Genome-wide identification, evolutionary and expression analyses of LEA gene family in peanut (Arachis hypogaea L.)

Abiotic stress-regulated LEA gene mediates the response to drought, salinity, and cold stress in Medicago sativa L

Late embryogenesis abundant (LEA) proteins are typical stress-related proteins widely distributed across various organisms. Their anti-stress functions in higher plants have garnered significant attention and have been extensively studied; however, no such studies have been reported on the entire protein family in Medicago sativa. In this study, we identified a total of 83 MsLEA proteins in M. sativa and conducted a comprehensive analysis to elucidate their functions in response to abiotic stresses. The results indicated that these proteins could be classified into seven groups and were distributed across eight chromosomes. Collineation analysis revealed that segmental duplication primarily drove the expansion of MsLEA genes. Furthermore, the promoters of MsLEA genes were found to be enriched with cis-acting elements associated with various stress responses. Through transcriptome and quantitative real-time PCR analysis, nine MsLEA genes related to drought, salinity, and cold stress were identified, with MsLEA69 selected for further validation. The ectopic expression of MsLEA69 improves osmotic and extreme temperature tolerance by increasing the activity of stress-related enzymes in both prokaryotic and eukaryotic cells. These comprehensive analyses and identifications lay the groundwork for future research into the functional mechanisms of MsLEA proteins and offer potential candidate genes for enhancing resistance breeding in M. sativa.

Late embryogenesis abundant gene GhLEA-5 of semi-wild cotton positively regulates salinity tolerance in upland cotton

The productivity and quality of cotton are significantly compromised by salt stress. In this study, the full length of encoding region and genomic DNA sequences of GhLEA_5A/D (Gh_A10G166600 and Gh_D10G188300), which belong to the late embryogenesis abundant gene family in allotetraploid upland cotton (Gossypium hirsutum L.) and semi-wild cotton (Gossypium purpurascens), were isolated and their salt tolerance was experimentally confirmed. Analysis of sequence alignments and phylogenetic trees indicated a significant level of homology between GhLEA-5A and GhLEA-5D. Additionally, a conserved protein motif was consistently identified across these sequences. The transcriptome data analysis showed that the expression level of GhLEA-5A/D was substantially enhanced in the leaves of salt-tolerant G. purpurascens accessions compared to salt-sensitive materials. In the real-time quantitative reverse transcription PCR (qRT-PCR) assays, notable expression levels of the GhLEA-5D gene were detected in salt-tolerant upland cotton materials following exposure to salt stress at 3 and 12-hour time points. The suppression of GhLEA-5A/D transcription via Virus-induced Gene Silencing (VIGS) technology significantly exacerbates salt sensitivity in cotton. This is evidenced by the nearly 50 % increase in malondialdehyde (MDA) content alongside a 60 % reduction in peroxidase (POD) levels in salt-treated plants when compared to the control group. The overexpression of the GhLEA-5A/D gene conferred enhanced salt tolerance in Arabidopsis, resulting in a 25 % increase in root length, a 30 % improvement in survival rate, a 15 % increase in water retention, and a 15 % boost in photosynthetic efficiency. The chlorophyll fluorescence parameters, enzyme activities, diaminobenzine, and nitroblue tetrazolium staining suggested that GhLEA-5A/D likely exhibited a positive regulatory role for cotton responding to salt stress. Furthermore, we identified 76 candidate proteins that potentially interact with GhLEA-5 in the yeast two-hybrid screening library. These results provide a theoretical basis for studying the mechanism of cotton salt tolerance and offer new resources for improving cotton salt tolerance genes.

Genome-Wide Identification, Phylogenetic Evolution, and Abiotic Stress Response Analyses of the Late Embryogenesis Abundant Gene Family in the Alpine Cold-Tolerant Medicinal Notopterygium Species

Late embryogenesis abundant (LEA) proteins are a class of proteins associated with osmotic regulation and plant tolerance to abiotic stress. However, studies on the LEA gene family in the alpine cold-tolerant herb are still limited, and the phylogenetic evolution and biological functions of its family members remain unclear. In this study, we conducted genome-wide identification, phylogenetic evolution, and abiotic stress response analyses of LEA family genes in Notopterygium species, alpine cold-tolerant medicinal herbs in the Qinghai-Tibet Plateau and adjacent regions. The gene family identification analysis showed that 23, 20, and 20 LEA genes were identified in three Notopterygium species, N. franchetii, N. incisum, and N. forrestii, respectively. All of these genes can be classified into six LEA subfamilies: LEA_1, LEA_2, LEA_5, LEA_6, DHN (Dehydrin), and SMP (seed maturation protein). The LEA proteins in the three Notopterygium species exhibited significant variations in the number of amino acids, physical and chemical properties, subcellular localization, and secondary structure characteristics, primarily demonstrating high hydrophilicity, different stability, and specific subcellular distribution patterns. Meanwhile, we found that the members of the same LEA subfamily shared similar exon-intron structures and conserved motifs. Interestingly, the chromosome distributions of LEA genes in Notopterygium species were scattered. The results of the collinearity analysis indicate that the expansion of the LEA gene family is primarily driven by gene duplication. A Ka/Ks analysis showed that paralogous gene pairs were under negative selection in Notopterygium species. A promoter cis-acting element analysis showed that most LEA genes possessed multiple cis-elements connected to plant growth and development, stress response, and plant hormone signal transduction. An expression pattern analysis demonstrated the species-specific and tissue-specific expression of NinLEAs. Experiments on abiotic stress responses indicated that the NinLEAs play a crucial role in the response to high-temperature and drought stresses in N. franchetii leaves and roots. These results provide novel insights for further understanding the functions of the LEA gene family in the alpine cold-tolerant Notopterygium species and also offer a scientific basis for in-depth research on the abiotic stress response mechanisms and stress-resistant breeding.

Comprehensive identification of LEA protein family genes and functional analysis of MdLEA60 involved in abiotic stress responses in apple (Malus domestica)

Late embryogenesis abundant (LEA) proteins are important proteins that exists widely in many plants and contribute to physiological processes of plant stress resistance. Despite LEA proteins being identified in many plants, none have been reported in apple (Malus domestica) until this study. In this study, a total of 87 MdLEA proteins were identified in apple, and a comprehensive analysis was conducted to elucidate the functions of MdLEA proteins in response to abiotic stress. Results showed that they were classified into 7 groups and distributed on 16 chromosomes. Collineation analysis revealed that segmental duplication primarily drove the expansion of MdLEA genes. The MdLEA promoters were enriched with elements associated with various stress responses. Through transcriptome and qRT-PCR analysis, several MdLEA genes related to drought/salinity/cold were excavated, and MdLEA60 was selected for transgenic validation. The ectopic expression of MdLEA60 enhanced osmotic and extreme temperature tolerance in both prokaryotic and eukaryotic cells, providing stress resistance support via antioxidant protection. Overall, the comprehensive analyses and identification not only establish a basis for future investigation into the functional mechanism of MdLEA proteins but also provide potential candidate genes for apple resistance breeding optimization.

Genome-wide identification of the LEA gene family in Panax ginseng: Evidence for the role of PgLEA2-50 in plant abiotic stress response

Ginseng frequently encounters environmental stress during its growth and development. Late Embryogenesis Abundant (LEA) proteins play a crucial role in combating adversity stress, particularly against abiotic challenges In this study, 107 LEA genes from ginseng, spanning eight subfamilies, were identified, demonstrating significant evolutionary conservation, with the LEA2 subfamily being most prominent. Gene duplication events, primarily segmental duplications, have played a major role in the expansion of the LEA gene family, which has undergone strong purifying selection. PgLEAs were unevenly distributed across 22 chromosomes, with each subfamily featuring unique structural domains and conserved motifs. PgLEAs were expressed in various tissues, exhibiting distinct variations in abundance and tissue specificity. Numerous regulatory cis-elements, related to abiotic stress and hormones, were identified in the promoter region. Additionally, PgLEAs were regulated by a diverse array of abiotic stress-related transcription factors. A total of 35 PgLEAs were differentially expressed following treatments with ABA, GA, and IAA. Twenty-three PgLEAs showed significant but varied responses to drought, extreme temperatures, and salinity stress. The transformation of tobacco with the key gene PgLEA2-50 enhanced osmoregulation and antioxidant levels in transgenic lines, improving their resistance to abiotic stress. This study offers insights into functional gene analysis, focusing on LEA proteins, and establishes a foundational framework for research on ginseng's resilience to abiotic stress.

Designing future peanut: the power of genomics-assisted breeding

KEY MESSAGE

Integrating GAB methods with high-throughput phenotyping, genome editing, and speed breeding hold great potential in designing future smart peanut cultivars to meet market and food supply demands. Cultivated peanut (Arachis hypogaea L.), a legume crop greatly valued for its nourishing food, cooking oil, and fodder, is extensively grown worldwide. Despite decades of classical breeding efforts, the actual on-farm yield of peanut remains below its potential productivity due to the complicated interplay of genotype, environment, and management factors, as well as their intricate interactions. Integrating modern genomics tools into crop breeding is necessary to fast-track breeding efficiency and rapid progress. When combined with speed breeding methods, this integration can substantially accelerate the breeding process, leading to faster access of improved varieties to farmers. Availability of high-quality reference genomes for wild diploid progenitors and cultivated peanuts has accelerated the process of gene/quantitative locus discovery, developing markers and genotyping assays as well as a few molecular breeding products with improved resistance and oil quality. The use of new breeding tools, e.g., genomic selection, haplotype-based breeding, speed breeding, high-throughput phenotyping, and genome editing, is probable to boost genetic gains in peanut. Moreover, renewed attention to efficient selection and exploitation of targeted genetic resources is also needed to design high-quality and high-yielding peanut cultivars with main adaptation attributes. In this context, the combination of genomics-assisted breeding (GAB), genome editing, and speed breeding hold great potential in designing future improved peanut cultivars to meet market and food supply demands.

Genome-wide identification of the LRR-RLK gene family in peanut and functional characterization of AhLRR-RLK265 in salt and drought stresses

Leucine-rich repeat receptor-like kinases (LRR-RLKs) play important roles in plant developmental regulations and various stress responses. Peanut (Arachis hypogaea L.) is a worldwide important oil crop; however, no systematic identification or analysis of the peanut LRR-RLK gene family has been reported. In present study, 495 LRR-RLK genes in peanut were identified and analyzed. The 495 AhLRR-RLK genes were classed into 14 groups and 10 subgroups together with their Arabidopsis homologs according to phylogenetic analyses, and 491 of 495 AhLRR-RLK genes unequally located on 20 chromosomes. Analyses of gene structure and protein motif organization revealed similarity in exon/intron and motif organization among members of the same subgroup, further supporting the phylogenetic results. Gene duplication events were found in peanut LRR-RLK gene family via syntenic analysis, which were important in LRR-RLK gene family expansion in peanut. We found that the expression of AhLRR-RLK genes was detected in different tissues using RNA-seq data, implying that AhLRR-RLK genes may differ in function. In addition, Arabidopsis plants overexpressing stress-induced AhLRR-RLK265 displayed lower seed germination rates and root lengths compared to wild-type under exogenous ABA treatment. Notably, overexpression of AhLRR-RLK265 enhanced tolerance to salt and drought stresses in transgenic Arabidopsis. Moreover, the AhLRR-RLK265-OE lines were found to have higher activities of superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) under salt and drought stress treatments. We believe these results may provide valuable information about the function of peanut LRR-RLK genes for further analysis.

Enzyme stabilization and thermotolerance function of the intrinsically disordered LEA2 proteins from date palm

In date palm, the LEA2 genes are of abundance with sixty-two members that are nearly all ubiquitous. However, their functions and interactions with potential target molecules are largely unexplored. In this study, five date palm LEA2 genes, PdLEA2.2, PdLEA2.3, PdLEA2.4, PdLEA2.6, and PdLEA2.7 were cloned, sequenced, and three of them, PdLEA2.2, PdLEA2.3, and PdLEA2.4 were functionally characterized for their effects on the thermostability of two distinct enzymes, lactate dehydrogenase (LDH) and β-glucosidase (bglG) in vitro. Overall, PdLEA2.3 and PdLEA2.4 were moderately hydrophilic, PdLEA2.7 was slightly hydrophobic, and PdLEA2.2 and PdLEA2.6 were neither. Sequence and structure prediction indicated the presence of a stretch of hydrophobic residues near the N-terminus that could potentially form a transmembrane helix in PdLEA2.2, PdLEA2.4, PdLEA2.6 and PdLEA2.7. In addition to the transmembrane helix, secondary and tertiary structures prediction showed the presence of a disordered region followed by a stacked β-sheet region in all the PdLEA2 proteins. Moreover, three purified recombinant PdLEA2 proteins were produced in vitro, and their presence in the LDH enzymatic reaction enhanced the activity and reduced the aggregate formation of LDH under the heat stress. In the bglG enzymatic assays, PdLEA2 proteins further displayed their capacity to preserve and stabilize the bglG enzymatic activity.

Genome-wide identification and expression analysis of late embryogenesis abundant (LEA) genes reveal their potential roles in somatic embryogenesis in hybrid sweetgum (Liquidambar styraciflua × Liquidambar formosana)

Late embryogenesis abundant (LEA) proteins are widely distributed in higher plants that play significant roles in embryonic development and abiotic stress response. Hybrid sweetgum is an important forest tree resource around the world, and somatic embryogenesis is an efficient way of reproduction and utilization. However, a systematic analysis of the LEA family genes in hybrid sweetgum is lacking, this is not conducive to the efficiency of its somatic embryogenesis. From the whole genome of the hybrid sweetgum, utilizing hidden Markov models, an identification of a total of 79 LEA genes was successfully conducted. They were classified into eight different groups based on their conserved domains and phylogenetic relationships, with the LsfLEA2 group of genes being the most abundant. The gene structure and sequence characteristics and chromosomal localization, as well as the physicochemical properties of LEA proteins were meticulously carried out. Analysis of the cis-acting elements shows that most of the LsfLEA genes are associated with light-responsive-elements. In addition, some genes are associated with biosynthetic pathways, such as abscisic acid response, growth hormone response, methyl jasmonate response, somatic embryogenesis, meristematic tissue expression. Furthermore, we systematically analyzed the expression patterns of hybrid sweetgum LEA genes in different stages of somatic embryogenesis and different tissues, in LEA family genes we also found significant specificity in gene expression during somatic embryogenesis. This study provides new insights into the formation of members of the LsfLEA family genes in hybrid sweetgum, while improving the understanding of the potential role of these genes in the process of hybrid sweetgum somatic embryogenesis and abiotic stress response. These results have a certain guiding significance for the future functional study of LsfLEA family genes, and provide a theoretical basis for exploring the regulatory mechanism of LsfLEA genes in the somatic embryo development stage of hybrid sweetgum.

Genome-wide identification of the myo-inositol oxygenase gene family in alfalfa (Medicago sativa L.) and expression analysis under abiotic stress

Myo-inositol oxygenase (MIOX), a pivotal enzyme in the myo-inositol oxygenation pathway, catalyzes the cleavage of myo-inositol to UDP-glucuronic acid and plays a major role in plant adaptation to abiotic stress factors. However, studies pertaining to the MIOX gene family in alfalfa (Medicago sativa L.) are lacking. Therefore, this study characterized ten MsMIOX genes in the alfalfa genome. These genes were divisible into two classes distributed over three chromosomes and produced 12 pairs of fragment repeats and one pair of tandem repeats. Physicochemical properties, subcellular location, protein structure, conserved motifs, and gene structure pertinent to these MsMIOX genes were analyzed. Construction of a phylogenetic tree revealed that similar gene structures and conserved motifs were present in the same MsMIOX groups. Analysis of cis-acting elements revealed the presence of stress- and hormone-induced expression elements in the promoter regions of the MsMIOX genes. qRT-PCR analysis revealed that MsMIOX genes could be induced by various abiotic stress factors, such as salt, saline-alkali, drought, and cold. Under such conditions, MIOX activity in alfalfa was significantly increased. Heterologous MsMIOX2 expression in yeast enhanced salt, saline-alkali, drought, and cold tolerance. Overexpression of MsMIOX2 in the hairy roots of alfalfa decreased O₂^- and H₂O₂ content and enhanced the abiotic stress tolerance. This study offers comprehensive perspectives on the functional features of the MsMIOX family and provides a candidate gene for improving the abiotic stress tolerance of alfalfa.

iTRAQ-Based Proteomic and Physiological Analyses Reveal the Mechanisms of Dehydration and Cryopreservation Tolerance of Sophora tonkinensis Gagnep. Seeds

Sophora tonkinensi is a shrub of the genus Sophora in the family Fabaceae with anti-inflammatory and pain-relieving effects. While the cultivation, chemical makeup, and medicinal properties of S. tonkinensis have been reported, the physiological mechanisms governing its dehydration and cryopreservation tolerance of seeds remain unclear. In this study, we investigated the morphological, physiological, biochemical, and protein expression characteristics of S. tonkinensis seeds subjected to dehydration and cryopreservation techniques via the observation of cell microstructure, determination of antioxidant enzyme activity, and iTRAQ-based proteomic analysis, respectively. The results of the study demonstrated that the seeds possessed a certain level of tolerance to dehydration. The highest germination percentage of 83.0% was observed after 2 h of dehydration (10.1% water content), which was identified as the optimal time point for cryopreservation. However, the germination percentage was reduced to only 30.5% when the water content reached 5.4%, indicating that S. tonkinensis seeds exhibit intermediate storage behavior. Further investigation revealed that during seed dehydration and cryopreservation treatment, liposomes were gradually and highly fused, whereas the activities of ROS scavenging and stress defense were significantly enhanced. During dehydration, the seed tissues formed a protective mechanism of stress resistance based on protein processing in the endoplasmic reticulum and antioxidant system, which was related to the dehydration tolerance. Moreover, only three differentially expressed LEA proteins were identified, and it is speculated that the strengthening of intracellular metabolism and the absence of specific LEA and dehydrins could be crucial factors for the reduced germination percentage after excessive dehydration and cryopreservation.

Genome-wide study and functional characterization elucidates the potential association of late embryogenesis abundant (LEA) genes with lotus seed development

Late embryogenesis abundant (LEA) proteins are extremely hydrophilic proteins imperatively associated with plant growth and development, as well as cell protection from abiotic stress. However, the genome-wide characterization of LEA gene family remains limited, especially in aquatic species such as lotus (Nelumbo spp.). Here, 57 putative LEA genes, including 28 NnLEAs and 29 NlLEAs were identified in the N.nucifera and N.lutea genomes, respectively. A total of 27 homologous LEA gene pairs were identified, indicating high degree of sequence homologies between the two Nelumbo species. Secondary structure prediction indicated high prevalence of alpha (α) helix structure among LEA proteins in the LEA_1, LEA_4, and SMP groups. Screening of putative promoter cis-elements revealed that NnLEA genes were involved in diverse biological processes. Most NnLEA genes were predominantly expressed in the late cotyledons and plumules development stages, suggesting their potential vital roles in lotus seed maturation. In addition, genes co-expressed with NnLEAs were involved in ABA signaling, seed maturation, and development processes. Overall, this study provides new insights for the in-depth understanding of the functions of NnLEA proteins in lotus seed development, and could act as a useful reference for the molecular breeding of seeds with prolonged lifespan.

Insights into sweet potato SR proteins: from evolution to species-specific expression and alternative splicing

SR proteins from sweet potato have conserved functional domains and similar gene structures as that of Arabidopsis and rice in general. However, expression patterns and alternative splicing regulations of SR genes from different species have changed under stresses. Novel alternative splicing regulations were found in sweet potato SR genes. Serine/arginine-rich (SR) proteins play important roles in plant development and stress response by regulating the pre-mRNA splicing process. However, SR proteins have not been identified so far from an important crop sweet potato. Through bioinformatics analysis, our study identified 24 SR proteins from sweet potato, with comprehensively analyzing of protein characteristics, gene structure, chromosome localization, and cis-acting elements in promotors. Salt, heat, and mimic drought stresses triggered extensive but different expressional regulations on sweet potato SR genes. Interestingly, heat stress caused the most active disturbances in both gene transcription and pre-mRNA alternative splicing (AS). Tissue and species-specific transcriptional and pre-mRNA AS regulations in response to stresses were found in sweet potato, in comparison with Arabidopsis and rice. Moreover, novel patterns of pre-mRNA alternative splicing were found in SR proteins from sweet potato. Our study provided an insight into similarities and differences of SR proteins in different plant species from gene sequences to gene structures and stress responses, indicating SR proteins may regulate their downstream genes differently between different species and tissues by varied transcriptional and pre-mRNA AS regulations.