Genome-Wide Identification and Expression Analysis of SWEET Family Genes in Sweet Potato and Its Two Diploid Relatives

Genome-wide identification of SWEET family genes and functional analysis of NtSWEET12i under drought and saline-alkali stresses in tobacco

BACKGROUND

SWEET (Sugar Will Eventually be Exported Transporter) proteins play vital roles in the transport of sugars, contributing to the regulation of plant development, hormone signaling, and responses to abiotic stress.

RESULTS

In this study, we identified 57 NtSWEETs in tobacco (Nicotiana tabacum L.), and then their physicochemical properties, chromosomal localization, synteny, phylogenetic relationships, genomic structure, promoter cis-elements, protein interaction network, tissue specificity, and expression pattern were systematically analyzed. In addition, NtSWEET12i improves drought and saline-alkali tolerance in tobacco by enhancing soluble sugars transport, ABA signaling, proline biosynthesis, and ROS scavenging. These findings illuminate the role of NtSWEETs, particularly NtSWEET12i, in regulating plant tolerance to drought and saline-alkali stresses.

CONCLUSIONS

This study offers new insights to enhance our understanding of the roles of NtSWEETs and identify potential genes involved in drought and saline-alkali tolerance of plants.

CLINICAL TRIAL NUMBER

Not applicable.

Genome-Wide Identification and Expression Analysis of Growth-Regulating Factor Family in Sweet Potato and Its Two Relatives

Growth-regulating factor (GRF) is a multi-gene family that plays an important role in plant growth and development and is widely present in plants. Currently, GRF gene members have been reported in many plants, but the GRF gene family has not been found in sweet potato. In this study, ten GRF genes were identified in sweet potato (Ipomoea batatas), twelve and twelve were identified in its two diploid relatives (Ipomoea trifida) and (Ipomoea triloba), which were unevenly distributed on nine different chromosomes. Subcellular localization analysis showed that GRF genes of sweet potato, I. trifida, and I. triloba were all located in the nucleus. The expression analysis showed that the expression of IbGRFs was diverse in different sweet potato parts, and most of the genes were upregulated and even had the highest expression in the vigorous growth buds. These findings provide molecular characterization of sweet potato and its two diploid relatives, the GRF families, further supporting functional characterization.

First systematic review of the last 30 years of research on sweetpotato: elucidating the frontiers and hotspots

Sweetpotato is an economically important crop, and it has various advantages over other crops in addressing global food security and climate change. Although substantial articles have been published on the research of various aspects of sweetpotato biology, there are no specific reports to systematically crystallize the research achievements. The current review takes the lead in conducting a keyword-centric spatiotemporal dimensional bibliometric analysis of articles on sweetpotato research using CiteSpace software to comprehensively clarify the development status, research hotspot, and development trend in the past 30 years (1993-2022). Quantitative analysis was carried out on the publishing countries, institutions, disciplines, and scholars to understand the basic status of sweetpotato research; then, visual analysis was conducted on high-frequency keywords, burst keywords, and keyword clustering; the evolution of major research hotspots and the development trend in different periods were summarized. Finally, the three main development stages-preliminary stage (1993-2005), rapid stage (2006-2013), and diversified mature stage (2014-2022)-were reviewed and analyzed in detail. Particularly, the development needs of sweetpotato production in improving breeding efficiency, enhancing stress tolerance, coordinating high yield with high quality and high resistance, and promoting demand were discussed, which will help to comprehensively understand the development dynamics of sweetpotato research from different aspects of biological exploration.

Genome-Wide Bioinformatics Analysis of SWEET Gene Family and Expression Verification of Candidate PaSWEET Genes in Potentilla anserina

Sugars act as the main energy sources in many fruit and vegetable crops. The biosynthesis and transportation of sugars are crucial and especially contribute to growth and development. SWEET is an important gene family that plays a vital role in plants' growth, development, and adaptation to various types of stresses (biotic and abiotic). Although SWEET genes have been identified in numerous plant species, there is no information on SWEETs in Potentilla anserina. In the present study, we performed a comprehensive genome-wide bioinformatics analysis and identified a total of 23 candidate PaSWEETs genes in the Potentilla anserina genome, which were randomly distributed on ten different chromosomes. The phylogenetic analysis, chromosomal location, gene structure, specific cis-elements, protein interaction network, and physiological characteristics of these genes were systematically examined. The identified results of the phylogenetic relationship with Arabidopsis thaliana revealed that these PaSWEET genes were divided into four clades (I, II, III, and IV). Moreover, tissue-specific gene expression through quantitative real-time polymerase chain reaction (qRT-PCR) validation exposed that the identified PaSWEETs were differentially expressed in various tissues (roots, stems, leaves, and flowers). Mainly, the relative fold gene expression in swollen and unswollen tubers effectively revealed that PaSWEETs (7, 9, and 12) were highly expressed (300-, 120-, and 100-fold) in swollen tubers. To further elucidate the function of PaSWEETs (7, 9, and 12), their subcellular location was confirmed by inserting them into tobacco leaves, and it was noted that these genes were present on the cell membrane. On the basis of the overall results, it is suggested that PaSWEETs (7, 9, and 12) are the candidate genes involved in swollen tuber formation in P. anserina. In crux, we speculated that our study provides a valuable theoretical base for further in-depth function analysis of the PaSWEET gene family and their role in tuber development and further enhancing the molecular breeding of Potentilla anserina.

Genome-wide identification and expression analysis of the glutamate receptor gene family in sweet potato and its two diploid relatives

Plant glutamate receptor (GLR) homologs are crucial calcium channels that play an important role in plant development, signal transduction, and response to biotic and abiotic stresses. However, the GLR gene family has not yet been thoroughly and systematically studied in sweet potato. In this study, a total of 37 GLR genes were identified in the cultivated hexaploid sweet potato (Ipomoea batatas), and 32 GLR genes were discovered in each of the two diploid relatives (Ipomoea trifida and Ipomoea triloba) for the first time. Based on their evolutionary relationships to those of Arabidopsis, these GLRs were split into five subgroups. We then conducted comprehensive analysis to explore their physiological properties, protein interaction networks, promoter cis-elements, chromosomal placement, gene structure, and expression patterns. The results indicate that the homologous GLRs of the cultivated hexaploid sweet potato and its two relatives are different. These variations are reflected in their functions related to plant growth, hormonal crosstalk, development of tuberous roots, resistance to root rot, and responses to abiotic stress factors, all of which are governed by specific individual GLR genes. This study offers a comprehensive analysis of GLR genes in sweet potato and its two diploid relatives. It also provides a theoretical basis for future research into their regulatory mechanisms, significantly influencing the field of molecular breeding in sweet potatoes.

Molecular Cloning, Expression Analysis, and Functional Analysis of Nine IbSWEETs in Ipomoea batatas (L.) Lam

Sugar Will Eventually be Exported Transporter (SWEET) genes play an important regulatory role in plants' growth and development, stress response, and sugar metabolism, but there are few reports on the role of SWEET proteins in sweet potato. In this study, nine IbSWEET genes were obtained via PCR amplification from the cDNA of sweet potato. Phylogenetic analysis showed that nine IbSWEETs separately belong to four clades (Clade I~IV) and contain two MtN3/saliva domains or PQ-loop superfamily and six~seven transmembrane domains. Protein interaction prediction showed that seven SWEETs interact with other proteins, and SWEETs interact with each other (SWEET1 and SWEET12; SWEET2 and SWEET17) to form heterodimers. qRT-PCR analysis showed that IbSWEETs were tissue-specific, and IbSWEET1b was highly expressed during root growth and development. In addition to high expression in leaves, IbSWEET15 was also highly expressed during root expansion, and IbSWEET7, 10a, 10b, and 12 showed higher expression in the leaves. The expression of SWEETs showed a significant positive/negative correlation with the content of soluble sugar and starch in storage roots. Under abiotic stress treatment, IbSWEET7 showed a strong response to PEG treatment, while IbSWEET10a, 10b, and 12 responded significantly to 4 °C treatment and, also, at 1 h after ABA, to NaCl treatment. A yeast mutant complementation assay showed that IbSWEET7 had fructose, mannose, and glucose transport activity; IbSWEET15 had glucose transport activity and weaker sucrose transport activity; and all nine IbSWEETs could transport 2-deoxyglucose. These results provide a basis for further elucidating the functions of SWEET genes and promoting molecular breeding in sweet potato.

Genome-Wide Identification and Expression Analysis of Malate Dehydrogenase Gene Family in Sweet Potato and Its Two Diploid Relatives

Malate dehydrogenase (MDH; EC 1.1.1.37) plays a vital role in plant growth and development as well as abiotic stress responses, and it is widely present in plants. However, the MDH family genes have not been explored in sweet potato. In this study, nine, ten, and ten MDH genes in sweet potato (Ipomoea batatas) and its two diploid wild relatives, Ipomoea trifida and Ipomoea triloba, respectively, were identified. These MDH genes were unevenly distributed on seven different chromosomes among the three species. The gene duplications and nucleotide substitution analysis (Ka/Ks) revealed that the MDH genes went through segmental duplications during their evolution under purifying selection. A phylogenetic and conserved structure divided these MDH genes into five subgroups. An expression analysis indicated that the MDH genes were omni-presently expressed in distinct tissues and responded to various abiotic stresses. A transcription factor prediction analysis proved that Dof, MADS-box, and MYB were the main transcription factors of sweet potato MDH genes. These findings provide molecular features of the MDH family in sweet potato and its two diploid wild relatives, which further supports functional characterizations.

Genome-Wide Identification and Expression Analysis of ACTIN Family Genes in the Sweet Potato and Its Two Diploid Relatives

ACTINs are structural proteins widely distributed in plants. They are the main components of microfilaments and participate in many crucial physiological activities, including the maintenance of cell shape and cytoplasmic streaming. Meanwhile, ACTIN, as a housekeeping gene, is widely used in qRT-PCR analyses of plants. However, ACTIN family genes have not been explored in the sweet potato. In this study, we identified 30, 39, and 44 ACTINs in the 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, via analysis of their genome structure and by phylogenetic characterization. These ACTINs were divided into six subgroups according to their phylogenetic relationships with Arabidopsis thaliana. The physiological properties of the protein, chromosome localization, phylogenetic relationship, gene structure, promoter cis-elements, protein interaction networks, and expression patterns of these 113 ACTINs were systematically investigated. The results suggested that homologous ACTINs are differentiated in the sweet potato and its two diploid relatives, and play various vital roles in plant growth, tuberous root development, hormone crosstalk, and abiotic stress responses. Some stable ACTINs that could be used as internal reference genes were found in the sweet potato and its two diploid relatives, e.g., IbACTIN18, -20, and -16.2; ItfACTIN2.2, -16, and -10; ItbACTIN18 and -19.1. This work provides a comprehensive comparison and furthers our understanding of the ACTIN genes in the sweet potato and its two diploid relatives, thereby supplying a theoretical foundation for their functional study and further facilitating the molecular breeding of sweet potatoes.

Sweet Potato as a Key Crop for Food Security under the Conditions of Global Climate Change: A Review

Sweet potato is one of the most economically important crops for addressing global food security and climate change issues, especially under conditions of extensive agriculture, such as those found in developing countries. However, osmotic stress negatively impacts the agronomic and economic productivity of sweet potato cultivation by inducing several morphological, physiological, and biochemical changes. Plants employ many signaling pathways to respond to water stress by modifying their growth patterns, activating antioxidants, accumulating suitable solutes and chaperones, and making stress proteins. These physiological, metabolic, and genetic modifications can be employed as the best indicators for choosing drought-tolerant genotypes. The main objective of sweet potato breeding in many regions of the world, especially those affected by drought, is to obtain varieties that combine drought tolerance with high yields. In this regard, the study of the physiological and biochemical features of certain varieties is important for the implementation of drought resistance measures. Adapted genotypes can be selected and improved for particular growing conditions by using suitable tools and drought tolerance-related selection criteria. By regulating genetics in this way, the creation of drought-resistant varieties may become cost-effective for smallholder farmers. This review focuses on the drought tolerance mechanisms of sweet potato, the effects of drought stress on its productivity, its crop management strategies for drought mitigation, traditional and molecular sweet potato breeding methods for drought tolerance, and the use of biotechnological methods to increase the tolerance of sweet potato to drought.

Identification and functional characterization of the SUMO system in sweet potato under salt and drought stress

Sumoylation is a crucial post-translation modification (PTM) that is the covalent attachment of SUMO molecules to the substrate catalyzed by enzyme cascade. Sumoylation is essential in almost every physiological process of plants, particularly in response to abiotic stress. However, little is known about sumoylation in sweet potato (Ipomoea batatas), the world's seventh most important food crop. In this study, 17 sweet potato SUMO system genes have been cloned and functionally characterized. Multiple sequence alignment and phylogenetic analysis showed sweet potato SUMO system proteins had conserved domains and activity sites. IbSUMOs, IbSAE1, and IbSCE1 were localized in the cytoplasm and nucleus. E3 SUMO ligases showed nuclear or punctate localization. In vitro sumoylation assay confirmed the catalytic activity of sweet potato SUMO system components. Heterologous expression of IbSIZ1 genes in Arabidopsis atsiz1 mutant rescued the defective germination and growth phenotype. IbSCE1a/b and IbSIZ1a/b/c were salt and drought responsive genes. Heterologous expression of IbSCE1a/b/c improved the drought tolerance of Arabidopsis thaliana, while IbSIZ1a/b/c significantly enhanced the salt and drought tolerance. Our findings define that the SUMO system in sweet potato shared with conserved function but also possessed specific characterization. The resources presented here would facilitate uncovering the significance of sumoylation in sweet potato.

Genome-Wide Comparative Analysis of the R2R3-MYB Gene Family in Six Ipomoea Species and the Identification of Anthocyanin-Related Members in Sweet Potatoes

Sweet potatoes (Ipomoea batatas) are one of the important tuberous root crops cultivated worldwide, and thier storage roots are rich in antioxidants, such as anthocyanins. R2R3-MYB is a large gene family involved in various biological processes, including anthocyanin biosynthesis. However, few reports about the R2R3-MYB gene family of sweet potatoes have been released to date. In the present study, a total of 695 typical R2R3-MYB genes were identified in six Ipomoea species, including 131 R2R3-MYB genes in sweet potatoes. A maximum likelihood phylogenetic analysis divided these genes into 36 clades, referring to the classification of 126 R2R3-MYB proteins of Arabidopsis. Clade C25(S12) has no members in six Ipomoea species, whereas four clades (i.e., clade C21, C26, C30, and C36), including 102 members, had no members in Arabidopsis, and they were identified as Ipomoea-specific clades. The identified R2R3-MYB genes were unevenly distributed on all chromosomes in six Ipomoea species genomes, and the collinearity analysis among hexaploid I. batatas and another five diploid Ipomoea species suggested that the sweet potato genome might have undergone a larger chromosome rearrangement during the evolution process. Further analyses of gene duplication events showed that whole-genome duplication, transposed duplication, and dispersed duplication events were the primary forces driving the R2R3-MYB gene family expansion of Ipomoea plants, and these duplicated genes experienced strong purifying selection because of their Ka/Ks ratio, which is less than 1. Additionally, the genomic sequence length of 131 IbR2R3-MYBs varied from 923 bp to ~12.9 kb with a mean of ~2.6 kb, and most of them had more than three exons. The Motif 1, 2, 3, and 4 formed typical R2 and R3 domains and were identified in all IbR2R3-MYB proteins. Finally, based on multiple RNA-seq datasets, two IbR2R3-MYB genes (IbMYB1/g17138.t1 and IbMYB113/g17108.t1) were relatively highly expressed in pigmented leaves and tuberous root flesh and skin, respectively; thus, they were identified to regulate tissue-specific anthocyanin accumulation in sweet potato. This study provides a basis for the evolution and function of the R2R3-MYB gene family in sweet potatoes and five other Ipomoea species.