Search Results (1,291)

As the fourth-largest global food crop, the quality and functional characteristics of processed potato products are closely linked to endogenous sugar metabolism in tubers, with the trehalose–sucrose metabolism playing a key role in processing adaptability. This study analyzed 333 accessions from a tetraploid potato natural population. The trehalose and sucrose content of potato tubers at harvest was quantified using the high-performance liquid chromatography (HPLC) method. Combined with whole-genome resequencing, a genome-wide association study (GWAS) was conducted to map regulatory loci and identify candidate genes. The results showed that relative trehalose content in tubers was 20.38–24.78, while relative sucrose content was 10.32–19.50. Frequency histograms for both sugars exhibited normal distributions characteristic of quantitative traits, and a positive correlation was observed between them. GWAS for trehalose identified 111 significant SNP loci, mainly on chromosomes 10 and 12, leading to the identification of 88 candidate genes. Kyoto encyclopedia of genes and genomes analysis (KEGG) revealed that trehalose-related genes were primarily involved in pathways such as ABC transporters, tricarboxylic acid (TCA) cycle, and cysteine and methionine metabolism. Candidate genes potentially regulating tuber trehalose content included GH10, GH28, GH127, UXS, UGT, PMEI, and MYB108. For sucrose, GWAS identified 279 significant SNP loci, mainly on chromosomes 5, 6, and 12, resulting in 111 candidate genes. KEGG enrichment analysis showed that sucrose-related genes were enriched in pathways including starch and sucrose metabolism, cyanoamino acid metabolism, and phenylpropanoid biosynthesis. Candidate genes potentially regulating tuber sucrose content included GH17, GH31,GH47, GH9A4, SPP1, BGLU12, GSA1, TPS8, cwINV4, HXK, UST, MYB5, MYB14, and WRKY11. Therefore, this study provides marker loci for trehalose and sucrose metabolism research, aiming to clarify their regulatory mechanisms and support potato variety improvement and superior germplasm development. Full article

Agronomic advancements have led to significant increases in maize yield per hectare in Northeast China, primarily through improved density tolerance. However, the genetic mechanism underlying grain yield responses to density stress remains poorly understood. Here, a population of 193 recombinant inbred lines (RILs) derived from the cross between ZM058 and PH1219 was employed to identify quantitative trait loci (QTLs) under two planting densities across three locations over two years. Six yield-related traits were investigated: ear tip-barrenness length (BEL), cob diameter (CD), ear diameter (ED), ear length (EL), kernel number per row (KNR), and kernel row number (KRN). These traits exhibited distinct and divergent responses to density stress, with the values of CD, ED, EL, KNR and KRN decreasing as planting density increased, except for BEL. A total of 81 QTLs were identified for these traits: 39 were unique to low planting density, 22 to high planting density, and 20 were shared across both conditions. Additionally, nine QTL clusters implicated in the development of multiple traits were detected. The results indicate that planting density significantly affects yield traits, primarily through the interaction of numerous minor QTLs with multiple effects. This insight enhances our understanding of the genetic basis of yield-related traits and provides valuable guidance for breeding high-density-tolerant varieties. Full article

Background: Host genetic factors significantly influence individual susceptibility to severe COVID-19, potentially explaining the observed disparities in clinical outcomes across populations. One of the key effectors in innate immunity and antiviral defense is the CD209 gene. This study explored the potential correlation of the CD209 gene SNP rs2287886 with diverse COVID-19 patient outcomes. Materials and Methods: A total of 176 patients (87 in the moderate group and 89 in the severe/critical/death group) were included in the study. Genotyping of patients was performed using the qPCR methodology, through the TAQMAN system. The results were analyzed adopting a significance level of p < 0.05. Results: The GG genotype (compared to AG + AA) and the G allele (compared to the A allele) of the rs2287886 SNP were significantly associated with an increased severity of COVID-19 (p = 0.0005 and p < 0.0001, respectively). The G allele was more frequent in individuals with more severe clinical outcomes (49.43% vs. 25.28%). Furthermore, expression quantitative trait loci (eQTL) analysis indicated that the GG genotype of rs2287886 is associated with higher CD209 gene expression. Furthermore, the observed interaction analysis suggests that the interactions between CD209 and its associated proteins may play a role in modulating the immune response. Conclusions: Our findings suggest that Brazilian patients homozygous for the GG genotype of the rs2287886 polymorphism in the CD209 gene may be at increased risk of severe COVID-19 in the Brazilian population and may act as a potential prognostic marker of disease severity. Full article

This study aimed to identify candidate genes associated with chlorophyll content in rice via genome-wide association studies (GWAS) and to develop molecular markers for the selection of genetic resources and breeding lines exhibiting high chlorophyll content. Measurement of the Soil and Plant Analysis Development (SPAD) values, indicative of chlorophyll content and photosynthetic potential, were measured in 198 rice genetic resources across three years under consistent nitrogen conditions. Nitrogen fertilizer (as urea) was applied at a rate of 90 kg N ha⁻¹. After analyzing the multi-year SPAD data, genetic resources with the coefficient of variation (CV) value exceeding 20% were excluded, and the remaining 175 accessions were used for subsequent analyses. Population structure analysis using the principal component analysis (PCA) and phylogenetic methods confirmed clear genetic differentiation, supporting the reliability of the GWAS. A GWAS using 289,569 SNPs identified 17 significant loci, among which four quantitative trait loci (QTLs)—qSV3-1, qSV3-2, qSV6, and qSV7—explained over 20% of phenotypic variance. Analysis of their additive effects revealed distinct SPAD distributions among QTL combination groups, with accessions harboring all four QTLs exhibiting the highest values. Candidate gene analysis within ± 200 kb of lead SNPs identified Os03g079100 (OsUCL8), involved in photosynthesis, near qSV3-2. A derived cleaved amplified polymorphic sequence (dCAPS) marker was developed to differentiate alleles at this locus and validated via restriction digestion. These results provide key genetic insights into chlorophyll accumulation and offer molecular markers for breeding high-yielding rice cultivars with enhanced chlorophyll content. The results of this study are expected to contribute to the development of sustainable rice varieties by utilizing the developed markers and identified candidate genes to increase SPAD values, thereby enhancing nitrogen use efficiency, improving photosynthetic capacity, and ultimately increasing rice productivity. Full article

Phenolic compounds contribute significantly to the nutritional and functional properties of wheat, particularly due to their antioxidant activity. In this study, a genome-wide association study was conducted to elucidate the genetic basis of total phenolic content (TPC) and antioxidant activity (AA) in a panel of 144 tetraploid wheat accessions representing diverse subspecies. The panel was evaluated under two different environments, located in Chile and Italy, to assess the influence of genotype, environment, and their interaction. Significant variability was observed for both TPC and AA, with TPC ranging from 0.26 to 0.82 mg gallic acid equivalent (GAE)/g and AA from 0.04 to 0.99 µmol Trolox equivalent (TE)/g. Substantial phenotypic variation and high broad-sense heritability were observed for both traits, underscoring the predominant genetic control. The genome-wide association study, using a mixed linear model (MLM), and the Bayesian information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) approaches identified 17 significant marker–trait associations, including quantitative trait loci on chromosomes 2B, 3A, 4B, 5A, 5B, and 6B. Notably, QTLs on chromosome 5A were co-localized for both TPC and AA, suggesting potential pleiotropic loci. Candidate genes linked to these loci included flavonol 3-sulfotransferase and peptidylprolyl isomerase, which are involved in phenylpropanoid metabolism and oxidative stress response, respectively. These findings offer valuable insights into the genetic basis of wheat phenolic traits and provide molecular targets for the development of biofortified cultivars through marker-assisted selection. Full article

Red epicarp in pears is an important trait for breeding. Exploring the genes regulating pear anthocyanin synthesis and developing molecular markers associated with these traits are important for obtaining new varieties of red pears. We performed whole-genome resequencing (WGS) on 127 ‘Yuluxiang (Pyrus bretschneideri)’ × ‘Xianghongli (Pyrus communis)’ F1 populations and identified a total of 510,179 single-nucleotide polymorphism (SNP) sites in the population. In total, 1972 bins were screened to form a high-density genetic map with a total map length of 815.507 cM, covering 17 linkage groups with an average genetic distance of 0.414 cM between markers. Three red skin quantitative trait loci (QTLs), located on LG4 and LG5, that explained 18.7% of the phenotypic variance, were detected. The QTL intervals contained 1658 genes, including 94 transcription factors (TF), subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Four key candidate genes (Pspp.Chr05.01969, Pspp.Chr05.01908, Pspp.Chr05.02419, and Pspp.Chr04.01087) that may play a role in promoting pear anthocyanin synthesis were screened and identified by a quantitative polymerase chain reaction (qPCR). Overall, our study deepens our understanding of the genetics of red peel traits in pears and accelerates pear breeding. Full article

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), represents a major global threat to wheat (Triticum aestivum. L). Planting varieties with adult-plant resistance (APR) is an effective approach for long-term management of this disease. The Chinese winter wheat variety Lantian 25 exhibits moderate-to-high APR against stripe rust under field conditions. To investigate the genetic basis of APR in Lantian 25, a set of 219 F₆ recombinant inbred lines (RILs) was created from a cross between Lantian 25 (resistant parent) and Huixianhong (susceptible parent). These RILs were assessed for maximum disease severity (MDS) in Pixian of Sichuan and Qingshui of Gansu over the 2020–2021 and 2021–2022 growing seasons, resulting in data from four different environments. Genotyping was performed on these lines and their parents using the wheat Illumina 50K single-nucleotide polymorphism (SNP) arrays. Composite interval mapping (CIM) identified six quantitative trait loci (QTL), named QYr.gaas-2BS, QYr.gaas-2BL, QYr.gaas-2DS, QYr.gaas-2DL, QYr.gaas-3BS and QYr.gaas-4BL, which were consistently found across two or more environments and explained 4.8–12.0% of the phenotypic variation. Of these, QYr.gaas-2BL, QYr.gaas-2DS, and QYr.gaas-3BS overlapped with previous studies, whereas QYr.gaas-2BS, QYr.gaas-2DS, and QYr.gaas-4BL might be novel. All the resistance alleles for these QTL originated from Lantian 25. Furthermore, four kompetitive allele-specific PCR (KASP) markers, Kasp_2BS_YR (QYr.gaas-2BS), Kasp_2BL_YR (QYr.gaas-2BL), Kasp_2DS_YR (QYr.gaas-2DS) and Kasp_2DL_YR (QYr.gaas-2DL), were developed and validated in 110 wheat diverse accessions. Additionally, we identified seven candidate genes linked to stripe rust resistance, including disease resistance protein RGA2, serine/threonine-protein kinase, F-box family proteins, leucine-rich repeat family proteins, and E3 ubiquitin-protein ligases. These QTL, along with their associated KASP markers, hold promise for enhancing stripe rust resistance in wheat breeding programs. 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

Soybean (Glycine max), as an important crop for both oil and grains, is a major source of high-quality plant proteins for humans. Among various natural disasters affecting soybean production, waterlogging is one of the key factors leading to yield reduction. It can cause root rot and seedling death, and in severe cases, even total crop failure. Given the significant differences in responses to waterlogging stress among different soybean varieties, traditional single-trait indicators are insufficient to comprehensively evaluate flood tolerance. In this study, relative seedling length (RSL) was used as a comprehensive evaluation index for flood tolerance. Using a chromosome segment substitution line (CSSL) population derived from SN14 and ZYD00006, we successfully identified seven quantitative trait loci (QTLs) associated with seed waterlogging tolerance. By integrating RNA-Seq transcriptome sequencing and phenotypic data, the functions of candidate genes were systematically verified. Phenotypic analysis indicated that Suinong14 had significantly better flood tolerance than ZYD00006. Further research revealed that the Glyma.05G160800 gene showed a significantly up-regulated expression pattern in Suinong14; qPCR analysis revealed that this gene exhibits higher expression levels in submergence-tolerant varieties. Haplotype analysis demonstrated a significant correlation between different haplotypes and phenotypic traits. The QTLs identified in this study can provide a theoretical basis for future molecular-assisted breeding of flood-tolerant varieties. Additionally, the functional study of Glyma.05G161800 in regulating seed flood tolerance can offer new insights into the molecular mechanism of seed flood tolerance. These findings could accelerate the development of submergence-tolerant rice varieties, enhancing crop productivity and stability in flood-prone regions. Full article

Backgroud. Endometriosis is a chronic, estrogen-dependent inflammatory disease characterized by the ectopic presence of endometrial-like tissue. Although genome-wide association studies (GWAS) have identified susceptibility variants, their tissue-specific regulatory impact remains poorly understood. Objective. To functionally characterize endometriosis-associated variants by exploring their regulatory effects as expression quantitative trait loci (eQTLs) across six physiologically relevant tissues: peripheral blood, sigmoid colon, ileum, ovary, uterus, and vagina. Methods. GWAS-identified variants were cross-referenced with tissue-specific eQTL data from the GTEx v8 database. We prioritized genes either frequently regulated by eQTLs or showing the strongest regulatory effects (based on slope values, which indicate the direction and magnitude of the effect on gene expression). Functional interpretation was performed using MSigDB Hallmark gene sets and Cancer Hallmarks gene collections. Results. A tissue specificity was observed in the regulatory profiles of eQTL-associated genes. In the colon, ileum, and peripheral blood, immune and epithelial signaling genes predominated. In contrast, reproductive tissues showed the enrichment of genes involved in hormonal response, tissue remodeling, and adhesion. Key regulators such as MICB, CLDN23, and GATA4 were consistently linked to hallmark pathways, including immune evasion, angiogenesis, and proliferative signaling. Notably, a substantial subset of regulated genes was not associated with any known pathway, indicating potential novel regulatory mechanisms. Conclusions. This integrative approach highlights the com-plexity of tissue-specific gene regulation mediated by endometriosis-associated variants. Our findings provide a functional framework to prioritize candidate genes and support new mechanistic hypotheses for the molecular pathophysiology of endometriosis. Full article

Disease resistance is one of the most important target traits for sugarcane genetic improvement. Sugarcane brown stripe (SBS) caused by Helminthosporium stenospilum is one of the most destructive foliar diseases, which not only reduces harvest cane yield but also sugar content. This study aimed to identify quantitative trait loci (QTL) and candidate genes associated with SBS resistance. Here, the phenotypic investigation in six field habitats showed a continuous normal distribution, revealing that the SBS resistance trait is a quantitative trait. Two high-density linkage maps based on the single-dose markers calling from the Axiom Sugarcane100K SNP chip were constructed for the dominant sugarcane cultivars YT93-159 (SBS-resistant) and ROC22 (SBS-susceptible) with a density of 2.53 cM and 2.54 cM per SNP marker, and mapped on 87 linkage groups (LGs) and 80 LGs covering 3069.45 cM and 1490.34 cM of genetic distance, respectively. A total of 32 QTL associated with SBS resistance were detected by QTL mapping, which explained 3.73–11.64% of the phenotypic variation, and the total phenotypic variance explained (PVE) in YT93-159 and ROC22 was 107.44% and 79.09%, respectively. Among these QTL, four repeatedly detected QTL (qSBS-Y38-1, qSBS-Y38-2, qSBS-R8, and qSBS-R46) were considered stable QTL. Meanwhile, two major QTL, qSBS-Y38 and qSBS-R46, could account for 11.47% and 11.64% of the PVE, respectively. Twenty-five disease resistance candidate genes were screened by searching these four stable QTL regions in their corresponding intervals, of which Soffic.01G0010840-3C (PR3) and Soffic.09G0017520-1P (DND2) were significantly up-regulated in YT93-159 by qRT-PCR, while Soffic.01G0040620-1P (EDR2) was significantly up-regulated in ROC22. These results will provide valuable insights for future studies on sugarcane breeding in combating this disease. Full article

Anaerobic germination (AG) is a pivotal trait for successful direct-seeded rice cultivation, encompassing rainfed and irrigated conditions. Elite rice cultivars are often vulnerable to flooding during germination, resulting in poor crop establishment. This drawback has led to the exploration of AG-tolerant rice landraces, which offer valuable insights into the genetic underpinnings of AG tolerance. Over the years, substantial progress has been made in identifying significant quantitative trait loci (QTLs) associated with AG tolerance, forming the basis for targeted breeding efforts. However, the intricate gene regulatory network governing AG tolerance remains enigmatic. This comprehensive review presents recent advances in understanding the physiological and genetic mechanisms underlying AG tolerance. It focuses on their practical implications in breeding elite rice cultivars tailored for direct-seeding systems. Full article

Vegetable oils are essential for human nutrition and industrial applications. With growing global demand, increasing oil content in oilseed crops has become a top priority. This review synthesizes recent progress in understanding the genetic, environmental, and molecular mechanisms regulating oil content, and presents biotechnological strategies to enhance oil accumulation in major oilseed crops. Oil biosynthesis is governed by intricate genetic–environmental interactions. Environmental factors and agronomic practices significantly impact oil accumulation dynamics. Quantitative trait loci (QTL) mapping and genome-wide association studies (GWAS) have identified key loci and candidate genes involved in lipid biosynthesis pathways. Transcription factors and epigenetic regulators further fine-tune oil accumulation. Biotechnological approaches, including marker-assisted selection (MAS) and CRISPR/Cas9-mediated genome editing, have successfully generated high-oil-content variants. Future research should integrate multi-omics data, leverage AI-based predictive breeding, and apply precision genome editing to optimize oil yield while maintaining seed quality. This review provides critical references for the genetic improvement and breeding of high- and ultra-high-oil-content varieties in oilseed crops. Full article

The functional components in cereals (rice and barley), such as gamma-aminobutyric acid (GABA), resistant starch (RS), and alkaloids, play crucial roles in human health, offering benefits such as improved cardiovascular function, enhanced gut microbiota, and potential anticancer properties. Rice (Oryza sativa) and barley (Hordeum vulgare) are key dietary staples with distinct genetic architectures influencing the biosynthesis and accumulation of these bioactive compounds. In this study, we explore the interaction and divergence of gene loci associated with GABA, RS, and alkaloid pathways in rice and barley, leveraging comparative genomics to identify conserved and species-specific regulatory mechanisms. We highlight key quantitative trait loci (QTLs) and candidate genes, such as GAD (glutamate decarboxylase) for GABA synthesis, SSIIa and GBSS for RS formation, and alkaloid biosynthesis genes including CYP80G2. Additionally, we discuss the health implications of these functional components, including their roles in reducing hypertension, managing diabetes, and exhibiting neuroprotective effects. Understanding the genetic differences between rice and barley in accumulating these compounds can guide biofortification strategies to enhance nutritional quality in cereal crops, ultimately benefiting human health and dietary outcomes. Full article

Background: Rheumatoid arthritis (RA) is an autoimmune disease that remains incurable. An increasing number of proteomic genome-wide association studies (GWASs) are emerging, offering immense potential for identifying novel therapeutic targets for diseases. This study aims to identify potential therapeutic targets for RA based on human plasma proteome. Methods: Protein quantitative trait loci were extracted and integrated from eight large-scale proteomic GWASs. Proteome-wide Mendelian randomization (Pro-MR) was performed to prioritize proteins causally associated with RA. Further validation of the reliability and stratification of prioritized proteins was performed using MR meta-analysis, colocalization, and transcriptome-wide summary-data-based MR. Subsequently, prioritized proteins were characterized through protein–protein interaction and enrichment analyses, pleiotropy assessment, genetically engineered mouse models, cell-type-specific expression analysis, and druggability evaluation. Phenotypic expansion analyses were also conducted to explore the effects of the prioritized proteins on phenotypes such as endocrine disorders, cardiovascular diseases, and other immune-related diseases. Results: Pro-MR prioritized 32 unique proteins associated with RA risk. After validation, prioritized proteins were stratified into four reliability tiers. Prioritized proteins showed interactions with established RA drug targets and were enriched in an immune-related functional profile. Four trans-associated proteins exhibited vertical or horizontal pleiotropy with specific genes or proteins. Genetically engineered mouse models for 18 prioritized protein-coding genes displayed abnormal immune phenotypes. Single-cell RNA sequencing data were used to validate the enriched expression of several prioritized proteins in specific synovial cell types. Nine prioritized proteins were identified as targets of existing drugs in clinical trials or were already approved. Further phenome-wide MR and mediation analyses revealed the effects and potential mediating roles of some prioritized proteins on other phenotypes. Conclusions: This study identified 32 plasma proteins as potential therapeutic targets for RA, expanding the prospects for drug discovery and deepening insights into RA pathogenesis. Full article