Genome-wide identification and expression analyses of late embryogenesis abundant (LEA) gene family in tobacco (Nicotiana tabacum L.) reveal their function in abiotic stress responses

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.

Saussurea involucrata SiLEA5 Enhances Tolerance to Drought Stress in Solanum lycopersicum

Drought adversely affects plant growth, which leads to reduced crop yields and exacerbates food insecurity. Late embryogenesis abundant (LEA) proteins are crucial for plants' responses to abiotic stresses. This research further investigates the role of SiLEA5 by utilizing transgenic tomatoes under drought stress. The expression of SiLEA5 was upregulated under drought and abscisic acid (ABA) treatment, resulting in decreased electrolyte leakage and malondialdehyde content, alongside increased levels of osmotic regulators and antioxidant enzyme activity. These biochemical alterations reduce oxidative damage and enhance drought resistance. qRT-PCR analysis revealed the upregulation of ABA signaling genes and key enzymes involved in proline biosynthesis (P5CS) and dehydrin (DHN) synthesis under drought stress. Additionally, overexpression of SiLEA5 increased the net photosynthetic rate (Pn) and fruit yield of tomatoes by regulating stomatal density and aperture. These findings suggest that SiLEA5 may be a potential target for improving drought tolerance in tomatoes and other crops.

Comparative Effects of Water Scarcity on the Growth and Development of Two Common Bean (Phaseolus vulgaris L.) Genotypes with Different Geographic Origin (Mesoamerica/Andean)

Drought stress is widely recognized as a highly detrimental abiotic stress factor that significantly impacts crop growth, development, and agricultural productivity. In response to external stimuli, plants activate various mechanisms to enhance their resistance or tolerance to abiotic stress. The common bean, a most important legume according to the FAO, serves as a staple food for millions of people worldwide, due to its rich protein, carbohydrate, and fiber content, concurrently, and water scarcity is the main factor limiting common bean production. The process of domestication and on-farm conservation has facilitated the development of genotypes with varying degrees of drought stress resistance. Consequently, using landraces as biological material in research can lead to the identification of variants with superior resistance qualities to abiotic stress factors, which can be effectively integrated into breeding programs. The central scope of this research was to find out if different geographic origins of common bean genotypes can determine distinct responses at various levels. Hence, several analyses were carried out to investigate responses to water scarcity in three common bean genotypes, M-2087 (from the Mesoamerican gene pool), A-1988 (from the Andean gene pool) and Lechinta, known for its high drought stress resistance. Plants were subjected to different water regimes, followed by optical assessment of the anatomical structure of the hypocotyl and epicotyl in each group; furthermore, the morphological, physiological, and biochemical parameters and molecular data (quantification of the relative expression of the thirteen genes) were assessed. The three experimental variants displayed distinct responses when subjected to 12 days of water stress. In general, the Lechinta genotype demonstrated the highest adaptability and drought resistance. The M-2087 landrace, originating from the Mesoamerican geographic basin, showed a lower resistance to water stress, compared to the A-1988 landrace, from the Andean basin. The achieved results can be used to scale up future research about the drought resistance of plants, analyzing more common bean landraces with distinct geographic origins (Mesoamerican/Andean), which can then be used in breeding programs.

Differential Gene Expression in Contrasting Common Bean Cultivars for Drought Tolerance during an Extended Dry Period

Common beans (Phaseolus vulgaris L.), besides being an important source of nutrients such as iron, magnesium, and protein, are crucial for food security, especially in developing countries. Common bean cultivation areas commonly face production challenges due to drought occurrences, mainly during the reproductive period. Dry spells last approximately 20 days, enough time to compromise production. Hence, it is crucial to understand the genetic and molecular mechanisms that confer drought tolerance to improve common bean cultivars' adaptation to drought. Sixty six RNASeq libraries, generated from tolerant and sensitive cultivars in drought time sourced from the R5 phenological stage at 0 to 20 days of water deficit were sequenced, generated over 1.5 billion reads, that aligned to 62,524 transcripts originating from a reference transcriptome, as well as 6673 transcripts obtained via de novo assembly. Differentially expressed transcripts were functionally annotated, revealing a variety of genes associated with molecular functions such as oxidoreductase and transferase activity, as well as biological processes related to stress response and signaling. The presence of regulatory genes involved in signaling cascades and transcriptional control was also highlighted, for example, LEA proteins and dehydrins associated with dehydration protection, and transcription factors such as WRKY, MYB, and NAC, which modulate plant response to water deficit. Additionally, genes related to membrane and protein protection, as well as water and ion uptake and transport, were identified, including aquaporins, RING-type E3 ubiquitin transferases, antioxidant enzymes such as GSTs and CYPs, and thioredoxins. This study highlights the complexity of plant response to water scarcity, focusing on the functional diversity of the genes involved and their participation in the biological processes essential for plant adaptation to water stress. The identification of regulatory and cell protection genes offers promising prospects for genetic improvement aiming at the production of common bean varieties more resistant to drought. These findings have the potential to drive sustainable agriculture, providing valuable insights to ensure food security in a context of climate change.

Identification and expression analysis of LEA gene family members in pepper (Capsicum annuum L.)

Pepper (Capsicum annuum L.) is an economically important crop containing capsaicinoids in the seed and placenta, which has various culinary, medical, and industrial applications. Late embryogenesis abundant (LEA) proteins are a large group of hydrophilic proteins participating in the plant stress response and seed development. However, to date there have been no genome-wide analyses of the LEA gene family in pepper. In the present study, 82 LEA genes were identified in the C. annuum genome and classified into nine subfamilies. Most CaLEA genes contain few introns (≤ 2) and are unevenly distributed across 10 chromosomes. Eight pairs of tandem duplication genes and two pairs of segmental duplication genes were identified in the LEA gene family; these duplicated genes were highly conserved and may have performed similar functions during evolution. Expression profile analysis indicated that CaLEA genes exhibited different tissue expression patterns, especially during embryonic development and stress response, particularly in cold stress. Three out of five CaLEA genes showed induced expression upon cold treatment. In summary, we have comprehensively reviewed the LEA gene family in pepper, offering a new perspective on the evolution of this family.

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.