Development of high yielding and stable cashew varieties is necessary to achieve sustainable cashew nut production under changing climate. Hence, the primary objective of this study was to identify the most stable cashew varieties that can be used as parents in a breeding programme. For this, twenty-five cashew varieties were evaluated across six agricultural seasons for nut yield. Two models viz., additive main effects and multiplicative interaction (AMMI) model and genotype plus G×E (GGE) biplots were used. Pooled analysis revealed significant differences (P < 0.01) among the varieties, environments and variety × environment interactions for nut yield and related traits across the six years. AMMI analysis for nut yield revealed significant PCs i.e., IPCA1, IPCA2, IPCA3, and IPCA4 accounting for 53.79
Rice productivity in Assam is constrained by highly diverse agro-ecological conditions, including recurrent seasonal flooding, which generate strong genotype × environment interaction (GEI) and complicate varietal recommendation. To identify broadly and specifically adapted cultivars, including submergence-tolerant Sub1 varieties suitable for flood-prone areas, 31 rice genotypes were evaluated across 21 environments representing seven locations in Assam over three consecutive years (2022–2024). Grain yield data were analysed using combined analysis of variance (ANOVA) and a mixed-model approach to estimate best linear unbiased predictions (BLUPs), followed by stability assessment using the weighted average of absolute scores from the BLUP-based GEI matrix (WAASB) and genotype–environment pattern analysis through GGE biplot. Combined ANOVA revealed highly significant effects of genotype, environment, and GEI, confirming substantial differential varietal responses across environments. WAASB-based selection identified BRRI Dhan 69 as the most stable genotype, while Dholi, Surma Dhan, Ranjit Sub1, and CR Dhan 801 combined high yield with broad adaptation across Assam. In contrast, GGE biplot analysis revealed distinct mega-environments, with Labanya, the highest-yielding genotype, winning the largest mega-environment, whereas Ranjit Sub1, CR Dhan 802, and IR64 Sub1 exhibited specific adaptation to other environment clusters. Environment evaluation further identified test locations combining high discriminative ability and representativeness, providing useful guidance for optimizing future multi-environment testing networks. These findings demonstrate that integrating WAASB and GGE biplot analyses provides a robust framework for identifying both broadly adapted and specifically adapted rice cultivars, thereby supporting evidence-based varietal deployment and climate-resilient rice production in Assam and similar rice-growing environments.
Understanding the factors governing crossability is fundamental for improving hybridization efficiency in groundnut (Arachis hypogaea L.). This study evaluated fertilization efficiency across ten half-diallel crosses involving five parental genotypes (GPBD4, JL24, K6, KDG123 and K1909) under three independent crossing environments (E₁, E₂ and E₃). A total of 80,766 pollinations produced 7,155 mature pods, corresponding to an overall fertilization efficiency of 8.86
Phosphorus (P) deficiency limits lentil productivity, but breeding progress depends on identifying traits that are genetically variable, independently predictive of biomass, and sufficiently stable across P environments. We evaluated 123 lentil genotypes under optimum P (OP; 250 µM) and low P (LP; 3 µM) conditions and integrated factorial ANOVA, broad-sense heritability, phenotypic plasticity, multivariate analysis, trait-network analysis, conditional Random Forest modelling, and a Trait Eligibility Index (TEI). Relative to optimum phosphorus, low phosphorus reduced shoot dry weight, root dry weight, and total dry weight by 27.46
Early seedling vigour (ESV) plays a crucial role in rapid crop establishment and is widely recognized as an indirect indicator of drought tolerance and weed competitiveness, particularly under direct-seeded rice (DSR) systems. Aim of present study is to assess genetic variability for ESV traits and identify superior genotypes suitable for DSR. A total of 150 rice landraces and four checks were evaluated at 15 and 30 days after sowing two locations (Thanjavur and Paramakudi) under natural DSR conditions, for sixteen seedling vigour related traits. Substantial variability was observed across locations, and traits such as seedling dry weight, root length, number of leaves, relative growth rate and crop growth rate exhibited high broad-sense heritability coupled with high genetic advance. Seedling dry weight showed strong positive correlations with key ESV traits including leaf width, number of leaves, tiller number, leaf length and shoot length. Stepwise regression identified seedling dry weight, root length, and number of leaves as the most informative predictors for ESV-based selection. Genotype-by-trait analysis highlighted RL8841, RL6010, RL9452, RL9975, and RL10156 as consistently superior across environments. These findings offer valuable genetic resources and trait-based selection strategies for improving early establishment, drought resilience, and weed competitiveness in rice cultivated under DSR conditions.
Drought stress is a major abiotic stress limiting rice productivity. Forty BC₂F₅ drought QTL pyramided lines (PLs) in the background of DRR dhan 50 cultivar, each carrying combinations of qDTY2.1, qDTY3.1, qDTY1.1 and qDTY2.2 were evaluated under drought and irrigated conditions during rabi 2025. The current study aimed to evaluate genetic variability and trait associations through correlation, principal component and cluster analyses among 40 PLs derived from DRR Dhan50*2/ SAB 4 -7-5 cross to identify superior drought tolerant donors. ANOVA revealed highly significant variability across eleven agro-morphological traits under both conditions. Reproductive stage drought stress drastically reduced yield and its components. Five superior PLs (QTV 108-4, 108-3, 189-2, 128-4, and 105-1) exhibited 36–82
Chia is an emerging nutraceutical crop with considerable potential for cultivation in the rainfed and semi-arid regions of India; however, its genetic improvement is constrained by a narrow genetic base and the absence of adapted varieties. The present study aimed to generate novel genetic variability through gamma irradiation and identify promising mutants with improved agronomic performance and distinct morphological traits. Two chia genotypes (CHIAmpion W-83 and Nira Black Chia-1) were exposed to gamma irradiation, and the resulting mutant populations were advanced through successive generations to obtain stable lines. Six stabilized mutants were characterized for qualitative traits, phenology, plant architecture, yield components, and seed yield under field conditions. The induced mutants exhibited diverse and stable variations, including altered pigmentation, crinkled leaves, chlorosis, and modified panicle architecture, demonstrating the effectiveness of mutation breeding in creating useful phenotypic diversity. Significant variability was also observed for flowering time, maturity, plant height, branching pattern, panicle length, test weight, and seed yield. Mutant 94 − 1 combined early flowering and maturity with superior branching, longer panicles, and the highest seed yield compared with its parental line, while mutant 74-1-5 also exhibited improved yield potential and desirable plant architecture. Other mutants provided valuable trait-specific genetic resources for studying pigmentation (94 − 1 and 125-1), leaf morphology (148-1-2), chlorophyll expression (31-1-1), and inflorescence shape (80 − 1). The study establishes induced mutagenesis as an effective strategy for broadening the genetic base of chia and generating elite breeding materials. The identified mutants represent valuable resources for developing improved chia varieties suited to Indian agro-ecological conditions and for accelerating future breeding and genetic studies.
The Protection of Plant Varieties and Farmers’ Rights Act (PPVFRA)of 2001 provides an important legal and institutional framework for protecting the rights of breeders and farmers over plant varieties developed, conserved or improved by them. This study presents an empirical analysis of 8,615 registered varieties belonging to 102 crops, grouped into 12 crop groups, as recorded in the PPVFR Registry as of March 2025 to visualize the temporal and categorical patterns, assess the contribution of applicant sectors (farmers, public institutions, and private companies), and evaluate the patterns of the duration of protection across crop groups and applicant categories. Descriptive statistics indicate that more than half (54.71
Transgenic technology enables the introduction of desirable genes into crop plants across sexual compatibility barriers, thereby accelerating cultivar development and expanding the scope of crop improvement. Major traits incorporated into transgenic crops include herbicide tolerance, insect resistance, abiotic stress tolerance, and nutritional enhancement. While the creation of novel gene combinations has raised concerns regarding potential risks to human and animal health, biodiversity, and the environment, such crops undergo rigorous evaluation for agronomic performance, food and feed safety, and compositional equivalence prior to commercialization. In India, the widespread adoption of Bt cotton demonstrates the potential of transgenic technology in enhancing agricultural productivity. However, the selection of suitable crops for transgenic intervention requires careful consideration of factors such as availability of target traits within the primary gene pool, consumption patterns, ecological risks, and lessons from past experiences. Based on these criteria, crops such as transgrafted fruits, sugarcane, forage crops, and maize emerge as promising candidates. For effective and socially acceptable deployment, strengthening regulatory frameworks and addressing public concerns through transparent communication are essential. Increasing awareness that transgenes are not inherently hazardous and may originate from plant sources is critical for building societal confidence. This review synthesizes global experiences and evidence to identify strategic priorities for advancing transgenic technologies in Indian agriculture.
Northeastern India has a diverse genetic reservoir of rice that remains largely underutilized for improving crop resilience against biotic and abiotic stresses. One of the most devastating threats to rice production worldwide is rice blast disease, caused by the fungus Magnaporthe oryzae. Despite this, the resistance genes present in local rice landraces have not been thoroughly explored. This study investigates the distribution of major blast resistance genes in rice germplasm from Northeastern India. A total of 58 genotypes from the region were screened, alongside one susceptible genotype (HR-12) and one resistant check (Tetep), in a uniform blast nursery to assess their responses to the disease. Fourteen gene-specific markers were employed to identify the presence of blast resistance genes. The results revealed that the blast resistance gene Pik-p was the most widely distributed, followed by Piz (96.66
Mungbean (Vigna radiata L. Wilczek) is a vital grain legume whose productivity is often constrained by limited phosphorus availability. Phosphorus deficiency hampers plant growth and alters root morphology, typically increasing the root-to-shoot ratio. Enhancing phosphorus-use efficiency (PUE) is therefore essential for improving mungbean performance under nutrient-limited conditions. To explore the genetic basis of PUE, transcriptome sequencing was performed on leaves, stems, and roots of two contrasting genotypes: Pusa 1333 (phosphorus-efficient) and PS 16 (phosphorus-inefficient). RNA-seq analysis revealed 833 upregulated and 1081 downregulated genes across tissues. In roots, 137 genes were upregulated and 477 downregulated; in stems, 365 were upregulated and 294 downregulated; and in leaves, 331 were upregulated and 310 downregulated. Gene Ontology (GO) classification indicated enrichment in biological processes related to growth, metabolism, and cellular organization. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that differentially expressed genes (DEGs) were predominantly associated with metabolic activity and secondary metabolite biosynthesis. Notably, eight DEGs were consistently expressed across all three tissues. Among these, Vradi05g03810 (polygalacturonase) interacted with cell wall–related genes, suggesting a role in modulating cell wall dynamics under phosphorus stress. Vradi05g03870 (RD22-like glycosyl transferase) interacted with stress-responsive proteins, indicating involvement in dehydration tolerance. These findings provide novel insights into the molecular regulation of PUE in mungbean and highlight candidate genes for breeding programs aimed at improving phosphorus efficiency and resilience under nutrient-limited conditions.
Water-deficit under drought and anoxia under flash flooding in the same field are recurring problems limiting rice production in rainfed lowland Agri-ecosystem. Hence, there is need to develop high-yielding rice varieties with inbuilt drought and submergence tolerance. Samba Mahsuri (SM) is a high-yielding mega variety of rice which is popular among the farmers due to its excellent eating quality despite long duration and sensitivity to drought and submergence. The objective of present study was to pyramid major QTL for drought and submergence tolerance in the genetic background of SM. A population of 990 F2 plants from a cross between SM-Sub1-DTY2.1 (DRR Dhan 50) and SM-Sub1-DTY3.2 was analysed using SSR markers linked to drought tolerance QTL qDTY2.1 and qDTY3.2 to select homozygous QTL-pyramided lines (QPL) in SM-Sub1 background. Sixty-two such lines were identified and advanced to F3 generation. Since both the parents matured earlier than SM, the QPL segregated for time to maturity, and only those showing uniform maturity were advanced to F4−6 generation. Of these, four lines were evaluated for agronomic and physiological performance under control and drought stress. The QPL showed significantly lower loss of grain yield under drought than SM and single-QTL parental lines. QPL 62 showed the least reduction in grain yield and was 16 days earlier in maturity than SM. It has over 95
In the present investigation five crosses out of twenty crosses made in line × tester mating design were utilized for inheritance studies of stem rot resistance. The five crosses were derived from crossing of five susceptible genotypes (TCGS 1694, TCGS 2245, Dheeraj, Kadiri-6 and Narayani) with one stem rot resistant genotype, TCGS 1862 (male parent). F₁s were moderately resistant to stem rot. The segregation pattern in the F₂ generation was good fit to a phenotypic ratio of 1 Susceptible: 2 Moderately resistant: 1 Resistant indicating that resistance to stem rot is governed by incomplete dominance. These F₂ findings were further confirmed by genetic analysis in the F3 generation.
Kernel row number (KRN) is one of the important breeding traits in maize which determines the grain yield. The trait is governed by pathways of core and many regulatory genes related to differentiation of floral meristems viz., fasciated 2 (fea2), fasciated 4 (fea4), tassel dwarf 1(td1) and tassel sheath 4 (tsh4). The presence and level of expression of such genes may influence the productivity of inbred lines vis-à-vis hybrids. Heterosis is a complex phenomenon, determined by many genetic and molecular mechanisms. The genes determining floral meristem differentiation may play role in deciding extent of hybrid yield in maize. To understand this, five lines (low KRN) and two testers (one each having high and low KRN) carrying these genes, viz., fea2, fea4, td1 and tsh4 were crossed in line (5) × tester (2) manner and generated hybrids were evaluated for various agronomic traits in a randomized complete block design (RCBD). The expression of targeted genes was undertaken to understand the interplay between the trait of interest and heterosis. Gene expression analysis was carried out by the quantitation of cDNA converted from a messenger RNA corresponding to the gene against an internal standard. The level of expression of fea2 gene was higher than the better parental value in both the hybrid combination viz., AI 5116 × AI 543 and AI 5116 × PML 105, which carries high KRN and low KRN testers respectively. Similarly, expression of fea4 gene was higher than mid parental value in hybrid, AI 5116 × AI 543 and better parental value in hybrid, AI 5116 × PML 105. High expression of td1 and tsh4 was associated with the high yielding hybrid (AI 5116 × AI 543) having one of its parents bearing high KRN. On the other hand, for these genes the expression level in hybrid, AI 5116 × PML 105 was lower than mid-parental value where both the parents were low in KRN. Hence, expression pattern of the studied genes seems to play key role in heterosis phenomenon of grain yield in maize and emphasises importance of testers in designing cross combinations and their finer analysis.
Climate change is expected to intensify drought stress, leading to yield instability and threatening wheat production, which poses serious risks to global food security. Thus, developing drought-tolerant cultivars is the most economical and sustainable approach to attain the required wheat production. In the current study, a total of 42 diverse hexaploid wheat lines were evaluated for drought tolerance using phenotypic and SSR marker data. Twelve traits including phenological, grain yield components and physiological were analysed. For most of the variables, analysis of variance showed substantial differences between genotypes, conditions, and genotype × condition. Strong genetic control is indicated by high heritability and genetic variability of yield, phenological, and yield-contributing traits. Based on the drought susceptibility index (DSI) for grain yield (GY), 25 genotypes were identified as drought-tolerant and 17 as susceptible. The genotypes, SPH66, SPH91, SYN42, SYN9, MACS6222, and DBW327 were identified as highly tolerant. The polymorphism information content (PIC) ranged from 0.28 (Xcfd43) to 0.70 (Xgwm111), and allelic richness was observed with 2 to 5 alleles per locus. Tolerant genotypes such as SPH 37, SPH 38, SPH 44, SPH 48, SYN42, SYN56, and SYN87 were consistently grouped together in both clusters based on phenotypic and molecular data and may serve as donors in future breeding programs. Further, the detection of five significant allelic associations for markers Xgwm484, Xwmc517, Xwmc702, and Xgwm108 suggests that these alleles may serve as functional indicators of drought tolerance and can be targeted for marker-assisted selection for the development of drought-resilient wheat varieties.
Self-incompatibility (SI) is a vital mechanism for promoting out-crossing in the production of hybrid seeds, understanding the reproductive behavior of Protogyny (PG) genotypes can assist in selecting appropriate parental plants for hybrid-breeding programs, enabling the creation of novel mustard hybrid in a more systematic and logical manner. The present study was focused on genetics and identification of putative candidate genes for PG-SI in Indian Mustard. F1s and F2 populations were developed by crossing Pusa Tarak with PG-SI and ten normal genotypes. F2 segregation pattern have shown that the PG-SI trait was controlled by digenic-duplicate gene action with 15:1 ratio. To understand the genetic basis of PG-SI trait in Indian mustard, we performed genotype-by-sequencing (GBS) of PG-SI and non-PG-SI lines developed in three different genetic background (Pusa Tarak, Pusa Bold and Pusa Mahak) using Illumina platform. Single nucleotide polymorphisms (SNPs) differentiating 3 PG-SI and 3 non-PG-SI genotypes were identified. A total of 4,88,663 SNPs and 4,01,301 SNPs found among 3 PG-SI genotypes and 3 Non-PG-SI genotypes, respectively. In this study, we identified corresponding alleles of 4 SNPs consistently associated with all protogynous (PG-SI) and non-protogynous (non-PG-SI) genotypes of Brassica juncea. SNPs, A10:9559612, A09:694111, B05:2480898 and A03:11891971 were co-segregated in these genotypes. We identified the putative candidate genes, namely, calcium-binding protein PBP1, serine/threonine-protein kinase and calcium-dependent protein kinase 5 associated with these identified SNPs. The present findings would enhance our understanding on the genetic basis of protogyny and self-incompatibility in Brassica juncea. In addition, associated SNPs and candidate genes predicted in the current study could be further useful in marker assisted breeding to transfer this trait to other genetic background and subsequently, can be useful in hybrid breeding program. Validating Digenic-duplicate gene action for Self-incompatibility and Protogyny in Indian Mustard. Identifying four key SNPs linked to candidate genes for protogyny and self-incompatibility. Valuable markers for efficient hybrid breeding in Indian Mustard.
