Search Results (2,409)

Plant architecture is a crucial agronomic trait significantly impacting soybean (Glycine max) yield. Traditional breeding has made some progress in optimizing soybean architecture, but it is limited in precision and efficiency. The Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated protein (CRISPR/Cas) system, a revolutionary gene-editing technology, provides unprecedented opportunities for plant genetic improvement. This review outlines CRISPR’s development and applications in crop improvement, focusing specifically on progress regulating soybean architecture traits affecting yield, such as node number, internode length, branching, and leaf morphology. It also discusses the technical challenges for CRISPR technology in enhancing soybean architecture, including that the regulatory network of soybean plant architecture is complex and the development of multi-omics platforms helps gene mining. The application of CRISPR enables precise the regulation of gene expression through promoter editing. Meanwhile, it is also faced with technical challenges such as the editing of homologous genes caused by genome polyploidy, the efficiency of editing tools and off-target effects, and low transformation efficiency. New delivery systems such as virus-induced genome editing bring hope for solving some of these problems. The review emphasizes the great potential of CRISPR technology in breeding next-generation soybean varieties with optimized architecture to boost yield potential. Full article

Prime editing (PE), a novel “search-and-replace” genome editing technology, demonstrates significant potential for crop genetic improvement due to its precision and versatility. However, since its initial application in plants, PE technology has consistently faced challenges of low and variable editing efficiency, representing a major bottleneck hindering its broader application. Therefore, this study conducted a systematic review following the PRISMA 2020 guidelines. We systematically searched databases—Web of Science, PubMed, and Google Scholar—for studies published up to June 2025 focusing on enhancing PE performance in crops. After a rigorous screening process, 38 eligible primary research articles were ultimately included for comprehensive analysis. Our analysis revealed that early PE systems such as PE2 could perform diverse edits, including all 12 base substitutions and small insertions or deletions (indels), but their efficiency was highly variable across species, targets, and edit types. To overcome this bottleneck, researchers developed four major optimization strategies: (1) engineering core components such as Cas9, reverse transcriptase (RT), and editor architecture; (2) enhancing expression and delivery via optimized promoters and vectors; (3) improving reaction processes by modulating DNA repair pathways or external conditions; and (4) enriching edited events through selectable or visual markers. These advancements broadened PE’s targeting scope with novel Cas9 variants and enabled complex, kilobase-scale DNA insertions and rearrangements. The application of PE technology in plants has evolved from basic functional validation, through systematic optimization for enhanced efficiency, to advanced stages of functional expansion. This review charts this trajectory and clarifies the key strategies driving these advancements. We posit that future breakthroughs will increasingly depend on synergistically integrating these strategies to enable the efficient, precise, and predictable application of PE technology across diverse crops and complex breeding objectives. This study provides an important theoretical framework and practical guidance for subsequent research and application in this field. Full article

Tomato is one of the most important vegetables due to its high production and nutritional value. With the development of digital agriculture, the tomato breeding and processing industries have seen a rapid increase in the need for simple, low-labor, and inexpensive methods for analyzing tomato composition. This study proposes a digital method to predict four minerals (calcium, potassium, phosphorus, and magnesium) in beef-type tomato using machine learning models, including k-nearest neighbors (kNN), artificial neural networks (ANNs), and Support Vector Regression (SVR). The models were discriminated using the coefficient of determination (R²), root mean square error (RMSE), mean absolute error (MAE), and mean absolute percentage error (MAPE). The kNN model showed the best performance for estimation of quantity of calcium, potassium, phosphorus, and magnesium. The results demonstrate that kNN consistently outperforms ANNs and SVR across all target nutrients, achieving the highest R² and the lowest error metrics (RMSE, MAE, and MAPE). Notably, kNN achieved an exceptional R² of 0.8723 and a remarkably low MAPE of 3.95% in predicting phosphorus. This study highlights how machine learning can provide a versatile, accurate, and efficient solution for tomato mineral analysis in digital agriculture. Full article

Spectral reflectance of plants can be readily associated with physiological and biochemical parameters. Thus, relating spectral data to amino acid contents in different genetic materials provides an innovative and efficient approach for understanding and managing genetic diversity. Therefore, this study had two objectives: (I) to differentiate genetic materials according to amino acid contents and spectral reflectance; (II) to establish the relationship between amino acids and spectral bands derived from hyperspectral data. The research was conducted with 32 soybean genetic materials grown in the field during the 2023–2024 crop year. The experimental design involved randomized blocks with four replicates. Leaf spectral data were collected 60 days after plant emergence, when the plants were in full bloom. Three leaf samples were collected from the third fully developed trifoliate leaf, counted from top to bottom, from each plot. The samples were taken to the laboratory, where reflectance readings were obtained using a spectroradiometer, which can measure the 350–2500 nm spectrum. Wavelengths were grouped as means of representative intervals and then organized into 28 bands. Subsequently, the leaf samples from each plot were subjected to quantification analyses for 17 amino acids. Then, the soybean genotypes were subjected to a PCA–K-means analysis to separate the genotypes according to their amino acid content and spectral behavior. A correlation network was constructed to investigate the relationships between the spectral variables and between the amino acids within each group. The groups formed by the different genetic materials exhibited distinct profiles in both amino acid composition and spectral behavior. Leaf reflectance data proved to be efficient in identifying differences between soybean genotypes regarding the amino acid content in the leaves. Leaf reflectance was effective in distinguishing soybean genotypes according to leaf amino acid content. Specific and high-magnitude associations were found between spectral bands and amino acids. Our findings reveal that spectral reflectance can serve as a reliable, non-destructive indicator of amino acid composition in soybean leaves, supporting advanced phenotyping and selection in breeding programs. Full article

The objective of this study was to characterize the sexual behavior and reproductive performance of Colombian Creole bulls from the Romosinuano (ROM) and Costeño con Cuernos (CCC) breeds, to support their strategic use in tropical production systems and sire selection programs. A standardized sexual behavior test, including nine behavioral indicators, was conducted over a 15 min observation period to assess libido and service capacity. Significant differences (p < 0.05) were found between the breeds in terms of the frequency of urination and mounting behaviors. ROM bulls exhibited a more uniform and rapid behavioral response, while CCC bulls showed greater individual variability and a broader behavioral repertoire, with courtship behaviors—such as smelling, the Flehmen reflex, and butting—strongly associated with ejaculation events. Libido scores were high in both breeds, with 80.35% of bulls rated as very good to excellent. CCC bulls also achieved mounts more frequently within the first five minutes of exposure. Additionally, bull age was inversely associated with mounting time (p < 0.05), suggesting that maturity and sexual experience influence behavioral efficiency. These findings represent the first quantitative assessment of sexual behavior in CCC bulls and provide comparative insights with ROM bulls, highlighting the functional reproductive potential of Colombian Creole bulls under low-input tropical conditions. Full article

The objective of this work was to analyse the genetic diversity of a population of Citrus spp. in the south of the State of Espírito Santo, Brazil, for pre-breeding studies. For that, a total of sixty genotypes were analysed, including ten citrus varieties from four species of the Citrus genus. The methodology involved DNA extraction, amplification via polymerase chain reaction, and the use of a set of 16 Simple Sequence Repeat markers. These markers identified 42 alleles, with a variation of one to four alleles per locus, an average heterozygosity value of 0.53, and an average polymorphic information content of up to 0.29 per species. After the analysis, a dissimilarity matrix was generated using Jaccard distance and a dendrogram, revealing the formation of two groups: Group I, comprising Citrus sinensis varieties, and Group II, comprising varieties of Citrus latifolia, Citrus aurantifolia, and Citrus reticulata. Our study demonstrated that the combination of these markers allowed for the differentiation of genotypes within the collection. The results obtained are valuable for the future management of the collection and the efficient use of genetic diversity estimation in Citrus spp. Full article

Background/Objectives: Loss and fragmentation of habitat from agricultural conversion led to the near extirpation of the pygmy rabbit (Brachylagus idahoensis Merriam, 1891) population in the Columbia Basin (CB) of Washington, USA. Recovery efforts began in 2002 and included captive breeding, translocations from other regions for genetic rescue, and reintroduction into native habitat in three sites: Sagebrush Flat (SBF), Beezley Hills (BH), and Chester Butte (CHB). Methods: We used noninvasive and invasive genetic sampling to evaluate demographic and population genetic parameters on three translocated populations of pygmy rabbits over eight years (2011–2020). For each population, our goal was to use fecal DNA sampling and 19 microsatellite loci to monitor spatial distribution, apparent survival rates, genetic diversity, reproduction, effective population size, and the persistence of CB ancestry. Over the course of this study, 1978 rabbits were reintroduced as part of a cooperative conservation effort between state and federal agencies. Results: Through winter and summer monitoring surveys, we detected 168 released rabbits and 420 wild-born rabbits in SBF, 13 released rabbits and 2 wild-born in BH, and 16 released rabbits in CHB. Observed heterozygosity (H_o) values ranged from 0.62–0.84 (SBF), 0.59–0.80 (BH), and 0.73–0.77 (CHB). Allelic richness (AR) ranged from 4.67–5.35 (SBF), 3.71–5.41 (BH), and 3.69–4.65 (CHB). Effective population (N_e) within SBF varied from 12.3 (2012) to 44.3 (2017). CB ancestry persisted in all three wild populations, ranging from 15 to 27%. CB ancestry persisted in 99% of wild-born juveniles identified in SBF. Apparent survival of juvenile rabbits differed across years (1–39%) and was positively associated with release date, release weight, and genetic diversity. Survival of adults (0–43%) was positively influenced by release day, with some evidence that genetic diversity also positively influenced adult apparent survival. Conclusions: Noninvasive genetic sampling has proven to be an effective and efficient tool in monitoring this reintroduced population, assessing both demographic and genetic factors. This data has helped managers address the goals of the Columbia Basin recovery program of establishing multiple sustainable wild populations within the sagebrush steppe habitat of Washington. Full article

Polyculture, or intercropping, is the practice of growing two or more crops simultaneously in time and space. The milpa is a systematic polyculture involving the simultaneous cultivation of maize (Zea mays), beans (Phaseolus spp.), squash (Cucurbita spp.), and other crops. Milpa polyculture initially emerged in the Mesoamerican region (Mexico and Central America) through the concurrent processes of managing, utilizing, and domesticating its constituent crops. It subsequently spread throughout the Americas via the diffusion of maize and the convergence of its domestication with that of its companion crops and other domesticated plants in the continent. Mesoamerican farmers made an outstanding contribution by domesticating and bringing together crops with contrasting morphological and physiological traits that are ecologically, agronomically, and nutritionally complementary. Despite its importance, few quantitative evaluations of this polyculture exist. However, these evaluations indicate that its productivity and land efficiency use (Land equivalent ratio = 1.34) are comparable to those of other intercrops studied on a global scale. We emphasize the importance of transdisciplinary efforts to study this polyculture and highlight its potential applications related to ecological interactions, plant microbiomes and breeding in order to reach sustainable production goals. Full article

Water-use efficiency (WUE) plays a crucial role in sustainable crop production, particularly in water-limited environments where maximizing natural resource use is essential. This study evaluated the physiological and agronomic performance of two Piper nigrum cultivars, Clonada and Uthirankotta, grown under different soil water potential conditions. The trial was conducted in a 1930 m² field using a randomized block design and drip irrigation system, calibrated to 3.55 L h⁻¹ with a uniformity of 97%. Soil water availability was managed based on daily tensiometer readings at 20 and 30 cm depths, triggering irrigation at defined tensions (10–55 kPa). Clonada exhibited higher net CO₂ assimilation rates (A) and stomatal conductance (g_s), but these responses did not lead to higher yields. In contrast, Uthirankotta consistently maintained superior water-use efficiency and yield across all soil moisture conditions by favoring water conservation and targeted biomass allocation over maximized gas exchange. Both cultivars performed optimally at a soil water potential range of 25–35 kPa, with declines in yield and gas exchange parameters at higher tensions (45–55 kPa). Under such conditions, Uthirankotta was 51.3% more water-use efficient and 40.8% more productive than Clonada. Based on this, a Principal Component Analysis (PCA) further demonstrated distinct physiological profiles, underscoring trade-offs between yield and water-use strategies. These results highlight the significance of cultivar selection for optimizing WUE and provide valuable insights into irrigation management and breeding programs aimed at boosting black pepper performance under water-limited conditions. Full article

Paeonia ostii is an economically significant species serving as an ornamental, medicinal herb, and woody oilseed crop. Gene function elucidation and molecular breeding are hindered by the lack of efficient, stable transformation methods due to tissue culture challenges. To enable year-round functional studies without material constraints, we established a novel transient transformation system mediated by Agrobacterium using in vitro embryo-derived seedlings (TTAES) in P. ostii. By optimizing embryo germination media, we achieved consistent seedling production. Orthogonal experiments with a GUS reporter identified optimal conditions: OD₆₀₀ = 1.0, 200 μM of acetosyringone, six negative-pressure treatments, and 2 h infection. Under this optimized system, maximum transformation efficiency was achieved at 35 days after germination. With this system, we demonstrated its application in investigating transcription factor-mediated regulation of target gene promoters using GUS as a reporter gene. To achieve non-destructive identification of transiently transformed plants, we employed GFP as a reporter gene. Using transient expression of VIGS (knockdown) and 35S constructs (overexpression), we characterized gene functions, thereby confirming the system’s effectiveness for functional analysis. This system facilitates the acquisition of plant experimental materials and significantly improves research efficiency for year-round gene function elucidation in P. ostii. Full article

Background: Genome-wide association studies (GWAS) have been extensively employed to elucidate the genetic architecture of body weight (BW) traits in chickens, which represent key economic indicators in broiler production. With the growing availability of genomic data from diverse commercial and resource chicken populations, a critical challenge lies in how to effectively integrate these datasets to enhance sample size and thereby improve the statistical power for detecting genetic variants associated with complex traits. Methods: In this study, we performed a multi-population GWAS meta-analysis on BW traits across three genetically distinct chicken populations, focusing on BW at 56, 70, and 84 days of age: P1 (N301 Yellow Plumage Dwarf Chicken Line; n = 426), P2 (F2 reciprocal cross: High Quality Line A × Huiyang Bearded chicken; n = 494), and P3 (F2 cross: Black-bone chicken × White Plymouth Rock; n = 223). Results: Compared to single-population GWAS, our meta-analysis identified 77 novel independent variants significantly associated with BW traits, while gene-based association analysis implicated 59 relevant candidate genes. Functional annotation of BW56- and BW84-associated SNPs (single-nucleotide polymorphisms) 1_170526144G>T and 1_170642110A>G, integrated with tissue-specific regulatory annotations, revealed significant enrichment of enhancer and promoter elements for KPNA3 and CAB39L in muscle, adipose, and intestinal tissues. Through this meta-analysis and integrative genomics approach, we identified novel candidate genes associated with body weight traits in chickens. Conclusions: These findings provide valuable mechanistic insights into the genetic mechanisms underlying body weight regulation in poultry and offer important references for selective breeding strategies aimed at improving production efficiency in the poultry industry. Full article

Light exposure during incubation can influence hatching characteristics, post-hatch growth, and physiological responses in poultry. This study aimed to evaluate the impact of pre-development exposure to different cold-colored light emitting diode (LED) lights on incubation characteristics, growth performance, stress physiology, and myogenic regulatory factors (MRFs) expression level in the slow-growing native Gerze chicken breed. Fertilized eggs were incubated under red, green, white, or dark conditions. The shortest hatch window was observed under red light (42 h), while the dark condition resulted in the longest (84 h) (p < 0.05). White light exposure reduced hatchability compared to the other groups (p < 0.05), whereas green and red lights enhanced both chick weight at hatch and egg-to-chick conversion efficiency (p < 0.001). Chicks incubated under green light exhibited superior body weight during the first four weeks (p < 0.05), but those from the red light group maintained consistently higher weights thereafter (p < 0.05). The highest serotonin levels were detected in chicks from the dark group, while the lowest were associated with green light exposure. Red light exposure was associated with the lowest corticosterone concentrations (p < 0.05). Gene expression analysis revealed no significant differences in MRFs across groups. In conclusion, the spectral level of light during incubation exerts measurable effects on hatch dynamics, post-hatch growth, and hormonal regulation in Gerze chicken. Full article

Dimensional stability is a key trait for structural wood applications such as flooring, yet its genetic basis in Eucalyptus pellita F.Muell. and its hybrids remain poorly understood. Addressing this gap is essential for improving processing efficiency and product quality through targeted breeding. This study assessed variation in shrinkage and density, their relationships with growth and chemical traits, and associated genetic markers. Wood samples from E. pellita, E. pellita × E. urophylla S.T.Blake, and E. pellita × E. brassiana S.T.Blake were collected from two plantation sites in northern Australia. Radial and tangential shrinkage and density were measured alongside growth and chemical traits. SNP genotyping was conducted to identify markers linked to these physical properties. Significant differences were observed among hybrid types. E. pellita × E. urophylla recorded the lowest tangential unit shrinkage (0.06%), while E. pellita × E. brassiana had the highest basic density (651 kg/m³). Shrinkage and density showed moderate to strong correlations with growth and chemical traits. Several SNPs were associated with these properties; all were located in the intergenic region near Eucgr.A00211. Among these, only one SNP exceeded the −log₁₀(p) significance threshold. These results provide early genetic insights and potential candidate markers for improving wood quality in Eucalyptus breeding programs. This exploratory study, constrained by a small sample size (n = 58), identifies putative SNPs for future validation in broader, multi-environment trials. Full article

Nitrogen (N) availability significantly influences plant metabolism and productivity. The aim of this study was to assess the effects of low N stress and subsequent N supplementation on key enzymes of nitrogen metabolism, nitrogen metabolism-related substances, and chlorophyll a fluorescence kinetic parameters in rice genotypes with different nitrogen utilization efficiencies. We used the Jijing 88 (low-N tolerant) and Xinong 999 (low-N sensitive) as test materials. During the seedling, tillering, and booting stages, the 1/2N and 1/4N treatments were restored to the 1N treatment level. Nine treatments were used in this experiment: CK (1N), A1 (1/2N), A2 (1/2N restored to 1N during the seedling stage), A3 (1/2N restored to 1N during the tillering stage), A4 (1/2N restored to 1N during the booting stage), B1 (1/4N), B2 (1/4N restored to 1N during the seedling stage), B3 (1/4N restored to 1N during the tillering stage), and B4 (1/4N restored to 1N during the booting stage). Key physiological responses, nitrogen compounds, enzymes activities, and chlorophyll a fluorescence kinetics were analyzed. Under low nitrogen conditions, the growth and nitrogen assimilation of rice were inhibited. Compared to XN 999, JJ 88 maintains higher levels of dry matter, nitrate reductase activity (NR), glutamine synthetase activity (GS), glutamate oxaloacetate transaminase activity (GOT), glutamate pyruvate transaminase activity (GPT), as well as nitrate (NO₃⁻) and ammonium (NH₄⁺) nitrogen contents. After N supplementation during the early growth stage, both JJ 88 and XN 999 exhibit recovery capabilities. However, in the late growth stage, JJ 88 demonstrates superior recovery capabilities. In addition to enhancing nitrogen metabolism levels, there is also an increase in the content of osmotic regulation substances such as soluble sugars, free amino acids, and proline, along with responses in chlorophyll fluorescence kinetic parameters. This was primarily manifested in the enhancement of performance index (PI_ABS, PI_total), and quantum yield (φ_EO, φ_RO, ψ_EO), which maintain photosynthetic performance and electron transport efficiency. The research findings indicated that reducing N supply during the early growth stage and restoring N levels in the later stage are beneficial for the recovery of low-nitrogen-tolerant rice varieties. Therefore, in the context of sustainable agricultural production, the breeding of low-nitrogen-tolerant rice varieties and the optimization of N fertilizer management are crucial. Full article

This review synthesizes advances in livestock genomics by examining the interplay between candidate genes, molecular markers (MMs), signatures of selection (SSs), and quantitative trait loci (QTLs) in shaping economically vital traits across livestock species. By integrating advances in genomics, bioinformatics, and precision breeding, the study elucidates genetic mechanisms underlying productivity, reproduction, meat quality, milk yield, fibre characteristics, disease resistance, and climate resilience traits pivotal to meeting the projected 70% surge in global animal product demand by 2050. A critical synthesis of 1455 peer-reviewed studies reveals that targeted genetic markers (e.g., SNPs, Indels) and QTL regions (e.g., IGF2 for muscle development, DGAT1 for milk composition) enable precise selection for superior phenotypes. SSs, identified through genome-wide scans and haplotype-based analyses, provide insights into domestication history, adaptive evolution, and breed-specific traits, such as heat tolerance in tropical cattle or parasite resistance in sheep. Functional candidate genes, including leptin (LEP) for feed efficiency and myostatin (MSTN) for double-muscling, are highlighted as drivers of genetic gain in breeding programs. The review underscores the transformative role of high-throughput sequencing, genome-wide association studies (GWASs), and CRISPR-based editing in accelerating trait discovery and validation. However, challenges persist, such as gene interactions, genotype–environment interactions, and ethical concerns over genetic diversity loss. By advocating for a multidisciplinary framework that merges genomic data with phenomics, metabolomics, and advanced biostatistics, this work serves as a guide for researchers, breeders, and policymakers. For example, incorporating DGAT1 markers into dairy cattle programs could elevate milk fat content by 15-20%, directly improving farm profitability. The current analysis underscores the need to harmonize high-yield breeding with ethical practices, such as conserving heat-tolerant cattle breeds, like Sahiwal. Full article