Search Results (462)

Soybean [Glycine max (L.) Merr.] is a commercially important oil and protein-producing crop. This study explored genetic variation in seed traits to improve soybean productivity. Phenotypic data, including seed size, length, width, thickness, and weight, were analyzed across 344 Korean soybean accessions, identifying 100-seed weight (100SW) as one of the important yield components in soybean. Using 4,472,823 high-density single-nucleotide polymorphism (SNP) markers, a genome-wide association study detected 10 novel loci associated with 100SW on chromosomes 3, 4, and 19. Haplotype analysis revealed that the accessions with alternative alleles at nine candidate loci displayed significant variation in 100SW, either increasing or decreasing weight. Allele stacking analysis further highlighted that favorable variants, particularly on chromosomes 3 and 19, had additive genetic effects on 100SW. Functional annotations suggest these genes influence seed weight through gibberellin synthesis and developmental pathways. By leveraging high-density genomic data, this study overcomes the limitations of previous studies relying on low-density markers, offering a foundation for more efficient soybean breeding strategies. These findings offer valuable insight into marker-assisted selection, providing a foundation to enhance soybean yield and adaptability under diverse environmental conditions and addressing the growing global demand for sustainable food production. Full article

A genetic linkage map of Grifola albicans f. huishuhua (Maitake) is an important resource for chromosome analysis and the genetic basis of phenotypic variation determination. A total of 92 monokaryotic isolates were selected from the F1 generation of Q3-8 × Y1-18 in this study. Restriction site-associated DNA sequencing, as well as identification of single nucleotide polymorphisms (SNPs), was performed, aiming to illustrate a high-density genetic linkage map. A total of 1122 high-quality SNP markers were located on a map with a length of 1473.60 centimorgan (cM) by screening 589534 SNPs. This map covers 12 linkage groups (LGs) with an average genetic distance of 122.80 cM. Three quantitative trait loci (QTLs) related to the growth rate of G. albicans f. huishuhua strains were identified using the composite interval mapping method. These QTLs were mapped to linkage groups (LGs) as follows: LG3 (qmgv), LG4 (qmb), LG5 (qmd), LG8 (qrdm1, qrdm2), and LG10 (qmgrc1, qmgrc2, qmgrc3). The genes associated with mycelial growth rate and biomass production of these strains were identified. This information could be used for molecular marker-assisted selective breeding in G. albicans f. huishuhua. Full article

Background: Beef tenderness is a key quality attribute that significantly influences consumer satisfaction; however, it exhibits considerable variability due to both genetic and environmental factors. While genomic selection based on Expected Progeny Differences (EPDs) has improved the accuracy of predictions, a substantial portion of tenderness variability remains unexplained. Metabolomics has emerged as a valuable approach to address this gap, as metabolites reflect gene–environment interactions and may serve as biomarkers for complex traits such as meat tenderness. Objectives: This study aimed to integrate genomic and metabolomic data to identify genetic loci associated with serum metabolites in Nellore calves, offspring of sires with contrasting EPDs for meat tenderness. Methods: Ninety-five male calves were evaluated and divided into two groups according to the sires’ genetic merit: FA-T (favorable EPD for tenderness, n = 45) and UN-T (unfavorable EPD for tenderness, n = 46). Blood serum samples were analyzed by ¹H NMR spectroscopy to quantify 40 metabolites, and genotyping was performed using a medium-density SNP panel. Metabolite quantitative trait loci (mQTL) were identified using the MatrixEQTL package, and metabolic enrichment analysis was performed in MetaboAnalyst 6.0. Results: In the FA-T group, SNPs were associated with metabolites such as phenylalanine, tyrosine, and succinate, suggesting enhanced oxidative metabolism and preservation of proteolysis. In the UN-T group, associations of pyruvate, creatinine, and glutamine with distinct SNPs indicated greater reliance on anaerobic glycolysis and early ATP consumption, potentially impairing phosphorylation and postmortem proteolytic activity. Conclusions: These findings suggest that genetic selection for tenderness may induce early divergent metabolic profiles, likely leading to persistent differences in postmortem biochemical pathways, with important implications for meat tenderness. Full article

Background: Polymorphisms in the FADS1 and FADS2 genes influence fatty acid metabolism. However, evidence of gene–diet interactions in population-based studies from Brazil remains limited. The objective of this study was to examine associations between FADS1–FADS2 single-nucleotide polymorphisms (SNPs) and erythrocyte fatty acid composition and serum lipid concentrations, as well as to explore potential gene–diet interactions. Methods: Data were analyzed from 294 adults (20–93 years) enrolled in the 2015 ISA-Nutrition study. Erythrocyte fatty acid composition and serum lipids were measured using standard enzymatic methods. Dietary intake was assessed by 24 h recalls, and participants were classified into tertiles according to fatty acid intake. Five SNPs were genotyped; FADS1 rs174546 and FADS2 rs174570 were prioritized based on linkage disequilibrium. Associations and interactions were assessed using generalized linear models, adjusting for confounders. Results: Carriers of the minor alleles for rs174546 and rs174570 had significantly lower erythrocyte levels of long-chain polyunsaturated fatty acids, particularly along the ω-6 pathway, suggesting reduced desaturase activity. The rs174546 TT genotype was associated with higher total, very-low-density lipoprotein cholesterol (VLDL), and non–high-density lipoprotein (non-HDL) cholesterolconcentrations. Higher dietary intakes of docosahexaenoic acid (DHA) or a higher linoleic acid to alpha-linolenic acid ratio(LA/ALA ratio) among these carriers were linked to lower serum lipid levels, indicating gene–diet interactions that attenuate adverse genotype effects. In addition, rs174570 TT carriers showed elevated VLDL concentrations, with a significant dietary interaction observed with the LA/ALA ratio. Conclusions: FADS1 and FADS2 polymorphisms influence fatty acid metabolism and interact with diet to shape lipid profiles. These findings highlight the importance of considering gene-diet interactions in cardiometabolic risk. Full article

Genomic prediction using whole-genome sequencing (WGS) data is challenged by the imbalance between a limited sample size (n) and an extensive number of single-nucleotide polymorphisms (SNPs) (p), where n $\ll$p. The high dimensionality of WGS data also increases computational demands, limiting its practical application. In this study, we introduce DAGP, a novel method that integrates deep autoencoder compression to reduce WGS data dimensionality by over 99% while preserving essential genetic information. This compression significantly improves computational efficiency, facilitating the effective use of high-dimensional genomic data. Our results demonstrated that DAGP, when combined with the genomic best linear unbiased prediction (GBLUP) method, maintained prediction accuracy comparable to WGS data, even at reduced marker densities of 50 K for sturgeon and 20 K for maize. Furthermore, integrating DAGP with Bayesian and machine learning models improved genomic prediction accuracy over traditional WGS-based GBLUP, with an average gain of 6.05% and 5.35%, respectively. DAGP provides an efficient and scalable solution for genomic prediction in species with large-scale genomic data, offering both computational feasibility and enhanced prediction performance. Full article

Osteoporosis is a multifactorial disease, the pathogenesis of which is caused by a complex interaction of genetic, hormonal, and metabolic factors. The challenges of early diagnosis highlight the need to identify genetic predictors to prevent bone mineral density (BMD) loss. Given the critical role of G-protein-coupled receptors (GPCRs) in bone development and remodeling, we investigated osteoporosis-associated single-nucleotide polymorphisms (SNPs) within GPCR genes using next-generation sequencing of patient cohorts. Subsequent screening via Sanger sequencing identified three SNPs for further analysis: rs1991517 in the thyroid-stimulating hormone receptor gene (TSHR), rs6166 in the follicle-stimulating hormone receptor gene (FSHR), and rs1042713 in the β2-adrenergic receptor gene (ADRB2). Our results reveal a significant association between osteoporosis and a specific homozygous genotype combination (TSHR rs1991517 CC, FSHR rs6166 AA, and ADRB2 rs1042713 AA). The functional impairment in osteodifferentiation was further validated in patient-derived cell lines harboring this triple-SNP combination. Thus, this study is the first to identify a specific combination of GPCR gene polymorphisms that may serve as a predictive biomarker for osteoporosis in early genetic screening. Full article

(1) Background: this study aimed to determine whether a serum parathyroid hormone (PTH) threshold of 40 pg/mL represents a clinically relevant risk factor for vitamin D (VitD) deficiency and reduced bone mineral density (BMD). It also investigated potential genetic interactions influencing PTH regulation and skeletal health in patients with periodontitis. (2) Methods: a cross-sectional analysis was conducted on 1038 periodontitis patients (35–75 years). Serum PTH, VitD, calcium (Ca), phosphate (P), and urinary parameters were assessed. Dual-energy X-ray absorptiometry (DXA) was used to evaluate BMD in 261 subjects. Vitamin D Receptor (VDR) and estrogen receptor alpha (ERα) polymorphisms were genotyped, and composite genetic risk scores were calculated. Statistical analyses included correlation tests, subgroup comparisons, and regression models. (3) Results: sixty-two percent of individuals had PTH > 40 pg/mL, which was associated with significantly lower 25(OH)D and Ca levels and reduced T-scores (p < 0.05). PTH levels negatively correlated with BMD (Pearson’s r = –0.159, p = 0.0105). Patients with higher ERα polymorphism scores showed increased PTH values (p < 0.05), while VDR variants demonstrated a positive but no significant trend. (4) Conclusions: a PTH threshold of 40 pg/mL identifies individuals at higher risk of VitD deficiency and skeletal fragility, even without overt hypercalcemia. Genetic factors, particularly ERα variants, may contribute to elevated PTH levels, suggesting value in integrating biochemical, densitometric, and genetic screening for early bone health risk stratification. Full article

Atherogenic dyslipidemia (AD) is a high-risk phenotype for cardiovascular disease, characterized by elevated triglycerides, increased small dense low-density lipoprotein cholesterol (sdLDL-C), and frequently coexisting hypertension. Although FTO gene variants have been implicated in lipid dysregulation, their role in AD among Latin American women remains poorly defined. We conducted a case–control study in 219 working perimenopausal women (97 AD cases and 122 controls). Sociodemographic, clinical, and biochemical variables were assessed. Three FTO SNPs (rs9939609, rs9940128, and rs8050136) were genotyped. Associations were evaluated using logistic regression models adjusted for age and BMI, with gene–environment interactions tested for smoking. Linkage disequilibrium (LD) and haplotype analyses were also performed. Women with AD exhibited significantly higher triglycerides, LDL-C, and sdLDL-C, along with increased hypertension prevalence, but no differences in BMI or glycemia. Multivariable models identified LDL-C (aOR ≈ 8), triglycerides, sdLDL-C, and systolic blood pressure as the strongest determinants of AD. The rs8050136 AA genotype was associated with a fourfold higher risk (aOR = 4.12; 95% CI: 1.49–11.95, p = 0.007). Smoking independently doubled AD risk (aOR = 2.33) and amplified the effect of rs8050136. Adjusted haplotype analysis revealed that the A-A-A (aOR = 5.33; 95% CI: 1.42–20.00) and A-G-A combinations (aOR = 2.54; 95% CI: 1.01–6.38) were significantly associated with AD. FTO polymorphisms, particularly rs8050136 and the A-A-A and A-G-A haplotypes, contribute independently and supra-additively to AD risk. The observed gene–environment interaction with smoking emphasizes the multifactorial nature of AD and supports genotype-based risk stratification and targeted preventive strategies in precision cardiovascular medicine. Full article

Lycium ruthenicum Murr. (Black goji), a medicinal and economically valuable crop rich in bioactive compounds, remains genomically understudied despite its expanding cultivation. To overcome limitations of traditional markers in genetic diversity analysis and molecular breeding, we employed specific-locus amplified fragment sequencing (SLAF-seq) to develop genome-wide SNP markers and elucidate the genetic structure of 213 L. ruthenicum accessions from natural and cultivated populations in Alxa, China. We identified 827,630 SLAF tags and 33,121 high-quality SNPs uniformly distributed across 12 chromosomes, establishing the first high-density SNP database for this species. Population genetic analyses revealed three distinct genetic clusters with <60% geographic origin consistency, indicating weakened isolation due to anthropogenic germplasm exchange. The Qinghai Nuomuhong population exhibited the highest genetic diversity (Nei’s index = 0.253; Shannon’s index = 0.352), while low overall polymorphism (average PIC = 0.183) likely reflects SNP biallelic limitations and domestication bottlenecks. Notably, SNP-based clustering showed <40% concordance with phenotypic trait clustering (31 traits), underscoring environmental plasticity as a key driver of morphological variation. This study provides the first genome-wide SNP resource for L. ruthenicum, enabling marker-assisted breeding and highlighting the need for standardized germplasm management to mitigate genetic erosion. Full article

Kernel row number (KRN) is a pivotal determinant for yield in maize breeding programs. However, the genetic basis underlying KRN remains largely elusive. To identify candidate genes regulating KRN, a population of 318 BC₄F₄ chromosomal segment substitution lines (CSSLs) was developed via backcrossing, with Baimaya (BMY) as the donor parent and B73 as the recurrent parent. Furthermore, a high-density genetic linkage map containing 2859 high-quality single-nucleotide polymorphism (SNP) markers was constructed for quantitative trait locus (QTL) mapping of KRN. Notably, 19 QTLs controlling KRN were detected across three environments and in the Best Linear Unbiased Prediction (BLUP) values; among these, a major-effect QTL (qKRN4.09-1) was consistently identified across all three environments and BLUP. Then, the integration of linkage mapping and transcriptome analysis of 5 mm immature ears from near-isogenic lines (NILs) uncovered a candidate gene, Zm00001eb205550. This gene exhibited significant downregulation in qKRN4.09-1^BMY, and two missense variants were detected between qKRN4.09-1^BMY and qKRN4.09-1^B73. Zm00001eb205550 exhibited preferential expression in developing ears. Moreover, the pyramiding of favorable alleles from the five stable QTLs significantly increased KRN in maize. These findings advance our genetic understanding of maize ear development and provide valuable genetic targets for improving KRN in maize breeding. Full article

Black tiger shrimp (Penaeus monodon) is the largest species of penaeid, being commercially cultured globally, ranking as the second most farmed species in the shrimp industry. However, with the transformation of shrimp aquaculture from semi-intensive to high-density farming, the concentration of ammonia nitrogen in the aquatic environment has increased, severely affecting the growth and survival of shrimps. To increase production efficiency, breeding new strains of shrimp with the trait of tolerance to high ammonia nitrogen is desired in the black tiger shrimp aquaculture. Previous studies have shown that glutamate dehydrogenase (GDH) and aspartate aminotransferase 2 (AST2) play important roles in the metabolism of ammonia nitrogen in crustaceans. In the present study, we conducted synteny analysis of PmGDH and PmAST2 in different species. The interactions of PmGDH with ammonium (NH₄⁺) and PmAST2 with aspartate were analyzed by docking. To develop molecule markers associated with ammonia nitrogen tolerance, SNPs of PmGDH and PmAST2 were identified by direct sequencing, genotyped by the SNaPshot technique, and characterized through genotype-phenotype association analysis by PLINK software version 1.9 in the three geographical populations, two families with different ammonia tolerance, and 120 susceptible and resistant individuals of black tiger shrimp. The results indicate that the GDH and AST2 genes are evolutionarily conserved in vertebrates, except for the black tiger shrimp, which suggests divergence in selective pressure between invertebrates and vertebrates. Notably, PmGDH may interact with NH₄⁺ via the residue Asp178 within loop 1 in the GdhA domain through a hydrogen bonding interaction, and PmAST2 may interact with aspartate via helix 1, sheet 1, loop 1, and loop 2, through both hydrogen bonding interactions and a salt bridge interaction. A total of 12 SNPs were detected in the exons of PmGDH and PmAST2. Among these candidate SNPs, the distributions of PmGDH-1227 and PmAST2-132 showed both significant differences in the genotype and allele association analysis between susceptible and resistant groups. Haplotype association analysis showed that three haplotypes exhibited significantly different distributions between susceptible and resistant groups. In conclusion, PmGDH-1227 and PmAST2-132 were associated with ammonia nitrogen tolerance, and these SNP markers are expected to contribute to marker-assisted selection (MAS) breeding programs to obtain new strains of Penaeus monodon. Full article

Yellow rust (YR), caused by Puccinia striiformis f. sp. tritici (Pst), is a global disease infecting wheat that seriously affects the yield and the quality of grains. Wheat breeding line C855 is immune to the mixed Pst isolates CYR32 + CYR33 + CYR34 under field conditions. To identify the Yr-loci carried by C855, in this study, an F₂ population derived from the crossing of C855 with Yannong 999, a YR-sensitive cultivar, was established, and the infection type (IT) of each F₂ individual was estimated. The correlation analysis results show that YR resistance was significantly positively correlated with grain weight and grain size. Using a 120K single-nucleotide polymorphism (SNP) array, the F₂ population was genotyped, and a high-density genetic map covering 21 wheat chromosomes and consisting of 5362 SNP markers was built. Then, five Yr-QTLs on chromosomes 1B, 2A, 2B, and 2D were identified. Of these, the QTL on chromosome 2A, temporarily named QYr.sxau-2A.1, is a major-effect QTL explaining 15.62% of the phenotypic variance. One PCR-based marker SSR2A-14 for QYr.sxau-2A.1 was developed, and the C855 allele of SSR2A-14 corresponded to the stronger Yr resistance. QYr.sxau-2A.1, located in the 228.02~241.58 Mbp physical interval, is different from all the known Yr loci on chromosomes 2A. Within the interval, there are 30 annotated genes, including a nucleotide-binding site and a leucine-rich repeat (NBS-LRR)-encoding gene with the linkage marker NRM2A-16 of QYr.sxau-2A.1. Our results reveal a novel major-effect QYr.sxau-2A.1, which provided resistance to YR and is a molecular marker for wheat breeding. Full article

Background: Longfin batfish (Platax teira) is an important economic species in southern China. In recent years, its wild population has significantly declined due to overfishing. Around 2015, breakthroughs in the artificial large-scale seedling technology for P. teira have promoted the growth of its aquaculture scale in regions such as Hainan and Guangdong. Methods: To study the genetic diversity, inbreeding status, and population structure of the current P. teira farming populations in China, we performed whole-genome resequencing technology and high-density SNP markers to analyze the genetics of four main farming populations. A total of 109 individuals from four populations (NA, ZP, XL, and XC) were sequenced, identifying 5,384,029 high-quality SNPs. Results: The results showed that the nucleotide diversity (π) of each population ranged from 0.00155 to 0.00165 and observed heterozygosity (Ho) ranged from 0.253 to 0.282, which indicated low levels of genetic diversity. The results of the ROH analysis show significant inbreeding in the NA population. Genetic differentiation analysis revealed that the genetic differentiation among NA, XC, and ZP populations was relatively low (F_ST = 0.021–0.029). Conclusions: NA, XC, and ZP populations likely share a common origin of their fry stocks. Based on a phylogenetic tree, principal component analysis (PCA), and population structure analysis, the four populations were divided into four genetic groups. This study is the first analysis of the genetic diversity and population structure of P. teira farming populations in China, laying the foundation for the establishment of a base breeding population and the implementation of genetic improvement programs. Full article

The structure and function of high-density lipoprotein (HDL), rather than its concentration, are more important factors in determining HDL activity. HDL particles (HDL-P) are heterogeneous in their composition, size, and antioxidative function. We investigated the levels of HDL subfractions and oxidized high-density lipoprotein (Ox-HDL) and validated their correlation with genetic determinants underlying peripheral artery disease (PAD). We recruited a PAD population stratified by claudication severity (group I) and critical limb ischemia (group II) according to the Rutherford classification. We found that the level of Ox-HDL was significantly increased with Rutherford classification (group II; p = 0.001). Conversely, the levels of high-density lipoprotein cholesterol (HDL-C), HDL-P, and small high-density lipoprotein particles (S-HDL-P) were significantly reduced in group II. Three single nucleotide polymorphisms (SNPs) were differentially associated with HDL particles and Ox-HDL. Briefly, rs117685211 and rs7934858 showed opposing effects, with rs117685211 and rs148877054 being associated with low levels of HDL subfractions; rs148877054 was significantly associated with M and S-HDL-P. Our study indicated the significance of HDL subfractions and Ox-HDL in the pathogenesis of PAD. Full article

Stomata on the leaves of wheat serve as important gateways for gas exchange with the external environment. Their morphological characteristics, such as size and density, are closely related to physiological processes like photosynthesis and transpiration. However, due to the limitations of existing analysis methods, the efficiency of analyzing and mining stomatal phenotypes and their associated genes still requires improvement. To enhance the accuracy and efficiency of stomatal phenotype traits analysis and to uncover the related key genes, this study selected 210 wheat varieties. A novel semantic segmentation model based on transformer for wheat stomata, called Wheat Stoma Former (WSF), was proposed. This model enables fully automated and highly efficient stomatal mask extraction and accurately analyzes phenotypic traits such as the length, width, area, and number of stomata on both the adaxial (Ad) and abaxial (Ab) surfaces of wheat leaves based on the mask images. The model evaluation results indicate that coefficients of determination (R²) between the predicted values and the actual measurements for stomatal length, width, area, and number were 0.88, 0.86, 0.81, and 0.93, respectively, demonstrating the model’s high precision and effectiveness in stomatal phenotypic trait analysis. The phenotypic data were combined with sequencing data from the wheat 660 K SNP chip and subjected to a genome-wide association study (GWAS) to analyze the genetic basis of stomatal traits, including length, width, and number, on both adaxial and abaxial surfaces. A total of 36 SNP peak loci significantly associated with stomatal traits were identified. Through candidate gene identification and functional analysis, two genes—TraesCS2B02G178000 (on chromosome 2B, related to stomatal number on the abaxial surface) and TraesCS6A02G290600 (on chromosome 6A, related to stomatal length on the adaxial surface)—were found to be associated with stomatal traits involved in regulating stomatal movement and closure, respectively. In conclusion, our WSF model demonstrates valuable advances in accurate and efficient stomatal phenotyping for locating genes related to stomatal traits in wheat and provides breeders with accurate phenotypic data for the selection and breeding of water-efficient wheat varieties. Full article