Search Results (366)

Branching is a critical agronomic trait in flowering Chinese cabbage (Brassica rapa subsp. chinensis), influencing plant architecture and yield. In this study, there was a highly significant difference between CX010 (single primary rosette branches) and BCT18 (multiple primary rosette branches). Phenotypic analysis revealed significant differences in primary rosette branch numbers, with BCT18 showing up to 15 branches and CX010 displaying only one main stem branch. Genetic analysis indicated that branching was controlled by quantitative trait loci (QTL) with a normal distribution of branch numbers. Using bulked segregant analysis coupled with sequencing (BSA-seq), we identified a candidate interval of approximately 2.96 Mb on chromosome A07 linked to branching. Fine mapping narrowed this to a 172 kb region containing 29 genes, with BraA07g032600.3C (BrTCP1) as the most likely candidate. cDNA cloning of the BrTCP1 gene revealed several variations in BCT18 compared to CX010, including a 6 bp insertion, 10 SNPs, and two single-nucleotide deletions. Expression analysis indicated that BrTCP1 was highly expressed in the rosette stems of CX010 compared to BCT18, consistent with its role as a branching suppressor. The heterologous mutants in Arabidopsis confirmed the conserved role of BrTCP1 in branch inhibition. These findings reveal that BrTCP1 might be a key regulator of branching in flowering Chinese cabbage, providing insights into the molecular mechanisms underlying this trait and offering a framework for genetic improvement in Brassica crops. Full article

Bacterial blight (BB) disease is a serious stress that affects up to 80% of rice yield. Utilizing an elite resistant variety was previously thought to be an alternative way to control disease outbreaks. The indigenous upland rice variety ULR207 is a high-potential donor for the BB resistance breeding program. However, the quantitative trait loci (QTLs) associated with bacterial blight resistance in this variety have not yet been discovered. Therefore, QTLs associated with BB resistance need to be identified. In this study, we identified the QTLs associated with BB resistance in the F_2:3 population crossed between the BB resistance variety ULR207 and Maled Phai, as well as a susceptible variety, via QTL-seq analysis and bulk-segregant analysis. We found a new QTL-associated BB resistance locus (qBBchr8) mapped on chromosome 8. Five positions were candidates, including Os08g0110700, Os08g0115200, Os08g0131300, Os08g0139500, and Os08g0163900. Afterwards, Kompetitive Allele-Specific PCR (KASP) markers specific to the SNP variant and the position of each gene were designed. These markers, associated with the disease lesion length phenotype, were validated with another 178 individual plants of the F₂ population via single-marker analysis. This analysis revealed that the position Os08g0110700 was the strongest locus, with a PVE of 15.00%. The results suggest that this KASP SNP marker could be used to improve elite rice for BB resistance. Full article

Fruiting body formation in edible fungi is a critical development process for both scientific understanding and industrial cultivation, yet the underlying genetic mechanisms remain poorly elucidated. This study aimed to identify key genes regulating monokaryotic fruiting in Flammulina filiformis. A genetic segregation population was constructed through selfing purification and hybrid segregation of the FF002 strain, followed by mapping candidate genes with bulked segregant analysis sequencing (BSA-seq). A 10 kb genomic region on scaffold19 was identified, pinpointing the gene FV-L110034160, which encodes a U2 snRNP complex component involved in pre-mRNA splicing. A T→G SNP located 121 bp downstream of the ATG codon caused a serine-to-alanine substitution, disrupting a conserved domain and altering fruiting phenotypes. Phylogenetic analysis further revealed conservation of this gene in fungal genera. These findings elucidate a key regulatory gene controlling monokaryotic fruiting in F. filiformis, providing novel insights into fruiting body formation mechanisms and establishing a foundation for genetic studies in other edible fungi. 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

Background/Objectives: Karyomapping, a genome-wide SNP analysis, has drastically changed the approach to preimplantation genetic testing for monogenic disorders (PGT-M). However, there are cases in which karyomapping cannot be applied due to an insufficient number of informative SNPs. In this study, we aimed to analyze for the first time whether an insufficient number of informative SNPs is related to the family member used as a reference. Methods: For the karyomapping pre-clinical test, in addition to the couple, one of the DNA samples from an additional family member (children, parent, sibling) is used as a reference for phasing the SNP allele. We analyzed 263 couples who underwent karyomapping for PGT-M at the CHA Fertility Center from May 2020 to December 2022. karyomapping data was scanned on an Illumina NextSeq and analyzed through the BlueFuse Multi software version 4.5. Results: Preclinical karyomapping tests were performed in 263 couples with 58 monogenic diseases. Karyomapping was applicable to PGT-M for 241 (91.6%) couples and not applicable for 22 (8.4%) couples. The percentages of “not applicable” cases according to the reference family member were 1.3% (1/80) in the children group, 5.4% (8/148) in the parent group, and 37.1% (13/35) in the sibling group. Among the genetic diseases studied, couples with neurofibromatosis type 1 (6/27, 22.2%) and Kennedy disease (5/5, 100%) had the highest rate of non-applicable cases. Conclusions: Our results suggest that a child or parent may be better than the sibling for karyomapping in PGT-M. These data provide useful information for selecting a reference among the family members for preclinical karyomapping tests. Full article

Single-cell RNA sequencing (scRNA-seq) enables expression quantitative trait locus (eQTL) analysis at cellular resolution, offering new opportunities to uncover regulatory variants with cell-type-specific effects. However, existing tools are often limited in functionality, input compatibility, or scalability for sparse single-cell data. To address these challenges, we developed scQTLtools, a comprehensive R/Bioconductor package that facilitates end-to-end single-cell eQTL analysis, from preprocessing to visualization. The toolkit supports flexible input formats, including Seurat and SingleCellExperiment objects, handles both binary and three-class genotype encodings, and provides dedicated functions for gene expression normalization, SNP and gene filtering, eQTL mapping, and versatile result visualization. To accommodate diverse data characteristics, scQTLtools implements three statistical models—linear regression, Poisson regression, and zero-inflated negative binomial regression. We applied scQTLtools to scRNA-seq data from human acute myeloid leukemia and identified eQTLs with regulatory effects that varied across cell types. Visualization of SNP–gene pairs revealed both positive and negative associations between genotype and gene expression. These results demonstrate the ability of scQTLtools to uncover cell-type-specific regulatory variation that is often missed by bulk eQTL analyses. Currently, scQTLtools supports cis-eQTL mapping; future development will extend to include trans-eQTL detection. Overall, scQTLtools offers a robust, flexible, and user-friendly framework for dissecting genotype–expression relationships in heterogeneous cellular populations. Full article

Guadua angustifolia, a native bamboo species of ecological and economic importance, has been widely studied in Colombia. This study focused on evaluating the genetic diversity and population structure of G. angustifolia from six natural populations in the Department of Nariño, Colombia, using restriction site-associated DNA sequencing (RADseq). A total of 224,996 high-quality SNPs were identified across 48 individuals. Observed heterozygosity (Ho) ranged from 0.398 in Consacá to 0.78 in Tumaco, while expected heterozygosity (He) was lower in all cases, ranging from 0.291 to 0.597. All populations exhibited negative inbreeding coefficients (FIS), from −0.316 to −0.763, indicating an excess of heterozygotes and suggesting predominantly outcrossing reproduction. Analysis of molecular variance (AMOVA) revealed that most genetic variation resides within individuals (92.54%), with low differentiation among populations (7.46%). Population structure and phylogenetic analyses identified two main genetic clusters, likely reflecting the origin of the planting material. Our results revealed that chromosomes CM070500.1, CM070502.1, CM070503.1, CM070504.1, CM070508.1, and CM070510.1 exhibited the highest SNP density, suggesting the presence of genomic regions with elevated variability. In contrast, chromosomes with lower SNP density suggested conservated genes related to Flavone Synthase II. This study is the first to evaluate genetic materials from the Department of Nariño. These findings highlight the significant genetic diversity in G. angustifolia and the density of SNPs, and provide suggestions for conservation planning and the development of targeted breeding programs for this non-model tropical species. Full article

Background/Objectives: The regulatory SNPs (rSNPs) that disturb the binding of transcription factors (TFs) and alter the transcription levels of genes play a paramount role in the formation of different traits and are associated with many pathologies. The search for allele-specific events in RNA-seq and ChIP-seq data is a powerful genome-wide approach to detect rSNPs. Using this approach, we have identified the T → A rs2072580 substitution in the bidirectional SART3/ISCU promoter as a potential rSNP and demonstrated its association with colorectal cancer, relying on International Cancer Genome Consortium data. The goal of this work was to identify the TF binding site that is affected by the T → A substitution and to study the effect of this substitution on reporter gene expression in different plasmid constructs. Methods: Electrophoretic mobility shift assay (EMSA), cross-competition analysis and supershift assay, plasmid construction, and dual luciferase reporter assay. Results: The T → A rs2072580 substitution is shown to damage the binding site for ubiquitous TF CREB1 and to significantly decrease the activity of the heterologous promoter carrying the cassettes of two or three repeated CREB binding sites inserted upstream of it. However, the substitution disturbing the CREB1 binding site within the bidirectional promoter shared by SART3 and ISCU inhibits the promoter activity of only the SART3 gene but has no effect on the activity of the ISCU promoter. Conclusions: The performed comprehensive functional analysis of the T → A rs2072580 in the bidirectional SART3/ISCU promoter unambiguously implies it is an rSNP. These results form the background for further studies of this rSNP and its potential significance for various pathologies. Full article

Haplotype phasing refers to determining the haplotype sequences inherited from each parent in a diploid organism. It is a critical process for various downstream analyses, and numerous haplotype phasing methods for genomic single nucleotide polymorphisms (SNPs) have been developed. Allele-specific (AS) expression and alternative splicing play key roles in diverse biological processes. AS studies usually focus more on exonic SNPs, and multiple phased SNPs need to be combined to obtain better inferences. In this paper, we introduce an alignment-free algorithm HPTAS for haplotype phasing in AS studies. Instead of using sequence alignment to count the number of reads covering SNPs, HPTAS constructs a mapping structure from transcriptome annotations and SNPs and employs a k-mer-based approach to derive phasing counts from RNA-seq data. Using both next-generation sequencing (NGS) and the third-generation sequencing (TGS) NA12878 RNA-seq data and comparing with the most advanced algorithm in the field, we have demonstrated that HPTAS achieves high phasing accuracy and performance and that transcriptome data indeed facilitates the phasing of exonic SNPs. With the continued advancement of sequencing technology and the improvement in transcriptome annotations, HPTAS may serve as a foundation for future haplotype phasing methods. Full article

Grain yield establishment is a complex progress and the genetic basis of one of the most important yield components, 100-kernel weight, remains largely unknown. Here, we employed a double haploid (DH) population containing 477 lines which was developed from a cross of two maize elite inbred lines, PHBA6 and Chang7-2, to identify quantitative trait loci (QTL) that related to 100-kernel weight. The phenotypes of the DH population were acquired over three years in two different locations, while the DH lines were genotyped by next-generation sequencing technology of massively parallel 3ʹ end RNA sequencing (MP3RNA-seq). Eventually, 28,874 SNPs from 436 DH lines were preserved after SNP calling and filtering and a genetic map with a length of 837 cM was constructed. Then, single environment QTL analysis was performed using the R/qtl program, and it was found that a total of 17 QTLs related to 100-kernel weight were identified and distributed across the whole genome except chromosomes 5 and 6. The total phenotypic variation explained by QTLs detected in three different environments (BJ2016, BJ2107, and HN2018) was 22.2%, 32.9%, and 51.38%, respectively. Among these QTLs, three of them were identified across different environments as environmentally stable QTLs and explained more than 10% of the phenotypic variance each. Together, the results provided in this study preliminarily revealed the genetic basis of 100-kernel weight and will enhance molecular breeding for key agronomic kernel-related traits in maize. Full article

A breeding program of Asian seabass (Lates calcarifer, also called barramundi) was established for sustainable aquaculture in Thailand. Estimated breeding values (EBVs) for growth of the base population (G0, 51 families, N = 1655) were evaluated. Fish exhibited either high (HEBV, averaged body weight = 1036.80 ± 250.80 g, N = 133) or low (LEBV, averaged body weight = 294.50 ± 167.20 g, N = 147) growth EBVs, and their parental fish (N = 26) were analyzed by Specific Locus Amplified Fragment Sequencing (SLAF-Seq). An average of 159,769 SLAF tags/sample was generated, covering 13.79-fold of the genome size, and 225,498 SNPs were applied for population genomics. Observed (H_o) and expected (H_e) heterozygosity values were 0.224 and 0.308, 0.178 and 0.246, and 0.184 and 0.305, respectively. Polymorphic information content (PIC) ranged from 0.205–0.251. A selective sweep was performed based on Fst, and nucleotide polymorphism (π) revealed significant differences between allelic contents of growth- and immune-related genes in HEBV and LEBV populations. Kinship analysis revealed that 84.38% of examined fish showed r values < 0.2, and population admixture analysis revealed three subpopulations in HEBV and four subpopulations in LEBV groups. Fish that possessed a single cluster were found in each subgroup of both populations, along with those exhibiting mixed ancestral clusters. This information is critically important for further applications in our ongoing seabass improvement breeding program. Full article

Maize is a crucial food crop and industrial raw material, significantly contributing to national food security. Aphids are one of the most prevalent and destructive pests in maize production, necessitating the exploration of pest-resistant germplasm and the development of resistant varieties as the most fundamental and effective strategy for mitigating aphid-induced damage. This study established an aphid resistance evaluation system and identified 17 elite resistant inbred lines through multi-year screening. A genome-wide association study (GWAS) revealed 22 significant single-nucleotide polymorphisms (SNPs) associated with aphid resistance, including genes involved in benzoxazinoid (Bx) biosynthesis (such as Bx2), insect resistance-related transcription factors (such as WRKY23), plant lectins, and other resistance pathways. RNA-seq analysis of the samples before and after aphid infestation detected 1037 differentially expressed genes (DEGs) in response to aphid infestation, with KEGG enrichment highlighting benzoxazinoid biosynthesis and starch/sucrose metabolism as primary response pathways. Integrating GWAS and RNA-seq results revealed the presence of several benzoxazinoid synthesis-related genes on the short arm of chromosome 4 (Chr4S). FMqRrm1, a Kompetitive Allele-Specific PCR (KASP) marker, was derived from the Chr4S region. We subsequently utilized this marker for marker-assisted selection (MAS) to introgress the Chr4S region from the aphid-resistant inbred line into two aphid-susceptible inbred lines. The results demonstrated that the Chr4S favorable allele significantly reduced aphid occurrence by 1.5 to 2.1 grades. This study provides a critical theoretical foundation and practical guidance for understanding the molecular mechanism of aphid resistance in maize and molecular breeding for aphid resistance. Full article

Background/Objectives: Whole-genome sequencing (WGS) data provide valuable information about the genetic architecture of local livestock but have not yet been applied to Russian native goats, in particular, the Orenburg and Karachay breeds. A preliminary search for selection signatures based on single nucleotide polymorphism (SNP) genotype data in these breeds was not informative. Therefore, in this study, we aimed to address runs of homozygosity (ROHs) patterns and find the respective signatures of selection overlapping candidate genes in Orenburg and Karachay goats using the WGS approach. Methods: Paired-end libraries (150 bp reads) were constructed for each animal. Next-generation sequencing was performed using a NovaSeq 6000 sequencer (Illumina, Inc., San Diego, CA, USA), with ~20X genome coverage. ROHs were identified in sliding windows, and ROH segments shared by at least 50% of the samples were considered as ROH islands. Results: ROH islands were identified on chromosomes CHI3, CHI5, CHI7, CHI12, CHI13, and CHI15 in Karachay goats; and CHI3, CHI11, CHI12, CHI15, and CHI16 in Orenburg goats. Shared ROH islands were found on CHI12 (containing the PARP4 and MPHOSPH8 candidate genes) and on CHI15 (harboring STIM1 and RRM1). The Karachay breed had greater ROH length and higher ROH number compared to the Orenburg breed (134.13 Mb and 695 vs. 78.43 Mb and 438, respectively). The genomic inbreeding coefficient (F_ROH) varied from 0.032 in the Orenburg breed to 0.054 in the Karachay breed. Candidate genes associated with reproduction, milk production, immunity-related traits, embryogenesis, growth, and development were identified in ROH islands in the studied breeds. Conclusions: Here, we present the first attempt of elucidating the ROH landscape and signatures of selection in Russian local goat breeds using WGS analysis. Our findings will pave the way for further insights into the genetic mechanisms underlying adaption and economically important traits in native goats. 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