Gautam Saripalli

Peanut ( Arachis hypogaea L.) is an economically important oilseed and food legume, yet genetic transformation remains challenging because of genotype dependence and the lengthy tissue-culture and regeneration process. A better understanding of the molecular mechanisms underlying callus development and proliferation could help identify candidate morphogenic genes and developmental regulators (DRs) for peanut improvement. Here, we used RNA sequencing to compare embryogenic calli from the cultivar Georgia Green that had been maintained for three months (new callus; NC) or repeatedly subcultured for four years (old callus; OC). The two callus types displayed distinct morphologies: NC was pale cream, expanded, and cauliflower-like, whereas OC was more yellow, compact, and nodular. We identified 1,141 genes significantly upregulated in NC and 2,086 in OC (adjusted p < 0.05; log fold change > 2). Transcription factors were prominent among 13 categories of differentially expressed genes, including members of the AP2/ERF, WOX, GRAS, LBD, and NAC families, several of which are known DRs in other crops. qRT-PCR analysis of seven selected genes strongly corroborated the RNA-seq results ( r = 0.944; R ² = 0.891). Highly upregulated candidates included C2H2/BED-type zinc-finger proteins, calreticulin/calnexin, a glycine-rich protein, a late embryogenesis abundant protein, glycoside hydrolases, and SWEET sugar transporters. These findings provide a resource for investigating callus development in peanut and prioritize candidate genes for functional validation and future improvement of transformation and regeneration systems.

Immune-mediated reactions to wheat gliadins, including celiac disease and wheat allergies, affect ∼1% of the U.S. population and are prevalent worldwide. Reducing the risk of inadvertent gluten exposure for individuals with celiac disease or wheat allergies requires the development of reduced immunogenicity wheat varieties which are suitable for human consumption. This study was designed with a view to improve our understanding of gene–protein relationships at the complex wheat Gli1/Glu3 and Gli2 loci, and to develop genetic and molecular resources for breeding reduced-immunogenicity wheat lines. We conducted comprehensive genomic, biochemical, and immunological analyses of diverse wheat genetic resources, including aneuploid stocks, chromosome deficiency and interstitial deletion lines, Wasko ^ω− , the landrace San Pastore, Pegaso near-isogenic lines lacking Gli1/Glu3/Gli2 loci, and progenies derived from a Wasko ^ω− × Pegaso ^{(6A–6D)α−} . Genomic characterization involved the targeted GlutEnSeq approach and PCR based DNA markers while biochemical and immunological analyses employed acid-urea PAGE, SDS-PAGE, and ELISA. Integration of these complementary approaches resolved gliadin gene–protein relationships at an unprecedented level. Notably, two F₂ lines exhibited substantial reductions (both α- and ω-gliadins) due to the successful stacking of parental mutations. The resulting F₂/F₃ progenies and associated DNA markers represent valuable resources for breeding wheat for reduced immunogenicity.

Peanut is a major oilseed crop in the U.S., which ranks third globally in production, with South Carolina ranking sixth nationally. Despite their economic and nutritional value, peanuts are unsuitable for 1–2% of the U.S. population due to allergic reaction, including anaphylaxis, making the development of reduced-allergen peanuts a priority. This study aimed to identify peanut lines with reduced Ara h1, h2, h3, and h6 levels and to elucidate their genetic regulation using genome-wide association studies (GWAS). Ninety-two accessions from the U.S. peanut mini-core collection were screened using ELISA and SDS-PAGE, and the resulting data were evaluated for association with 5,532 SNP markers. Substantial phenotypic diversity was observed. Twenty-three lines with extreme protein phenotypes were further evaluated by RP-UPLC, and nine by LC-MS. GWAS identified 165 marker-trait associations (MTAs) across raw and log-transformed datasets, with 13 MTAs common to both analyses. These MTAs were grouped into protein quantitative loci (PQLs), revealing six trans -PQLs and cis -PQLs for two of the five Ara h genes. Seed-expressed candidate transcription factors (TFs), including MYB, MYC, ERF, and bZIP, and pleiotropic PQLs were identified. Promoter analysis (1 kb upstream of transcription start site or TSS) of the corresponding Ara h genes revealed binding sites for TFs underlying these PQLs. We hypothesize that these TFs trans-regulate the Ara h genes either directly or through a regulatory cascade. These findings provide initial insights into the regulatory landscape of Ara h genes and will facilitate breeding for reduced allergen content in peanut.

The growing unpredictability of climate and resource constraints continues to challenge global agriculture, demanding innovative strategies for crop improvement. This special issue "Harnessing Resilient Flora for Maximized Crop Efficiency and Stress Tolerance" brings together a diverse yet interconnected set of studies that collectively advance our understanding of plant resilience from genetic regulation to field productivity. This research topic highlights advances in genomics (epigenetics, transcriptomics) and nanobiotechnology for stress tolerance (mainly abiotic stresses like drought, salinity and nitrogen use efficiency) not only in major cereals like wheat and rice, but also in other plant species like halophytes (mangroves), ornamental plants (sweet osmanthus) and bioenergy crops.In cereals, optimum application of nitrogen fertilizers plays a significant role in enhancing grain micronutrient composition (especially zinc and iron) and efforts are being made to identify markers linked to the associated traits which could aid in molecular breeding for improved NUE. Malakondaiah et al. (2025) identified genomic regions controlling nitrogen use efficiency (NUE) in wheat which can be targeted for breeding purposes. In total, eight important QTLs under NUE conditions were identified using biparental mapping. These QTLs were linked to metal concentrations like zinc, calcium, iron, nickel and potassium. Twelve recombinant inbred lines (RILs) were also identified which were superior for multiple traits simultaneously as revealed through multi-trait genotype-ideotype distance index (MGIDI). The study revealed the genetic and molecular basis of micronutrient accumulation under nitrogen deficient conditions in wheat and identified important genomic and genetic resources for breeding wheat for improved NUE.Drought is another important abiotic stress which is responsible for significant yield losses in major cereals. A recent news report suggests a reduction of 13% in grain yields due to climate change, especially severe dry and warmer conditions in last 50 years (https://resoilfoundation.org/en/agricultural-industry/climate-grain-yields-reduced/). Elsherif et al. ( 2025) used a nanobiotechnology-based approach to enhance drought tolerance in barley. The authors-imposed drought stress on barley plants under pot conditions by irrigating at 30% field capacity. After drought stress, the plants were treated with biogenic calcium phosphate nanoparticles and showed significant improvement in growth and plant functions despite drought stress, not only in morphophysiological parameters but also in molecular responses as revealed through gene expression studies. Altogether, their study explored a novel approach for enhancing drought tolerance using nanobiology-based tools.The impact of salt stress was studied in rice and a mangrove species by Xu 2025) examined the impact of mixed oligosaccharides on the growth of rice seedlings under salinity (100 mmol L-1 NaCl) and alkalinity (10 mmol L-1 Na₂CO₃) stresses. Significant improvements in growth, physiology, and root morphology were observed following oligosaccharide priming. Transcriptomics was undertaken for studying differential gene expression patterns associated to photosynthesis under salt stress conditions, thus revealing the enhancement of photosynthesis and mitigated oxidative damage.In mangrove tree species (Avicennia marina), Wang et al. (2025) identified an endogenous promoter, AMGT1P33, and examined its role in driving the expression of genes for enhanced salt tolerance in Arabidopsis through GUS assay. Their findings suggest that such regulatory elements from extremophytes can be effectively utilized in crop systems to elucidate and enhance salt tolerance mechanisms, thereby facilitating the development of transgenic approaches for functional validation and improvement of salinity tolerance in important crop species.Yield is a complex trait controlled by many genes/QTL and therefore, studying the genetics of yield improvement has always been challenging for breeders and geneticists. Total yield is determined by a number of associated traits like grain number, grain size, tiller number, plant architecture. etc. Chachar et al. (2025) compiled literature focused on genetics and molecular aspects of tiller development and yield improvement in the form of a comprehensive review. Their detailed literature survey revealed the involvement of complex genetic, molecular and environmental interactions in controlling grain yield in cereals. Available GWAS and biparental mapping studies were deeply analyzed for pinpointing the genomic regions controlling tiller development. By combining transcriptomic studies with genetic mapping, TaMAX1, TaMOC1, and TN1 in wheat, ZmTB1, ZmD14, and ZmMOC1 in maize, along with MAX1-like genes, OsMAX1, and OsHAM2 in rice were highlighted along with phytohormonal regulation. As tillering directly influences crop productivity, advances in this area hold significant promise for sustainable yield enhancement.Epigenetic regulation, encompassing DNA methylation, histone modifications, and non-coding RNAs, orchestrate dynamic changes in chromatin architecture without altering the underlying DNA sequence. Epigenetic memory enables priming responses to recurrent environmental cues, thereby enhancing resilience and nutrient use efficiency. Vela and Steadman (2026), reviewed in detail the progress made and research gaps in the epigenetic research in bioenergy crops. Zhang et al. ( 2025) studied the spatio-temporal tissue specific expression of important microRNAs (based on miRNA sequencing) in Osmanthus fragrans under different abiotic stresses (cold, salinity and drought), hormonal and metal ion treatments in different tissues to examine their suitability as candidate reference genes. This study provides the first validated set of reference miRNAs for accurate normalization in miRNA expression analyses under abiotic...

Soybean is the primary oilseed crop in the United States, with significant industrial value. Understanding the molecular mechanisms of heat stress tolerance in soybean plants is critical for developing stress-resistant cultivars. Current knowledge about the role of fatty acid desaturases (FADs) in modulating membrane fluidity under abiotic stress prompted this investigation into the impact of mutations in the FAD genes on seed germination from heat-stressed plants. In soybean plants, exposure to heat stress during anthesis is known to significantly reduce seed germination. In silico expression analysis indicated high expression levels of the soybean FAD2 and FAD3 genes in the leaves. Therefore, a detailed expression analysis of these genes was conducted using qRT-PCR from leaf tissue. Generally, downregulation of these genes was observed in the mutants; however, two genes, FAD3A and FAD2-3, showed a more than 2-fold increase in expression in six out of ten mutants under heat stress. This upregulation was particularly pronounced (7-fold) in the mutant S17CR-170. Correlation analysis revealed a positive correlation (up to 0.48) between the expression level of FAD3A, FAD3B, FAD3C, and FAD2-3 and the decline in germination from heat-stressed plants. This suggests these FAD genes may act as negative regulators of germination under heat stress conditions.

Soybean is the primary oilseed crop in the United States, with significant industrial value. Understanding the molecular mechanisms of heat stress tolerance in soybean is critical for developing stress-resistant cultivars. Current knowledge about the role of fatty acid desaturases (FADs) in modulating membrane fluidity under abiotic stress prompted this investigation into the impact of mutations in the FAD genes on seed germination from heat-stressed plants. In soybean, exposure to heat stress during anthesis is known to significantly reduce seed germination. In silico expression analysis indicated high levels of expression of the soybean FAD2 and FAD3 genes in leaves. Therefore, a detailed expression analysis of these genes was conducted using qRT-PCR from leaf tissue. Generally, downregulation of these genes was observed in the mutants; however, two genes, FAD3A and FAD2-3, showed a more than 2-fold increase in expression in six out of ten mutants under heat stress. This upregulation was particularly pronounced (7-fold) in mutant S17CR-170. Correlation analysis revealed a positive correlation (0.5) between the expression level of FAD3A, FAD3B, FAD3C, and FAD2-3 and the decline in germination from heat-stressed plants. This suggests these FAD genes may act as negative regulators of germination under heat stress conditions.

In wheat, a genome-wide association study (GWAS) and genomic prediction (GP) analysis were conducted for pre-harvest sprouting (PHS) tolerance and two of its related traits. For this purpose, an association panel of 190 accessions was phenotyped for PHS (using sprouting score), falling number, and grain color over two years and genotyped with 9904 DArTseq based SNP markers. GWAS for main-effect quantitative trait nucleotides (M-QTNs) using three different models (CMLM, SUPER, and FarmCPU) and epistatic QTNs (E-QTNs) using PLINK were performed. A total of 171 M-QTNs (CMLM, 47; SUPER, 70; FarmCPU, 54) for all three traits, and 15 E-QTNs involved in 20 first-order epistatic interactions were identified. Some of the above QTNs overlapped the previously reported QTLs, MTAs, and cloned genes, allowing delineating 26 PHS-responsive genomic regions that spread over 16 wheat chromosomes. As many as 20 definitive and stable QTNs were considered important for use in marker-assisted recurrent selection (MARS). The gene, TaPHS1, for PHS tolerance (PHST) associated with one of the QTNs was also validated using the KASP assay. Some of the M-QTNs were shown to have a key role in the abscisic acid pathway involved in PHST. Genomic prediction accuracies (based on the cross-validation approach) using three different models ranged from 0.41 to 0.55, which are comparable to the results of previous studies. In summary, the results of the present study improved our understanding of the genetic architecture of PHST and its related traits in wheat and provided novel genomic resources for wheat breeding based on MARS and GP.