plants from cold wave, and phytohormones importantly participate in the cold injury recovery of tea leaves.

Overexpression of IbFAD8 Enhances the Low-Temperature Storage Ability and Alpha-Linolenic Acid Content of Sweetpotato Tuberous Roots

Sweetpotato is an emerging food crop that ensures food and nutrition security in the face of climate change. Alpha-linoleic acid (ALA) is one of the key factors affecting plant stress tolerance and is also an essential nutrient in humans. In plants, fatty acid desaturase 8 (FAD8) synthesizes ALA from linoleic acid (LA). Previously, we identified the cold-induced IbFAD8 gene from RNA-seq of sweetpotato tuberous roots stored at low-temperature. In this study, we investigated the effect of IbFAD8 on the low-temperature storage ability and ALA content of the tuberous roots of sweetpotato. Transgenic sweetpotato plants overexpressing IbFAD8 (TF plants) exhibited increased cold and drought stress tolerance and enhanced heat stress susceptibility compared with non-transgenic (NT) plants. The ALA content of the tuberous roots of TF plants (0.19 g/100 g DW) was ca. 3.8-fold higher than that of NT plants (0.05 g/100 g DW), resulting in 8-9-fold increase in the ALA/LA ratio in TF plants. Furthermore, tuberous roots of TF plants showed better low-temperature storage ability compared with NT plants. These results indicate that IbFAD8 is a valuable candidate gene for increasing the ALA content, environmental stress tolerance, and low-temperature storage ability of sweetpotato tuberous roots via molecular breeding.

Overexpression of IbLfp in sweetpotato enhances the low-temperature storage ability of tuberous roots

Sweetpotato (Ipomoea batatas [L.] Lam) is a prospective food crop that ensures food and nutrition security under the dynamic changes in global climate. Peroxidase (POD) is a multifunctional enzyme involved in diverse plant physiological processes, including stress tolerance and cell wall lignification. Although various POD genes were cloned and functionally characterized in sweetpotato, the role of POD in lignification and low-temperature storage ability of sweetpotato tuberous roots is yet to be investigated. In this study, we isolated the cold-induced lignin forming peroxidase (IbLfp) gene of sweetpotato, and analyzed its physiological functions. IbLfp showed more predominant expression in fibrous roots than in other tissues. Moreover, IbLfp expression was up-regulated in leaves and roots under cold stress, and was altered by other abiotic stresses. Tuberous roots of transgenic sweetpotato lines overexpressing IbLfp (LP lines) showed improved tolerance to low temperature, with lower malondialdehyde and hydrogen peroxide contents than non-transgenic sweetpotato plants under cold stress. The enhanced cold tolerance of LP lines could be attributed to the increased basal activity of POD, which is involved in reactive oxygen species (ROS) scavenging. Moreover, greater accumulation of lignin could also contribute to the enhanced cold tolerance of LP lines, as lignin acts as a protective barrier against invading pathogens, which is a secondary symptom of chilling injury in sweetpotato. Overall, the results of this study enhance our understanding of the function of POD in low-temperature storage of sweetpotato tuberous roots.

Genome-Wide Identification and Expression Analysis of JAZ Family Involved in Hormone and Abiotic Stress in Sweet Potato and Its Two Diploid Relatives

Jasmonate ZIM-domain (JAZ) proteins are key repressors of a jasmonic acid signaling pathway. They play essential roles in the regulation of plant growth and development, as well as environmental stress responses. However, this gene family has not been explored in sweet potato. In this study, we identified 14, 15, and 14 JAZs in cultivated hexaploid sweet potato (Ipomoea batatas, 2n = 6x = 90), and its two diploid relatives Ipomoea trifida (2n = 2x = 30) and Ipomoea triloba (2n = 2x = 30), respectively. These JAZs were divided into five subgroups according to their phylogenetic relationships with Arabidopsis. The protein physiological properties, chromosome localization, phylogenetic relationship, gene structure, promoter cis-elements, protein interaction network, and expression pattern of these 43 JAZs were systematically investigated. The results suggested that there was a differentiation between homologous JAZs, and each JAZ gene played different vital roles in growth and development, hormone crosstalk, and abiotic stress response between sweet potato and its two diploid relatives. Our work provided comprehensive comparison and understanding of the JAZ genes in sweet potato and its two diploid relatives, supplied a theoretical foundation for their functional study, and further facilitated the molecular breeding of sweet potato.

Tuberous roots of transgenic sweetpotato overexpressing IbCAD1 have enhanced low-temperature storage phenotypes

Lignin is associated with cell wall rigidity, water and solute transport, and resistance to diverse stresses in plants. Lignin consists of polymerized monolignols (p-coumaryl, coniferyl, and sinapyl alcohols), which are synthesized by cinnamyl alcohol dehydrogenase (CAD) in the phenylpropanoid pathway. We previously investigated cold-induced IbCAD1 expression by transcriptome profiling of cold-stored tuberous roots of sweetpotato (Ipomoea batatas [L.] Lam). In this study, we confirmed that IbCAD1 expression levels depended on the sweetpotato root type and were strongly induced by several abiotic stresses. We generated transgenic sweetpotato plants overexpressing IbCAD1 (TC plants) to investigate CAD1 physiological functions in sweetpotato. TC plants displayed lower root weights and lower ratios of tuberous roots to pencil roots than non-transgenic (NT) plants. The lignin contents in tuberous roots of NT and TC plants differed slightly, but these differences were not significant. By contrast, monolignol levels and syringyl (S)/guaiacyl (G) ratios were higher in TC plants than NT plants, primarily owing to syringyl unit accumulation. Tuberous roots of TC plants displayed enhanced low-temperature (4 °C) storage with lower malondialdehyde and H₂O₂ contents than NT plants. We propose that high monolignol levels in TC tuberous roots served as substrates for increased peroxidase activity, thereby enhancing antioxidation capacity against cold stress-induced reactive oxygen species. Increased monolignol contents and/or increased S/G ratios might contribute to pathogen-induced stress tolerance as a secondary chilling-damage response in sweetpotato. These results provide novel information about CAD1 function in cold stress tolerance and root formation mechanisms in sweetpotato.

Chilling and Heat Stress-Induced Physiological Changes and MicroRNA-Related Mechanism in Sweetpotato (Ipomoea batatas L.)

Sweetpotato (Ipomoea batatas (L.) Lam.) is an important industrial and food crop. Both chilling and heat stress inhibits sweetpotato growth and development and then affects yield. However, the physiological and molecular mechanisms of sweetpotato response to chilling and heat stress is unclear. In this study, we investigated the effect of extreme temperature on sweetpotato physiological response, with a focus on oxidative stress and the potential microRNA (miRNA)-mediated molecular mechanism. Our results showed that both chilling and heat stress resulted in accumulation of reactive oxygen species (ROS), including H₂O₂ and O₂ ^-, and caused oxidative stress in sweetpotato. This further affected the activities of oxidative stress-related enzymes and products, including SOD, POD, and MDA. Both chilling and heat stress inhibited POD activities but induced the enzyme activities of SOD and MDA. This suggests that sweetpotato cells initiated its own defense mechanism to handle extreme temperature-caused oxidative damage. Oxidative damage and repair are one mechanism that sweetpotato plants respond to extreme temperatures. Another potential mechanism is miRNA-mediated gene response. Chilling and heat stress altered the expression of stress-responsive miRNAs in sweetpotato seedlings. These miRNAs regulate sweetpotato response to extreme stress through targeting individual protein-coding genes.