Search Results (71)

Growth is a key genetic improvement target in aquaculture. The giant grouper (Epinephelus lanceolatus), the largest and fastest-growing grouper species, is an important aquaculture species and also an ideal male parent in grouper hybrid breeding, such as hulong hybrid grouper (E. fuscoguttatus ♀ × E. lanceolatus ♂). However, the genetic basis of this rapid growth is unclear. In this study, we established a hulong hybrid grouper self-cross population, observing significant growth segregation. Using Bulked Segregant Analysis (BSA) and RNA-seq on extreme growth groups, we identified a significant growth-related quantitative trait locus (QTL) on chromosome 2, containing 23 candidate genes and 5 growth-correlated non-synonymous SNPs. Transcriptome analysis revealed 4074 differentially expressed genes. Integrating these results, we identified three critical genes: iqgap1, mex3b, and ndufs3, involved in cell proliferation, embryonic development, and energy metabolism, respectively. Their expression patterns further supported their association with giant grouper’s rapid growth. Our findings provide crucial insights into giant grouper growth mechanisms and valuable molecular markers for grouper breeding. Full article

Background: Individual differences in immune responses to African swine fever virus (ASFV), whether induced by vaccination or natural infection, may be linked to genetic variation in the genes involved in antigen presentation. Methods: A total of nine pigs from the 112-population were selected for RNA-seq analysis. To pinpoint key transcription factors (TFs) regulating gene expression in the lymph nodes, weighted Kendall’s Tau rank correlation analysis was performed to link the TF binding potential with the extent of differential expression of target genes. Results: CD8⁺ T cells expressing a specific epitope of the ASFV p72 protein (ACD8⁺) accounted for 41% of the total CD8⁺ T cells in peripheral blood. A total of 2062 transcripts were identified as differentially expressed across the nine pigs (q-value < 1 × 10⁻⁸). Differential expression levels of the target genes for MECP2, ETS1, ZBTB33, ELK4, and E2F4 were significantly correlated with their TF binding potential (p < 0.05). Six SNPs were identified in the promoter region of ELK4. Analysis of the 112-pig population revealed that SNPs at S.-404A>G and S.-668C>T loci were significantly associated with ACD8⁺ levels (q-value < 0.01). Individuals with the AA genotype at S.-404A>G had significantly higher ACD8⁺ counts compared to those with AG and GG genotypes (q-value < 0.05). At the S.-668C>T locus, ACD8⁺ levels were highest in the CC genotype, followed by CT and TT genotypes, with CC showing notably higher ACD8⁺ counts (q-value < 0.05). Notably, the S.-404A>G site overlaps with potential binding sites for TFs FOXA2, GATAs, and TRPS1, while the S.-668C>T site lies within the binding regions for NR1H3, RARA, VDR, and NR1I3. Conclusion: These mutations may disrupt TFs binding to the ELK4 promoter, potentially reducing ELK4 expression and impairing antigen processing and presentation. Full article

Understanding the genetic regulatory mechanisms of fat accumulation is crucial for improving beef quality. Hanwoo (Korean native cattle) is renowned for its high intramuscular fat (marbling), yet the genetic regulation of adipose gene expression remains insufficiently understood. In this study, we performed expression quantitative trait loci (eQTL) analysis using RNA-Seq data and genotype data from backfat tissue of 75 Hanwoo steers to identify regulatory variants associated with adipose deposition. A total of 25,042 significant cis-eQTL associations (FDR < 0.05) were identified, and 5362 unique top cis-eQTL pairs were retained after gene-wise filtering. Key cis-regulated genes included AGBL1, CACNG1, MYO18B, and DUSP29, which are involved in cytoskeletal organization, muscle development and calcium signaling. Three major cis-regulatory hotspots were located on BTA15 (BTA15:50354741) and BTA21 (BTA21:21526143, and BTA21:21541921). Permutation-based analysis (100,000 iterations) was conducted to control false positives, identifying 12 statistically significant trans-eQTL hotspots (FDR q < 0.05), of which SNP 6:60512276 and SNP 21:17035557 exhibited extensive trans-regulatory activity influencing 429 and 161 genes, respectively. In particular, SNP 21:17035557 acted as a shared cis- and trans-regulatory hub, indicating hierarchical control of adipose gene networks. Functional enrichment analyses revealed significant involvement of cytoskeleton- and calcium-dependent pathways, highlighting the interplay between structural remodeling and metabolic regulation in adipose tissue. These findings provide a comprehensive, system-level view of adipose gene regulation in Hanwoo cattle and highlight candidate molecular targets for genome-assisted and precision breeding. Moreover, this study offers quantitative genomic resources that can support the development of prediction models and decision-support systems for improving carcass traits in Hanwoo breeding programs. Full article

Type 1 Diabetes Mellitus (T1D) is an autoimmune disease characterized by the destruction of pancreatic β-cells, predominantly manifesting in childhood or adolescence. The lack of clearly interpretable biological markers in the early stages, combined with the insidious onset of the disease, poses significant challenges to early diagnosis and the implementation of preventive strategies. The applicability of classic T1D biomarkers for understanding the mechanisms of the autoimmune process, preclinical diagnostics and treatment efficiency is limited. Despite advances in next-generation sequencing (NGS) technologies, which have enabled large-scale genome-wide association studies (GWASs) and the identification of polygenic risk scores (PRSs) associated with T1D predisposition, as well as progress in bioinformatics approaches for assessing dysregulated gene expression, no universally accepted risk assessment model or definitive predictive biomarker has been established. Until now, the use of new promising biomarkers for T1D diagnostics is limited by insufficient evidence base. However, they have great potential for the development of diagnostic methods on their basis, which has been shown in single or serial large-scale studies. This critical review covers both well-known biomarkers widely used in clinical practice, such as HLA-haplotype, non-HLA SNPs, islet antigen autoantibodies, C-peptide, and the promising ones, such as cytokines, cfDNA, microRNA, T1D-specific immune cells, islet-TCR, and T1D-specific vibrational bands. Additionally, we highlight new approaches that have been gaining popularity and have already demonstrated their potential: GWAS, single-cell transcriptomics, identification of antigen-specific T cells using scRNA-seq, and FTIR spectroscopy. Although some of the biomarkers, in our opinion, are still limited to a research context or are far from being implemented in clinical diagnostics of T1D, they have the greatest potential of being applied in clinical practice. When integrated with the monitoring of the classical autoimmune diabetes markers, they would increase the sensitivity and specificity during diagnostics of early and preclinical stages of the disease. This critical review aims to evaluate the current landscape of classical and emerging biomarkers in autoimmune diabetes, with a focus on those enabling early detection—prior to extensive destruction of pancreatic islets. Another goal of the review is to focus the attention of the scientific community on the gaps in early T1D diagnostics, and to help in the selection of markers, targets, and methods for scientific studies on creating novel diagnostic panels. Full article

This study examines the genetic diversity and population structure of silver carp (Hypophthalmichthys molitrix), an ecologically and economically important freshwater species. Samples were collected from 17 sites along the Yangtze River, including LCH, LCS, LJHK, and LXZX, as well as one population from the United States (SV). Restriction-site associated DNA sequencing (RAD-seq) generated 759,453 high-quality single-nucleotide polymorphisms (SNPs) for population genomic analyses, including genetic differentiation (F_ST), population structure, and linkage disequilibrium (LD) decay. Genetic variation was primarily found within populations (78.05%), with 21.94% among populations. Most sites exhibited low genetic differentiation (F_ST < 0.05), suggesting high admixture along the river, although a few sites displayed elevated values (F_ST > 0.15). Rapid LD decay in LCH, LCS, and LJZ indicated frequent recombination and moderate to large effective population sizes. These patterns reflect the influence of geographic and ecological factors on population structure. Conservation strategies should maintain genetic connectivity while protecting distinct genetic resources. Populations with high differentiation, such as LXZX and LWZ, warrant targeted management to preserve unique genetic diversity. Full article

The skin color of radish taproots is an important commodity character that directly affects the choice behavior of consumers. Here, we identified a skin color gene carried by a red-skinned inbred line, SXAU-R2. Genetic population was constructed by the crossing of SXAU-R2 and a white-skinned inbred line, SXAU-W2, and the taproots of F₁ plants exhibited intermediate color. In the F₂ population, the separation ratio of taproot skin color indicated that the phenotype was controlled by one major locus, named RST1 (Red-Skinned Taproot 1). Combined with bulked segregant analysis and RNA sequencing (BSA-seq), 2640 single nucleotide polymorphisms (SNPs) were detected between the annotated genes of the red skin bulk and white skin bulk. Molecular markers were developed in the SNP-enriched 27~32 Mbp region of chromosome 7, and then RST1 was mapped in the genetic interval between flanking markers SSR-14 and SSR-22. Using F_2:3 lines derived from a key F₂ heterozygote, RST1 was narrowed down into a 530 Kbp interval. There were 46 expressed annotated genes in the fine-mapping region, and a gene encoding MYB was selected as the candidate of RST1. Finally, based on Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and RT-qPCR, we identified the potential interacting genes RsbHLH and RsWD, as well as the latent target genes RsDFR and RsANS of RST1 in the anthocyanin synthesis pathway. These results provide an understanding of the genetic mechanisms regulating anthocyanin synthesis and offer an efficient molecular marker for the radish breeding of skin color. Full article

Nitrogen is an essential macronutrient for crop growth. Although sorghum can tolerate poor soils, its low-nitrogen (LN) tolerance mechanisms remain underexplored. We conducted a genome-wide association study (GWAS) and RNA sequencing (RNA-seq) to dissect LN tolerance mechanisms in a diverse panel of 232 sorghum accessions. Phenotypic analyses revealed extensive variation in nitrogen-use efficiency traits, with shoot dry weight and shoot nitrogen accumulation in (SNAcc) showing the highest diversity. GWAS identified 10 quantitative trait loci harboring pleiotropic single-nucleotide polymorphisms (SNPs), including q1 (Chr3: 8.59–8.68 Mb), which is associated with biomass and nitrogen accumulation. Transcriptome profiling under LN stress revealed 6208 differentially expressed genes, with nitrate transporters showing genotype-specific regulation. Integration prioritized SORBI_3004G286700, where Hap2 accessions (14.66%) showed superior agronomic performance under LN conditions. We also identified pivotal transcription factors (TFs) that govern LN tolerance in sorghum, notably bHLH35 (SORBI_3007G051800) and three WRKY TFs, demonstrating constitutive upregulation in tolerant genotypes, whereas three previously uncharacterized TFs (MYB, bZIP, and B3) exhibited > 5-fold genotype-specific induction under LN. The integration of GWAS and transcriptome analyses offers an effective strategy for exploring candidate genes and elucidating nitrogen adaptation mechanisms in sorghum, while providing actionable molecular targets for precise breeding of nitrogen-efficient cultivars. Full article

As a globally significant fruit crop, litchi (Litchi chinensis Sonn.) exhibits substantial variation in seed size, which is a key determinant of fruit quality. However, the lack of molecular markers closely associated with seed-related traits has hindered targeted breeding efforts. In this study, we systematically evaluated six critical traits—single fruit weight, seed weight, seed length, seed width, edible rate, and seed-to-fruit weight ratio—across 131 early-maturing litchi accessions. Hierarchical clustering analysis (HCA) and principal component analysis (PCA) revealed a clear bifurcation of these accessions into two distinct groups based on seed size-related traits. Using bulked segregant analysis sequencing (BSA-seq), we identified a candidate genomic region (24.93–25.69 Mb) on chromosome 5, potentially regulating litchi seed size. Within this region, 1600 single-nucleotide polymorphisms (SNPs) and 314 insertion/deletion mutations (InDels) exhibited significant divergences between the extreme pools. To validate these findings, we performed PCR-based screening on 87 litchi accessions. Two InDel markers demonstrated strong phenotypic associations: Chr5_25610680_InDel showed highly significant correlations with seed weight, edible rate, seed length, seed width, and seed-to-fruit weight ratio, explaining 22.60–35.54% of phenotypic variation. Meanwhile, Chr5_25585686_InDel was significantly associated with seed weight and edible rate, accounting for 18.66% and 18.94% of the phenotypic variation, respectively. These findings provide valuable molecular markers for marker-assisted breeding of litchi seed size, offering a promising avenue to advance precision breeding in this economically important crop. Full article

Cotton fiber quality improvement remains a fundamental challenge in breeding programs due to the complex genetic architecture underlying fiber development. The narrow genetic base of upland cotton (Gossypium hirsutum L.) and the quantitative nature of fiber quality traits necessitate innovative approaches for identifying and incorporating superior alleles from related species. We developed a BC₆F₂ population by introgressing chromosome segments from the sea island cotton variety Xinhai 36 (G. barbadense) into the upland cotton variety Xinluzhong 60 (G. hirsutum). Based on fiber strength phenotyping, we constructed two DNA bulks representing extreme phenotypes (20 superior and 12 inferior individuals) for bulked segregant analysis sequencing (BSA-Seq). High-throughput sequencing generated 225.13 Gb of raw data with average depths of 20× for parents and 30× for bulks. SNP calling and annotation were performed using GATK and ANNOVAR against the upland cotton reference genome (TM-1). BSA-Seq analysis identified 13 QTLs primarily clustered within a 1.6 Mb region (20.6–22.2 Mb) on chromosome A10. Within this region, we detected nonsynonymous mutation genes involving a total of six genes. GO and KEGG enrichment analyses revealed significant enrichment for carbohydrate metabolic processes, protein modification, and secondary metabolite biosynthesis pathways. Integration with transcriptome data prioritized GH_A10G1043, encoding a β-amylase family protein, as the key candidate gene. Functional validation through overexpression and RNAi knockdown in Arabidopsis thaliana demonstrated that GH_A10G1043 significantly regulates starch content and β-amylase activity, though without visible morphological alterations. This study successfully identified potential genomic regions and candidate genes associated with cotton fiber strength using chromosome segment substitution lines combined with BSA-Seq. The key candidate gene GH_A10G1043 provides a valuable target for marker-assisted selection in cotton breeding programs. Our findings establish a foundation for understanding the molecular mechanisms of fiber quality formation and offer genetic resources for developing superior cotton varieties with enhanced fiber strength. Full article

As the laying cycle is prolonged, the egg albumen quality exhibits a declining trend. A Haugh unit (HU) is a standard measure of the albumen quality, which reflects viscosity and freshness. During the late laying period, the HU not only decreased significantly, but also exhibited greater variability among individuals. The magnum, as the primary site of albumen synthesis, plays a central role in this process; however, the mechanisms by which it regulates the albumen quality remain unclear. To address this, we obtained genomic and transcriptomic data from 254 individuals, along with single-cell RNA sequencing (scRNA-seq) data of the magnum tissue. Genome-wide association studies (GWAS) across five laying stages (66, 72, 80, 90, and 100 weeks of age) identified 77 HU-associated single-nucleotide polymorphisms (SNPs). Expression quantitative trait locus (eQTL) mapping linked these variants to the expression of 12 genes in magnum tissue. In addition, transcriptomic analysis using linear regression and random forest models identified 259 genes that significantly correlated with the HU. Single-cell RNA sequencing further revealed two key cell types, plasma cells and a subset of epithelial cells, marked by ADAMTSL1 and OVAL, which are functionally relevant to the HU. Through integrated Transcriptome-Wide Association Study (TWAS) and Summary-data-based Mendelian Randomization (SMR) analyses, we identified four robust regulators of the albumen quality: CISD1, NQO2, SLC22A23, and CMTM6. These genes are functionally involved in mitochondrial function, antioxidant defense, and membrane transport. Overall, our findings uncovered the genetic and cellular mechanisms underlying age-related decline in the albumen quality and identified potential targets for improving the egg quality in aging flocks. Full article

Body weight (BW) is a critical economic trait closely linked to livestock meat production performance and producer profitability. In the present study, we measured individual BW of 1070 male Hu sheep at six growth stages (80, 100, 120, 140, 160, and 180 days of age) and conducted descriptive statistical analyses. Results showed that the coefficient of variation (CV) for BW at each stage was higher than 13%. Additionally, we investigated the expression patterns of the FGF9 gene and its associations with single nucleotide polymorphisms (SNPs) and BW. Quantitative real-time PCR (qRT-PCR) revealed FGF9 is significantly higher expressed in the hypophysis tissues that in the other tested tissues. Association analyses indicated that the SNP FGF9:c.382-1264C>T was significantly associated with BW across different measurement periods. Finally, we performed assay for transposase-accessible chromatin using sequencing (ATAC-seq) and cleavage under targets and tagmentation (CUT&Tag) techniques to identify the OCRs (open chromatin regions) and regulatory regions in the hypophysis tissues of Hu sheep, and we obtained an average of 221243, 52692, and 20957.5 peaks in the ATAC-seq, H3K27ac, and H3K4me3 data per sample. Simultaneously, by integrating the SNPs of FGF9 and hypophysis tissue’s epigenomic data, we found that the SNP FGF9:c.382-1264C>T was located in the adjacent OCR- and H3K27ac-modified peaks. Therefore, we propose that the SNP FGF9:c.382-1264C>T plays an important role in regulating body weight in sheep. Overall, this study generated a valuable epigenetic dataset (ATAC-seq, H3K27ac, and H3K4me3) in sheep hypophysis tissue and identified a novel functional regulatory variant for improving body weight in sheep. Full article

Growth traits are the most important economic traits in red tilapia (Oreochromis spp.) production, and are the main targets for its genetic improvement. Increasing salinity levels in the environment are affecting the growth, development, and molecular processes of aquatic animals. Red tilapia tolerates saline water to some degree. However, few credible genetic markers or potential genes are available for choosing fast-growth traits in salt-tolerant red tilapia. This work used genome-wide association study (GWAS) and RNA-sequencing (RNA-seq) to discover genes related to four growth traits in red tilapia cultured in saline water. Through genotyping, it was determined that 22 chromosomes have 12,776,921 high-quality single-nucleotide polymorphisms (SNPs). One significant SNP and eight suggestive SNPs were obtained, explaining 0.0019% to 0.3873% of phenotypic variance. A significant SNP peak associated with red tilapia growth traits was located on chr7 (chr7-47464467), and plxnb2 was identified as the candidate gene in this region. A total of 501 differentially expressed genes (DEGs) were found in the muscle of fast-growing individuals compared to those of slow-growing ones, according to a transcriptome analysis. Combining the findings of the GWAS and RNA-seq analysis, 11 candidate genes were identified, namely galnt9, esrrg, map7, mtfr2, kcnj8, fhit, dnm1, cald1, plxnb2, nuak1, and bpgm. These genes were involved in ‘other types of O-glycan biosynthesis’, ‘glycine, serine and threonine metabolism’, ‘glycolysis/gluconeogenesis’, ‘mucin-type O-glycan biosynthesis’ and ‘purine metabolism signaling’ pathways. We have developed molecular markers to genetically breed red tilapia that grow quickly in salty water. Our study lays the foundation for the future marker-assisted selection of growth traits in salt-tolerant red tilapia. Full article

MYB transcription factors constitute a diverse and functionally versatile family, playing central roles in regulating plant responses to a range of abiotic stressors. Based on previous research, we identified and characterized a maize MYB transcription factor gene, ZmMYBR24, which is involved in responses to salt, alkali, and low-temperature stress. This study aimed to investigate the function and mechanism of ZmMYBR24 in response to salt, alkali, and low-temperature stresses. We hypothesized that ZmMYBR24 regulates biosynthetic pathways to influence maize resistance to multiple abiotic stresses. The results indicate that ZmMYBR24 expression was markedly upregulated (p < 0.01) and the fold-change in gene expression ranged from 1.54 to 25.69 when plants were exposed to these combined stresses. Phenotypically, the zmmybr24 mutant line exhibited more pronounced inhibition of seedling and root growth under stress compared to the wild-type B73 line. Based on a correlation expression pattern analysis and mutant line evaluation, ZmMYBR24 was confirmed to be a positive regulatory transcription factor for multiple types of abiotic stress resistance. An RNA-seq analysis of both lines revealed differentially expressed genes (DEGs), with gene ontology (GO) and KEGG enrichment analyses indicating that ZmMYBR24 may mediate stress responses by modulating the expression of genes involved in flavonoid biosynthesis. Notable differences were observed in the expression of pathway-associated genes between the mutant and wild-type plants. A haplotype analysis across 80 inbred maize lines revealed 16 ZmMYBR24 coding region haplotypes—comprising 25 SNPs and 17 InDels—with HAP12 emerging as a superior haplotype. These results demonstrate that ZmMYBR24 enhances maize yields by regulating the flavonoid biosynthesis pathway in response to adverse climatic conditions including salt, alkaline conditions, and low temperatures. Collectively, these findings offer novel insights into the molecular mechanisms underlying maize adaptation to combined abiotic stresses and lay the groundwork for breeding programs targeting multi-stress resistance. Full article

In this study, 172 Single-Nucleotide Polymorphisms (SNPs) (94 identity-informative SNPs, 56 ancestry-informative SNPs, and 22 phenotypic-informative SNPs) included in the ForenSeq™ DNA Signature Prep kit/DNA Primer Mix B (Verogen) were used for genotyping DNA samples from a population of twenty-one unrelated subjects, native to Northeast Italy. SNP sequencing was performed with the MiSeq FGx™ Forensic Genomics System (Illumina-Verogen), and data were analyzed using the Universal Analysis Software (UAS) v1.2. Raw data underwent further examination with STRait Razor v3 (SRv3) to compare the target SNPs’ genotype calls made with UAS and to identify the presence of microhaplotypes (MHs) due to SNPs associated with the same target SNP’s amplicon. The allele (haplotype) frequencies, Hardy–Weinberg equilibrium, linkage disequilibrium, number of effective alleles (A_e), and relevant forensic statistic parameters were calculated. Among the 172 SNPs evaluated, 45 unique microhaplotypes were found, comprising a novel sequence variant never previously described. The presence of MHs resulted in an 8.00% rise in the typologies of unique sequences, leading to changes in A_e. Notably, for 12 out of the 94 iiSNPs, the values of A_e exceeded 2.00, which is generally associated with a higher expected heterozygosity and increased power of discrimination. Full article

Background: Germline alleles near genes encoding certain immune checkpoints (CTLA4, CD200) are associated with autoimmune/autoinflammatory disease and cancer, but in opposite ways. This motivates a systematic search for additional germline alleles with this pattern with the aim of identifying potential cancer immunotherapeutic targets using human genetics. Methods: Pairwise fixed effect cross-disorder meta-analyses combining genome-wide association studies (GWAS) for breast, prostate, ovarian and endometrial cancers (240,540 cases/317,000 controls) and seven autoimmune/autoinflammatory diseases (112,631 cases/895,386 controls) coupled with in silico follow-up. Results: Meta-analyses followed by linkage disequilibrium clumping identified 312 unique, independent lead variants with p < 5 × 10⁻⁸ associated with at least one of the cancer types at p < 10⁻³ and one of the autoimmune/autoinflammatory diseases at p < 10⁻³. At each lead variant, the allele that conferred autoimmune/autoinflammatory disease risk was protective for cancer. Mapping led variants to nearest genes as putative functional targets and focusing on immune-related genes implicated 32 genes. Tumor bulk RNA-Seq data highlighted that the tumor expression of 5/32 genes (IRF1, IKZF1, SPI1, SH2B3, LAT) was each strongly correlated (Spearman’s ρ > 0.5) with at least one intra-tumor T/myeloid cell infiltration marker (CD4, CD8A, CD11B, CD45) in every one of the cancer types. Tumor single-cell RNA-Seq data from all cancer types showed that the five genes were more likely to be expressed in intra-tumor immune versus malignant cells. The five lead SNPs corresponding to these genes were linked to them via the expression of quantitative trait locus mechanisms and at least one additional line of functional evidence. Proteins encoded by the genes were predicted to be druggable. Conclusions: We provide population-scale germline genetic and functional genomic evidence to support further evaluation of the proteins encoded by IRF1, IKZF1, SPI1, SH2B3 and LAT as possible targets for cancer immunotherapy. Full article