Search Results (1,743)

Powdery mildew is a prevalent wheat disease that affects yield and quality. The characterization and fine mapping of genes associated with powdery mildew resistance can benefit marker-assisted breeding. In this study, quantitative trait loci (QTL) associated with powdery mildew were mapped using a high-density 35K DArT genetic linkage map developed from a population of double haploid lines (DHs) created by crossing “Jinmai 33 (a highly resistance line) with Yannong 19 (a highly susceptible line)”. Three stable QTLs for powdery mildew were identified on chromosomes 1B, 2B, and 6A combined with the composite interval graphing method and multiple interval mapping, explaining phenotypic variations (PVE) that range from 4.98% to 13.25%. Notably, Qpm.sxn-1B and Qpm.sxn-2B were identified across three environments, with the PVE ranging from 9.37% to 13.25% and from 4.98% to 5.23%, respectively. The synergistic effects of these QTLs were contributed by the parental line “Jinmai 33”. Qpm.sxn-1B was the major stable QTL, and Qpm.sxn-2B was close to Pm51. Furthermore, Qpm.sxn-6A was identified in two environments, accounting for PVE values of 7.13% and 7.65%, respectively, with the resistance effects originating from the male parent. Remarkably, this locus has not been reported previously, indicating that Qpm.sxn-6A represents a newly dis-covered QTL governing powdery mildew genes. Conclusions Five molecular markers available for mark-er-assisted selection were selected for tracking Qpm.sxn-1B and Qpm.sxn-2B in the program. The identification of this novel newly discovered QTL and markers reported in this study will be useful for marker-assisted selection of powdery mildew resistance. Full article

DNA markers have broad applications, including marker-assisted selection (MAS) for breeding new cultivars. Currently, single nucleotide polymorphisms (SNPs) have become a preferred choice of markers for molecular geneticists and breeders. They offer many advantages, such as high abundance and coverage in the genome, codominant inheritance, locus specificity, and flexibility for high-throughput genotyping/detection formats, and they are relatively inexpensive. The availability of reference genome sequences enables precise identification of candidate genes and SNPs associated with a trait of interest through quantitative trait loci mapping and genome-wide association studies. Such SNPs can be converted into markers for their application in MAS in crop breeding programs. Cleaved amplified polymorphic sequence (CAPS) markers amplify short genomic sequences around the polymorphic endonuclease restriction site. This review provides insight into the recent advancements made in the development and application of CAPS markers in several horticultural plants. We discussed many new tools that aid faster and more accurate design of CAPS markers from the whole genome resequencing data. The developed CAPS markers offer immense application in germplasm screening and field trials, genomic loci mapping, identifying candidate genes, and MAS of important horticultural traits such as disease resistance, fruit quality and morphology, and genetic purity. Full article

As a common fungal disease, powdery mildew (PM) is one of the main diseases that harm the growth and development of cucumbers. Understanding the types of pathogenic fungus and analysis of the genetic and molecular mechanisms of cucumber resistance to PM at the molecular level are important when breeding disease-resistant varieties. The present review summarizes the hazards, prevention, and control of PM, and it discusses resistance inheritance rules, molecular markers, quantitative trait locus (QTL) mapping, gene cloning, omics, and gene editing technology, providing research insights on cucumber breeding varieties resistant to PM. Full article

The breeding of disease-resistant pigs has consistently been a topic of significant interest and concern within the pig farming industry. The study of pig blood indicators has the potential to confer economic benefits upon the pig farming industry, whilst simultaneously providing valuable insights that can inform the study of human diseases. In this study, an F2 resource population of 489 individuals was generated through the intercrossing of Large White boars and Min pig sows. A total of 17 haematological parameters and T lymphocyte subpopulations were measured, including white blood cell count (WBC), lymphocyte count (LYM), lymphocyte count percentage (LYM%), monocyte count (MID), monocyte count percentage (MID%), neutrophilic granulocyte count (GRN), percentage of neutrophils (GRN%), mean platelet volume (MPV), platelet distribution width (PDW), platelet count (PLT), CD4+/CD8+, CD4+CD8+CD3+, CD4+CD8−CD3+, CD4−CD8+CD3+, CD4−CD8−CD3+, and CD3+. The Illumina PorcineSNP60 Genotyping BeadChip was obtained for all of the F2 animals. Subsequently, a genome-wide association study (GWAS) was conducted using the TASSEL 5.0 software to identify associated variants and candidate genes for the 17 traits. Significant association signals were identified for PCT and PLT on SSC7, with 1 and 11 significant SNP loci, respectively. A single nucleotide polymorphism (SNP) on SSC12 was identified as a significant predictor of the white blood cell (WBC) trait. Significant association signals were detected for the T lymphocyte subpopulations, namely CD4+/CD8+, CD4+CD8+CD3+, CD4+CD8−CD3+, and CD4−CD8+CD3+, with the majority of these signals observed on SSC7. The genes CLIC5, TRIM15, and SLC17A4 were identified as potential candidates for influencing CD4+/CD8+ and CD4−CD8+CD3+. A missense variant, c.2707 G>A, in the SLC17A4 gene has been demonstrated to be significantly associated with the CD4+/CD8+ and CD4-CD8+CD3+ traits. Three missense variants (c.425 A>C, c.500 C>T, and c.733 A>G) have been identified in the TRIM15 gene as being linked to the CD4+/CD8+ trait. Nevertheless, only c.425 A>C has been demonstrated to be significantly associated with CD4-CD8+CD3+. In the CLIC5 gene, one missense variant (c.957 T>C) has been identified as being associated with the CD4+/CD8+ and CD4-CD8+CD3+ traits. Additionally, significant association signals were observed for CD4+CD8+CD3+ and CD4+CD8−CD3+ on SSC2 and 5, respectively. Subsequently, a gene ontology (GO) enrichment analysis was conducted on all genes within the quantitative trait loci (QTL) intervals of platelet count, CD4+/CD8+, and CD4−CD8+CD3+. The MHC class II protein complex binding pathway was identified as the most significant pathway among the three immune traits. These results provide guidance for further research in the field of breeding disease-resistant pigs. Full article

The Ningxiang pig, one of the well-known Chinese native pig breeds, has the advantages of tender meat, high intramuscular fat (IMF) content, and roughage tolerance, compared to the commercial lean pig breeds. The genetic basis for complex traits in Ningxiang pigs has been previously studied through other genetic markers, such as Single Nucleotide Polymorphism (SNP), while the characteristics of copy number variation (CNV) and the selection signal have not been investigated yet. In this study, GGP 50 k genotyping data of 2242 Ningxiang pigs (NX) and 1137 Duroc pigs (Duroc) were involved in CNV atlas construction and selection signals identification. Annotations of genes and quantitative trait locus (QTLs) were performed on the target candidate regions, as follows: (1) 162 CNVs were detected in Ningxiang pigs, while 326 CNVs were detected in Duroc pigs, and there are 21 copy number variation regions (CNVRs) shared between them; (2) The CNVRs of Duroc are more abundant, with 192 CNVRs, accounting for 1.61% of the entire genome, while those of Ningxiang pigs only have 98 CNVRs, accounting for 0.49%; (3) The QTLs annotated on CNVs and selected regions of Ningxiang pigs were mainly associated with meat quality and fertility. In contrast, the Duroc QTLs’ notes relate primarily to the carcass and immunity, and explain why they have a higher slaughter rate and immunity; (4) There is a presence of high-frequency acquired CNVs, specifically in Ningxiang pigs, with 24 genes significantly enriched in the sensory receptor-related pathway in this region; (5) Based on the CNVs atlas, candidate genes such as 3 inositol 1,4,5-triphosphate receptor, type 3 (ITPR3), forkhead box protein K2 (FOXK2), G-protein coupled estrogen receptor 1 (GPER1), Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), triosephosphate isomerase 1 (TPI1), and other candidate genes related to fat deposition and differentiation were screened. In general, this study improved our knowledge about copy number variation and selection signal information of Ningxiang pigs, which can not only further explain the genetic differences between Chinese native and Western commercial pig breeds, but also provide new materials for the analysis of the genetic basis of complex traits. Full article

Maize tassel spindle length is closely related to the number of pollen grains and the duration of the flowering stage, ultimately affecting maize yield and adaptations to stress conditions. In this study, 182 maize inbred lines were included in an association population. A genome-wide association study was conducted on maize tassel spindle length using the Q + K model. With p ≤ 1.0 × 10⁻⁴ applied as the significance threshold, 240 SNPs significantly associated with tassel spindle length were detected, which were associated with 99 quantitative trait loci (QTLs), with 21 QTLs detected in two or more environments. Moreover, 51 candidate genes were detected in 21 co-localized QTLs. A KEGG enrichment analysis and candidate gene expression analysis indicated that Zm00001d042312 affects plant hormone signal transduction and is highly expressed in maize tassels. A haplotype analysis of Zm00001d042312 revealed three main haplotypes, with significant differences between Hap1 and Hap2. In conclusion, we propose that Zm00001d042312 is a gene that regulates maize tassel spindle length. This study has further elucidated the genetic basis of maize tassel spindle length, while also providing excellent genetic targets and germplasm resources for the genetic improvement of maize tassel spindle length and yield. Full article

Autoimmune diseases are among the most prevalent diseases across the world with genetic and environmental factors that contribute to their etiology. Because the exact causes of autoimmune diseases are largely unknown, a Mendelian randomization (MR) approach is used here to examine the potential causal association between gene expression levels and disease risk across various tissues. Specifically, this study focuses on six autoimmune diseases including Crohn’s disease, ulcerative colitis, rheumatoid arthritis, multiple sclerosis, type 1 diabetes mellitus, and systemic lupus erythematosus. Several of these diseases are currently treatable with immunosuppressants that target specific genes, such as TNF-alpha, IL-23, CD20, and more. In this study, a two-sample MR analysis is performed with multitissue expression quantitative trait loci (eQTLs) and large-scale genome-wide association studies to investigate how gene expression can influence the risk of developing these diseases. Our results show that genes HLA-DQA1/2, HLA-DRB1/6, HLA-DQB2, C4A, CYP21A2, and HLA-DQB1-AS1 have a high causal effect across several diseases and tissues, and almost all of these findings originate from the major histocompatibility complex (MHC) region on Chromosome 6. Our findings support the current knowledge of genes associated with these diseases while also revealing novel genes that can be used for drug therapies in the future. Although several drug therapies currently exist to treat this selection of autoimmune diseases, we provide further insights into the main, common pathways responsible for autoimmune disease pathogenesis and discuss novel genes that lack research focus. Full article

The shape of fruits is a critical trait affecting the commercial value and consumer acceptance of horticultural crops. Genetic regulation of fruit shape involves complex interactions among multiple genes and environmental factors. This review summarizes recent advances in understanding the genetic mechanisms controlling fruit shape in several key horticultural crops, including tomato, pepper, cucumber, peach, and grape. We present the identification and characterization of genes and quantitative trait loci (QTLs) that influence fruit shape, focusing on the roles of genes such as OVATE, SUN, FAS, LC, ENO, GLOBE, CsSUN, CsFUL1, CsCRC, PpCAD1, PpOFP1, and VvSUN. This review highlights the importance of hormonal pathways, particularly those involving synthesis and concentration of cytokinins and brassinosteroids in shaping fruit morphology, and explores how these genes interact and form regulatory networks that collectively determine the final fruit shape. This knowledge provides a foundation for developing strategies to improve fruit quality and yield through genetic modification and breeding programs. Full article

Endometriosis (EMT) is a common gynecological disease with a strong genetic component, while its precise etiology remains elusive. This study aims to integrate transcriptome-wide association study (TWAS), Mendelian randomization (MR), and bioinformatics analyses to reveal novel putatively causal genes and potential mechanisms. We obtained summary-level data of the Genotype-Tissue Expression Project (GTEx), v8 expression quantitative loci (eQTL) data, and the genome-wide association study (GWAS) data of EMT and its subtypes from the R11 release results of the FinnGen consortium for analysis. GWAS data of modifiable risk factors were collected from IEU Open GWAS. Cross-tissue TWAS analyses were performed using the unified test for molecular signature (UTMOST), while functional summary-based imputation (FUSION) was employed for single-tissue TWAS analyses. Furthermore, we also conducted multi-marker analysis of genomic annotation (MAGMA) analyses to validate the significant associations. Subsequent Mendelian randomization (MR) and colocalization analysis elucidated the causal associations between the identified genes across various tissues and EMT. To further delve into mechanisms, two-sample network MR analyses were conducted. At last, bioinformatics analyses were employed to enhance our understanding of the functional implications and expression patterns of these identified genes. For EMT, 22 significant gene signals were identified by UTMOST, 615 by FUSION, and 354 by MAGMA. Ultimately, six genes, including CISD2, EFRB, GREB1, IMMT, SULT1E1, and UBE2D3, were identified as candidate susceptibility genes for EMT. Through similar procedures, we identified GREB1, IL1A, and SULT1E1 for EMT of the ovary, and we identified GREB1 for EMT of the pelvic peritoneum, EMT of rectovaginal septum and vagina, and deep EMT. In MR analyses, the expression of IMMT in 21 tissues, EFR3B in the adrenal gland, CISD2 in 17 tissues, and UBE2D3 in 7 tissues demonstrated causal relationships with EMT risk. In addition, CISD2, IMMT, and UBE2D3, across different tissues, exhibited strong colocalization with EMT (PPH4 > 0.7). Two-sample network MR analyses revealed that CISD2, EFR3B, and UBE2D3 could potentially regulate the levels of blood lipids and hip circumference so as to influence the risk of EMT. Furthermore, bioinformatics analyses confirmed our findings and delved into the biological functions of the identified genes. Our study unveiled seven novel candidate genes whose predicted expression was associated with the risk of EMT, providing new insights into the underlying genetic framework of EMT. These findings will facilitate a deeper comprehension of the tissue-specific transcriptional regulatory mechanisms associated with EMT, paving the way for optimizing the management and treatment of EMT. Full article

Fatty acid composition and its proportions are critical to the nutritional value and storage quality of rice (Oryza sativa L.) as the third major nutrient component in this staple food. This study involved crossing an indica rice variety, Huazhan (HZ), as the male parent, with a japonica variety, Nekken2, as the female parent, to produce the F1 generation. Subsequently, a population of 120 recombinant inbred lines (RILs) was developed through multiple generations of self-breeding. By utilizing a high-density molecular genetic linkage map and phenotypic data of four fatty acid components, we identified a total of 14 quantitative trait loci (QTLs) related to fatty acid composition across chromosomes 1, 3, 4, 6, 8, and 9. These included two QTLs for C₁₄ content, three for C_16:0 content, six for C_18:1 content, and three for C_18:2 content. Notably, the QTL qCOPT4.2 exhibited a high LOD score of 5.22. Within QTL intervals, genes such as OsACX3 and SLG affecting grain length were identified. The expression of candidate genes within these intervals was assessed and further analyzed by using quantitative real-time PCR. Genes such as LOC_Os01g15000, LOC_Os04g47120, LOC_Os04g49194, LOC_Os06g22080, LOC_Os06g23870, LOC_Os06g24704, LOC_Os06g30780, LOC_Os08g44840, and LOC_Os09g36860 were found to regulate fatty acid synthesis or metabolic pathways, potentially enhancing fatty acid content in rice. These QTLs are indispensable for breeding rice varieties with improved fatty acid profiles, offering new genetic resources for enhancing the nutritional and storage qualities of rice. Full article

The genetic regulation of goose meat quality traits remains relatively unexplored, and the underlying mechanisms are yet to be elucidated. This study aims to employ single nucleotide polymorphism (SNP) genotyping in conjunction with genome-wide association studies (GWAS) to investigate critical candidate regions and genes associated with the pH trait of meat in Sichuan white geese. A cohort of 203 healthy male Sichuan white geese was randomly selected and slaughtered at 70 days of age. Measurements were taken of meat pH, growth parameters, body dimensions, and post-slaughter traits. High-throughput sequencing on the Illumina HiSeq X Ten platform facilitated gene resequencing and SNP evaluation, and GWAS was employed to detect key genes within quantitative trait loci (QTL) intervals. The sequencing of 203 individuals yielded a total of 2601.19 Gb of genomic data, with an average sequencing depth of 10.89×. Through GWAS analysis, a total of 30 SNPs associated with pH were identified. These SNPs were identified on multiple chromosomes, including on chromosome 17 (chr: 23.57–23.68 Mb) and chromosome 13 (chr13: 31.52–31.61 Mb). By annotating these associated SNPs, nine candidate genes (including C19L2, AMFR, POL, RERGL, ZN484, GMDS, WAC) associated with the pH of goose meat were identified. The matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) genotyping of 10 SNPs centered on these nine candidate genes was confirmed. GO enrichment analysis revealed that genes within 1 Mb of the associated SNPs are significantly enriched in pathways involved in lymphocyte activation, in response to hydrogen peroxide, Salmonella infection, and other metabolic processes. This study explores the gene regulatory pathways influencing pH traits in goose meat and provides molecular markers for enhancing meat quality. These findings are expected to facilitate the advancement of molecular breeding programs in geese. Full article

Strategies to enhance rice productivity in response to global demand have been the paramount focus of breeders worldwide. Multiple factors, including agronomical traits such as plant architecture and grain formation and physiological traits such as photosynthetic efficiency and NUE (nitrogen use efficiency), as well as factors such as phytohormone perception and homeostasis and transcriptional regulation, indirectly influence rice grain yield. Advances in genetic analysis methodologies and functional genomics, numerous genes, QTLs (Quantitative Trait Loci), and SNPs (Single-Nucleotide Polymorphisms), linked to yield traits, have been identified and analyzed in rice. Genome editing allows for the targeted modification of identified genes to create novel mutations in rice, avoiding the unintended mutations often caused by random mutagenesis. Genome editing technologies, notably the CRISPR/Cas9 system, present a promising tool to generate precise and rapid modifications in the plant genome. Advancements in CRISPR have further enabled researchers to modify a larger number of genes with higher efficiency. This paper reviews recent research on genome editing of yield-related genes in rice, discusses available gene editing tools, and highlights their potential to expedite rice breeding programs. Full article

Flesh firmness is an important quality of pear fruits. Breeding cultivars with suitably low flesh firmness is one of the popular pear breeding goals. At present, SNP markers related to pear flesh firmness and genes affecting flesh firmness are still uncertain. In this study, a QTL analysis was performed, and the result showed that the position of 139.857 cM in lineage group 14 (LG14) had the highest average logarithm of odds (3.41) over two years. This newly discovered locus was identified as a flesh firmness-related QTL (qFirmness-LG14). The ‘C/T’ SNP was found in corresponding Marker1512129. The ‘C’ genotype is the high-firmness genotype, which is a dominant trait. The average firmness of fruits with genotype C is 21.4% higher than genotype without the C genotype. Transcriptome profiling was obtained between ‘Zaoshengxinshui’ and ‘Qiushui’ at five time points. Three candidate genes in the interval of qFirmness-LG14 might affect firmness. A gene of xyloglucan endotransglucosylase 1 (PpXTH1) was upregulated in ‘Qiushui’ at all five time points. Two transcription factors (PpHY5 and PpERF113) were upregulated in ‘Zaoshengxinshui’, which might be negative regulatory genes for high flesh firmness. The transcriptome results also isolated a large number of cell wall-related genes (e.g., Pectate lyase, Pectin acetylesterase, Pectin methylesterase, and 4-coumarate-CoA ligase) and transcription factors (e.g., ERF, WRKY). These genes are all potential upstream and downstream genes related to flesh firmness. In conclusion, this study provides valuable insights into the QTLs and molecular mechanisms associated with fruit firmness in Pyrus pyrifolia. Full article

The sunflower, an important oilseed crop and food source across the world, is susceptible to several pathogens, which cause severe losses in sunflower production. The utilization of genetic resistance is the most economical, effective measure to prevent infectious diseases. Based on the sunflower pangenome, in this study, we explored the variability of resistance gene analogs (RGAs) within the species. According to a comparative analysis of RGA candidates in the sunflower pangenome using the RGAugury pipeline, a total of 1344 RGAs were identified, comprising 1107 conserved, 199 varied, and 38 rare RGAs. We also identified RGAs associated with resistance against Sclerotinia sclerotiorum (S. sclerotiorum) in sunflower at the quantitative trait locus (QTL). A total of 61 RGAs were found to be located at four quantitative trait loci (QTLs). Through a detailed expression analysis of RGAs in one susceptible and two tolerant sunflower inbred lines (ILs) across various time points post inoculation, we discovered that 348 RGAs exhibited differential expression in response to Sclerotinia head rot (SHR), with 17 of these differentially expressed RGAs being situated within the QTL regions. In addition, 15 RGA candidates had gene introgression. Our data provide a better understanding of RGAs, which facilitate genomics-based improvements in disease resistance in sunflower. Full article

Exchangeable aluminum (Al) ions released from acidic soils with pH < 5.5 inhibit root elongation of crops, ultimately leading to yield reduced. It is necessary to identify the quantitative trait locus (QTLs) and candidate genes that confer toxicity resistance to understand the mechanism and improve tolerance of rapeseed. In this study, an F₂ segregating population was derived from a cross between Al-tolerance inbred line FDH188 (R178) and -sensitive inbred line FDH152 (S169), and the F_2:3 were used as materials to map QTLs associated with the relative elongation of taproot (RET) under Al toxicity stress. Based on bulked segregant analysis sequencing (BSA-seq), three QTLs (qAT-A07-1, qAT-A07-2, and qAT-A09-1) were detected as significantly associated with RET, and 656 candidate genes were screened. By combined BSA and RNA-seq analysis, 55 candidate genes showed differentially expressed, including genes encoding ABC transporter G (ABCG), zinc finger protein, NAC, ethylene-responsive transcription factor (ERF), etc. These genes were probably positive factors in coping with Al toxicity stress in rapeseed. This study provides new insight into exploring the QTLs and candidate genes’ response to Al toxicity stress by combined BSA-seq and RNA-seq and is helpful to further research on the mechanism of Al resistance in rapeseed. Full article