This study aimed to evaluate the impact of partial-record egg production selection on egg production performance, serum biochemical constituents, and egg quality traits in Dokki-4 laying hens. A selection experiment was conducted over four generations involving 2,880 hens distributed across three experimental lines: high egg number line (SHEN₉₀), heavy egg weight line (SHEW₉₀), and a random-bred control line (RBCL). Selection criteria were based on performance during the first 90 days of production. Line effects were highly significant for all egg production traits, serum calcium concentrations, yolk cholesterol levels, and most egg quality traits. The SHEN₉₀ line showed superior egg number, annual egg mass production performance, and exhibited favorable metabolic profiles with reduced serum cholesterol and triglycerides. The SHEW₉₀ line achieved significantly heavier egg weights and improved shell quality traits compared to other lines. Genetic gain estimates revealed significant improvements in economically important traits. The SHEN₉₀ line showed favorable genetic gains for EN₉₀, EM₉₀, EM₃₆₅, and favorable reductions in serum cholesterol, triglycerides, and yolk cholesterol. The SHEW₉₀ line exhibited significant positive genetic gains in EW₉₀, EM₉₀, EM₃₆₅, and favorable yolk weight and yolk index percentages. Heritability estimates were moderate for selection criteria (EN₉₀: 0.22; EW₉₀: 0.17) and ranged from 0.09 to 0.31 for correlated traits. Genetic correlations revealed strong positive relationships between EN₉₀ and egg mass traits. EW₉₀ showed positive correlations with most external quality parameters. Selection for partial-record egg production represents an effective breeding strategy for simultaneously improving multiple economically important traits in Dokki-4 laying hens.

Plant Breeder’s Rights (PBR) were introduced in Australia (1987-94) to protect intellectual property (IP) and foster private investment in new plant cultivars. Their introduction coincided with an incremental withdrawal of the public sector from cultivar development, and a downsizing of the wool industry that had previously funded pasture research. This Viewpoint assesses the status of pasture cultivar development three decades later, contrasting PBR with the old Register of Australian Herbage Plant Cultivars (RAHPC). A desktop analysis of cultivars registered under PBR or RAHPC is compared to cultivars recently marketed by six major seed companies, followed by detailed case studies of three cultivars, to explore modern trends. As of April 2024, 807 cultivars were registered in Australia from 127 pasture species, most of which (>100) could be considered niche species. There was poor support for PBR by the companies sampled, with only 31% of marketed cultivars having PBR protection, 48% having never been registered and signs of low availability of many species. There was limited evidence of genetic gain in pasture cultivars post-2010, attributable to the lack of commercial return in minor species, little requirement for ‘characters of merit’ and poor cultivar descriptions that obscure independent assessment. It is our view that further genetic gain in most Australian pasture species seems unrealistic without public investment, due to the wide diversity of species requiring development and the lack of end-point royalties in pasture cultivars. Preserving previous gains by maintaining availability of older cultivars of merit may be a more realistic objective.

Speed breeding (SB) has emerged as a technology that helps in developing new, improved crop varieties by dramatically shortening the time period taken for their generation. This is achieved by optimizing environmental parameters such as photoperiod, temperature and soil moisture. This process enables the development of multiple generations per year, thereby speeding up the development of homozygous lines and elite cultivars. Integration with modern molecular tools, including marker-assisted selection (MAS) and genomic selection (GS) with SB, enhances the precision and efficiency of trait selection, leading to faster genetic gain. Despite these advantages, adoption of this technique faces challenges such as infrastructure demands, shortage of skilled personnel, energy requirements and regional disparities in technology access. Addressing these bottlenecks through targeted investment, capacity building and policy support is required to harness SB technique for global food security. This review elucidates the principles, applications and limitations of SB and highlights its pivotal role in modern plant breeding and sustainable agriculture.

Characterization of the genetic and molecular architecture underlying egg production traits in chickens is essential for improving the rate of genetic gain through intensive artificial selection. Here, to explore the dynamic landscape of regulatory effects across egg-laying stages in chickens, we generated 1272 RNA-seq samples of four tissues, i.e., the hypothalamic–pituitary–ovarian axis and liver, and paired whole-genome sequence data from 358 hens. We detected 1008 genes with stage-specific regulatory effects in at least one tissue excluding the pituitary. Out of them, 12.60, 52.78 and 32.84% were mediated by alterations in cell type composition, transcriptional factor activity, and gene co-expression networks among laying stages, respectively. Out of 80 significant loci associated with egg production traits that were detected in a large population (n = 12,952), 37 and 5 colocalized by shared and stage-specific regulatory effects, respectively. Furthermore, orthologues of these colocalized genes are enriched for the heritability of reproductive traits in pigs, cattle, and humans. In summary, we provide a resource for understanding reproduction-relevant gene regulation and highlight the importance of context-specific regulatory effects in deciphering complex traits.

The response to the diverse economic and ecological needs from trees requires an increase in genetic gain and will necessitate investment in public tree breeding programs. Breeding for small spaces in agroforestry and urban places should especially be targeted, given the reduced space for plantations and their roles in strengthening climate change resilience of communities while contributing to food access, income, health, and environmental stability. No systematic tree breeding programme exists in Uganda. However, use of improved planting stock exists in timber and pole plantations where improved tree genetic resources have been mostly imported and tested, although some plus trees now exist for Eucalyptus and Pine species. The National Forestry Resources Research Institute (NaFORRI) and the Forestry Department at Makerere University undertake some tree breeding activities, mostly limited to research. However, many opportunities exist that can support the development of a fully functional tree breeding programme. At national level, these include; (1) enhanced capacity in terms of necessary resources, human capital, and technical expertise, (2) enabling policies and instruments such as the formation of a national forestry research institute, (3) enhanced awareness of the importance of trees that has also led to (4) the diversification of users, including the private sector. Enablers at a wider scale include (1) the enhanced appreciation of trees for non-commodity values such as climate change adaptation, (2) technological developments to enhance data collection and management, such as phenotyping tools and next-generation sequencing, and (3) enhanced tree genetic and genomic resources such as published tree genomes. However, there is a need to design and implement sustainable tree breeding programs that ensure genetic progress. The lack of a national tree breeding strategy and financial resources remains a key constraint. Significant sustained investment, especially from public funds for the tree breeding programme, is paramount, given the very long nature of the activities.

Climate change intensifies abiotic stresses heat, drought, and flooding jeopardizing global food security by disrupting crop physiology and causing substantial yield losses. While conventional breeding has developed resilient varieties like submergence-tolerant "Scuba" rice and drought-tolerant maize, its slow pace and limited genetic diversity are inadequate for rapidly changing climates. This review synthesizes advances in breeding for climate resilience, highlighting the integration of traditional methods with modern tools. Genomic selection accelerates genetic gain for complex traits, CRISPR enables precise editing of genes for root architecture and stomatal regulation, and speed breeding shortens generation cycles. High-throughput phenomics and artificial intelligence further enhance predictive breeding. However, critical gaps persist, including a lack of multi-stress field validation, underutilized crop wild relatives, and trade-offs between stress tolerance and yield. Future efforts must prioritize integrative strategies that combine genomics, phenomics, and participatory approaches to develop resilient crops capable of sustaining productivity under compound climatic stresses, ensuring food security in the 21st century.

Teak (Tectona grandis L.) is a valuable tropical timber species known for its durability, strength, and economic significance. Clonal seed orchards (CSOs) are crucial for improving genetic gain and seed quality. However, phenological variation among clones influences synchronization and productivity. This study evaluated vegetative phenophases and genetic parameters among teak clones in a 45-year-old CSO at Karka, Karnataka. Fifteen teak clones representing northern, central, and southern provenances were assessed for leaf shedding initiation, leafless period, and leaf flushing traits through fortnightly observations from May 2024 to April 2025. Results revealed significant clonal differences across all vegetative phenophases. Northern clones exhibited delayed leaf shedding and prolonged dormancy, whereas southern and central clones showed earlier leaf flushing and shorter leafless periods, reflecting adaptation to local climatic conditions. Genetic analysis indicated high heritability and genetic gain for leaf flushing initiation (78.04%, 52.66%) and duration (73.23%, 27.16%), suggesting strong genetic control. Schematic phenograms illustrated temporal variation among clones, confirming distinct growth rhythms and genotype-specific responses to environmental cues. Vegetative phenology in teak is predominantly genotype-governed with moderate environmental influence. Traits such as leaf flushing initiation and duration are reliable for selecting superior clones with synchronized growth and enhanced adaptability, supporting effective teak improvement and sustainable orchard management.

Cinnamomum zeylanicum Blume is an economically important tree spice valued for its bark, leaves and increasingly for its fruits. The present study was undertaken to assess genetic variability, heritability and inter-relationships among fruit and seed traits in half-sib progenies of C. zeylanicum under humid tropical conditions of the Western Ghats, India. Six-year-old half-sib progenies representing five seed sources were evaluated during 2023-2025 in a randomized complete block design. Genetic parameters including genotypic and phenotypic coefficients of variation, heritability and genetic advance were estimated, along with genotypic and phenotypic correlations among traits. Substantial variability was observed for most fruit and seed characters. Fruit traits such as mature fruit length (84.58%), fruit width (60.26%) and test weight (69.92%) exhibited high heritability coupled with moderate genetic gain, indicating predominance of additive gene action and suitability for direct selection. Seed length (81.33%) and seed dry weight (73.72%) recorded high heritability and moderate genetic gain, suggesting strong genetic control and potential for improving seed quality and vigour. Traits related to fruit number and fruit set showed greater environmental influence and lower selection efficiency. Correlation analysis revealed strong positive associations among size and weight-related fruit traits, as well as among seed morphological traits, indicating that selection for one trait could lead to simultaneous improvement of related characters. The study identifies key selection traits for cinnamon improvement and provides valuable insights for breeding, conservation and sustainable cultivation of C. zeylanicum.

Wheat ranks third among cereal crops in terms of global production, and its demand is expected to increase as the human population grows. Plant breeding can increase crop production without burdening natural resources, and one way to accelerate genetic gain is through shortening breeding cycles with speed breeding (SB). Speed breeding protocols for winter wheat have been adapted by adding a vernalization phase to existing spring wheat protocols. Although a protocol for the vernalization phase was previously developed, it was not tested for genotypes grown in the Midwest US, which may have higher vernalization requirements. The transition from vegetative to reproductive stages in winter wheat depends mainly on photoperiod, vernalization temperature, and vernalization length, which determines the time needed to reach flowering. Optimizing vernalization under SB in a greenhouse setting is important for applications in breeding programs. Our objectives were to develop a speed breeding protocol for winter wheat that meets the vernalization requirements of all genotypes and to evaluate the interaction between vernalization temperature and sowing depth. A significant reduction in the time to flowering via speed breeding was achieved. Compared with normal vernalization, high-throughput vernalization adds on average ten days to the time to harvest. A shallow planting depth results in maturity five days earlier than a deep planting depth. A combination of speed breeding, shallow planting, and high-throughput vernalization will shorten the breeding cycle by 22 days per generation or 44 days per year compared to normal greenhouse conditions. This system is suitable for genotypes with high vernalization requirements and can be combined with high-throughput systems.

Genetic selection against methane emissions is one of the levers to reduce the environmental impact of dairy production. Once genetic evaluation of methane emissions is available, the next step is to include this trait in breeding objectives. In this study, we investigated the consequences of three selection scenarios on methane emission and traits currently under selection for the Montbéliarde dairy cattle breed. We estimated the expected genetic progress based on genetic (co)variances between traits currently under selection and two methane traits predicted from milk mid-infrared spectra. The first scenario, representing the current total merit index, revealed the necessity of incorporating a methane trait to reduce methane emissions. The second scenario demonstrated the feasibility of achieving -1% annual methane emissions, but at the expense of a reduced genetic progress on the other selected traits, in particular milk production and fertility, which reached only 66 and 65%, respectively, of the progress achieved in the first scenario. The third scenario, maintaining 90% of the current genetic gain on existing traits while incorporating methane traits, achieved approximately -0.38% annual methane emissions. These preliminary results illustrate the feasibility of genetically reducing methane emissions through including methane traits into breeding objectives.

The nature of gene action and the number of genes controlling the traits are the vital criteria for the selection of traits. The present study is to analyze the range of variations within the population and as well as the skewness and kurtosis in backcross and selfed sweet corn populations USC1-2-3-1× UMI1230β+ and SC1107×UMI1230β+. In the BC2 F2 population of SC1107×UMI1230β+, most of the traits showed positive skewness and platykurtic distribution which indicated that complementary gene action played a role and more number of genes is controlling the traits. In USC1-2 3-1× UMI1230β+, single plant yield recorded positive skewness. In some traits such as, the number of tassel branches, cob girth, and leaf breadth showed negative skewness and platykurtic distribution was also observed in both the cross combination which indicated prevalence of duplicate gene action. In order to fix an individual trait and for rapid genetic gain, duplicate gene action is required.

The study investigates provenance-based variation in fruit characters of teak (Tectona grandis L. f.) collected from eleven provenances across the Western Ghats of Kerala and Karnataka. Significant variability was observed among provenances for fruit traits, including fruit length, width, thickness, number of locules per fruit and number of seeds per fruit. Fruit length ranged from 11.8 mm (Naragakkanam) to 14.5 mm (Kokilbana), while fruit width and thickness varied between 12.6 to 16.3 mm and 11.3 to 13.7 mm, respectively. The highest number of locules per fruit (3.8) was recorded in Nayarupara and the highest number of seeds per fruit (2.8) in Madanaru. The number of locules per fruit exhibited the highest genotypic (34.0%) and phenotypic (31.44%) coefficients of variation, high heritability (70.48%) and the greatest genetic gain (45.43%), indicating strong additive genetic control. Significant positive correlations were recorded among fruit length, width and thickness (r = 0.88-0.89), while the number of seeds per fruit was positively associated with locule number (r = 0.68). Provenances such as Kokilbana, Nayarupara and Madanaru demonstrated superior performance for different fruit traits, suggesting their potential as promising seed sources. The observed genetic diversity among provenances highlights ample scope for selection and improvement in teak breeding programs.

Genetic diversity is the cornerstone of crop improvement, as the identification and effective utilization of variation within germplasm determine the success of breeding programs. Indian mustard (Brassica juncea L.), a major oilseed crop of India, possesses a relatively narrow genetic base, highlighting the need for systematic molecular diversity analysis. In the present investigation, 40 promising breeding lines developed through the pedigree method at BAU, Sabour, along with four check varieties, were evaluated for genetic diversity using simple sequence repeat (SSR) markers. Out of 22 SSR markers screened, six markers (gi258659503gbGT070143.1, BRMS-018F, gi407345453gbJK615950.1, cnu_m612aF, cnu_m606aF and PBCESSRJU9) were polymorphic and used for diversity analysis. Cluster analysis based on SSR polymorphism grouped the genotypes into distinct clusters, revealing substantial molecular variability and heterogeneous divergence within clusters. Based on dendrogram topology and branch length, genotypes R.Suflam, BRBJ55, BRBJ45, BRBJ42 and BRBJ46 from Cluster I and BRBJ02, BRBJ03, BRBJ07, BRBJ101, BRBJ106 and BRBJ53 from Cluster II were identified as genetically most divergent. Inter-cluster crosses such as R × BRBJ02, BRBJ55 × BRBJ03, BRBJ45 × BRBJ07, BRBJ42 × BRBJ101 and BRBJ46 × BRBJ106 were suggested to exploit maximum genetic diversity. The identified diverse genotypes and proposed crosses provide a strong molecular basis for parent selection and can be effectively utilized for broadening the genetic base and enhancing genetic gain in Indian mustard breeding programs.

Enhancing faba bean breeding efficiency through insect pollination and smart crossing schemes

The implementation of genomics‐assisted breeding methodologies is helping to drive the genetic gain required to meet the grand challenge of producing more food using fewer resources in the face of a changing climate. Despite the documented usefulness of genomics‐assisted breeding toward this end, its full infusion into most small‐ and medium‐sized breeding programs is still incomplete. One major reason for limited routine application of genomic selection among most such programs is the lack of a single integrated software tool capable of assisting breeders throughout the entire genomic prediction pipeline. To help address this need, we have implemented a streamlined genomic prediction and selection pipeline designed for plant breeding programs using open‐source tools. The steps implemented in the pipeline include processing genotypic data (e.g., filtering and imputing genotypic data), merging genotypic and phenotypic data, collecting enviromics covariates, estimating environmental kinship, optimizing training sets, cross‐validating genomic prediction models, and implementing genomic prediction for single or multiple traits across single or multiple environments. Herein, we describe an R Shiny web application named “GS4PB” (Genomic Selection For Plant Breeding) that implements the above steps in the pipeline and discuss the rationale for each of the tools in the pipeline. We used this GS4PB application to conduct an experiment comparing phenotypic and genomic selection, and showed genomic selection worked as well as phenotypic selection for advancement of breeding lines. This publicly available analysis tool will help to lower entry barriers into advanced techniques of genomic prediction, enabling breeders to take advantage of these technologies to help drive genetic gain.

Bitter gourd is an important cucurbitaceous crop grown in the summer and rainy seasons. However, its improvement requires genotypes with high yield and stability across the seasons. We evaluated 22 (gynoecious and monoecious) lines across four environments (spring–summer and rainy seasons over 2 years) for number of fruits per plant (NFP), fruit length (FL), fruit circumference (FC), fruit weight (FW), and yield per plant (YP), with the goal of determining the genotype-by-environment interaction (GEI) for yield and yield-contributing traits. Analysis of variance indicated a highly significant variation among the genotypes, environments, and GEI for all the traits under study. The environmental influence on yield accounted for 70.38% of the total variation. The presence of a strong environmental effect on complex traits such as yield indicates a substantial difference among different growing seasons. AMMI, WAASBY/ASV, and YSI all identified broadly stable genotypes; G3, G5, and G8 (notably high NFP), with G8 and G7 combining stability and high YP. Best performers included G16, G19, and G7 for FL; G9, G2, and G11 for FC; and G13, G16, and G21 for FW, with G12 expressing the most FW. GGE biplots identified two mega-environments; E2 and E3, which were the most discriminative for NFP and YP, respectively, with environment-specific “winners” allowing for targeted deployment. BLUPs and BLUEs were consistent across environments, with G20, G8, and G7 consistently leading in YP. The high-yield group (BLUP ≥ 1.79 kg: G14, G20, G9, G5, G6, G4, G8, G7) outperformed the grand mean. These findings support a need for a dual breeding strategy to advance broadly adapted, high-YP lines (G20, G8, G7, and G3, G5) for wide release and hybrid production, while exploiting specific adaptation for market-defining traits (FC and FW) using E2/E3 as primary selection sites. Integrating stability indices with BLUPs accelerates genetic gain and makes gynoecious lines more suitable for hybrid seed production.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-29704-w.

SummaryTracking parental genome contributions in segregating populations is crucial for accelerating genetic gain in plant breeding. We introduce GCCVision (Genome Contribution Calculator and Visualizer), an integrated bioinformatics toolkit to simplify this process. GCCVision uses an efficient Python-based backend and a user-friendly web-based frontend to analyze Variant Call Format (VCF) files from biparental crosses. The software identifies informative single-nucleotide polymorphisms (SNPs), calculates parental contribution rates, and generates clear, customizable graphical genotype maps where chromosome segments are color-coded by parental origin. By providing clear visualizations of genomic composition, GCCVision assists breeders in selection decisions for backcrossing, F2 analysis, quality control of hybrid seeds, and other breeding programs. This streamlined workflow shortens breeding cycles and accelerates the development of improved crop varieties.

BackgroundHundred-seed weight (HSW) is a critical yield component in soybean that directly influences productivity and seed quality. Despite its agronomic importance, the genetic architecture underlying natural variation in seed weight remains incompletely understood.MethodsWe conducted a comprehensive genome-wide association study (GWAS) using 554 globally diverse soybean accessions, comprising 453 Chinese varieties (81.8%) and 101 international accessions (18.2%) from 15 countries. Accessions were evaluated across three consecutive years (2022-2024) and genotyped with 78,050 high-quality single-nucleotide polymorphisms (SNPs).ResultsMixed linear model (MLM) analysis revealed a major QTL on Chr.20 that consistently explained the largest proportion of phenotypic variation across all environments. This QTL demonstrated exceptional temporal stability, maintaining genome-wide significance with peak -log10(P) values of 13.4, 12.1, and 10.2 across the three evaluation years. Fine mapping narrowed the critical interval to 493.69 kb containing 25 annotated genes. The lead SNP within Glyma.20G223200 explained 8-12% of phenotypic variance, while multi-SNP models incorporating five high-priority candidates cumulatively explained 14-18% of variance. Expression analysis of candidate genes revealed differential patterns between large-seeded and small-seeded varieties during seed development, with up to 32-fold expression differences.ConclusionsThe environmentally stable Chr. 20 QTL provides immediate opportunities for marker-assisted selection (MAS) in soybean breeding programs. Genomic prediction modeling suggests 35% greater genetic gain compared to phenotypic selection alone, supporting broad applicability for global soybean improvement programs.

The present study was conducted at Department of Tree improvement and Forest Genetics Resources, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan, Himchal Pradesh. A study investigating the stability of leaf traits in Populus deltoides clones was conducted across three locations: Nauni-Solan (HP), RHR&TS center Dhaula Kuan, Sirmaur (HP), and Laddhowal farm, PAU, Ludhiana. Analysis of variance revealed significant clone x site interaction for leaf blade length, midrib length, distance between petiole junction and leaf base, and total leaf length. Utilizing the Eberhart and Russell (1966) model, clone L-621/84 was identified as exhibiting the highest stability for leaf blade length and midrib length. Conversely, clone G-48 demonstrated the greatest stability for the distance between the petiole junction and the leaf base. Both clones L- 621/84 and G-48 displayed stable performance for total leaf length. Broad-sense heritability estimates were substantial, with leaf blade length (83.03) exhibiting the highest value, followed by total leaf length (78.29) and midrib length (77.85). Expected genetic gain, expressed as a percentage of the population mean, ranged from 16.42 to 26.68 percent across the evaluated traits. Moderate heritability estimates for most traits suggest the potential benefits of clonal propagation in poplar. The combination of heritability and genetic gain provides a valuable indicator of the potential for trait improvement through breeding programs.

The genetic potential of black gram genotypes which were introduced from Bhava Atomic Research Centre (BARC) along with national check PU-31 and VBN-11 and local check were evaluated to find out 14 genotypes of their quantitative characters for future crop improvement programme. The current investigation was carried out in a Complete Randomized Block Design (CRBD) in the University Research Farm of Uttar Banga Krishi Viswavidyalaya. Fourteen black gram genotypes including local and national checks were sown on Pre- Kharif (March) 2023 at Research Farm, Uttar Banga Krishi Viswavidyalaya, Pundibari. The data were recorded for 9 morphological characters and biometrical analysis was done to estimate Analysis of Variance (ANOVA) along with Genotypic and Phenotypic Co-efficient of Variation, heritability in broad sense, genetic advance. From the ANOVA, all the genotypes were found significant in the investigation for all the quantitative characters. High GCV were observed for Peduncle length (41.38) followed by no. of primary branches (37.17), Yield (28.94), Number of seeds (25.85), No. of leaves (20.02) and No. of pods (20.92). Highest heritability was found in peduncle length (93.21%) followed by number of seeds (91.03%), number of primary branches (89.49%), Numbers of pods (87.22%), yield (86.41%), Number of secondary branches (72.54%), Pod length (71.80%), Number of leaves (70.36%) and Plant height (67.11%). High-genetic advance as percent of mean was higher for Peduncle length (82.61%) followed by number of primary branches (72.44%), yield (55.41%), number of seeds (50.81%), Numbers of pods (40.25%), Number of leaves (34.60%), Number of secondary branches (34.30%), Plant height (24.74%) and Pod length (23.95%). So the characters which were found to have high GCV, heritability and Genetic gain can be utilized for future crop improvement programme because of the presence of additive genetic effects with less environmental interactions and higher stability of heritable characters in future generations.