Bromodomain-containing (BRD) proteins are epigenetic readers that can identify acetylated lysine on histones and play a vital role in chromatin remodeling, transcriptional regulation, and stress modulation. Despite extensive investigation in animals, the identity and functions of BRDs in soybean are poorly understood. In the present study, we identified 52 BRD genes across the soybean genome, which were unevenly distributed across 15 chromosomes. Phylogenetic analysis categorized the GmBRDs into 16 different clades along with the BRD proteins of Arabidopsis thaliana, Triticum aestivum and Oryza sativa, associated with conserved domain organizations. The gene structure and motif analysis revealed high structural divergence, while most of the duplication pairs have retained similar domain compositions. Furthermore, collinearity and duplication studies revealed that segmental duplication contributed most to the family expansion of GmBRDs, and duplicated genes have been under strong purifying selection. Comparative synteny analysis between G. max and G. soja revealed a high level of conservation. The presence of several cis-acting elements for phytohormone signaling, development, and abiotic stress responses suggests a possible role of GmBRDs in stress regulation. Gene ontology analysis showed that GmBRDs are enriched in transcriptional regulation, chromatin-based complexes and histone acetylation. In addition, protein-protein interaction prediction identified GmBRD3 and GmBRD16 as putative hub genes. Based on publicly available RNA-seq data, 14 GmBRD genes were expressed and induced under drought and heat stress. Among these, GmBRD16 was strongly induced under both drought and heat stress, and qRT-PCR confirmed its upregulation, suggesting that GmBRD16 may take part in abiotic stress responses. The study provides a genome-wide characterization of BRD genes in soybean and describes their evolutionary pattern, structural diversity, functional roles in transcription mediated by chromatin and expression pattern of GmBRD genes in response to abiotic stress. These findings provide a basis for functional studies aimed at improving soybean tolerance to abiotic stress.
Moisture deficit stress severely limits tomato productivity by affecting cellular homeostasis, photosynthesis, and thereby growth. In this study, 111 recombinant inbred lines (RILs) derived from contrasting parents were screened under polyethylene glycol (PEG)-induced osmotic stress to evaluate seedling growth responses. Based on seedling length reduction, tolerant and susceptible bulks were subjected to QTL-seq analysis, identifying four quantitative trait loci (QTLs) associated with moisture deficit tolerance (one on chromosome 1 and three on chromosome 9). Transcriptome profiling of parental lines under PEG stress revealed that the tolerant genotype preferentially upregulated genes involved in abiotic stimulus detection, RNA splicing, cytosolic ribosome function, fatty acid metabolism, and lipoic acid metabolism, suggesting coordinated post-transcriptional regulation and membrane remodeling. Five candidate genes within QTL intervals namely, chlorophyll synthase, chlorophyll a/b binding protein, small heat shock protein, major latex protein, and HMG protein, showed contrasting expression patterns between parents, and are confirmed by qRT-PCR. Further, co-expression network analysis identified a small heat-shock protein (SHSP) gene as the most strongly stress-induced hub in tomato, which could be a candidate regulator of osmotic stress response in tomato. The identified QTLs and also the candidate genes may provide genomic targets for genetic engineering and marker-assisted breeding of climate-resilient tomato cultivars.
Mango (Mangifera indica L.) (2n = 40) is a globally vital horticultural fruit crop with significant economic, nutritional, and cultural value. Pakistan, as one of the leading mango-producing countries, holds a rich diversity of mango germplasm. However, genomic diversity based on single nucleotide polymorphism (SNP) markers remains poorly characterized, restricting the effective use of this germplasm in molecular breeding programs. The present study aimed to evaluate the genetic diversity, population structure, and evolutionary relationships among 80 mango genotypes, representing diverse geographic origins conserved in Pakistan, using whole-genome resequencing. Evolutionary relationships were further elucidated using 47 single-copy nuclear genes. After filtering the raw dataset, 7.2 to 25.7 Gb of sequencing data per genotype was obtained, with sequencing depth ranging from 18.2× to 64.3×. Over 98
A study on variability among sixteen exotic genotypes of mango was carried out under subtropical conditions of the Indian subcontinent at ICAR-Central Institute for Subtropical Horticulture. These genotypes were evaluated for twenty morphometric traits, including four leaf morphometric traits and ten biochemical traits, including three leaf-based biochemical parameters. Fruit weight, number of fruits, pulp weight and peel weight displayed maximum variance. For biochemical traits, ascorbic acid content in fruits, leaf total flavonoids and total leaf phenol were most variable. For most of the economic traits viz., the high broad sense heritability (h2) and high genetic advance over mean (GAM) for traits viz., fruit weight (85
Coconut (Cocos nucifera L.) is one of the most economically important perennial crops worldwide, yet the molecular basis of variation among cultivars remains comparatively understudied relative to other major oilseed crops. Fiji Tall and Fiji Dwarf are two contrasting coconut cultivars of agronomic relevance to the Pacific Island region, differing substantially in growth habit, plant architecture, and developmental characteristics. To investigate the molecular basis of these differences, we performed a comprehensive reference-guided transcriptome analysis of leaf, stem, and root tissues from both cultivars using Illumina paired-end RNA sequencing. Clean reads were aligned to the Hainan Tall chromosome-level reference genome using HISAT2, and gene-level expression was quantified with featureCounts. Differential expression analysis using DESeq2 identified 3,155, 6,904, and 7,448 differentially expressed genes (DEGs) in leaf, stem, and root tissues, respectively, with 716 DEGs shared across all three tissues. Gene Ontology (GO) and KEGG pathway enrichment analyses revealed that genes upregulated in Fiji Tall were consistently associated with biosynthetic, structural, and primary metabolic processes across tissues, while genes more highly expressed in Fiji Dwarf were enriched in stress-responsive, defense-related, and regulatory pathways. Targeted analysis of stem growth-associated genes identified differential expression of key phytohormone-related genes, including CnGA20ox1 and other gibberellin metabolism genes, together with auxin, cytokinin, and brassinosteroid-related genes, suggesting coordinated hormonal regulation underlying the contrasting growth habits of Fiji Tall and Fiji Dwarf. Integration of alternative splicing analysis identified an additional post-transcriptional regulatory dimension, with stress- and signaling-related genes particularly subject to differential splicing in root tissue. This study provides a primary comprehensive, multi-tissue transcriptomic resource for Fiji coconut cultivars and establishes a foundational molecular framework for coconut genomics and breeding programs in the Pacific.
