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

Abstract

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.

Introduction

Sweet potato (Ipomoea batatas [L.] Lam.) is the third most important storage root crop in the world after potato and cassava, with an annual production of approximately 113 million tons [1]. Sweet potatoes have become in widespread demand due to their high nutritive value, carbohydrate content, and health-promoting secondary metabolites [2]. Sweet potatoes possess a remarkable ability to grow in a wide range of environmental conditions [1] and have grown in many countries around the globe, such as tropical and sub-tropical countries in Asia, Africa, and Latin America [3]. Due to high adaptability to environments, sweet potatoes are primarily grown in arid, hilly regions with marginal soil conditions and exposed to various abiotic stresses. Recent climate change has also been a rising threat to global crop production; hence, the abiotic stresses to crop cultivation are becoming more severe and frequent, impairing plant growth development and reducing crop yield. Sweet potato production is also constrained by various biotic stresses, which cause typical sweet potato diseases and significantly threaten sweet potato quality. The co-evolution of sweet potatoes with different biotic diseases and their potato-microbe interaction study will be advantageous in improving the efficiency of breeding new biotic stress-resistant cultivars. The plants, being sessile, acclimatize to changes in environmental conditions and have developed various mechanisms to combat biotic and abiotic stresses. Thus, biotic and abiotic stress tolerance is necessary for sustainable sweet potato production.

Improving the crop traits is highly desired for developing superior varieties to deal with climate change and associated biotic and abiotic stress challenges. Biotic and abiotic stress tolerance mechanisms are complex, influenced by many external factors, and involve many cellular processes [4]. Climate change-driven global warming can trigger higher insect pest pressures and plant diseases, thus affecting sweet potato production sternly and influencing the storage root yield and quality [5, 6]. The sweet potato plant has evolved various anatomical, morphological, and metabolic adaptations under biotic/abiotic stresses [7, 8]. Stress signaling in sweet potatoes generally begins from energy sensing via many players, e.g., receptors, secondary messengers, transcriptional actors, regulatory enzymes, stress-responsive proteins, reactive oxygen species (ROS), and different organic–inorganic molecules involved in these complex processes [9]. Various transcription factors (TFs) play crucial roles in generating the earliest response under any stressful condition by acting as coordinators for signal transmission and controlling the regulation of stress-responsive genes. To date, the role of many TF families has been reported in regulating plant stress responses [10]. Understanding how sweet potato plants deal with different stresses helps to develop strategies for breeding high-productivity and high-quality sweet potatoes.

Crop breeding is a decision-making process where plant breeders select the individual plants harboring the best traits. Conventional breeding has been widely applied in sweet potato via hybridization and then subsequent rounds of selection, but these practices mostly remain very slow and inadequate to enhance the development of sweet potato varieties. The whole process takes multi-year testing at different locations to detect the genetic potential of candidate genotypes across a wide range of environmental conditions [11]. The development and application of molecular markers in sweet potato facilitated this process to some extent for the identification of desirable gentotypes [12]; however, improving the quantitative traits is quite challenging because they are controlled by numerous quantitative trait nucleotides. The traits controlling the genes for disease or stress tolerance are economically imperative in crop plants, therefore the extensive exploration of available germplasm resources and unraveling their genetic diversity remains vital for stress breeding programs. The advanced molecular breeding approaches provide unprecedented opportunities to accelerate the development of cultivars with desired traits and enhanced adaptation to mitigate the effects of climate change. With the advancement in genome sequencing and the latest genome editing technologies, the discovery and accumulation of valuable traits in a single genotype can now be done more efficiently. These innovative technologies provide a better understanding of genome structures and underlying trait architectures for precise crop improvement. The recent development in high-throughput next-generation sequencing technology during a couple of decades has led to the advent of ‘omics’ technologies: genomics, proteomics, transcriptomics, metabolomics, and phenomics. The integrated use of different omics approaches called multi-omics, such as pan-omics and trans-omics, also provides deep insights into data analysis, visualization, and interpretation to conclude the mechanism of any biological process, especially stress-related cellular mechanisms of plant responses and their relationships with the environmental clues to producing a characteristic phenotype. The efficient combination of different molecular breeding approaches, from markers to recent genomic and post-genomic era technologies, provide a basis to develop a successful breeding strategy that would be helpful to understand better the complex genetic control of biotic/abiotic related genes and their underlying plant resistance to obtain resistant crop varieties [13]. The integration of transcriptomic and metabolomic data was successfully applied in sweet potatoes to identify the candidate genes and corresponding metabolites [14]. The genome-wide analysis of expression QTLs has also been applied and reveal the regulatory architecture of gene expression profile in sweetpotato [15]. These approaches also facilitate the prompt identification of putative genes and their corresponding loci associated with stress resistance. Furthermore, omics technology also guides us in exploring stress-related pathways, which further helps plant functional and metabolic engineering. With the latest next-generation sequencing technologies, the extended information regarding the whole genome sequence and functional genomics resources facilitates stress breeding in tuber crops.

In this review, we comprehensively describe the impact of major biotic and abiotic stresses on sweet potato, their adaptive mechanisms, and how the integration of different omics approaches such as functional genomic, transcriptomic, and proteomic processes enable the different researchers to combat the challenges of various diseases/pests as well as climate change posed by global warming. The updated consequences of major omics in sweet potatoes have been listed, and the impact/mechanism of the individual and multiple biotic and abiotic stresses have been drawn, which helps to explore the genetic regulatory networks for stress tolerance. It is important to identify the various component traits contributing to the stress tolerance mechanism, investigate the relative importance of these traits in various crops and production systems, and understand the genetic architecture of these component traits. The integrated use of various omics approaches in sweet potatoes helps design crops that perform better under environmental stresses and assist future sweet potato breeding for disease and environmental-stress-resilient cultivars (Fig. 1).

Figure 1.

The use of the omics roadmap to develop stress-resilient sweet potato. Sweet potato usually grows on marginal lands, thus facing multiple biotic and abiotic stresses that cause considerable losses in sweet potato production worldwide. Recent genomics, transcriptomics, proteomics, and metabolomics approaches are used individually or in combination to understand the cellular mechanisms of sweet potato responses to multiple stresses, thus developing stress-tolerant sweet potato plants. AOS, alternative oxidase; ROS, reactive oxygen species.

Sweet potato whole genome sequencing and re-sequencing

High-throughput sequencing technology eases the way for whole-genome sequencing in different crops. An enormous amount of sequencing information is gathered as per the continuous reduction in sequencing cost per unit. However, there is limited information regarding whole-genome sequencing for sweet potatoes due to the highly heterozygous hexaploid genome of I. batatas, which further complicates genetic studies. Due to these limitations, sweet potatoes need further information and more sophisticated modern technologies that can process all the available information and draw a better perspective to explore the molecular mechanisms for biotic and abiotic tolerance in sweet potatoes. The first whole-genome de novo sequencing in diploid relatives of sweet potato (Ipomoea trifida) was reported in 2015 [16], facilitating the research in sweet potato studies as first reference genomes to better understand the stress resilance [17]. Furthermore, bacterial artificial chromosome library was constructed by using a stem nematode resistance line ‘Xu-781’, which provides a valuable source of polymorphic markers in the form of repetitive DNA sequences called simple sequence repeats (SSRs) for disease resistance and gives deep insights into the diploid closest wild relative of sweet potato genome (I. trifida) composition and their utilization in gene cloning and marker development [18]. Furthermore, the expression pattern of sporamin, which account for 80% of the total protein content in sweet potato, was also highlighted and its enzymatic activities were found to be related to plant defenses such as insects, plant diseases, and abiotic stresses (osmotic stress) [19]. The first chromosome-level references genome was constructed in wild relatives of sweet potato: Ipomoea trifida and Ipomoea triloba [20]. Yan et al. sequence the chloroplast genome in the sweet potato cultivar ‘Xushu18’, which facilitates and signifies the roles of chloroplast-related genes in response to future stress-responsive gene expression [21]. The whole-genome de novo assembly of carotenoid-rich (role as antioxidants during plant stresses) sweet potato cultivar was drawn, which provided helpful information regarding the complexity of chromosome sequence composition in a polyploidy genome [22]. The OutcrossSeq strategy was also applied in sweet potatoes to dissect loci for complex quantitative traits and identify several candidate genes for stress-related agronomic traits in sweet potato [23]. The re-sequencing of 314 sweet potato germplasm reveals several novel significant loci (Iba_chr02a, Iba_chr05a, Iba_chr06a, Iba_chr07a, Iba_chr10a) associated with stress-tolerance mechanisms related pathways such as carotenoid metabolism and anthocyanin metabolism [24]. The accessibility of this reference genome information permits its application in different polyploidy crops, and such technologies in sweet potatoes predicted significant progress and sped up the future precision breeding program for abiotic tolerance.

Genome-wide survey of TF families and their response to various stresses in sweet potato

Different genome-wide surveys were conducted in sweet potatoes to identify TF families and their corresponding roles/expression under various stresses. Recently, a combined approach was adopted to study both biotic and abiotic stress responses in sweet potatoes and identified the role of IbPIF3.1 TF under drought and Fusarium wilt stresses [25]. The comparative genome-wide study was performed between four Ipomoea species to evaluate valine glutamine motif-containing genes and found 40 differentially expressed genes (DEGs) referring to various abiotic stresses [26]. The other genome-wide studies in different Ipomoea species were conducted for important TF families such as NAC (NAM, ATAF, and CUC) TFs family [27], hydroxycinnamate-CoA quinate hydroxycinnamoyl transferase gene family [28], DNA-binding with one finger (Dof) TF family [29], myeloblastosis (MYB) gene family [30], phytochrome-interacting factors [25], domain of unknown function gene family [31], two-component system genes [32], xyloglucan endotransglucosylase/hydrolase gene family [33], expansin gene family [34], glycine-rich RNA-binding proteins [35], WRKY TFs family [36], zinc-finger domain-containing stress-associated proteins [37], plant-specific GRAS TFs [38], APETALA2/ethylene responsive factor (AP2/ERF) TFs family [38], jasmonate-ZIM (JAZ) TF family [39], and bZIP TF family [10]. These studies provide new insights for understanding the different TFs families-mediated stress responses and lays the foundation for future functional investigation of sweet potato TFs families.

The functional genomics studies for resilience against abiotic and biotic stresses in sweet potato

Functional omics data from multiple platforms are useful for positional cloning. The stress signaling in sweet potatoes generally evolves by signal perception, which then leads toward the stress responses. Many players from receptors, regulatory enzymes, and different organic–inorganic molecules are involved in this complex process. Signal extension and transduction by secondary messengers cause differential regulation of TFs and stress-responsive genes (Fig. 2). The plant functional omics data are helpful for positional cloning and utilized to unravel the various stress-related molecular mechanisms, thereby contributing to the development of functional genomics for stress tolerance in tuber crops [40].

Figure 2.

General overview of stress signaling pathway in sweet potato. Sweet potato biotic and abiotic stress signaling pathways are initiated by signal perception and lead toward stress responses. The early occurrence of stress sensing via receptors/sensors cascades activates the downstream stress-responsive genes via reactive oxygen species (ROS), Ca²⁺/calmodulin (CaM), and phytohormone signaling. Moreover, the signal transduction is facilitated by secondary messengers such as nitric oxide (NO), cyclic adenosine monophosphate (cAMP), cyclic guanosine monophosphate (cGMP), inositol triphosphate (IP3), and calcium ion (Ca²⁺). These signaling pathways induce the differential regulation of transcription factors (TFs) and other stress-responsive genes. Furthermore, regulating TFs/genes leads to adjusting sweet potato physiological, biochemical, and molecular responses, thus improving stress tolerance. The boxes on the left side indicate the essential genes/TFs that act and protect sweet potato plants under extreme environmental and biotic stresses.

Role of TF families and other resistance genes incorporating stress resistance

The advancement in functional genomics has accelerated the studies to dissect the complex role of TFs in biotic and abiotic stress tolerance mechanisms and led to the identification of novel candidate genes/alleles. Different plant-specific TF families such as NAC, MYC/MYB, c-repeat binding factor (CBF)/dehydration response element binding (DREB), ABA-responsive elements (ABRE), and AP2/ERF regulate multiple abiotic stress-related gene expression. NAC family TFs function in different regulatory networks in response to numerous abiotic stresses. Recently, IbNAC3 TF was found as a crucial component for incorporating combined stress tolerance via integrating different regulatory events as well as ubiquitin pathways [41]. A dynamic network biomarker analysis was performed on sweet potato and identified IbNAC083 as a core regulator and its gene ontology (GO) enrichment revealed most of the stress and hormonal-responsive genes [42]. In another study, sweet potato NAC006 and NAC143 had prominent transactivation activities and were strongly induced by multiple abiotic stress (Fig. 3) [27]. The gene expression analysis of 12 novel NAC genes (designated as IbNAC1L and IbNAC3 through IbNAC13) were significantly induced by implying multiple abiotic stresses as well as when treated with various hormones, depicting distinct roles of IbNAC genes in sweet potato stress tolerance [51]. The IbNAC1-overexpressing (OE) sweet potato plants increased the sporamin expression and elevated resistance against herbivores via the jasmonic acid (JA)-mediated pathway [52]. Furthermore, nucleotide-binding sites and leucine-rich repeat domains containing genes are plants’ predominant type of resistance genes. Four NBS encoding genes’ (IbNBS258, IbNBS88, IbNBS10, and IbNBS20) expression were significantly induced in response to stem nematode infection in sweet potato [53].

Figure 3.

The molecular mechanism of sweet potato responses to multiple abiotic stresses. Sweet potatoes’ salt, drought, and oxidative stresses induce various transcription factors (TFs) in the nucleus. The B-box (BBX) TF IbBBX24 directly binds to the promoter of sweet potato peroxidases (IbPRX17) and stimulates the IbPRX17 expression, leading to enhanced peroxidase activity along with the lower H₂O₂ accumulation [43]. A novel GAGA gene, IbGATA24 (a kind of transcription factor), induces the expression by polyethylene (PEG) 6000, NaCl, and abscisic acid (ABA) treatments found in salt and drought tolerance [44]. Under salt and drought stresses, sweet potato with high IbGATA24 expression shows increases in ABA, jasmonic acid (JA), and proline contents as well as high activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) [44]. In addition, it is found that low contents of malondialdehyde (MDA) and H₂O₂ ultimately result in salt and drought stresses [44]. The sweet potato IbABF4 encoding the ABA-responsive element binding factor is induced in its expression by ABA, drought, salt, and high-temperature signals leading to an increase in the photosynthetic efficiency and a decrease in the contents of MDA and H₂O₂ against salt, drought, and oxidative stresses [45]. Moreover, tolerance of sweet potato to salt and drought is involved in the up-regulation of IbARF5, IbRAP2–12, and IbMYB48. PEG6000, ABA, and NaCl trigger the up-regulation of IbARF5 contributing to an increase in ABA and proline contents as well as the SOD activity along with the reduction of H₂O₂ [46]. Meanwhile, IbRAP2–12 expression is induced by NaCl, PEG6000, ABA, and methyl jasmonate (MeJA), causing increases in ABA, JA, and proline contents with the reduction of H₂O₂ content [47]. The up-regulation of IbMYB48 promotes the contents of ABA, JA, and proline as well as the SOD activity through the presence of PEG6000, NaCl, ABA, MeJA, SA, and H₂O₂ [48]. In plastid, IbLCYB2 and IbTC play a significant role in salt, drought, and oxidative tolerance. The overexpression of lycopene β-cyclase gene IbLCYB2 contributes to an increase in α-carotene, β-carotene, lutein, β-cryptoxanthin, ABA, and proline zeaxanthin contents [9], whereas the up-regulation of IbTC shows high accumulation of α-tocopherol and chlorophyll contents and high levels of photosystem II activity [49]. Additionally, the down-regulation of IbLCY-ε increases the contents of total carotenoid, β-carotene, and photosynthetic rate, thus reducing the membrane permeability, resulting in salt and drought tolerance [50]. In the cytoplasm, Myo-inositol-1-phosphate synthase gene (IbMIPS1) is induced by NaCl, PEG6000, and ABA and its overexpression significantly enhances salt and drought tolerance [64]. IbMIPS1 up-regulation increases IP3, PA, Ca^2+, ABA, K⁺, proline, and trehalose contents whereas the reduction was observed in MDA, Na^+, and H₂O₂ contents [64]. Besides the up-regulation of trehalose-6-phosphate synthase (TPS), IbTPS1 is induced by environmental stresses including, drought, salt, and heat shock, resulting in salt, drought, and heat shock tolerance with the increased trehalose-6-phosphate (TP6) content [77]. Moreover, a sucrose transporter plays a crucial role in plant growth and response to salt, low temperature, and exogenous ABA treatments. The overexpression of IbSUT4 enhances sucrose accumulation in roots under various stress conditions as well as induces the expression of genes involved in ABA signaling pathways and inhibits the negative regulator of ABA signal transduction pathway gene expression, that is, ABA insensitive 1 (ABI1) [63].

The role of a basic helix–loop–helix (bHLH) TF IbbHLH33 was reported as a positive regulator in cold tolerance and fine-tune signaling pathways for chilling stress [54]. In another study, Zhang et al. [55] reported the role of 72 putative sweet potato IbGRAS genes in responses to multiple abiotic stresses (salt, drought, heat, and cold). Three sweet potato expansin (IbEXP1, IbEXP2, and IbEXPL1) activities were found significant under chilling stress, and their transcriptional regulation provides a way forward to enhance the chilling tolerance in tropical crops [56]. Moreover, sweet potato zinc finger protein gene-1 (IbZFP1) develops drought and salt tolerance in transgenic Arabidopsis plants via modulating abscisic acid (ABA) signaling, ROS scavenging, proline biosynthesis, and stress-responsive genes [57]. The functional study of a PIFs TFs IbPIF3.1 revealed that IbPIF3.1 enhances drought and Fusarium wilt tolerance in transgenic tobacco plants and is significantly induced by salt, H₂O₂, cold, and heat stresses [25].

Role of sweet potato secondary metabolic pathways to mitigate stress responses

The role of plant secondary metabolites is well known to cope with adverse environmental conditions. The genes involved in the carotenoid biosynthesis pathway were induced under abiotic stress responses. A recent report suggested the role of IbNAC29 in carotenoid accumulation via inducing the expression of carotenoid biosynthesis gene IbPSY and directly binds to sweet potato STAY-GREEN-1 (IbSGR1) and inhibits the promoter activity of IbSGR1 [58]. Under salt stress, IbOr-Ins OE plants showed increased carotenoid contents, which is closely associated with higher DPPH radical-scavenging activity [59]. In another report, IbARF5 transgenic Arabidopsis plants showed increased carotenoid contents and enhanced tolerance to salt and drought stresses [46]. The overexpression of sweet potato lycopene beta-cyclase (IbLCYB2) gene enhances the drought, salt, and oxidative stress tolerance via increasing the contents of α-carotene, β-carotene, β-cryptoxanthin, lutein, and zeaxanthin [9]. Moreover, down-regulation of CHY-β and LCY-ε genes showed tolerance to salt stress compared to wild-type control cells and calli of sweet potato [60]. Anthocyanin’s natural pigments belong to the main subgroup of flavonoids, which not only gives plants distinguishable colors but also provides them with resistance against biotic and abiotic stresses. The transcriptomics data screening from rich anthocyanin cultivars identified a R2R3-MYB gene IbMYB48, for which the expression is induced by various stresses, and enhances the drought and salt tolerance in sweet potatoes [48]. In another study, the down-regulation of sweet potato dihydroflavonal-4-reductase gene IbDFR increases susceptibility to abiotic stress while decreasing the anthocyanin accumulation [61].

The hormonal interplay to incorporate stress resilience in sweet potato

ABA is widely known for its pivotal roles in responding to various abiotic stresses and regulating plant adapting metabolism and gene expression profiles to cope with stress responses. The antagonistic roles of two bHLH were established under ABA-mediated drought responses; that is, OE of IbbHLH118 enhances drought susceptibility, whereas the OE of IbbHLH66 increases drought tolerance [62]. In another study, sucrose transporter gene IbSUT4 behaves through the ABF-dependent ABA signaling pathway and plays critical roles under abiotic stresses [63]. ABA-induced expression of IbbZIP37 and IbMIPS1 under various environmental stresses thus enhances the salt and drought tolerance under field conditions [64, 65]. The OE of different sweet potato genes, i.e., IbSPCP2, IbNFU1, IbP5CR, IbMas, IbPSS1, and IbMYB308, significantly enhances salt and drought tolerance in transgenic plants by protecting membrane integrity, regulating osmotic balance, photosynthesis, maintaining Na⁺ homeostasis, Na⁺ exclusion in the root, and activating the ROS scavenging system [66–69] (Fig. 4). The JAZ domain is a core JA-signaling module that regulates the expression of JA-responsive genes. The OE of the IbBBX24 gene increases the resistance against Fusarium wilt disease via modulating the JA biosynthesis pathway via directly binding to the promoter region of JA signaling repressor IbJAZ10 and activating its transcription. These findings suggested that JA responses play a crucial role in regulating Fusarium wilt resistance in sweet potato [76] (Table 1).

Figure 4.

The molecular characterization of sweet potato responses under salt and drought stresses. Salinity is a genetically complex abiotic stress affected by several physiological and biochemical processes. Several physiological mechanisms that improve salt tolerance include ion exclusion from roots, ion compartmentalizing into vacuoles, regulation of ion transport from root to shoot, accumulation of organic compatible solutes in tissues, and increased tissue tolerance to toxic ions [70]. During salt stress, proline accumulation is common in plants. Pyrroline-5-carboxylate reductase (P5CR) is a critical enzyme in proline biosynthesis and is strongly induced by salt stress [66]. The overexpression (OE) of IbP5CR stimulates the expression of ROS scavenging genes, whereas it down-regulates the proline dehydrogenase (PRODH) and P5C dehydrogenase (P5CDH) genes and enhances proline accumulation [66]. The OE of sweet potato Maspardin gene (IbMas) contributes to an increase in both proline accumulation and superoxide dismutase (SOD) activity and decreases H₂O₂ accumulation. Moreover, IbMas expression also causes the up-regulation of P5CS, P5CR, SOD, PsbA (D1 protein of PSII), and Phosphoribulokinase (PRK) genes [67]. Sweet potato phosphatidylserine synthase-1 (IbPSS1) encodes the enzyme involved in phosphatidylserine (PS) synthesis [68]. Under salt stress, an apoplastic H₂O₂ burst is rapidly triggered [71]. The OE of IbPSS1 causes a reduction in cellular Na⁺ accumulation, but also elevates salt-induced Na⁺/H⁺ antiport activity and plasma membrane (PM) Ca²⁺ permeable channel sensitivity to NaCl and H₂O₂ [68]. The sweet potato stress-associated protein (SAP) gene IbSAP16 is present in the endoplasmic reticulum and responds under salinity stress [37]. Sweet potato C2-Domain Abscisic Acid-Related Gene IbCAR1 [72], RING-H2 type E3 ubiquitin ligase gene IbATL38 [73], and APETALA2/ethylene responsive factor (AP2/ERF) transcription factor (TF) IbRAP2.4 [74] and Myeloblastosis (MYB) TF IbMYB308 [69] play significant roles in salinity stress. The two bHLH proteins have antagonistic roles in ABA-mediated drought responses. IbbHLH118 directly binds to the promoter of IbABF2 (ABA-responsive element binding factor 2), IbABI5 (ABA-insensitive 5), and IbTIP1 (Tonoplast intrinsic protein 1) at the E-box region to suppress their transcription. ABA accumulates during drought stress, promoting the IbPYL8–IbbHLH66–IbbHLH118 complex formation, repressing the ABA-responsive genes, and improving drought tolerance [62]. An open reading frame (sORF) gene in sweet potato [75], IbEGF, and sweet potato phytochrome-interacting factors (IbPIF3.3) also play significant roles in drought tolerance [25, 75]. IbEGF protein is present in the nucleus and cell membrane and it interacts with the IbCOP9-5α and enhances drought tolerance by increasing the accumulation of proline, ABA, methyl-jasmonate (MeJA), brassinosteroid (BR) and activating ROS scavenging system as well as up-regulating genes involved in SOD, catalase (CAT), and peroxidase (POD) [75].

Table 1.

A detailed overview of abiotic and biotic stress studies in sweet potato.

Host cultivar	Resistance gene/ candidate gene/ target gene	Abiotic/biotic stresses	Defense mechanism/ catabolism/ signaling/ significant compounds involving stress tolerance	Ref.
Xushu 18	Trehalose-6-phosphate synthase 1 (IbTPS1)	Salt, drought, and heat shock (47°C)	The increase in T6P content acting as a secondary messenger for inducing the expression of genes related to signal transduction in response to abiotic stresses	[77]
HVB-3; Shangshu 19	Lycopene β-cyclase (IbLCYB2)	Salt, drought, and oxidative stresses	The upregulated genes involved in carotenoid and ABA biosynthesis pathways	[9]
Xushu 29	Tocopherol cyclase (IbTC)	Salt, drought, and oxidative stresses	The increases in photosynthesis II activity, chlorophyll, and α-tocopherol content contents	[49]
Yulmi	Lycopene ε-cyclase (IbLCY- ε)	Salt and drought	The increases in carotenoid and ABA accumulation, β-carotene, and ROS	[50]
ND98 (salt-tolerant); Lizixiang (salt-sensitive)	The B-box (IbBBX24) and peroxidase (IbPRX17)	Salt and drought	The higher peroxidase activity along with lower H2O2 accumulation	[43]
Xushu55-2	IbGATA24	Salt and drought	Genes involved in ABA and JA signaling pathways and ROS scavenging were upregulated IbGATA24 binding with IbCOP9-5a protein through the activation of ABA, and ROS accumulation enhanced salt and drought stress resistance	[44]
Yulmi; Sinhwangmi; Sinzami	Orange protein of sweet potato (IbOr) and carotenoid cleavage dioxygenase 4 (IbCCD4)	High temperature (47°C) and drought	The increases in carotenoid contents	[78]
Sinzami; Yulmi;Sinhwangmi	IbMPK3/6	Pseudomonas syringae pv. tabaci and cold temperature	IbMPK3/6 phosphorylation Upregulation of PR gene expression Upregulation of IbMPK3/6 against cold stress	[79]
Nongda 603; Lizixiang	IbMIPS1	Salt and drought tolerance, and stem nematodes	Upregulation of genes involved in inositol biosynthesis, PI and ABA signaling pathways, stress responses, photosynthesis, and ROS scavenging system The increases in the contents of inositol. IP3, PA, Ca2+, ABA, callose, and lignin	[40, 64]
HVB-3	IbARF5	Salt and drought	The increases in the contents of carotenoids, ABA, proline, and SOD activity The reduction of H2O2 content The upregulation of genes related to carotenoid and ABA biosynthesis and abiotic stress response	[46]
ND98	IbRAP2–12	Salt and drought	The increases in the contents of ABA, JA, and proline with the reduction of H2O2 content The upregulation of genes involved in ABA and JA signalling, proline biosynthesis and ROS scavenging process	[47]
Xushu 55–2	IbWRKY2	Salt and drought	The increases in the contents of ABA and proline with the reduction of MDA and H2O2 contents The upregulation of genes involved in ABA signalling, proline biosynthesis, and ROS scavenging process	[80]
Xushu 18	IbABF4	Salt, drought, and oxidative stress	The increases in ABA sensitivity and photosynthetic efficiency with the reduction of MDA and H2O2 contents	[65]
Taizhong 6	IbSUT4	Salt, low temperature, and exogenous ABA	The reduction of MDA content A higher accumulation of sucrose content in roots and the lower sucrose content in leaves. The changes of sucrose distribution between source and sink tissues were responsible for salt, low temperature, ABA treatment	[63]
Jingshu 6 and JS6-5	IbMYB48	Salt and drought	The increases in ABA, JA, and proline contents with the enhance of SOD activity The upregulation of genes involved in ABA and JA biosynthesis, and ROS scavenging system	[48]
Xushu 18	Myo-inositol-1-phosphate synthase (IbMIPS1)	Salt stress	Salt stress-responsive genes including MIPP, P5CS, P5CR, PRK, and SOD were upregulated The contents of inositol, proline, SOD, and photosynthesis activities were increased	[81]
Whitestar	Peroxidase (swpa4)	Oxidative stress and high salinity	Peroxidase (swpa4) played a role in the regulation of peroxidase metabolism against stress responses Interplay among diverse peroxidases regulated stress responses	[82]
Yeonjami (YJM, tolerant); Jeonmi (JM, highly sensitive)	Ethylene response factor VII (ERFVII)	Flooding	Genes involved in ET, ROS, NO biosynthesis were upregulated ERFVII, a gene related to low oxygen signaling, was upregulated	[5]
Lushu 3	Trehalose-6-phosphate synthase (IbTPS)	Salt tolerance	High accumulation of trehalose, and proline contents	[83]
Xushu 29	Invertase inhibitor (IbINH)	Drought	The increases in sucrose content and upregulation of ABA biosynthesis genes were noticed during water deficit	[84]
Xushu55-2; Lizixiang	IbEGF	Drought	High accumulation of ABA, MeJA, BR, and proline contents and upregulation of genes encoding SOD, CAT, and POD were reported under stress conditions IbEGF-IbCOP9-5α interaction increased drought tolerance through the regulation of phytohormone signalling pathways	[75]
Xushu 29	Basic/helix-loop-helix (IbbHLH79, an ICE1-like gene)	Cold tolerance	Induction of an active C-repeat binding factor (CBF) pathway mediated a broad range of signals in sweet potato	[85]
Xushu 29	Lignin-forming peroxidase (IbLfp)	Low-temperature storage ability	The increases in POD activity and lignin accumulation Reduction of MDA and H2O2 contents	[86]
Xushu 29	IbFAD8	Low-temperature storage ability	The increases in ALA content, membrane fluidity and POD activity	[87]
Xushu 29	Orange gene (IbOr-R96H)	Heat tolerance (47°C)	The increases in the contents of carotenoid, Β-carotene, and ABA as well as the DPPH radical scavenging activity	[88]
G87 × N73 (F1)	SPWR1 and SPWR2	Sweet potato weevil	Increase in quinate derivative metabolites	[89]
Guangshu No. 87	IbPAL, IbC4H, and IbHQT	Sweet potato weevil	The increases in JA, SA, and ABA The levels of IbPAL, IbC4H, and IbHQT expression were up-regulated	[90]
Kyushu No. 166; Tamayutaka	The terpenoid-related genes (itf09g05600.t1, itf09g05580.t1, and itf12g13950.t1)	Sweet potato weevil	The suppression of pupation during larval development An increase in the expression of terprnoid-related genes	[91]
Ayamurasaki	Cry1Aa	Spodoptera litura	Cry1Aa toxin expressing in BT transgenic sweet potato lines could prevent S. litura infestation Cry1Aa toxin severely damages the columnar cells of midgut of S. litura	[92]
Xushu29	IbSPF1	P. syringae pv. tabaci	IbSPF1 interacted with IbMPK3/6 and was phosphorylated at Ser75 and Ser110 by IbMPK3/6 The increase in the affinity of IbSPF1 for W-box element	[93]
ND98; Lizixiang	IbSWEET10	Fusarium oxysporum	Sugar contents decreased in leaves and the remaining compact cells in the pith were observed	[94]
ND98; Lizixiang	IbBBX24	F. oxysporum	High accumulation of JA. JA biosynthesis and signaling played a significant role in Fusarium wilt resistance in sweetpotato	[76]
Tainong 57	IbNAC1	Wounding	A forming protein complex of IbbHLH3-IbbHLH3 binding the G-box motif to activate IbNAC1 expression	[52]
Kokei No.14; Tamayutaka	α-hordothionin (αHT) from barley endosperm	Ceratocystis fimbriata (Black rot)	Plant thionin peptide had an anti-fungal activity against C. fimbriata Thionin inhibits the fungal growth at the inoculated site through the action at their membranes	[95]
Chikei 682–11	Coat protein (CP) gene of SPFMV	Sweet potato feathery mottle virus (SPFMV)	CP-mediated resistance	[96]
Blesbok	CP genes of SPFMV, Sweet potato chlorotic stunt virus (SPCSV), Sweet potato virus G (SPVG), and Sweet potato mild mottle virus (SPMMV)	Multiple viruses (SPFMV, SPCSV, SPVG, and SPMMV)	CP-mediated resistance manifested the delayed symptoms of chlorosis and mottling of lower leaves	[97]
15 sweet potato diallel progenies (1352 genotypes)	spcsv1 and spfmv1	SPCSV and SPFMV	The recessive genes, spcsv1 and spfmv1 associated with the resistance to SPCSV and SPFMV, respectively	[98]
Huachano	An intron-spliced hairpin contruct targeting the RNA-dependent RNA polymerase (RdRp) encoding sequence of SPCSV	SPCSV	RNA silencing-mediated resistance	[99]
HZHK2	chit42 from Trichoderma harzianum	Sclerotinia sclerotiorum (white rot)	The increase in the endochitinase activity caused a reduction of S. sclerotiorum virulence	[100]
Xushu 29	SPCSV-RNase3	Sweet potato virus disease (SPVD)	CRISPR-Cas13 system An RNase3-targeted RfxCas13d system improved the SPVD resistance	[101]

ABA, abscisic acid; ALA, alpha-linoleic acid; ARF, auxin response factor; BR, brassinosteroid; BT, Bacillus thuringiensis; CAT, catalase; C4H, cinnamate 4-hydroxylase; CRISPR-Cas, clustered regularly interspaced short palindromic repeat CRISPR-associated protein; DPPH, 2,2-diphenyl-1-picrylhydrazyl; ET, ethylene; GB, glycine betaine; H₂O₂, hydrogen peroxide; HQT, hydroxycinnamoyl-CoA quinate hydroxycinnamoyl transferase; inositol-1,4,5-triphosphate, IP3; JA, jasmonic acid; MDA, malondialdehyde; MeJA, methyl-jasmonate; NO, nitric oxide; PEG, polyethylene glycol; PI, phosphatidylinositol; POD, peroxidas; PR, pathogenesis-related; ROS, reactive oxygen species; SA, salicylic acid; SOD, superoxide dismutase.

The activation of various stress-responsive signaling pathways/cascades during multiple stresses

The stress-responsive signaling pathways/cascades significantly mitigate the detrimental factors posed by various stresses in plants. During multiple abiotic stresses, various signaling cascades in sweet potato activate and induce different TFs via signal transduction pathways and initiate gene regulatory networks. In sweet potato, IbBBX24-IbTOE3-IbPRX17 signaling cascades co-regulate the PRX-mediated ROS-scavenging and crucial role in maintaining the H₂O₂ homeostasis in response to multiple abiotic stresses [43]. Another report highlighted the role of the IbPYL8-IbbHLH66-IbbHLH118 complex in sweet potato in an ABA-dependent fashion under drought stress and enhanced drought tolerance [62]. The mitogen-activated protein kinase (MAPK) signaling pathway plays a crucial role in the signal transduction pathway and is induced by various abiotic and biotic stresses. IbMPK3/6 enhanced the tolerance against bacterial pathogens and increased the expression of pathogenesis-related genes [79]. IbMPK3 and IbMPK6 physically interact and phosphorylate IbSPF1 (transcriptional regulator during biotic stress signaling), thus playing a crucial role in plant immunity via up-regulating the downstream genes [93] (Fig. 5).

Figure 5.

The cellular responses under biotic stress to incorporate tolerance mechanism in sweet potato. The fusarium wilt in sweet potatoes is caused by Fusarium oxysporum f. sp batatas (Fob). Fob infection induced the expression of a sucrose transporter gene IbSWEET10, which confers resistance to Fob infection [94]. Moreover, the IbBBX24 also plays a significant role in fusarium wilt resistance caused by Fob in sweet potato by competition with IbMYC2 to interact with IbJAZ10 and enhance the function of IbMYC2 to activate jasmonic acid (JA) signaling, leading to Fob resistance [76]. Sweet potato SP8-binding factor (IbSPF1) acts as a transcriptional regulator of biotic stress signaling in sweet potatoes. IbSPF1 is phosphorylated by IbMPK3 and IbMPK6 at Ser75 and Ser110, respectively, which increases the binding affinity with the w-box element in target gene promoters, resulting in tolerance to Pseudomonas syringae [93]. The overexpression of IbMIPS1 enhances the expression of genes involved in inositol biosynthesis, phosphatidylinositol (PI) as well as increases the content of inositol, inositol-1,4,5-trisphosphate (IP₃), phosphatidic acid (PA), Ca²⁺, abscisic acid (ABA), callose, and lignin to protect stem nematode infection [64]. IbNAC1 plays an important role in the defense responses against herbivores in sweet potatoes through the binding of the IbbHLH3-IbbHLH3 protein complex at G-box motif to activate IbNAC1 expression [52]. In addition, α-hordothionin (αHT) encoding the antimicrobial peptide induces the expression in the fusion forms of E12Ω:αHT and β-Amy:αHT on sweet potato [95]. Storage roots of sweet potato harboring the αHT show the reduction of black rod lesion caused by Ceratocystis fimbriata [95]. Sweet potato weevils (SPWs) or Cylas formicarius are among the most significant pests, which cause substantial losses in sweet potato yield [89]. Wounding from SPWs activates the increases in phytohormones, jasmonic acid (JA), salicylic acid (SA), and abscisic acid (ABA) and subsequently induces the expression of genes involved in chlorogenic acid (IbPAL, IbC4H, and IbHQT) to enhance the accumulation of chlorogenic acid, resulting in resistance against SPWs [90]. A recent study reveals the SPW resistance through the functions of both SPWR1 and SPWR2 by activating the quinate biosynthesis [89]. Moreover, transcriptomics of SPW-resistant sweet potato, Kyushu No. 166 (K166), exhibits that terpenoid-related genes play an important role in SPW resistance [91]. Spodoptera litura is one of the crucial insect pests of sweet potato [92]. Feeding sweet potato leaves with overexpressing Cry1Aa on S. litura caused the reduction of larval growth by destroying its midgut, indicating that overexpressing Cry1Aa sweet potato can prevent S. litura infestation [92]. In addition, coat protein-mediated resistance to sweet potato feathery mottle virus (SPFMV) is reported by inducing the expression of the coat protein (CP) gene of SPFMV in sweet potato var. Chikei 682–11 [96]. The chitinase gene, chit42, from Trichoderma harzianum is introduced into sweet potato and promotes the activity of endochitinase, resulting in resistance to white rod disease caused by Sclerotinia sclerotiorum [100].

The transgenic sweet potato plants expressing the antimicrobial peptide incorporate the resistance against black rot disease caused by Ceratocystis fimbriata pathogenic fungus [95]. Another study also elucidated the function of small open reading frames (sORFs) in stress responses via functional polypeptides. In sweet potato, IbEGF (sORF gene) directly interacts with IbCOP9-5α to increase drought tolerance via modulating the phytohormone signaling pathways [75]. In plants, sumoylation is a post-translation modification process in which SUMO molecules are attached covalently to the substrate and catalyzed by an enzyme cascade. In sweet potatoes, the SUMO genes IbSCE1a/b and IbSIZ1a/b/c enhance the drought and salt tolerance, respectively [102]. Furthermore, the roles of other transporters and antiporters were also reported in stress-related responses in sweet potatoes. The OE of IbSWEET10 (sucrose transporter) in sweet potato increases the resistance against the fungal pathogen Fusarium oxysporum via reducing the overall sugar content in transgenic plants [94]. In sweet potato, the higher level of sodium ion compartmentalization into vacuoles also improves the salt and cold stress tolerance and signifies the roles of Na⁺/H⁺ antiporter in sweet potato plant abiotic stress tolerance mechansim [103].

Role of sweet potato transcriptomics for incorporating stress tolerance

Transcriptomics is the functional map of total mRNA gene expression in a cell/tissue/organism during a definite biological process or stress, which helps to reveal the molecular mechanisms underlying such processes. Transcriptomics studied in non-model crops without a reference genome effectively identifies genes under stress conditions. It also helps understand the molecular mechanisms and provides information about the plant responses under various stresses, thus providing a basis for incorporating stress tolerance via genetic engineering. Several transcriptome analyses were performed in sweet potatoes, allowing us to dissect numerous pathways’ molecular mechanisms during stresses. The first de novo transcript assembly was generated using the diploid and hexaploid sweet potatoes and identified 1661 gene-based microsatellite sequences for drought-stressed conditions [104].

Several other transcriptomics studies were conducted to dissect the molecular mechanism of drought tolerance in sweet potatoes and identified the important genes involved in ABA, ethylene, and JA signaling, drought-inducible TFs such as bHLH, MYB, NAC, WRKY, bZIP, HD-ZIP, thiol specific antioxidant [105], anthocyanin, pentose-phosphate, and photosynthesis biosynthesis pathway [106]. A three-way combined de novo transcriptome sequencing in sweet potato identified the positive role of Ca²⁺-ATPase gene in drought tolerance mechanism via promoting ABA singling pathway [107]. The genotypic effect and genotype-specific responses under drought stress conditions were also significant in sweet potatoes [106]. The previous study highlighted the role of several important candidate genes in different drought responses such as leucine-rich repeat (LRR) protein kinases reported roles in dehydration response. The two effectors proteins—light-harvesting chlorophyll A/B-binding-6 (LHCSB6) and slow anion channel-associated-1 (SLAC1)—were found to have roles in the chlorophyll-binding component of PS-II and a guard cell anion efflux protein, respectively [106].

A few studies have also surveyed the global transcriptomic responses under combined abiotic stresses in different Ipomoea species. The purple flesh sweet potato (hexaploid) was re-sequenced to dissect the molecular regulation of drought and salinity pathways [108] and depicted the role of glutathione S-transferases family genes which are involved in the accumulation of mono-caffeoylquinic acids to incorporate resistance against abiotic stress [109]. The NBS genes IbNBS80, IbNBS90, and IbNBS240 were significantly induced under cold stress, while IbNBS71, IbNBS159, and IbNBS208 responded to PEG treatment [53]. Furthermore, the responses of three genes in purple flesh sweet potato were strongly induced (itb11g07110, itb11g02640, and itb13g03940) by drought and oxidative stresses [109]. Guo et al. [27] identified several sweet potato NAC TFs (IbNAC006, IbNAC029, IbNAC138, and IbNAC143) that have roles under salt stress. Furthermore, a transcriptomics analysis dissected the molecular mechanism of cadmium accumulation in sweet potatoes and shows that cell wall biosynthesis and heavy metal transport pathways are strongly associated with heavy metal toxicity [110]. Another transcriptomics analysis of sweet potato roots under K⁺ deficiency found the crucial roles of hormonal interplay of JA, ethylene, auxin in K⁺ nutrient signaling [111]. The transcriptomic analysis revealed the mechanisms of chilling responses in sweet potato and identified the genes related to carbohydrate metabolism, antioxidant enzymes, hormone metabolism, and cell membrane system under chilling responses [112]. The transcriptomics study of orange-fleshed sweet potato identified the essential secondary metabolic pathways (e.g., carotenoid biosynthesis) involved in stress tolerance and identified important DEGs that participated in metabolite biosynthesis, signal transduction, fatty acid metabolism, and terpenoid backbone biosynthesis [113]. Another report uncovered 55 and 78 different uni-genes involved in the biosynthesis of carotenoid and terpenoid backbone biosynthesis pathways, respectively, via Kyoto Encyclopedia of Genes and Genomes analysis [114]. During the tuber development in sweet potato, an increase in MAPK and calcium signaling-related genes such as nine CDPKs, eight CBLs, and one CaM [115], which were previously reported to have roles in stress responses [116, 117].

Different studies were conducted to identify the key genes involved in disease resistance as well as genes induced by other pathogens in sweet potatoes. The RNA sequencing technology was used to investigate the dynamic changes in root transcriptome profiles at different root development stages after infection with Fusarium solani and identified several candidate genes related to plant-pathogen interaction and TFs that could be used to increase the biotic resistance in sweet potato [118]. De novo transcriptome assembly and digital gene expression profile of sweet potato identified various differentially expressed genes during defense, such as chitin elicitor receptor kinase-1, MAPK, NAC, WRKY, MYB, ERF TFs, as well as resistance, pathogenesis, SA and JA signaling pathways related genes against Fusarium wilt [119]. The combined de novo transcriptome assembly also identified the significant and tissue-specific transcripts abundance pattern in seven different tissues of sweet potatoes—plant proteinase inhibitor (kunitz-type protease (sporamins), cysteine protease, and trypsin)—which reported roles in potential stress tolerance, viral genomes and insect resistance [120]. The sweet potato viruses pose a great risk to sweet potato quality and production. Sweet potato feathery mottle virus and sweet potato chlorotic stunt virus are the common viruses in sweet potatoes. To identify the biological mechanism of host responses against these viral pathogens, deep sequencing was performed in the SPVD-susceptible cultivar ‘Beauregard’ upon viral infection. These findings identify several novel responsive elements that can target the NBS-LRR mediated disease resistance genes and involve the downregulation of SA-mediated defense responsive pathway [121]. Another genome-wide study was conducted to identify and characterize the nucleotide-binding site (NBS) encoding genes in a wild ancestor of sweet potatoes (I. trifida) and found that four NBS genes (IbNBS258, IbNBS88, IbNBS10, and IbNBS20) were significantly induced in response to stem nematode infection, while IbNBS240, IbNBS90, and IbNBS80 respond to cold stress, whereas IbNBS208, IbNBS71, and IbNBS159 respond to polyethylene glycol (PEG) treatment in sweet potato [53].

Metabolomics studies in sweet potato for abiotic and biotic stresses

In metabolomics-based crop improvement, the crop phenotype is related to a metabolite; thus, metabolic datasets under stress conditions are significant in understanding the plant responses to stresses. Their corresponding phenotypic information helps improve stress tolerance and adaptability. The metabolomics studies provide comprehensive information regarding the gene’s final products (i.e., metabolites). During abiotic stresses, plant changes the total metabolite profile, which strongly reveals the molecular phenotype of an organism and helps plants under stress adaptation and accumulates a large number of primary and secondary metabolites. Therefore, it is imperative to understand the molecular mechanism of pigmentation in crops. Recently, the integrated metabolic and transcriptional analysis was performed in different flesh colors of sweet potatoes to dissect the role of carotenoid cleavage dioxygenase-4 (IbCCD4) in carotenoid disposition during different tuberous root developmental stages [122]. The same approach has been applied to study the molecular mechanisms of anthocyanin and flavonoid accumulation [123]. The OE of sweet potato plants for IbMYB1 [124] and IbOr possessed higher levels of anthocyanins and carotenoids with greater antioxidant activities and showed enhanced tolerance against heat, oxidative [125, 126], and drought stresses [127]. In another report, the same approach was applied and revealed the significant co-annotation of ABA and carotenoid pathway genes and provided helpful information to understand the mechanism governing carotenoid biosynthesis and plant stress mechanism [128]. The sugar molecules act as a significant metabolite in plants that maintain ionic homeostasis, thus retaining structure under stress-induced injury and playing a role in signal transduction mechanisms for abiotic stresses. In sweet potato, the SUT transporter plays a significant role in the molecular regulation of plant stress adaptability via the ABF-dependent ABA signaling pathway [129].

The metabolic engineering in sweet potatoes with low-molecular-weight antioxidants such as carotenoids and vitamins leads to cultivars with enhanced antioxidants and tolerance to abiotic stresses [130]. Furthermore, other metabolic engineering studies in sweet potato IbGGPS, IbZDS, IbLCYB2, and IbARF5 lead to an increase in the level of carotenoids, such as α-carotene, β-carotene, lutein, β-cryptoxanthin, zeaxanthin and thus incorporate the tolerance against osmotic stress, salt, and drought stresses [46]. RNA interference strategy was also applied to silence the IbCHY-β and IbLCY-ε genes, which increase the metabolites in sweet potato and enhance tolerance against salt and methyl viologen-mediated oxidative stress, respectively [60]. The metabolite profile of a plant under stress conditions serves as a significant biomarker for plant adaptability and provides a basis for metabolomics-assisted breeding.

Proteomics: a key for understanding protein structure, function, and regulation under stresses

Proteome analysis elucidates the role of genes related to a specific protein associated with stress [131]. There are relatively few studies on the proteome in sweet potatoes. The comparative proteome and transcriptome analysis between salt-tolerant and salt-sensitive sweet potatoes revealed significant up-regulation of genes involved in stress signaling, plant hormone signal transduction, secondary metabolite accumulation, ion accumulation, redox reactions, and transcriptional regulation. These are the potential pathways to be involved in response to salt stress in sweet potatoes [132]. Furthermore, 93 differentially expressed proteins (DEPs) were found that are specifically expressed in salt-tolerant genotype [132]. In another study, the comparative proteomics analysis highlighted the significant expression level of an extrinsic subunit of PSII (PsbP) under heat-stressed IbOr-overexpressing (At-OX) Arabidopsis plants via directly stabilizing PSII system. The (At-OX) Arabidopsis plants also showed an increase in carotenoid biosynthesis, thus enhancing the plant’s adaptability under environmental stress [126]. Omics-based biomarkers were developed for identifying sweet potato cultivars by applying the proteomic and metabolomic approaches [133], suggesting that the proteins and metabolites that accumulate differentially may be used as biomarkers to identify stress breeding material for developing new cultivars. The proteogenomic study was performed to functionally characterize the proteomes of sweet potatoes that contribute to map peptides on the haplotype-resolved genome and predicted transcriptome [134]. A recent study reported SUMO system protein’s critical role in salt and drought stress response in sweet potato [102]. Proteomics was also applied to study the disease resistance in sweet potato. The comparative quantitative proteomic analysis was performed to examine the defense mechanisms involved against Fusarium wilt in two sweet potato cultivars with differential Fob infection responses. Different proteins related to the signaling transduction pathway, chitinase pathway, subtilisin-like protease, and plant resistance were identified, which depicted significant roles for disease-resistant response. In a nutshell, the omics studies provide a better perspective on precision breeding for developing stress-resilient sweet potatoes and understanding the stress-tolerant mechanism in tuber crops.

Challenges for stress tolerance in sweet potato and future perspectives

The genetic analysis and breeding of sweet potato has been challenging. Traditional and molecular breeding approaches are used to enhance the tolerance against stresses in sweet potatoes; however, getting novel germplasm with the desirable traits is quite challenging due to various reasons. Firstly, sweet potato is a highly heterozygous hexaploid and posseses a large, complex genome which complicates the inheritance pattern of alleles. Secondly, a large number of possible genotypes are observed in segregating populations because of the diverse combinations of parental chromosomes, which poses a significant challenge to genetic mapping. Lastly, sweet potato plants are almost always self-incompatible and sometimes cross-incompatible. Cross-incompatibility restricts breeding progress when parental lines with desirable traits belong to the same incompatibility group [135]. These factors limit genetic analysis and applications of modern breeding strategies in sweet potato. However, the recent technological advancements in genetic analysis and biotechnology are opening new ways to overcome such challenges in sweet potato genetics (Fig. 6).

Figure 6.

The existing bottlenecks in the utilization of omic approaches to develop stress-resilient sweet potatoes. Modern omics technologies provide a way to overcome the bottlenecks in hexaploid sweet potato breeding via utilizing different molecular/bioinformatics tools, which will help us exploit the new manifesto to develop stress-resilient sweet potato cultivars and assure global food security problems.

The plant’s responses to different abiotic stresses can disturb the equilibrium between energy consumption and energy harvest, thus affecting the overall plant’s growth capacity. Therefore, it is dispensable to gather and process deep information underlying the trade-off mechanisms between plant growth and stress tolerance mechanisms that help to develop crops which can sustain growth and development under adverse environmental conditions. There is also a lack of knowledge about the sweet potato responses to various stress-related environmental stimuli and how these responses coordinate effectively in different cell/tissue types to make long-distance communication.

There is also a need to develop more sophisticated tools to analyse and integrate the vast amount of data generated via the latest sequencing technologies and other omics approaches in sweet potatoes, which can help to draw a better perspective to explore the mechanisms behind biotic and abiotic stresses. The integration of omics data from different apporoaches helps to characterize the dispensable genes and non-coding regions functionally.

Another big challenge plant breeders have recently faced is phenotyping the effects of major stresses and precisely measuring their damage. The commonly used classical ways for evaluating abiotic tolerance are based on the visual scoring system, destructive measurements, and with the help of hand-held equipment to evaluate plant performance under stress. Phenotyping the effects of abiotic stress in crops has conventionally been relatively manual and laborious; however, combining various high-throughput plant phenotyping, such as the latest imaging techniques, machine learning, artificial intelligence etc, could open up new avenues for efficient and cost-effective phenotyping.

The latest genome editing technologies are creating new opportunities for crop improvement through precise genome engineering as transgene-free applications. CRISPR-Cas9 genome-editing technology has been successfully applied in sweetpotato [1], which thus facilitates the development of novel breeding lines for stress tolerances.

Summary and conclusion

The biotic and environmental stresses are becoming more frequent and long-lasting due to climate change, which seriously threatens global crop production and overall plant development. The plants have developed sophisticated mechanisms to perceive multiple, fluctuating environmental cues and respond precisely. Advanced molecular biology approaches have made it possible to better understand the complex nature of biotic and abiotic stresses, their regulatory networks, and signaling pathways, as well as open new ways to design stress-resilient crops via new breeding programs. This review highlighted the recent omics technologies used in sweet potatoes and gathered knowledge about integrating different technologies to dissect the candidate genes, biosynthetic pathways, and their cross-talk during plant responses under various stressful conditions. The latest omics information helps to understand sweet potato plant functioning and their interactions at the cell and tissue level under adverse environmental conditions. This study will accelerate the characterization of sweet potato plant functional architecture, their responses, and hormonal interplay during biotic and abiotic stress conditions, thus facilitating the progress of genetic improvement in tuber crops. Integrating different omics technologies with conventional breeding approaches paves new ways to incorporate stress tolerance mechanisms in sweet potato, thus ensuring a solution to future food security problems.

Author contributions

S.A. and J.C. conceived the idea, wrote and edited the manuscript. S.A. and P.T. designed the figures and tables. M.S.S.K., S.X., F.I., A.U.I., M.A., S.L., and P.T. reviewed and edited the manuscript. All the authors have read and approved the final version of the manuscript.

Data availability

Data sharing is not applicable to this article, as no datasets were generated or analysed during the current study.

Conflict of interest statement

The authors declare that they have no conflicts of interest.