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.

The North-eastern India is a hotspot of genetic biodiversity of flora and fauna. Among rice landraces, indigenous black rice varieties such as Chakhao Amubi and Chakhao Poireton have gained attention due to their superior grain quality and nutritional attributes. These genotypes are recalcitrant to Agrobacterium tumefaciens mediated genetic transformation. Although transformation protocols have been reported for these landraces, but their transformation and regeneration efficiencies remain moderate. We developed and optimized a tissue culture-based Agrobacterium-mediated transformation protocol for the black rice landraces Chakhao Amubi and Chakhao Poireton and optimized the callus induction and shoot regeneration media for above genotypes. Incorporation of a short resting phase following Agrobacterium infection significantly improved callus recovery and shoot regeneration. The hygromycin concentration previously reported for black rice (50 mg L⁻¹ during regeneration) was excessively stringent, resulting in poor regeneration and delayed shoot development, indicating higher hygromycin sensitivity compared with japonica varieties. Evaluation of lower selection pressures identified 25 mg L⁻¹ as the optimal concentration, enabling efficient regeneration of positive transformants. Using these genotype-specific protocols, transgenic rice could be successfully regenerated within 90–100 days, with efficiencies of 48

Optimising root system architecture (RSA) is essential for improving maize resilience to drought, salinity, and nutrient stress, yet its regulatory landscape remains fragmented. Here, we integrated gene mining, cross-species orthology, in silico expression profiling, and gene regulatory network (GRN) analysis to identify RSA regulators under abiotic stress. Curated literature and comparative genomics identified 127 non-redundant maize RSA-associated genes (v5; 69 transcription factor (TF)-coding, 58 non-TF) enriched for lateral root formation, adventitious root development, root system development, hormone-mediated signalling, and cytokinin metabolism, indicating representation of RSA-shaping developmental processes. Spatial and stress-specific transcriptomes revealed expression of root-system-modulating genes, that is Zm00001eb091920 (AASR2), Zm00001eb429540 (CCDP), Zm00001eb405590 (NACTF25), Zm00001eb256650 (CCAAT-HAP2), and Zm00001eb121500 (CKO1), preferentially in the root cortex and elongation zone. The GRN comprised 616 unique nodes and 3295 regulatory edges, identifying KN1 (Zm00001eb055920), EREB147 (Zm00001eb150840), and D8 (Zm00001eb054480) as major transcriptional hubs and miR167d-3p as the most connected miRNA, supporting hormone- and auxin-linked RSA plasticity. qRT-PCR analysis confirmed co-expression of Zm00001eb234120 (WRKY48), Zm00001eb212120 (NACTF6), and Zm00001eb386990 (TIPD1) with regulators Zm00001eb051660 (EREB142), D8, and KN1 in drought- and salinity-stressed CML579. Expression modules further suggest that Zm00001eb403030 (RTCL1) and auxin-associated regulators modulate post-embryonic root initiation and branching. The current investigation outlines a stress-responsive maize RSA network and identifies targets for functional validation, genome editing, and breeding climate-resilient cultivars.

Heat stress is a major abiotic constraint that increasingly threatens plant survival, growth, and productivity under changing climatic conditions. Like many crops, chilli is also highly sensitive to heat stress. This study was planned to understand the biochemical response, identify the critical growth phase and physio-reproductive parameters of chilli genotypes under heat stress. The present study elucidates heat stress mediated alterations in lipid peroxidation and antioxidant defense mechanisms in chilli genotypes during dual phases of plant growth I.e. vegetative and reproductive stages. Twenty-two chilli genotypes were exposed to conditions of ambient temperature (Control/AT; 30–35 °C) and Heat stress (HT; 36–42 °C) regimes to evaluate oxidative stress responses and adaptive defense strategies. Key biochemical indicators, including proline accumulation, hydrogen peroxide (H₂O₂), malondialdehyde (MDA) content, and activities of major antioxidant enzymes, were quantified to assess reactive oxygen species (ROS) scavenging efficiency. Among the evaluated genotypes, A-17-10, A-17-2, and A-5-4 exhibited markedly higher proline accumulation under heat stress. Lipid peroxidation, as indicated by MDA content, was highest in LCA-424 (32.95µmol/gFw) and lowest in A-17-10 (26.34µmol/gFw), highlighting substantial genotypic variability in membrane stability. Hydrogen peroxide levels across both growth stages peaked in Anugraha (2.21 μmol g⁻1 FW), indicating its sensitivity to heat stress. Antioxidant enzyme profiling revealed maximum peroxidase activity in A-17-2 and minimum activity in Swati Palampur. Superoxide dismutase (SOD) activity during the vegetative stage was highest in A-17-10 and lowest in Swati Palampur, while catalase activity ranged from 14 Unit activity/gFw in A-17-2 to 10.08 Unit activity/gFw in Pusa Sadabahar. Heat stress had a greater impact at the reproductive stage, as shown by higher catalase, SOD, and peroxidase activities. The strong antioxidant response in A-17-2 and A-17-10 indicates inherent, stage-specific mechanisms that limit oxidative damage under high temperatures. Factorial analysis grouped genotypes into four clusters, revealing distinct adaptive responses to heat stress. The study identifies key antioxidant traits and elite genotypes that can be utilized for developing climate-resilient chilli cultivars to sustain productivity under rising temperatures. Future research focusing on molecular mechanisms in chilli will further elucidate cellular responses to heat stress and support advanced breeding strategies.

Accurate detection of wheat spikes and reliable yield prediction are critical for optimizing crop production and resource management. This study presents an integrated framework for spike detection and yield estimation using pseudo-RGB images derived from hyperspectral data. A YOLOv8 model was trained on 1,050 images, achieving high precision, recall, and mean average precision values. The bounding boxes and masks generated byYOLOv8 were used to quantify spike count and spike area, while six vegetation indices were extracted from hyperspectral images acquired at the booting stage. Three multiple linear regression models were developed for yield prediction: one based on spike features, another on vegetation indices, and a third combining both. The combined model achieved the highest accuracy, with a five-fold cross-validation R2of 0.902 +/- 0.007, RMSE of 1.739 +/- 0.133 g,and MAE of 1.289 +/- 0.066 g. Compared with previous approaches, the proposed framework demonstrated improved performance, highlighting the value of integrating spike morphology and spectral data for yield prediction. Overall, the study shows that hyperspectral imaging can simultaneously provide morphological and physiological traits, reducing reliance on high-resolution RGB data in wheat phenotyping

Photosynthesis is a key determinant for plant productivity, understanding its genetic basis will aid its improvement. The photosynthesis trait is primarily measured in terms of carbon and light utilization, using gas exchange and chlorophyll fluorescence methods. We report in this study, the extent of variability for photosynthetic trait in wild rice relatives, comprising a total of 26 taxa (22 wild species), using an infrared gas analyzer. The scale of measures used were, PN (net photosynthetic rate), E (transpiration), gs (stomatal conductance), Ci (intercellular CO2), Ci/Ca (ratio of intercellular to ambient CO2), WUE (water use efficiency), CE (carboxylation efficiency), Fv′/Fm′ (ratio of variable to maximum fluorescence, photosynthesis efficiency), qP (photochemical quenching), qN (non-photochemical quenching), ΦPSII (quantum yield of photosystemII), and ETR (electron transport rate). These were subjected to variability (ANOVA and PCA) and association (correlation matrices and path analysis) studies. The maximum PN was observed in Oryza australiensis, followed by Oryza officinalis and Oryza barthii. Maximum qP was observed in Oryza latifolia which was at par with O. australiensis, and Oryza alta. Highest CE was observed in O. australiensis. The CE values for O. barthii, Oryza grandiglumis and O. latifolia were at par with O. australiensis. Transcriptomic analysis for flag leaf between APO, the high efficient photosynthetic genotype with indica rice cultivar BAM4234 revealed key candidate genes underlying photosynthesis traits. These findings underscore the value of wild species and their alleles in expanding the photosynthetic capacity of rice potentially using classical breeding approaches.

Increasing yield is of major importance for Asian and African food security. Knock out mutants in the rice cytokinin oxidase gene CKX2 had shown potential for yield improvement. Here we explored whether subtle changes in CKX2 activity by editing FAD and cytokinin binding site sequences could improve the Indian mega-variety Samba Mahsuri. Knock out and single mutants in FAD and cytokinin binding sites induced by CRISPR/Cas12a caused moderate yield increases. Among 80 CKX2 alleles, five lines with in-frame mutations in both FAD and cytokinin binding domains produced even higher yield. One line, KAMALA, showed superior agronomic performance in 18 field locations (irrigated and rainfed ecologies) over three seasons in trials conducted by AICRPR (All India Coordinated Research Project on Rice), with an average 19% grain yield increase, early maturity, complete panicle emergence, and unaltered grain quality. KAMALA was registered as the first genome-edited variety ready for cultivation by Indian farmers. ### Competing Interest Statement The authors have declared no competing interest. ICAR-NASF, NASF/CRISPR-Cas-7003/2017-18, NASF/ BGAM-9021/2022-23

Finger millet (Eleusine coracana) is a nutritionally important and climate-resilient cereal cultivated in rainfed regions of India and Eastern Africa, yet its genetic improvement has been limited by the lack of efficient and reproducible transformation systems. In this study, we developed a rapid and efficient Agrobacterium tumefaciens–mediated transformation and regeneration system using shoot apical meristem (SAM) explants, enabling direct, callus-free shoot organogenesis. Optimal regeneration and shoot elongation were achieved on Murashige and Skoog (MS) medium supplemented with 3.5 mg L⁻1 6-benzylaminopurine (BAP), 1.5 mg L⁻1 kinetin, 0.1 mg L⁻1 2,4-dichlorophenoxyacetic acid (2,4-D), and 0.2 mg L⁻1 gibberellic acid (GA₃). Genotype-dependent responses were observed, with PR-202 requiring 2 mg L⁻1 AgNO3 to reduce phenolic browning, whereas VL-376 regenerated efficiently without AgNO3. Transformation efficiencies of 30–32

Strategic optimisation of Root System Architecture (RSA) represents a critical frontier for stabilising crop productivity amid increasingly unpredictable moisture-deficit regimes. Understanding key root traits underlying effective drought response is necessary to harness the genetic diversity associated with root growth patterns and environmental adaptations. Many functionally significant root architectural traits have been reported, and the mechanistic importance of some of the anatomical ideotypes, such as the increased metaxylem vessel diameter to reduce axial hydraulic resistance to maintain leaf water potential and change in root growth angle to promote geotropic deep-soil moisture foraging, are discussed in this review. Despite the identification of these characteristics, the knowledge gap in their integration into predictive breeding frameworks remains. This review addresses this fragmentation by critically evaluating how the bottleneck of the ‘phenotyping’ process is being broken down through non-invasive high-throughput phenotyping modalities. Dynamic root-soil interfaces can be spatio-temporally quantified in situ using non-destructive technologies such as X-ray computed tomography and MRI, which can detect developmental plasticity masked by destructive sampling. Artificial Intelligence (AI), especially Convolutional Neural Networks, enables automated extraction of high-dimensional topological parameters from complex digital rhizograms. Present review integrates recent advances in phenotyping with molecular regulatory mechanisms, bridging two traditionally disparate fields. By focusing on the DRO1/qSOR1 loci and ABA-auxin crosstalk, we establish critical connections between molecular regulation and field-scale architectural performance. The resulting multi-scale roadmap may help in targeted selection of climate-resilient cultivars to maximize resource use efficiency.

Root traits during post-tillering stages in wheat are critical for adapting to moisture-deficit stress. This study mapped 24 traditional quantitative trait loci (QTLs) of root and yield traits in wheat across 14 chromosomes using 198 recombinant inbred lines (RILs), developed by crossing two contrasting parents, HD 3086 and HI 1500. Genotyping was done with the 35 K Axiom Wheat Breeder’s Array, followed by QTL mapping through Inclusive Composite Interval Mapping (ICIM) software. From the 5 conditional QTLs (Y75|Y45) mapped, QARFC.iari-2 A was mapped as the major stable QTL for root fresh weight, explaining 11.23

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.

Variations in reproductive stage stress tolerance account for the significant variations in salt tolerance of glycophytes, such as chickpeas. There is a dearth of understanding about the traits and donors for reproductive stage salinity tolerance in chickpeas. Previous studies focus on screening for seedling-stage tolerance or selection based solely on yield without examining component traits. In the present study, observations were recorded from stress and control treatments at the flowering stage from a hydroponic experimental setup. The traits measured in the study were significantly impacted by salinity, showing noticeable differences between the tolerant checks (ICCV-10 and CSG-8962) and sensitive (DCP-92-3 and Pusa-256) chickpea genotypes. The tolerant lines showed comparatively better shoot and root growth than the two sensitive genotypes. Osmotic component traits, such as retention of photosynthetic pigments, biomass, and photosynthetic rate, as well as stomatal conductance, partially contributed to the tolerance. We also found significant variations in the Na+/K+ ratio among genotypes differing in salinity tolerance, sampled at the flowering stage, suggesting variation in ionic stress and tissue tolerance. The expression of salinity tolerance-related genes in contrasting genotypes also uncovered differences in their genetic mechanisms. The key physiological traits and gene expression during the flowering stage are important in selecting salinity-tolerant chickpea genotypes.

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.

Citrus yellow vein clearing virus (CYVCV) is an emerging mandarivirus globally, commonly present in citrus orchards in India. Early detection of CYVCV is essential to prevent its spread through propagative material and to support integrated disease management. Conventional RT-PCR, although reliable and widely used, are time-intensive, require RNA extraction, and depend on sophisticated laboratory infrastructure, which limits their application for rapid on-site surveillance and large-scale indexing. In this study, we developed and validated a CRISPR-Cas12a-assisted reverse transcription recombinase polymerase amplification (RT-RPA) assay using crude-sap as template for rapid, sensitive, and sequence-specific detection of CYVCV. A 241 bp RT-RPA amplicon derived from the RNA-dependent RNA polymerase (RdRp) region of CYVCV was specifically recognized by a Cas12a-crRNA-complex, which activated collateral cleavage of a fluorescent single-stranded DNA-reporter, generating robust and unambiguous signals within 40-50 min. The analytical sensitivity of the CRISPR-based system was established at the 10-6 dilution of RT-RPA product by quantitative fluorescence measurement and was further translated into absolute copy numbers using a plasmid-based SYBR Green qPCR standard curve, while endpoint visualization using a UV transilluminator was feasible up to the 10-3 dilution. Validation on symptomatic citrus field samples revealed strong fluorescence signals in infected plants (up-to 91,447 AU), whereas healthy and non-template controls consistently remained at baseline. Importantly, visible fluorescence in infected samples under UV light further underscored the field-deployable potential of the assay. Compared with conventional RT-PCR, the CRISPR-based RT-RPA platform demonstrated an approximately similar to 1.4-fold per-sample cost reduction, supported by itemized reagent-level cost analysis. These attributes establish the assay as robust, user-friendly, and scalable diagnostic-tool for CYVCV detection, offering strong potential for nursery indexing, orchard surveillance, and certification programs.

Histone methylation is a key epigenetic mechanism that modulates gene expression, particularly during developmental processes and in response to environmental stresses. In this study, we investigated genome-wide patterns of histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 trimethylation (H3K27me3) in two contrasting rice (Oryza sativa L.) cultivars: IR-64, which is sensitive to terminal drought stress, and Nagina-22 (N-22), a drought-tolerant genotype. Under terminal drought stress, a pronounced enrichment of H3K4me3 mark was observed in the panicles of N-22, whereas IR-64 exhibited a marked increase in H3K27me3 levels. H3K4me3 was predominantly localized to promoter regions, while H3K27me3 displayed a broader distribution across exons, introns, transcription termination sites, and intergenic regions. In N-22, H3K27me3 peaks were associated with 3052 genes, including 799 genes uniquely expressed in this cultivar. In contrast, IR-64 showed H3K27me3 enrichment across 7521 genes, of which 5268 were uniquely expressed in the sensitive cultivar. Notably, N-22 exhibited a substantially higher number of H3K4me3-marked genes under drought stress, reflecting enhanced transcriptional activity in the tolerant cultivar. Of the 19,430 genes carrying H3K4me3 modifications, 18,785 were exclusive to N-22, whereas only 283 genes were uniquely marked in IR-64. In N-22, H3K27me3 enrichment was detected in nine genes associated with drought tolerance, and these epigenetic changes were consistent with their transcript abundance. A positive correlation between H3K4me3 enrichment and gene expression was observed for 646 genes in N-22, compared with only five genes in IR-64 under terminal drought stress. Differential enrichment of histone modification peak was prominent in genes involved in regulatory and stress-related functions, including transcription factors, detoxification pathways, and redox signaling. Coordinated changes in histone modifications and gene expression were observed in only a small subset of genes, which included key stress-responsive families such as AP2/ERF and MYB transcription factors, chloroplast precursor proteins, cytochrome P450s, oxidoreductases, and glutathione S-transferases. Together, these findings highlight distinct epigenetic landscapes associated with drought tolerance and sensitivity in rice and provide a valuable resource for understanding the epigenetic regulation of gene expression under terminal drought stress.

Drought stress is a primary abiotic constraint limiting lentil (Lens culinaris Medik.) productivity globally, and identifying genotypes with stable physiological tolerance across multiple growth stages is essential for developing climate-resilient varieties. This study combined multi-season field screening of diverse lentil germplasm panel using seedling vigour derived stress susceptibility index (SSI), a measure of proportional reduction in seedling vigour under stress relative to control adjusted by overall stress intensity followed by physiological and biochemical validation of contrasting genotypes under drought stress at seedling and reproductive stages. Multi-season screening identified 11 tolerant genotypes (IC560051, IC560246, IC560032, IG134349, IC201678, P3227, IC559924,. IC559666, IG130033 and P3208 including check FLIP-96-51) with lower mean SSI rank values. Seedling vigour-derived SSI provided a proxy for selection of stress-tolerant genotypes at an early growth stage. Contrasting genotypes tolerant IC560246 and highly sensitive IC424523 along with their checks FLIP-96-51 (tolerant) and JL3 (sensitive) were evaluated for physiological traits (NDVI, canopy temperature), antioxidant enzyme activities (SOD, CAT, POX), lipid peroxidation (TBARS), root system architecture (RSA), biomass, and yield components. Tolerant genotypes maintained superior trait values under drought, with markedly smaller reductions in NDVI, biomass, and root architecture, along with elevated antioxidant enzyme activities and lower lipid peroxidation compared to sensitive genotypes. Principal component analysis indicated that antioxidant enzymes (SOD, CAT, POX) and growth traits were the key contributors to drought-stress-related variance at both stages. Correlation analysis identified traits strongly associated with seed yield (r > 0.80), including shoot and root fresh weight, number of branches, and antioxidant enzyme activities that were correlated to seed yield, while shoot dry weight, total root length, surface area, NDVI, and number of pods had strong correlations at the reproductive stage only. These traits were subsequently integrated into a multi-trait composite drought tolerance index. A promising tolerant genotype, IC560246 was identified with validated tolerance stability across growth stages, offering potential as a donor for developing climate-resilient lentil varieties.

CRISPR/Cas9 mediated genome editing is a highly powerful and versatile tool for accelerating crop improvement. The editing efficiency of CRISPR/Cas9 system in planta has been highly variable owing to the variable binding affinity between native CRISPR RNA and Cas9 protein in vivo. In plant systems, systematic, large-scale engineering and benchmarking of guide RNA (gRNA) scaffold variants is still relatively limited compared with work in mammalian systems, despite several important studies demonstrating that scaffold and expression-cassette engineering can substantially improve CRISPR/Cas9 efficacy. Current study addresses the limitations of commonly used gRNA scaffold architecture by incorporating a stabilized stem-loop RAR (tetra loop) extension and a transcription-termination site mutation, resulting in improved RNA folding, increased Cas9 binding affinity, and enhanced in vivo editing outcomes. The synthesized scaffold boosted CRISPR/Cas9 efficiency in monocot or dicot plants across the 19 diverse target sites in Arabidopsis, rice and tomato. Furthermore, the synthetic scaffold is compatible with multiplex genome editing architectures, including polycistronic tRNA-gRNA (PTG) expression systems, enabling efficient simultaneous targeting of multiple genomic loci. The findings of this study have broad applications in precision plant breeding, functional genomics, and agricultural biotechnology, facilitating reliable gene modification across diverse plant species and transformation platforms.

Improving water-use efficiency and seed yield stability under moisture deficit stress is a major challenge in Brassica juncea cultivation. The present study evaluated Brassica carinata-derived B. juncea introgression lines (ILs) to elucidate the role of source-sink relationships in enhancing seed yield under moisture deficit stress conditions. A set of 191 ILs, along with their parental lines, was assessed under rainfed and irrigated conditions for various agromorphological and physiological traits. Results revealed that ILs consistently outperformed parents for dry matter accumulation at maturity, seed yield per plant, harvest index, flowering duration, and reproductive-stage dry matter accumulation across environments. Under moisture-deficit stress, ILs maintained comparable crop growth rate and net assimilation rate to those of parents, while exhibiting enhanced physiological plasticity under irrigated conditions. Trait association and scatterplot analyses revealed that balanced source-sink ratio and efficient dry matter partitioning in ILs were critical determinants of seed yield under rainfed conditions. Principal component analysis further demonstrated strong multivariate associations of seed yield with crop growth rate, net assimilation rate, leaf area index, reproductive dry matter accumulation, and source-sink traits, clearly differentiating superior ILs from their parents. Several introgression lines, including IL11, IL33, IL54, IL73, IL83, IL112, IL124, IL128, IL134, IL135, IL155, IL161, and IL165, emerged as promising for moisture deficit stress conditions. Overall, the study highlights that integrating physiological efficiency with source-sink traits provides a robust framework for improving drought resilience and yield stability in Brassica juncea breeding programs through interspecific hybridization.

Developing dwarf plant ideotypes is a crucial strategy for optimizing plant architecture for high-density planting, thereby augmenting productivity. Dominant DELLA mutants confer short plant stature and have been utilized to improve the harvest index since the ‘Green Revolution’. In this study, we unravelled a novel polymorphism in the maize DELLA gene, dwarf8 (d8), by characterizing a set of nine wild-type and one mutant inbreds. Sequencing the 4651-bp-long d8 gene revealed a single exon, with the mutant allele harbouring a unique G-to-A transition (SNP_1458), resulting in a glycine-to-arginine substitution within the highly conserved DELLA domain. Sequence and motif enrichment analysis of 185 orthologues and paralogues further supported glycine as a highly conserved amino acid within the DELLA domain. Genetic and molecular analysis of 48 diverse inbred lines, using eight InDels and an SNP polymorphism (SNP_1458), revealed 19 distinct d8 haplotypes (hap1 to hap19), with the mutant allele included in hap1. To streamline molecular breeding, we developed and validated two breeder-friendly functional markers, viz., (i) allele-specific SNP (MGU-D8mutSNP1458) and (ii) CAPS marker (MGU-D8mutCAPS) specific to the G-to-A mutation to effectively differentiate wild-type and mutant alleles. Genotyping of F1 and F2 progenies revealed that the SNP mutation was semi-dominant, as heterozygotes (D8d8) exhibited a semi-dwarf plant architecture, while homozygotes (D8D8) exhibited a dwarf phenotype. The identification of this novel SNP (SNP_1458) and the development of cost-effective functional markers are of great significance for breeding programmes aimed at developing short-statured maize hybrids. These maize hybrids possess great potential to meet global productivity demands through high-density planting.

A composite hypocotyl–epicotyl–cotyledonary tri-complex (HECC) explant significantly improves soybean regeneration and Agrobacterium-mediated transformation efficiency (40.3