Pepper (Capsicum annuum L.) holds significant global importance as both a spice and a vegetable, extensively cultivated for its unique pungency, nutritional value, and diverse pharmaceutical uses. Being a warm tropical fruit vegetable, it is highly sensitive to heat stress (HS). However, temperature above 33 °C impairs its reproduction, subsequently impacting fruit yield and seed quality. Despite this vulnerability, pepper harbors substantial genetic diversity for key morphological, fruit, and seed traits. Therefore, studying this genetic diversity and identifying genome-wide candidate genes through GWAS for these traits under heat-stress conditions is crucial for advancing heat-resilient pepper improvement. We assessed the genotypic and phenotypic variance among 146 diverse accessions in two seasons (S1: 2022 and S2: 2023) under HS condition. Key morphological, fruit, and seed traits exhibited significant genotypic effects (P < 0.001) across seasons. A pooled ANOVA revealed significant genotype × season interactions for a number of traits, including leaf length (LL), number of primary branch (NPB), average fruit width (AFW), average fruit weight (AF Wt), and hundred-seed weight (HSW). The majority of traits exhibited high heritability (>60

SUMMARY:Phylogenetic trees are ubiquitous and central to biology, but most published trees are available only as visual diagrams and not in the machine-readable Newick format. There are, thus, thousands of published trees in the scientific literature that are unavailable for follow-up analyses, comparisons, and supertree construction. Experts can easily read such diagrams, but the manual construction of a Newick string from a diagram is laborious, error-prone, and time-consuming. Previous attempts to semi-automate the reading of tree images relied on image processing techniques. These often encounter difficulties as typical published tree diagrams contain various graphical elements and annotations that overlap the branches, such as error bars on internal nodes. Here we introduce Treemble, a user-friendly desktop application for generating Newick strings from tree images. The user simply clicks to mark node locations, assisted by a deep learning-based node detection tool, and Treemble algorithmically assembles the tree from the node coordinates alone. Treemble also facilitates the automatic reading of tip name labels and can be used for both rectangular and circular trees. AVAILABILITY AND IMPLEMENTATION:Treemble is a native desktop application for macOS and Windows and is freely available, with documentation, at treemble.org. Source code is available at github.com/John-Allard/Treemble. The trained node detection model is available at huggingface.co/John-Allard/treemble-1.

Convergent phenotypic evolution, the independent acquisition of similar or nearly identical traits in multiple species, is widespread throughout the tree of life. These cases of repeated evolution offer an opportunity to investigate shared genetic changes underlying shared traits, thereby linking genotypes to phenotypes. Genetic convergence can take many forms: identical amino acid or nucleotide substitutions; non-identical changes in orthologous genes or other elements; losses or gains of the same genetic elements; or convergent shifts in molecular evolutionary characteristics, such as substitution rates, amino acid preferences and selection strength. However, identifying adaptive genetic convergence, whereby evolved traits provide a fitness advantage, is challenging due to a pervasive background of random convergence that causes low signal-to-noise ratios. Numerous computational methods, including machine learning and artificial intelligence approaches, have been developed to detect, interpret and predict molecular convergence across multiple levels of genetic organization in multicellular organisms. These emerging approaches offer novel avenues to uncover the genetic foundations of complex and biomedically important traits. Convergent phenotypic evolution, the independent acquisition of similar or nearly identical traits in multiple species, is widespread. Allard and Kumar explore the spectrum of molecular convergence in multicellular organisms, evaluate computational and artificial intelligence-based methods for detecting adaptive genetic convergence, and highlight how comparative genomics of convergent phenotypes informs complex trait evolution and human health.

Viruses contain some of the most interesting origins, biology, and relationships in the noncellular world. They are also visually alien looking to students and obviously different from cellular life. They are, in their parasitic mode, the consummate intimate associate, the genetic and evolutionary collaborator at the level closest to the cell’s inner life. Viruses are, by their very structure and nature, dependent and interdependent. The concept of interdependency is an often-overlooked critical thinking skill, spoken of but rarely consolidated in biology curriculum yet at the root of understanding every tier of biological systems. Interdependency links all life together at all scales. To address the importance of interdependency in biological systems we propose a genomic medicine authentic STEAM-based experience that explores interdependency through the phage viruses. Phages are the most abundant and diverse biological entities on the planet (Batinovic et al., 2019). In this paper we outline the phage’s universality and interesting attributes to provide background for a critical thinking prospectus that utilizes fine art skills and biological knowledge for students to experience and discover phage morphology, evolution, and therapy. We explore both the portrait of a phage (its structure and proximal relationships) and the landscape of its interdependence (global relationships) through the GM lens.

High temperature causes harmful effects on growth, quality and yield of rice (Oryza sativa L.). Higher spikelet fertility is the most desirable trait for mitigating the effects of climate change, and thus need to develop rice varieties with climate resilience under future climate scenario for sustainable rice productivity. In our study, spikelet fertility and panicle weight were investigated under controlled environmental conditions in a set of 241 rice genotypes, which were sequenced in 3000 rice genomes project. High temperature significantly reduced the spikelet fertility and panicle wight by over 50% in this study. Genome wide association mapping was performed on spikelet fertility and panicle weight with 1 million SNPs using an efficient mixed model. Three promising MTAs viz., qHTSF19_5.2, qHTSF19_5.4 and qHTPW19_9.2 and haplotype variants of four putative candidate genes namely, LOC_Os05g15160 (a triose phosphate/phosphate translocator 2), LOC_Os05g16420 (SHR5-receptor-like kinase), LOC_Os09g15670 (an ABA-induced protein phosphatase 2Cs) and LOC_Os09g15700 (a receptor like protein kinase) were identified. The variations of non-synonymous SNPs (nsSNPs) in the gene sequences were used to group the association panel and identify superior donors and haplotypes. IRIS 313-8704 and IRIS 313-11307 were identified as superior donors with higher spikelet fertility and panicle weight under HT stress. Moreover, both the identified donors were found to be in the same haplotype group, highlighting their significance in developing haplotype specific markers that could be beneficial for marker-assisted breeding and making reproductive stage high temperature stress tolerant rice globally.

Pyrimidine analogues, essential nitrogen-containing heterocycles, play vital roles in nucleic acid architecture and cellular metabolism, with growing applications in aquatic animal health. This review synthesizes current knowledge on their pharmacological potential, focusing on the freshwater catfish Heteropneustes fossilis. An analysis of peer-reviewed literature revealed pyrimidine derivatives’ broad-spectrum bioactivities, including anticancer and antimicrobial properties. Notably, recent investigations demonstrate that waterborne exposure to the synthetic analogue 4,6-dimethyl-2-hydroxypyrimidine hydrochloride (4,6-DHP) (10 pg/mL) has been reported to improve physiological resilience in H. fossilis. Observed benefits include enhanced oxygen transport capacity, reduced markers of immune-stress, and elevated tissue energy reserves. Crucially, this derivative has been shown to provide neuroprotection by reducing oxidative stress and effectively remediating hypoxia-induced brain alterations; furthermore, short-term observations suggest a rapid clearance, though long-term bioaccumulation studies remain necessary. Despite these robust systemic benefits, a significant knowledge gap persists regarding reproductive endocrinology. While the compound’s stress-mitigating and metabolic-enhancing profile may contribute to positive modulation of the Brain-Pituitary-Gonad axis, direct evidence concerning hormonal regulation (GnRH, LH, steroids) and gametogenesis remains absent. Because reproductive regulation in teleosts is highly complex and sensitive to both direct endocrine signalling and indirect metabolic factors, this lack of direct gonadal data represents a critical limitation. Therefore, rigorous experimental validation is required to definitively confirm any reproductive efficacy. Future research must prioritize dose-dependent investigations into reproductive outcomes, including fecundity and larval viability, and evaluate interactions with induced breeding protocols. Addressing these gaps could help develop sustainable aquaculture methods by using pyrimidine analogues that do not accumulate in the body and act on multiple biological processes. This review highlights the need to connect mechanistic understanding with practical reproductive studies to improve aquaculture productivity.

Cancer genomes accumulate somatic mutations over time, influenced by both intrinsic and extrinsic mutational processes. In metastatic cancer, disseminated tumor cells may acquire additional mutations at metastatic sites, shaped by extrinsic factors distinct from those at the primary tumor. As a result, cancer genomes at metastatic sites may bear mutational signatures originating from both primary and metastatic environments. However, the patterns and relative contributions of mutational signatures specific to metastatic sites remain poorly understood. To investigate this, we analyzed mutational signatures from seven metastatic cancer patients. We observed distinct mutational patterns between early and late mutation profiles within individual patients, where the early and late categories were based on their relative timing during tumor evolution. Early mutations were often dominated by a single mutational signature that accounted for more than half of the total signature burden. These dominant signatures tended to be shared among tumors of the same cancer type, suggesting that early mutations in metastatic cancers may be shaped by a single, highly active mutational process at the primary tumor site. In contrast, late mutations were often more poorly decomposed into distinct mutational signatures, reflecting more complex and diverse compositions. Overall, early mutations tended to preserve clearer signals of their origin.

Winged bean (Psophocarpus tetragonolobus L.) is a nutritionally rich underutilized tropical legume. It requires short-day (SD) conditions for flowering, which limits its cultivation across seasons and regions. In this study, 81 winged bean accessions were evaluated over three years under contrasting natural photoperiods, identifying five genotypes capable of flowering under both short- and long-day conditions. However, only one accession (IIAB-PIS1) achieved full reproductive development under long-day (LD) conditions. To understand the molecular basis of this trait, we conducted a genome-wide identification and analysis of the phosphatidylethanolamine-binding protein (PEBP) genes, which are key regulators of flowering-time pathways. Ten PEBP genes were identified and classified into FT-like, TFL1/CEN-like, and MFT-like groups, each of which displayed conserved domain structures and features. Divergence time analysis indicated recent diversification within subfamilies. Expression profiling under LD conditions showed that FT2 may be the potential candidate gene for florigen production in both photoperiod-sensitive and -insensitive genotypes. In contrast, differential expression of FT1, FT4, TFL1, and CEN2 suggested genotype-specific regulation of floral transition pathways. The discovery of a truly photo-insensitive genotype, along with the identification of key regulatory PEBP genes, offers valuable resources for developing high-yielding, photoperiod-insensitive winged bean cultivars.

The study utilized high-throughput phenotyping (HTP) techniques, including red-blue-green (RGB), infra-red (IR), near infra-red (NIR) imagings, and chlorophyll fluorescence, along with biochemical indices to evaluate the drought tolerance and recovery potential (after two weeks of rewatering) of novel citrus rootstock genotypes. The RGB imaging quantified geometric traits such as projected shoot area, convex hull area, object extent Y, compactness and eccentricity, revealing reductions in plant canopy size, height, and density under drought stress. IR imaging highlighted the plant canopy temperatures, while NIR imaging detected reduced water content, which provided an early indication of drought stress. Chlorophyll fluorescence analysis identified genotype-specific changes in photosynthetic activity, with a significant decline observed in drought-sensitive genotypes such as SCSH 17 − 12 and Cleopatra mandarin. Rewatering enabled partial recovery in several genotypes, with X639 demonstrating the highest drought tolerance and recovery, followed by the hybrid CRH 21 − 13, which emerged as a promising rootstock for water-limited conditions. The biochemical analysis of the tested rootstocks under normal and drought stress conditions also proved that the hybrid CRH 21 − 13 can be utilized in the drought-prone areas for citrus cultivation. The integration of advanced imaging technologies showed strong correlations between image-based traits and physiological drought responses, highlighting their utility for non-destructive screening of plants under drought stress and genetic evaluation.

Heat stress poses a significant challenge to wheat productivity, necessitating the identification of genetic loci conferring yield stability and resilience. This study evaluated a multi-parent advanced generation intercross (MAGIC) population for biomass (BM), grain weight per spike (GWPS), thousand grain weight (TGW), yield per plot (YLD), and heat susceptibility indices (HSI_BM, HSI_GWPS, HSI_TGW, HSI_YLD) under timely-sown irrigated (TSIR) and late-sown irrigated (LSIR) conditions across Delhi, Dharwad, and Pune. The population exhibited substantial phenotypic variation and yield and biomass positively correlated and inversely related to heat susceptibility, highlighting potential for selection under stress conditions. Genome-wide association studies identified SNPs across nearly all wheat chromosomes associated with BM, GWPS, TGW, YLD and their corresponding heat susceptibility indices (HSIs), with phenotypic variance explained (PVE) ranging from 3-15%. Major-effect loci (e.g., AX-94529210, AX-95104040 and AX-95204353 for GWPS; AX-95210025 for TGW, AX-94496657 for BM; AX-94877518, AX-94942005 and AX-95118494 for YLD) and numerous minor-effect SNPs contributed to trait variation, reflecting a polygenic architecture. Allelic effect analysis demonstrated consistent enhancement of yield and reduction of heat susceptibility across environments. Collectively, this study underscores the MAGIC population as a valuable resource for dissecting complex traits and provides genomic insights for marker-assisted breeding of high-yielding, heat-tolerant wheat varieties.

Winged bean (Psophocarpus tetragonolobus) is a nutritionally rich but genomically underexplored legume with potential for climate-resilient agriculture. We report a near chromosome-scale genome assembly ( 697.69 Mb; N50 = 85.98 Mb; 98.25

A comprehensive evaluation of 248 MAGIC population-derived wheat lines and their eight founder lines revealed significant genetic variation and adaptive diversity for key physiological traits- NDVI_1-3, SPAD chlorophyll content, canopy temperature (CT), and chlorophyll fluorescence (Fv/Fm UP and LW) under timely sown (TSIR) and late-sown (LSIR) irrigated conditions across multiple locations. Genotypes under TSIR exhibited higher canopy greenness, chlorophyll stability, and photosynthetic efficiency, whereas LSIR induced elevated CT and reduced SPAD, indicating genotypic differences in heat tolerance. Correlation and PCA analyses showed strong interrelationships among traits, with NDVI positively correlated with SPAD and Fv/Fm (r = 0.52-0.86) and negatively with CT (r = -0.13 to -0.60). PCA identified two principal adaptive axes- vigour/biomass (NDVI-CT) and pigment/stress (SPAD-Fv/Fm), explaining 65-82% of total variation. GWAS detected 54 significant marker-trait associations, predominantly on chromosome 5A, with major loci AX-95210025, AX-94980357, and AX-94448771 influencing NDVI, SPAD chlorophyll content, CT, and Fv/Fm (UP and LW). Favorable alleles enhanced canopy vigour and chlorophyll content while reducing CT, signifying integrated genetic control of photosynthetic resilience and thermal regulation. In-silico and gene regulatory network (GRN) analyses identified key heat-responsive candidate genes including TraesCS5A02G078000 (Heat shock cognate 70 kDa protein), TraesCS5A02G077900 (DnaJ co-chaperone), TraesCS1A02G098800 (DUF4408 domain protein), TraesCS7A02G143900 (Hydroxyproline O-arabinosyltransferase-like protein), and TraesCS7B02G083500 (Small heat shock protein) that regulate chlorophyll maintenance, PSII repair, and canopy cooling under stress. Collectively, this study elucidates the genetic and physiological basis of heat tolerance in the MAGIC population and identifies robust targets for marker-assisted selection and genomic improvement of thermotolerant wheat.

Heat stress negatively impacts key yield-contributing physiological traits in wheat, leading to a decrease in grain yield. Scanning of genomic regions linked to these traits, along with the identification of the most relevant candidate genes (CGs), is an effective strategy for developing heat-tolerant wheat cultivars in the near future. In this context, a genome-wide association mapping approach has been employed to identify chromosomal regions associated with these traits, along with to identify the putative CGs for heat tolerance in wheat. Genotyping was performed using the 35 K Axiom Wheat Breeder Array. From our study, principal component analysis (PCA) revealed that biomass (BM), canopy temperature (CT), and seed weight per pot (SWPP) explained a higher cumulative variance. Population structure and diversity analysis filtered 13,947 markers and revealed three subpopulations with sufficient diversity. A large whole-genome LD block size of 7.15 MB was obtained at a half LD decay value. We have mapped 14 significant MTAs linked to these traits with − log10(p) value > 5.44 after Bonferroni correction and also identified 14 high-confidence CGs. Our study also identified four haplotype groups, suggesting the potential for a haplotype-based breeding program under heat stress. Promoter analysis revealed 174 cis-regulatory elements (CREs). Phylogenetic analysis of the pleiotropic gene TraesCS7A02G200200 revealed three major clades of closely related species. We have also reported several orthologous genes related to our 14 major CGs. Untranslated regions (UTRs) analysis found several upstream Open Reading Frames (uORFs) in few identified genes, which can be employed to understand the stringent mechanism of gene regulation under heat stress. By using the Multitrait-genotype ideotype index (MGIDI), we have selected 13 high-performance genotypes for their use as donor parent for heat tolerance. Henceforth, after successful validation, these SNPs can be utilized for marker-assisted transfer of genes/QTLs to develop heat-tolerant wheat cultivars. Mapped 14 significant marker-trait associations (MTAs) for yieldcontributingtraits in wheat under heat stress. Identified 14 high-confidence CGs and four haplotype groups. Promoter analysis revealed 174 cis-regulatory elements (CREs) in identified CGs.

Drought significantly limits plant growth and productivity by reducing water availability and disrupting physiological processes. Root system architecture and its plasticity play a vital role in plant adaptation to water limited environments by regulating soil water acquisition and resources allocation. Root plasticity enables dynamic modulation of key traits, including, root depth, growth angle, diameter, branching pattern, root hairs, and root-to-shoot ratio, allowing plants to optimize water uptake under variable soil moisture conditions. This review highlights recent advances in understanding of root trait plasticity by integrating anatomical, physiological, hormonal, and genetic mechanisms governing drought adaptations in crop plants. It also summarises, how coordinated changes in root architecture and their functions, determine plant resilience under transient and prolonged drought conditions. Major emphasis is on functional root traits, hormonal and molecular regulation, and their integration in to breeding strategies to improve drought stress tolerance. The review also highlights the importance of root trait trade-offs and specific root ideotypes for developing drought-resilient cultivars in different crops under changing climatic conditions.

Homologous proteins evolve from a common ancestral sequence, constrained by intricate patterns of co-evolving residues. Accurate reconstruction of evolutionary histories remains a challenge, primarily due to the inability of the existing approaches to capture long-range coevolutionary ties and lack of a precise metric to represent the evolutionary distance between sequences. Standard approaches are based on p-distance or substitution-corrected measures such as Jukes-Cantor. These methods saturate in cases of deep evolutionary divergence, losing all evolutionary signal after enough time. We present HyperEvoGen, a Poincaré variational autoencoder with adversarial training, hyperbolic latent geometry, and a compound loss function that learns evolutionarily meaningful representations from single-family alignments. The arrangement of protein sequences in HyperEvoGen's hyperbolic embedding aims to preserve phylogenetic structure and produce latent distances which scale with true evolutionary divergence. HyperEvoGen enables fast, scalable modeling of protein evolution while preserving hierarchical relatedness in a geometry-aware representation. On Potts-coupled simulation benchmarks, it produces more accurate ancestral reconstructions than conventional baselines, and offers higher-quality sequence generation with less training time than Potts models. This combination of accuracy and throughput supports large-family evolutionary studies and accelerates design-oriented applications.

A comprehensive evaluation of the MAGIC wheat population under timely sown irrigated (TSIR) and late sown irrigated (LSIR) conditions revealed wide phenotypic variability in agro-morphological and flag leaf traits, including plant height (PH), spike length (SL), spikelet number per spike (SN), grains per spike (GPS), harvest index (HI), flag leaf length (FLL), flag leaf width (FLW) and flag leaf area (FLA), highlighting rich genetic diversity and environmental sensitivity. Genotypes under TSIR showed superior performance, where LSIR induced heat stress effects, resulting in reduced trait expression. Genome-wide association studies identified 97 significant marker-trait associations (MTAs), with key significant SNPs such as AX-94,533,666 (1B) associated with flag leaf area (FLA) and flag leaf width (FLW); AX-94,980,357 (5 A) associated with flag leaf area (FLA), flag leaf length (FLL), and spike length (SL); AX-94,818,117 (5 A) associated with spike length (SL); AX-94,514,616 (7 A) associated with spikelet number per spike (SN); and AX-95,210,025 (5 A) explaining 16.1

Viruses contain some of the most interesting origins, biology, and relationships in the noncellular world. They are also visually alien looking to students and obviously different from cellular life. They are, in their parasitic mode, the consummate intimate associate, the genetic and evolutionary collaborator at the level closest to the cell's inner life. Viruses are, by their very structure and nature, dependent and interdependent. The concept of interdependency is an often-overlooked critical thinking skill, spoken of but rarely consolidated in biology curriculum yet at the root of understanding every tier of biological systems. Interdependency links all life together at all scales. To address the importance of interdependency in biological systems we propose a genomic medicine authentic STEAM-based experience that explores interdependency through the phage viruses. Phages are the most abundant and diverse biological entities on the planet (Batinovic et al., 2019). In this paper we outline the phage's universality and interesting attributes to provide background for a critical thinking prospectus that utilizes fine art skills and biological knowledge for students to experience and discover phage morphology, evolution, and therapy. We explore both the portrait of a phage (its structure and proximal relationships) and the landscape of its interdependence (global relation ships) through the GM lens.

The winged bean (Psophocarpus tetragonolobus) is a fast-growing, underutilized legume adapted to hot and humid regions and valued for its high nutritional content and symbiotic nitrogen fixation, making it suitable for crop rotation and intercropping systems. In this study, we generated high-coverage short-read sequencing data and assembled the complete chloroplast genome of winged bean. The plastome is 151,571 bp in length and comprises 130 genes, including 85 protein-coding genes, 37 tRNAs, and eight rRNAs, organized in a typical quadripartite structure. We identified 84 simple sequence repeats (SSRs), two compound SSRs, and 15 variable number tandem repeats (VNTRs). Comparative analyses with representative legume plastomes revealed strong clade-wise conservation of genome organization, gene content, and GC composition, together with localized variation at IR–SSC junctions consistent with plastome isomerism rather than fixed structural rearrangements. Phylogenomic reconstruction based on complete chloroplast gene sets robustly placed P. tetragonolobus within the Phaseoleae (Millettioid) lineage, consistent with current legume systematics. Molecular evolutionary analyses indicated pervasive purifying selection across chloroplast protein-coding genes, with limited relaxation of constraint in a small subset of loci, while codon usage patterns showed a pronounced A/U-ending bias typical of legume plastomes. Overall, this study provides the first complete chloroplast genome resource for winged bean and supports future comparative genomics, evolutionary studies, and crop improvement in legumes.

Abstract Background Substitutional entrenchment arising from epistatic interactions renders previously acceptable amino-acid states unfavorable over evolutionary time and has often been attributed to novel adaptive processes. However, recent simulations based on Potts-Hamiltonian models have suggested that entrenchment may also emerge during protein evolution governed by the neutral theory of molecular evolution (NTME). Results Here, we re-examine this conclusion by assessing whether substitutions permitted in such simulations are consistent with empirical expectations of NTME. Since Potts models are inferred from a large collection of homologous rather than orthologous sequences, they may allow substitutions that are incompatible with NTME. Our analysis revealed that Potts-based simulations permit amino-acid substitutions whose Hamiltonian energies (PHE, φ ) often fall outside empirically derived NTME φ neighborhoods, thus allowing non-neutral evolution of domain sequences. To prevent such transgressions, we implement simulations that impose purifying selection whenever Potts-acceptable substitutions depart from the NTME φ neighborhood. When these substitutions are eliminated, we observed limited substitutional entrenchment, with site-specific amino-acid preferences remaining stable over biologically relevant timescales in neutral protein evolution. We further find that overdispersion of the molecular clock is modest and scales directly with the proportion of evolutionary lineages displaying epistasis-driven among-site rate heterogeneity, independent of entrenchment. Conclusions These results demonstrate that significant entrenchment is not an inherent property of epistasis during protein evolution consistent with NTME. Our findings establish baseline expectations for neutral evolution with epistasis and suggest that pronounced entrenchment observed in natural protein evolution likely reflects non-neutral evolutionary histories, including adaptation.

The present study aimed to validate the identified marker trait associations (MTAs) for stay-green (SG) and stem reserve mobilisation (SRM) using 12 wheat genotypes. Out of 12 genotypes, equal number of genotypes (6 each) had higher and lower SG and SRM traits. These genotypes were selected from our previous genome-wide association study for SG and SRM traits. Validation of mapped MTAs have been accomplished by using physiological and gene expression approach. Gene expression analysis of the identified genes in the MTAs region were carried out in these selected contrasting lines in a pot experiment site at Division of Plant Physiology, Indian Agricultural Research Institute (IARI), New Delhi, India. For SG traits, canopy temperature (CT), soil plant analysis development (SPAD) value, leaf senescence rate (LSR) was recorded, whereas for SRM, stem reserve mobilisation efficiency (SRE) was measured. The experiment was carried out in completely randomized design (CRD), under control and combined heat and drought stress (HD) condition. Plants in the control condition (timely sown) were irrigated at their critical phenological stages throughout the cropping period, while under combined stress (50 days late sown), irrigation was withheld at the flowering stage to impose drought stress. Candidate genes found in the overlapping region and within the region of 100 Kb intervals flanking either side of the associated markers were identified through BioMart tool in Ensemble Plants platform. Real-time gene expression analysis was performed on SG-associated genes in the flag leaf and SRM- associated genes in the peduncle. Phenotypic assessment showed that there was significant genotypic variation for the SG and SRM traits and yield. Low SG and SRM performing genotypes showed around 27% and 37% faster leaf senescence rate (LSR) than high SG and SRM performing genotypes under control and HD conditions, respectively, which confirming to our mapped MTAs for SG and SRM traits. HD3366 showed highest stem reserve mobilisation efficiency (SRE) of around 85% under combined stress, while lowest of around 27% was recorded in MP1369 under control condition. Thousand grain weight (TGW) showed negative association with LSR, while positive correlation with SRE. However, highest relative gene expression of cytokinin dehydrogenase 11-like (TaCKX11) was recorded in low performing SG and SRM genotypes, while lowest expression was recorded in high performing SG and SRM genotypes. Expression analysis of candidate genes like protein phosphatase 2C (TaPP2C), TaCKX11, protein detoxification 40-like (TaPD), F-box protein (TaFBP) and pentatricopeptide repeat (TaPPR) were associated with leaf senescence (SG- linked). Genes linked with SRE, such as serine/threonine-protein kinase 2 (TaSK2) and wall-associated receptor kinase 4- like (TaWAK) exhibited the highest expression levels during 12 days after anthesis, suggesting their involvement in enhanced carbon reserve mobilization to the grain under stress conditions. Our study confirmed the association of mapped markers and its linked traits, which can be used in further marker-assisted selection (MAS) using efficient breeding tools.