Search Results (1,301)

The Xinjiang Brown cattle (XJBC) is one of China’s five major dual-purpose dairy and beef breeds. Analyzing the genetic diversity of the Xinjiang Brown cattle population lays the theoretical groundwork for identifying and conserving its genetic resources. This study employed the Illumina Bovine SNP 150K chip to analyze genetic diversity, inbreeding coefficient, kinship, and genetic distance in a population of 750 Xinjiang Brown cattle from three breeding farms in Xinjiang. Genetic diversity was assessed by calculating minimum allele frequency (MAF), observed heterozygosity (Ho), expected heterozygosity (He), polymorphic information content (PIC), and linkage disequilibrium (LD). Population structure was analyzed using PCA. ROH was calculated to derive ROH-based inbreeding coefficients, pedigree-based inbreeding coefficients (F_PED) were estimated using CFC software for comparison, and candidate genes within high-frequency ROH regions in Xinjiang Brown cattle were identified. A G matrix was constructed to analyze population kinship. Results revealed 94,173 high-quality SNP loci in Xinjiang Brown cattle, with an average MAF of 0.276, PIC of 0.376, Ho of 0.345, and He of 0.376. Breeding farm 3 exhibited the fastest LD decay, indicating relatively high genetic diversity across Xinjiang Brown cattle populations, with farm 3 demonstrating greater diversity. The IBS genetic distance was 0.313. The G matrix results aligned with the IBS distance matrix, both indicating close kinship among some individuals within the Xinjiang Brown cattle population. The ranges for average F_PED and average F_ROH across farms were 0.0017–0.0189 and 0.0609–0.0878, respectively. Short ROH segments (0.5–2 Mb) constituted the largest proportion (51.31%) of all ROHs. Within high-frequency ROH enrichment regions, 61 genes, including LCORL, FAM110B, NR4A1, and PER2, were identified as potentially associated with economic traits in Xinjiang Brown cattle. These findings provide relevant marker sites for genomic selection in Xinjiang Brown cattle and lay a theoretical foundation for subsequent research. Full article

Sweet corn is widely cultivated and valued for its palatability and nutritional quality, with kernels accumulating substantial carotenoids, which serve as essential antioxidants and vitamin A precursors. This study elucidated the genetic basis of carotenoid variation in sweet corn kernels by integrating quantitative trait loci (QTL) mapping with a candidate region association study. Seven carotenoid-related traits were quantified in a recombinant inbred line (RIL) population and its parental lines. QTL mapping based on a high-density genotyping-by-target sequencing (GBTS) map and BLUE values across two environments identified 15 loci on chromosomes 5, 6, 7, 8, and 9, explaining 3.83–17.25% of the phenotypic variance. Notably, chromosome 6 harbored a cluster of major-effect QTLs regulating β-cryptoxanthin, zeaxanthin, lutein, total carotenoids, and provitamin A contents. A regional association study within these linkage-defined intervals detected 71 significant SNPs (Bonferroni p < 1/n) and identified Zm00001d036238, encoding a GDSL esterase/lipase, as a strong candidate gene associated with β-cryptoxanthin accumulation. This gene exhibited kernel-specific expression in the endosperm and harbored a downstream cis-variant (Chr6: 78,466,427) correlated with increased carotenoid content. Allelic effect analysis indicated that the A/A genotype conferred markedly higher β-cryptoxanthin levels than other genotypes. Collectively, these findings provide valuable genetic resources for marker-assisted selection and biofortification breeding to enhance the nutritional quality of sweet corn. Full article

Soybean (Glycine max (L.) Merr.), as a crucial source of oil and protein globally, is widely cultivated in many countries. Low-temperature stress has become one of the major environmental factors affecting soybean production, especially in colder regions, making the improvement of cold tolerance traits in soybean a key breeding objective. This study integrates Genome-Wide Association Studies (GWAS) and Marker-Assisted Selection (MAS) to enhance the predictive performance of soybean cold tolerance traits. First, three GWAS methods—Fast3VmrMLM, fastGWA, and FarmCPU—were used to analyze soybean cold tolerance traits, and significant SNP markers were identified. Principal Component Analysis (PCA) was employed to reveal genetic differences among various soybean germplasm. Then, based on the identified SNP markers, multiple Genomic Selection (GS) models, such as GBLUP, BayesA, BayesB, BayesC, BL, and BRR, were used for prediction to evaluate the contribution of genetic effects to phenotypic variation. The results showed that the markers selected through GWAS significantly improved the prediction accuracy of genomic selection, especially with the Fast3VmrMLM and FarmCPU methods in larger datasets. Finally, Gene Ontology (GO) analysis was performed to further identify candidate genes associated with cold tolerance traits and their biological functions, providing theoretical support for molecular breeding of cold-tolerant soybean varieties. Full article

Reproductive traits are essential in dairy cattle breeding, and improving body conformation is considered beneficial for reproductive performance. This study systematically analyzed the genetic relationships between six key conformation traits—stature (ST), body depth (BD), loin strength (LS), rump angle (RA), rump width (RW), bone quality (BQ)—and reproductive performance in 1631 Jersey cattle from China. Heritability estimates for conformation traits ranged from 0.05 to 0.62. We identified significant phenotypic and genetic correlations between conformation and reproductive traits, and regression analyses confirmed the predictive value of conformation traits for reproductive outcomes. Genome-wide association studies detected 24 significant SNPs associated with ST, RW, RA, and BQ. Subsequent bioinformatics analysis revealed seven candidate genes (AZIN1, OR2H1, HS6ST3, ERCC4, KCNH5, KRT19, KRT35) involved in embryonic development and estrous cycle regulation. Notably, incorporating six SNPs, which are linked to these candidate genes, into genomic prediction models significantly improved the accuracy for predicting Age at First Calving (AFC) and Gestation Length (GL). These results elucidate the shared genetic basis of conformation and reproduction, providing theoretical support for using conformation traits in marker-assisted selection to enhance reproductive efficiency in Jersey cattle. Full article

Climate change in the Pannonian region is accelerating a shift toward autumn sowing of cool-season grain legumes (pea, faba bean, lentil, chickpea, lupine) to achieve higher yields, greater biomass production, enhanced nitrogen fixation, improved soil cover, and superior resource use efficiency compared with spring sowing. However, successful overwintering depends on the availability of robust winter-hardy cultivars. This review synthesizes recent breeding advances, integrating traditional approaches—such as germplasm screening, hybridization, and field-based selection—with genomics-assisted strategies, including genome-wide association studies (GWAS), quantitative trait locus (QTL) mapping, marker-assisted selection (MAS), and CRISPR/Cas-mediated editing of CBF transcription factors. Key physiological mechanisms—LT₅₀ determination, cold acclimation, osmoprotectant accumulation (sugars, proline), and membrane stability—are assessed using field survival rates, electrolyte leakage assays, and chlorophyll fluorescence measurements. Despite challenges posed by genotype × environment interactions, variable winter severity, and polygenic trait control, the release of cultivars worldwide (e.g., ‘NS-Mraz’, ‘Lavinia F’, ‘Ghab series’, ‘Pinklevi’, and ‘Rézi’) and ongoing breeding programs demonstrate substantial progress. Future breeding efforts will increasingly rely on genomic selection (GS), high-throughput phenomics, pangenomics, and G×E modeling to accelerate the development of climate-resilient legume cultivars, ensuring stable and sustainable production under increasingly unpredictable winter conditions. Full article

Ancient wheat cultivars play a crucial role in human and animal nutrition and health, serving as rich sources of bioactive compounds, essential nutrients, and functional metabolites. This study investigated Triticum turgidum subsp. durum (cv. Saragolla), an ancient wheat variety from the Campania region of Southern Italy, to comprehensively characterize its morphological, functional, and nutritional attributes in support of germplasm conservation and valorization. Standard AOAC methods, including HPLC profiling, antioxidant assays, and quantification of total polyphenols and flavonoids, were applied to characterize the grain’s composition. The results revealed a balanced distribution of proteins, lipids, dietary fibers, and carbohydrates, that defines the nutritional and functional quality of Saragolla grains. Microscopic investigation through SEM coupled with EDX analysis provided high-resolution visualization of caryopsis morphology, ultrastructure, and mineral distribution, confirming its distinct varietal characteristics. Additionally, SSR marker analysis revealed notable genetic diversity within the Saragolla germplasm, identifying loci associated with key agronomic traits, including kernel weight, grain number, and stress tolerance parameters essential for future breeding programs. Overall, this integrated assessment highlights Saragolla as a valuable heritage wheat and a strategic genetic resource for breeding durum cultivars with enhanced nutritional quality, technological performance, and resilience to environmental stress. Full article

Nitrogen (N) is essential for maize (Zea mays L.) productivity, yet its acquisition is limited by the low N uptake efficiency of current varieties. Root cortical aerenchyma (RCA) formation provides a carbon-saving strategy that enhances soil exploration and N acquisition by reducing the metabolic cost of root tissue. However, the genetic basis of RCA formation remains poorly characterized. This study employed an association panel of 295 maize inbred lines to dissect the genetic architecture of RCA formation under low nitrogen (LN) stress. Phenotypic analysis demonstrated that LN stress significantly induced RCA area (RCAA) and proportion (RCAP), with responses ranging from −0.31 to 1.16 mm² for RCAA and −11.34% to 40.18% for RCAP. The non-stiff stalk (NSS) subpopulation exhibited 29.19% higher RCAA under LN than the stiff stalk subgroup. Genome-wide association analysis detected a total of 560 significant SNPs and 810 candidate genes associated with RCA-related traits. Transcriptomic profiling further identified 537 differentially expressed genes between inbred lines with contrasting RCA phenotypes. Integrated GWAS and transcriptomic analysis pinpointed 12 co-localized candidates, subsequently refined to four core genes (GRMZM2G033570, GRMZM2G052422, GRMZM2G080603, and GRMZM2G472266), which were implicated in ethylene signaling and stress-responsive root development. Favorable haplotypes of three genes were predominantly distributed in the NSS (25.64–56.00%) and tropical/subtropical (20.51–46.67%) subpopulations. These findings elucidate the genetic basis of LN-responsive RCA formation and provide fundamental resources for marker-assisted breeding of N-efficient maize. Full article

Salinity stress is a major abiotic constraint limiting soybean (Glycine max L.) productivity in saline–alkali soils; however, the physiological and biochemical mechanisms underlying genotypic tolerance remain poorly understood. This study aimed to identify key traits that underpin salinity tolerance and can inform breeding and agronomic strategies to enhance soybean performance under saline conditions. Two contrasting soybean genotypes, YAKARTA and POCA, were exposed to 25, 50, 75, and 100 mM NaCl from the first to the fourth trifoliate stage (V1–V4) under controlled conditions for 30 days. YAKARTA maintained higher relative water content (75.51% vs. 66.97%), stomatal conductance (342 vs. 286 mmol H₂O m⁻² s⁻¹), proline (6.15 vs. 4.36 µmol g⁻¹ fresh weight), K⁺/Na⁺ ratio (61.8 vs. 32.2), and H₂O₂ (833.8 vs. 720.2 µmol g⁻¹ fresh weight) compared with POCA, whereas POCA exhibited elevated solute leakage (87.1% vs. 79.21%), malondialdehyde (122 vs. 112 µg g⁻¹), and ascorbic acid (334 vs. 293 µg g⁻¹), indicating greater sensitivity. At 100 mM NaCl, relative water content, stomatal conductance, K⁺/Na⁺ ratio, and H₂O₂ declined by 44.5%, 81.9%, 99.8%, and 49.5%, respectively, while proline, solute leakage, malondialdehyde, and ascorbic acid increased by 56-, 1.27-, 11.6-, and 1.68-fold, respectively. The contrasting physiological and biochemical responses between these genotypes highlight key traits, such as relative water content, stomatal conductance, proline accumulation, malondialdehyde content, and the K⁺/Na⁺ ratio, as promising potential markers associated with salinity tolerance in soybean. These findings provide a foundational understanding that can guide future research to validate these markers across a wider genetic pool and under field conditions. Full article

Background/Objectives: Understanding the genetic basis of growth and fat deposition is crucial for improving beef productivity in Kalmyk cattle, a breed well adapted to the extreme climatic conditions of Kazakhstan. The present study aimed to determine the effects of single-nucleotide polymorphisms (SNPs) in the CRTC2 and ELOVL6 genes on intramuscular fat content and to evaluate their associations with growth and meat quality traits in 18-month-old Kalmyk heifers raised under different environmental conditions. Methods: A total of 400 clinically healthy Kalmyk heifers (200 from LLP “Qazaq Asyldary” and 200 from LLP “Agrofirma Turikpen”) were examined. All animals originated from closed breeding herds, and only unrelated individuals without common ancestors to the third generation were included. Zootechnical measurements— live weight, withers height, chest depth, chest girth, and body length—were performed twice by a trained specialist. Backfat thickness and musculus longissimus dorsi depth were measured postmortem. Blood samples were collected for genomic DNA extraction using the GeneJET purification kit, and DNA quality was assessed by Nanodrop, Qubit, and agarose gel electrophoresis. Target fragments of CRTC2 and ELOVL6 were amplified (150–200 bp) and sequenced on an ABI 3500 system. SNP identification, allele frequencies, and genotyping were performed by alignment to the Bos taurus ARS-UCD1.2 reference genome. Statistical analyses were conducted in RStudio using linear and mixed models with “farm” as a random effect. Results: Only one informative polymorphism, g.133528A>G in ELOVL6, was detected. Three genotypes (AA, AG, GG) were observed, with the heterozygous AG genotype showing significantly higher live weight, greater body length, and improved linear measurements compared to AA and GG. No significant associations were detected with backfat thickness or muscle depth. The g.133528A>G polymorphism in ELOVL6 positively influences growth traits without increasing fatness, aligning with the naturally lean phenotype of Kalmyk cattle. Conclusions: The AG genotype may serve as a promising marker for selecting faster-growing animals in marker-assisted breeding programs. Full article

Egg quality is a critical economic trait in poultry production, influencing consumer preference and production efficiency. The genetic and epigenetic regulation of egg quality involves complex biological pathways across various traits such as shell quality, albumen composition, and yolk biochemistry. This review synthesizes recent advances in the genetic, molecular, and epigenetic mechanisms that determine poultry egg quality. Specifically, it focuses on external traits such as eggshell strength, color, and thickness, and internal traits including albumen height, yolk composition, and the Haugh unit. Through genome-wide association studies (GWAS), quantitative trait loci (QTL) mapping, whole-genome sequencing (WGS), and multi-omics approaches, key candidate genes such as OC-116, CALB1, CA2 (shell formation), OVAL, SPINK5, SERPINB14 (albumen quality), and FGF9, PIAS1, NOX5 (lipid metabolism) have been identified. These genes play a pivotal role in shell biomineralization, albumen protein regulation, and yolk lipid transport. This review also explores the heritability of these traits, emphasizing the challenges posed by polygenic architecture and the influence of environmental factors. Furthermore, it addresses the dynamic spatiotemporal regulation of egg quality traits, including epigenetic layers such as DNA methylation, histone modifications, RNA methylation, and post-translational protein modifications. This paper highlights the application of these findings to breeding programs via genomic selection, marker-assisted breeding, and epigenetic engineering approaches. Future directions for precision breeding and the development of functional eggs with enhanced quality are also discussed. Full article

Grain weight, a highly heritable yield component, is a primary breeding target for enhancing wheat productivity. Unraveling the molecular dynamics underlying grain development is essential for identifying key regulators controlling this trait. In this study, we employed an integrated multi-omics approach to analyze transcriptomic and proteomic profiles in developing grains using pairwise near-isogenic lines with contrasting grain weight across four grain developmental stages. Our analysis revealed that early grain development, particularly at 7 days post-anthesis, serves as a critical window during which differential regulation of genes and proteins involved in carbohydrate biosynthesis and metabolic pathways establishes the final grain weight. By combining weighted gene co-expression network analysis (WGCNA) and K-means clustering, we identified a grain weight-associated module and pinpointed four high-confidence candidate genes. Among these, TaYAK1-2D, which encodes a YAK family protein kinase, was functionally validated as a positive regulator of grain weight through mutational analysis. Sequence analysis revealed two major natural haplotypes of TaYAK1-2D, with TaYAK1-2D-Hap2 being significantly associated with higher grain weight across multiple environments. Our findings not only delineate a crucial metabolic window governing grain weight but also provide both a novel genetic target and a practical haplotype marker for molecular breeding aimed at yield improvement in wheat. Full article

This study aimed to investigate the relationship between GH, GHR, IGF-1R, VIP, and NPY genes and egg quality traits in laying hens. Atak-S laying hens aged 54 weeks were monitored for 6 weeks. Egg production and egg weight were recorded daily, while egg quality traits and feed consumption were assessed weekly. Genotyping was performed using PCR-RFLP. The GH, GHR, IGF-1R, VIP, and NPY genes were cut with MspI, HindIII, HinfI, HinfI, and DraI, respectively. The AA genotype of the GH gene was associated with increased egg shape index, eggshell weight, and eggshell thickness (p < 0.05). In the IGF-1R region, significant associations were found with egg weight and egg shape index (p < 0.05). Additionally, the VIP12 TT genotype was linked to higher egg production (p < 0.05). These findings suggest that the GH gene may serve as a selection marker for shell-related traits, IGF-1R for egg weight and egg shape, and VIP for improving egg production. Overall, the results obtained in this study indicate that the genes studied have the potential to be candidate markers for improving egg performance and quality; however, their use in marker-assisted selection requires further studies in larger and more diverse populations. Full article

In animals and humans, nutrients influence signaling cascades, transcriptional programs, chromatin dynamics, and mitochondrial function, collectively shaping traits related to growth, immunity, reproduction, and stress resilience. This review synthesizes evidence supporting nutrient-mediated regulation of DNA methylation, histone modifications, non-coding RNAs, and mitochondrial biogenesis, and emphasizes their integration within metabolic and developmental pathways. Recent advances in epigenome-wide association studies (EWAS), single-cell multi-omics, and systems biology approaches have revealed how diet composition and timing can reprogram gene networks, sometimes across generations. Particular attention is given to central metabolic regulators (e.g., PPARs, mTOR) and to interactions among methyl donors, fatty acids, vitamins, and trace elements that maintain genomic stability and metabolic homeostasis. Nutrigenetic evidence further shows how genetic polymorphisms (SNPs) in loci such as IGF-1, MSTN, PPARs, and FASN alter nutrient responsiveness and influence traits like feed efficiency, body composition, and egg quality, information that can be exploited via marker-assisted or genomic selection. Mitochondrial DNA integrity and oxidative capacity are key determinants of feed conversion and energy efficiency, while dietary antioxidants and mitochondria-targeted nutrients help preserve bioenergetic function. The gut microbiome acts as a co-regulator of host gene expression through metabolite-mediated epigenetic effects, linking diet, microbial metabolites (e.g., SCFAs), and host genomic responses via the gut–liver axis. Emerging tools such as whole-genome and transcriptome sequencing, EWAS, integrated multi-omics, and CRISPR-based functional studies are transforming the field and enabling DNA-informed precision nutrition. Integrating genetic, epigenetic, and molecular data will enable genotype-specific feeding strategies, maternal and early-life programming, and predictive models that enhance productivity, health, and sustainability in poultry production. Translating these molecular insights into practice offers pathways to enhance animal welfare, reduce environmental impact, and shift nutrition from empirical feeding toward mechanistically informed precision approaches. Full article

Cannabis sativa L. has been cultivated for millennia as a source of food and fibre. Increasing demand for functional foods has renewed interest in C. sativa seeds (hempseeds), which are rich in essential fatty acids and amino acids. However, a near-global moratorium on C. sativa cultivation and research throughout most of the 20th century has delayed crop improvement using modern breeding approaches. As a result, genetic loci contributing to key agronomic traits, including with respect to maximizing yield as a seed crop, remain largely unknown. In this study, a feminized segregating F₂ mapping population, derived from a tall parent with spacious inflorescences and large seeds and a short-stature parent with compact inflorescences and small seeds, was phenotyped for key seed and agronomic traits related to yield. A mid-density Single Nucleotide Polymorphism (SNP) genotyping panel was used to generate a genetic linkage map of 291.5 cM with 455 SNPs. Quantitative Trait Locus (QTL) mapping identified major loci for hundred-seed weight—qHSW3, 26.59 percent variance explained (PVE), seed volume—qSV1, 33.24 PVE, and plant height—qPH9, 46.99 PVE. Our results provide novel target regions, associated molecular markers, and candidate genes for future breeding efforts to improve C. sativa. Full article

Objective: Genetic and environmental factors influence the expression of personality pathology and subsequent treatment efforts. This study associates genetics with a contemporary nosology of personality pathology represented in the Alternative Model for Personality Disorders (AMPD). We hypothesized traits from Criterion B of the AMPD would differ between genotypes of the catechol-O-methyltransferase (COMT) polymorphism (rs4680/Val158Met variation), given this genetic marker’s role in the metabolism of dopamine and norepinephrine, especially in the prefrontal cortex. Methods: The Personality Inventory for DSM-V (PID-5) was used to quantify personality traits, and the Genomind platform was used to identify the genotypes of the Val158Met COMT polymorphism in 84 psychiatric outpatients. Results: One of the five Criterion B personality domains and three of the twenty-five traits were significantly different among genotypes. Met/Met carriers had significantly higher pathological scores on the broad domain of negative affect and specific traits of perceptual dysregulation and separation insecurity, while the Val/Val carriers had significantly higher scores on the restricted affectivity trait. The COMT Val158Met polymorphism’s association with personality pathology was sexually dimorphic, with the two domains and nine traits significantly different across genotypes in males, but no differences were found in females. A substantial improvement in the regression of domains/traits score when gene–sex interactions were included further confirmed the dimorphism, e.g., the R-squared (adjusted) for the psychoticism improved from 0.03 (p = 0.15) to 0.19 (p < 0.001). Conclusions: Findings offer preliminary support for a link, potentially dimorphic across sexes, between the COMT Val158Met polymorphism and personality pathology as represented by the AMPD. Full article