Genome-Wide Identification and Comprehensive Analysis of the GASA Gene Family in Peanuts (Arachis hypogaea L.) under Abiotic Stress

Peanut (Arachis hypogaea L.) is a globally cultivated crop of significant economic and nutritional importance. The role of gibberellic-acid-stimulated Arabidopsis (GASA) family genes is well established in plant growth, development, and biotic and abiotic stress responses. However, there is a gap in understanding the function of GASA proteins in cultivated peanuts, particularly in response to abiotic stresses such as drought and salinity. Thus, we conducted comprehensive in silico analyses to identify and verify the existence of 40 GASA genes (termed AhGASA) in cultivated peanuts. Subsequently, we conducted biological experiments and performed expression analyses of selected AhGASA genes to elucidate their potential regulatory roles in response to drought and salinity. Phylogenetic analysis revealed that AhGASA genes could be categorized into four distinct subfamilies. Under normal growth conditions, selected AhGASA genes exhibited varying expressions in young peanut seedling leaves, stems, and roots tissues. Notably, our findings indicate that certain AhGASA genes were downregulated under drought stress but upregulated under salt stress. These results suggest that specific AhGASA genes are involved in the regulation of salt or drought stress. Further functional characterization of the upregulated genes under both drought and salt stress will be essential to confirm their regulatory roles in this context. Overall, our findings provide compelling evidence of the involvement of AhGASA genes in the mechanisms of stress tolerance in cultivated peanuts. This study enhances our understanding of the functions of AhGASA genes in response to abiotic stress and lays the groundwork for future investigations into the molecular characterization of AhGASA genes.

Molecular, genetic, and genomic basis of seed size and yield characteristics in soybean

Soybean (Glycine max L. Merr.) is a crucial oilseed cash crop grown worldwide and consumed as oil, protein, and food by humans and feed by animals. Comparatively, soybean seed yield is lower than cereal crops, such as maize, rice, and wheat, and the demand for soybean production does not keep up with the increasing consumption level. Therefore, increasing soybean yield per unit area is the most crucial breeding objective and is challenging for the scientific community. Moreover, yield and associated traits are extensively researched in cereal crops, but little is known about soybeans' genetics, genomics, and molecular regulation of yield traits. Soybean seed yield is a complex quantitative trait governed by multiple genes. Understanding the genetic and molecular processes governing closely related attributes to seed yield is crucial to increasing soybean yield. Advances in sequencing technologies have made it possible to conduct functional genomic research to understand yield traits' genetic and molecular underpinnings. Here, we provide an overview of recent progress in the genetic regulation of seed size in soybean, molecular, genetics, and genomic bases of yield, and related key seed yield traits. In addition, phytohormones, such as auxin, gibberellins, cytokinins, and abscisic acid, regulate seed size and yield. Hence, we also highlight the implications of these factors, challenges in soybean yield, and seed trait improvement. The information reviewed in this study will help expand the knowledge base and may provide the way forward for developing high-yielding soybean cultivars for future food demands.

Development of InDels markers for the identification of cytoplasmic male sterility in Sorghum by complete chloroplast genome sequences analysis

Cytoplasmic male sterility (CMS) is predominantly used for F1 hybrid breeding and seed production in Sorghum. DNA markers to distinguish between normal fertile (CMS-N) and sterile (CMS-S) male cytoplasm can facilitate F1 hybrid cultivar development in Sorghum breeding programs. In this study, the complete chloroplast (cp) genome sequences of CMS-S and Korean Sorghum cultivars were obtained using next-generation sequencing. The de novo assembled genome size of ATx623, the CMS-S line of the chloroplast, was 140,644bp. When compared to the CMS-S and CMS-N cp genomes, 19 single nucleotide polymorphisms (SNPs) and 142 insertions and deletions (InDels) were identified, which can be used for marker development for breeding, population genetics, and evolution studies. Two InDel markers with sizes greater than 20 bp were developed to distinguish cytotypes based on the copy number variation of lengths as 28 and 22 bp tandem repeats, respectively. Using the newly developed InDel markers with five pairs of CMS-S and their near isogenic maintainer line, we were able to easily identify their respective cytotypes. The InDel markers were further examined and applied to 1,104 plants from six Korean Sorghum cultivars to identify variant cytotypes. Additionally, the phylogenetic analysis of seven Sorghum species with complete cp genome sequences, including wild species, indicated that CMS-S and CMS-N contained Milo and Kafir cytotypes that might be hybridized from S. propinquum and S. sudanese, respectively. This study can facilitate F1 hybrid cultivar development by providing breeders with reliable tools for marker-assisted selection to breed desirable Sorghum varieties.

Genome-Wide Identification of Aquaporin Genes in Adzuki Bean (Vigna angularis) and Expression Analysis under Drought Stress

The adzuki bean Vigna angularis (Wild.) is an important leguminous crop cultivated mainly for food purposes in Asian countries; it represents a source of carbohydrates, digestible proteins, minerals, and vitamins. Aquaporins (AQPs) are crucial membrane proteins involved in the transmembrane diffusion of water and small solutes in all living organisms, including plants. In this study, we used the whole genome sequence of the adzuki bean for in silico analysis to comprehensively identify 40 Vigna angularis aquaporin (VaAQP) genes and reveal how these plants react to drought stress. VaAQPs were compared with AQPs from other closely-related leguminous plants, and the results showed that mustard (Brassica rapa) (59), barrel medic (Medicago truncatula) (46), soybean (Glycine max) (66), and common bean (Phaseolus vulgaris L.) (41) had more AQP genes. Phylogenetic analysis revealed that forty VaAQPs belong to five subfamilies, with the VaPIPs (fifteen) subfamily the largest, followed by the VaNIPs (ten), VaTIPs (ten), VaSIPs (three), and VaXIPs (two) subfamilies. Furthermore, all AQP subcellular locations were found at the plasma membrane, and intron-exon analysis revealed a relationship between the intron number and gene expression, duplication, evolution, and diversity. Among the six motifs identified, motifs one, two, five, and six were prevalent in VaTIP, VaNIP, VaPIP, and VaXIP, while motifs one, three, and four were not observed in VaPIP1-3 and VaPIP1-4. Under drought stress, two of the VaAQPs (VaPIP2-1 and VaPIP2-5) showed significantly higher expression in the root tissue while the other two genes (VaPIP1-1 and VaPIP1-7) displayed variable expression in leaf tissue. This finding revealed that the selected VaAQPs might have unique molecular functions linked with the uptake of water under drought stress or in the exertion of osmoregulation to transport particular substrates rather than water to protect plants from drought. This study presents the first thorough investigation of VaAQPs in adzuki beans, and it reveals the transport mechanisms and related physiological processes that may be utilized for the development of drought-tolerant adzuki bean cultivars.

Enhanced Resistance of atbzip62 against Pseudomonas syringae pv. tomato Suggests Negative Regulation of Plant Basal Defense and Systemic Acquired Resistance by AtbZIP62 Transcription Factor

The intrinsic defense mechanisms of plants toward pathogenic bacteria have been widely investigated for years and are still at the center of interest in plant biosciences research. This study investigated the role of the AtbZIP62 gene encoding a transcription factor (TF) in the basal defense and systemic acquired resistance in Arabidopsis using the reverse genetics approach. To achieve that, the atbzip62 mutant line (lacking the AtbZIP62 gene) was challenged with Pseudomonas syringae pv. tomato (Pst DC3000) inoculated by infiltration into Arabidopsis leaves at the rosette stage. The results indicated that atbzip62 plants showed an enhanced resistance phenotype toward Pst DC3000 vir over time compared to Col-0 and the susceptible disease controls, atgsnor1-3 and atsid2. In addition, the transcript accumulation of pathogenesis-related genes, AtPR1 and AtPR2, increased significantly in atbzip62 over time (0–72 h post-inoculation, hpi) compared to that of atgsnor1-3 and atsid2 (susceptible lines), with AtPR1 prevailing over AtPR2. When coupled with the recorded pathogen growth (expressed as a colony-forming unit, CFU mL⁻¹), the induction of PR genes, associated with the salicylic acid (SA) defense signaling, in part explained the observed enhanced resistance of atbzip62 mutant plants in response to Pst DC3000 vir. Furthermore, when Pst DC3000 avrB was inoculated, the expression of AtPR1 was upregulated in the systemic leaves of Col-0, while that of AtPR2 remained at a basal level in Col-0. Moreover, the expression of AtAZI (a systemic acquired resistance -related) gene was significantly upregulated at all time points (0–24 h post-inoculation, hpi) in atbzip62 compared to Col-0 and atgsnor1-3 and atsid2. Under the same conditions, AtG3DPH exhibited a high transcript accumulation level 48 hpi in the atbzip62 background. Therefore, all data put together suggest that AtPR1 and AtPR2 coupled with AtAZI and AtG3DPH, with AtAZI prevailing over AtG3DPH, would contribute to the recorded enhanced resistance phenotype of the atbzip62 mutant line against Pst DC3000. Thus, the AtbZIP62 TF is proposed as a negative regulator of basal defense and systemic acquired resistance in plants under Pst DC3000 infection.

Genetic diversity analysis of Korean peanut germplasm using 48 K SNPs 'Axiom_Arachis' Array and its application for cultivar differentiation

Cultivated peanut (Arachis hypogaea) is one of the important legume oilseed crops. Cultivated peanut has a narrow genetic base. Therefore, it is necessary to widen its genetic base and diversity for additional use. The objective of the present study was to assess the genetic diversity and population structure of 96 peanut genotypes with 9478 high-resolution SNPs identified from a 48 K 'Axiom_Arachis' SNP array. Korean set genotypes were also compared with a mini-core of US genotypes. These sets of genotypes were used for genetic diversity analysis. Model-based structure analysis at K = 2 indicated the presence of two subpopulations in both sets of genotypes. Phylogenetic and PCA analysis clustered these genotypes into two major groups. However, clear genotype distribution was not observed for categories of subspecies, botanical variety, or origin. The analysis also revealed that current Korean genetic resources lacked variability compared to US mini-core genotypes. These results suggest that Korean genetic resources need to be expanded by creating new allele combinations and widening the genetic pool to offer new genetic variations for Korean peanut improvement programs. High-quality SNP data generated in this study could be used for identifying varietal contaminant, QTL, and genes associated with desirable traits by performing mapping, genome-wide association studies.

A Novel DUF569 Gene Is a Positive Regulator of the Drought Stress Response in Arabidopsis

In the last two decades, global environmental change has increased abiotic stress on plants and severely affected crops. For example, drought stress is a serious abiotic stress that rapidly and substantially alters the morphological, physiological, and molecular responses of plants. In Arabidopsis, several drought-responsive genes have been identified; however, the underlying molecular mechanism of drought tolerance in plants remains largely unclear. Here, we report that the “domain of unknown function” novel gene DUF569 (AT1G69890) positively regulates drought stress in Arabidopsis. The Arabidopsis loss-of-function mutant atduf569 showed significant sensitivity to drought stress, i.e., severe wilting at the rosette-leaf stage after water was withheld for 3 days. Importantly, the mutant plant did not recover after rewatering, unlike wild-type (WT) plants. In addition, atduf569 plants showed significantly lower abscisic acid accumulation under optimal and drought-stress conditions, as well as significantly higher electrolyte leakage when compared with WT Col-0 plants. Spectrophotometric analyses also indicated a significantly lower accumulation of polyphenols, flavonoids, carotenoids, and chlorophylls in atduf569 mutant plants. Overall, our results suggest that novel DUF569 is a positive regulator of the response to drought in Arabidopsis.

Evaluation potential of PGPR to protect tomato against Fusarium wilt and promote plant growth

Soilborne fungal diseases are most common among vegetable crops and have major implications for crop yield and productivity. Eco-friendly sustainable agriculture practices that can overcome biotic and abiotic stresses are of prime importance. In this study, we evaluated the ability of plant growth-promoting rhizobacterium (PGPR) Bacillus aryabhattai strain SRB02 to control the effects of tomato wilt disease caused by Fusarium oxysporum f. sp. lycopersici (strain KACC40032) and promote plant growth. In vitro bioassays showed significant inhibition of fungal growth by SRB02. Inoculation of susceptible and tolerant tomato cultivars in the presence of SRB02 showed significant protection of the cultivar that was susceptible to infection and promotion of plant growth and biomass production in both of the cultivars. Further analysis of SRB02-treated plants revealed a significantly higher production of amino acids following infection by F. oxysporum. Analysis of plant defense hormones after inoculation by the pathogen revealed a significantly higher accumulation of salicylic acid (SA), with a concomitant reduction in jasmonic acid (JA). These results indicate that B. aryabhattai strain SRB02 reduces the effects of Fusarium wilt disease in tomato by modulating endogenous phytohormones and amino acid levels.

Functional Insight of Nitric-Oxide Induced DUF Genes in Arabidopsis thaliana

Advances in next-generation sequencing technologies facilitate the study of plant molecular functions in detail and with precision. Plant genome and proteome databases are continually being updated with large transcriptomic or genomic datasets. With the ever-increasing amount of sequencing data, several thousands of genes or proteins in public databases remain uncharacterized, and their domain functions are largely unknown. Such proteins contain domains of unknown function (DUF). In the present study, we identified 231 upregulated and 206 downregulated DUF genes from the available RNA-Seq-based transcriptome profiling datasets of Arabidopsis leaves exposed to a nitric oxide donor, S-nitroso-L-cysteine (CysNO). In addition, we performed extensive in silico and biological experiments to determine the potential functions of AtDUF569 and to elucidate its role in plant growth, development, and defense. We validated the expression pattern of the most upregulated and the most downregulated DUF genes from the transcriptomic data. In addition, a loss-of AtDUF569 function mutant was evaluated for growth, development, and defense against biotic and abiotic stresses. According to the results of the study, AtDUF569 negatively regulates biotic stress responses and differentially regulates plant growth under nitro-oxidative stress conditions.

Effects of Bacterial Fermentation on the Biochemical Constituents and Antioxidant Potential of Fermented and Unfermented Soybeans Using Probiotic Bacillus subtilis (KCTC 13241)

Fermented soybeans, cheonggukjang (CKJ), are considered to be more wholesome than soybeans in Korea. To select the best soybean cultivar for making functional CKJ, a comparison was made between the biological activities of four soybean cultivars in their unfermented soybean (UFS) and CKJ states. Changes in 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging activity, 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) assays, superoxide dismutase (SOD)-like activity, total phenolic compounds, total amino acids, and isoflavones were investigated. The levels of DPPH, ABTS, SOD-like activity, and total phenolic compounds increased in CKJ among all cultivars. The isoflavone aglycone and total amino acids showed the highest amount in CKJ prepared from soybean cultivar Aga 3. These results suggest that the improved antioxidant activity of CKJ in all cultivars might occur because of the higher levels of aglycones and total phenolic compounds achieved during fermentation. Moreover, CKJ prepared from soybean cultivar Aga 3 showed higher antioxidant activity than the other cultivars and so can be considered for the commercial production of functional foods in the future.