Search Results (356)

Fruit size is an important agronomic trait affecting the yield and commercial value of melon and a key trait selected for during domestication. In this study, two respective melon accessions (large-fruited M202008 and small-fruited M202009) were crossed, and developed biparental mapping populations of the F₂ generation (160 and 382 plants) were checked across two subsequent experimental years (2023 and 2024). The phenotypic characterization and genetic inheritance analysis showed that melon fruit size is modulated by quantitative genetics. Bulked segregant sequencing analysis (BSA-seq) identified a stable and effective quantitative trait locus (QTL, named Cmfs) controlling fruit size, localized to a 3.75 Mb region on chromosome 9. To better delineate the main-effect Cmfs locus, co-dominant polymorphic molecular markers were developed in this genetic interval, and genotyping was performed within the F₂ mapping populations grown across two years. QTL analysis of the phenotypic and genotypic datasets delimited the major-effect Cmfs locus interval for fruit length [2023: logarithm of odds (LOD) value = 6.16, 16.20% phenotypic variation explained (PVE); 2024: LOD = 5.44, 6.35% PVE] and fruit diameter (2023: LOD value = 5.48, 14.59% PVE; 2024: LOD = 6.22, 7.22% PVE) to 1.88 and 2.20 Mb intervals, respectively. The annotation analysis across the melon genome and comparison of resequencing data from the two parental lines led to the preliminary identification of MELO3C021600.1 (annotated as cytochrome P450 724B1) as a candidate gene related to melon fruit size. These results provide a better understanding for further fine mapping and functional gene analysis related to melon fruit size. Full article

Background/Objectives: Cardiovascular diseases are a global health issue with an increasing burden and are exacerbated by hypertension. High blood pressure is partly attributed to genetic variants that are generally not well understood or extensively studied in sub-Saharan African populations. Variants linked to blood pressure have been found through genome-wide association studies (GWASs), which were mostly conducted among European ancestry populations; however, limited research has been undertaken in Africa. The current study evaluated single-nucleotide polymorphisms (SNPs) of PCSK9, ABCA1, LPL, and PON1 in relation to blood pressure measurements of 1839 Ghanaian adults. Methods: Genotypes were extracted from data generated by the H3Africa SNP array. After adjusting for sex, age, smoking, and body mass index (BMI), inferential statistics were used to investigate the relationships between SNPs and blood pressure (BP) indices. Additionally, Bonferroni correction was used to adjust for multiple testing. Results: Diastolic blood pressure (DBP) and the minor allele T of the PCSK9 variant (rs17111557) were positively associated at p = 0.006 after covariate adjustments. Although this novel DBP-associated variant is located in the 3′ untranslated region (3′ UTR) of the PCSK9 gene, in silico functional prediction suggests it is an expression quantitative trait locus (eQTL) that may change the binding site of transcription factors, potentially altering the rate of transcription and impacting DBP in this Ghanaian population. Conclusions: Our findings highlight the role of genetics in hypertension risk and the potential of discovering new therapies targeting isolated diastolic blood pressure in this rural African population. 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

Wheat stripe rust (Puccinia striiformis f. sp. tritici, Pst) resistance and agronomic traits are crucial determinants of wheat yield. Elucidating the quantitative trait loci (QTLs) associated with these essential traits can furnish valuable genetic resources for improving both the yield potential and disease resistance in wheat. Lantian 31 is an excellent Chinese winter wheat cultivar; multi-environment phenotyping across three ecological regions (2022–2024) confirmed stable adult-plant resistance (IT 1–2; DS < 30%) against predominant Chinese Pst races (CYR31–CYR34), alongside superior thousand-kernel weight (TKW) and kernel morphology. Here, we dissected the genetic architecture of these traits using a total of 234 recombinant inbred lines (RILs) derived from a cross between Lantian 31 and the susceptible cultivar Avocet S (AvS). Genotyping with a 15K SNP array, complemented by 660K SNP-derived KASP and SSR markers, identified four stable QTLs for stripe rust resistance (QYrlt.swust-1B, -1D, -2D, -6B) and eight QTLs governing plant height (PH), spike length (SL), and kernel traits. Notably, QYrlt.swust-1B (1BL; 29.9% phenotypic variance) likely represents the pleiotropic Yr29/Lr46 locus, while QYrlt.swust-1D (1DL; 22.9% variance) is the first reported APR locus on chromosome 1DL. A pleiotropic cluster on 1B (670.4–689.9 Mb) concurrently enhanced the TKW and the kernel width and area, demonstrating Lantian 31’s dual utility as a resistance and yield donor. The integrated genotyping pipeline—combining 15K SNP discovery, 660K SNP fine-mapping, and KASP validation—precisely delimited QYrlt.swust-1B to a 1.5 Mb interval, offering a cost-effective model for QTL resolution in common wheat. This work provides breeder-friendly markers and a genetic roadmap for pyramiding durable resistance and yield traits in wheat breeding programs. Full article

Advances in spinning technology have increased the demand for upland cotton (Gossypium hirsutum L.) cultivars with superior fiber quality. However, progress in breeding for traits such as fiber length is constrained by limited phenotypic and genetic diversity within upland cotton. Introgression from Gossypium barbadense, a closely related species known for its superior fiber traits, offers a promising strategy. Sealand 883 is an obsolete upland germplasm developed through G. barbadense introgression and is known for its long and fine fibers. Previous studies have identified a fiber length quantitative trait locus (QTL) on Chromosome 25, designated qFL-Chr.25, in Sealand 883, conferred by an allele introgressed from G. barbadense. This study evaluated the effect of qFL-Chr.25 in near-isogenic introgression lines (NIILs) using Advanced Fiber Information System (AFIS) measurements. Across four genetic backgrounds, NIILs carrying qFL-Chr.25 consistently exhibited longer fibers, as reflected in multiple length parameters, including UHML, L(n), L(w), UQL(w), and L5%. Newly developed TaqMan SNP diagnostic markers flanking the QTL enable automated, reproducible, and scalable screening of large populations typical in commercial breeding programs. These markers will facilitate the incorporation of qFL-Chr.25 into commercial breeding pipelines, accelerating fiber quality improvement and enhancing the competitiveness of cotton against synthetic fibers. 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

Grain size is a crucial agronomic trait that significantly impacts yield potential in sorghum (Sorghum bicolor), making it a key focus for genetic improvement. In this study, we investigated the genetic basis of grain size variation using two contrasting sorghum accessions, PI302232 (small grain, Sg) and PI563512 (large grain, Lg). The 1000-grain weight, grain length, and grain width of Lg were 3.63-fold, 1.22-fold, and 1.65-fold higher than Sg, respectively. The 1000-grain weight in the F₂ segregating population derived from the cross Sg and Lg parents exhibited the highest phenotypic variation and followed a normal distribution in the three traits. Using bulked segregant analysis sequencing (BSA-seq) with small- and large-grain bulks from the F₂ population, two major quantitative trait loci (QTLs) for grain size were identified on chromosomes 1 and 3. Fine mapping with SSR markers narrowed the qGS1 locus to a 1.03 Mb region on chromosome 1 (Chr01: 22,001,448–23,035,593), containing 49 candidate genes. To narrow down potential candidate genes, transcriptome analysis of spike tissues from Sg and Lg at 0 and 14 days after heading revealed 3719 differentially expressed genes (DEGs), primarily enriched in “starch and sucrose metabolism” and “phenylpropanoid biosynthesis” pathways. Integrating fine mapping intervals and RNA-seq data, 6 DEGs were identified within the qGS1 region. Quantitative real-time PCR confirmed that 6 genes exhibited different expression at two stages. The expression and bioinformatics analysis showed Sobic.001G230700 was the most likely candidate gene for the qGS1 locus. This study provides new insights into the genetic regulation of grain size and a new target to improve grain size in sorghum. Full article

Background: Hippocampal sclerosis (HS) is a hallmark of mesial temporal lobe epilepsy (MTLE). However, genetic studies on MTLE patients with HS (MTLE-HS) remain limited, especially in East Asian populations. This study aimed to identify genetic variants associated with MTLE-HS and elucidate their biological relevance through integrative genomic and transcriptomic analyses. Methods: We conducted a genome-wide association study (GWAS) on 157 Korean epilepsy patients, including 52 MTLE-HS subjects and 105 non-acquired focal epilepsy individuals without HS as controls. The splicing and expression quantitative trait locus (sQTL and eQTL, respectively) effects of significant variants were analyzed using GTEx datasets. Transcriptomic data from the hippocampi of MTLE-HS subjects and an epilepsy mouse model were examined to assess TMEM14A expression. Gene correlation enrichment analysis was performed to investigate potential associations with epilepsy-related phenotypes. Results: The GWAS identified rs6924849, located downstream of TMEM14A, as significantly associated with MTLE-HS. The sQTL analysis revealed that rs6924849 induces abnormal TMEM14A splicing in hippocampal tissue. Transcriptomic analyses showed reduced TMEM14A expression in MTLE-HS hippocampi, while mice with pilocarpine-induced epilepsy exhibited a transient increase in TMEM14A expression during the acute phase post-status epilepticus. Gene correlation enrichment analyses linked TMEM14A to seizure-related phenotypes in both humans and mice. Conclusions: This study identifies rs6924849 as a novel genetic variant associated with MTLE-HS in an East Asian population. The dysfunctional splicing and altered expression of TMEM14A may contribute to the neuronal loss characteristic of HS, as TMEM14A regulates apoptosis. These findings emphasize the potential role of TMEM14A in MTLE-HS pathogenesis from genomic and transcriptomic perspectives. Full article

Overweight and obese individuals show lower mortality rates or better prognoses than those of normal weight in a variety of diseases, a phenomenon called the “obesity paradox”. An inverse association of adiposity with atherosclerosis has been observed in both humans and mice. To dissect phenotypic and genetic connections between the traits, 154 female and 145 male F2 mice were generated from an intercross between BALB/cJ and LP/J apolipoprotein E-deficient mice and fed a Western diet for 12 weeks. Atherosclerotic lesion size in the aortic root, body weight, plasma lipids, and glucose were measured, and genotyping was performed on miniMUGA SNP arrays. Quantitative trait locus (QTL) analyses on all F2 mice with sex as a covariate revealed four significant QTLs on chromosomes (Chr) 3, 6, 13, and 15 for atherosclerosis and three significant QTLs on Chr2, 7, and 15 for body weight. Chr15 QTL for atherosclerosis overlapped with one for body weight near 36 Mb. After adjusting for variation in body weight, Chr15 atherosclerosis QTL was downgraded from significant to suggestive linkage. Body weight was inversely correlated with atherosclerotic lesion sizes and accounted for more variance than a single other risk factor for atherosclerosis among F2 mice. Analysis of public data collected from two backcross cohorts revealed strong correlations between body weight and fat mass in adult mice (r ≥ 0.93; p ≤ 1.6 × 10⁻¹³⁶). Thus, the obesity paradox in atherosclerosis is partially attributable to shared genetic components that have an opposite effect on adiposity and atherosclerosis. Full article

Exploring the characteristics of maize’s tolerance to low-temperature stress is of great significance for enhancing maize’s adaptability to such stress and for developing valuable germplasm resources. In this study, a combined analysis of genomics, transcriptomics, and metabolomics was conducted on maize 245 F7 recombinant inbred lines (RILs) to screen for candidate genes and differential metabolites controlling the cold tolerance of maize during the germination stage. Bulked segregant analysis-sequencing (BSA-seq) located four candidate regions on chromosome 1 (qSGRL1-2, qSGRL1-3, and qSGRL1-4) and chromosome 10 (qSGRL10), which altogether contained 109 candidate genes. Combined with the transcriptome sequencing results, among the genes screened by quantitative trait locus sequencing (QTL-seq), seven genes (Zm00001eb043000, Zm00001eb043620, Zm00001eb043650, Zm00001eb043680, Zm00001eb043720, Zm00001eb043400, and Zm00001eb043490) were identified as common candidate genes related to the cold tolerance of maize during the germination stage. Combined with the metabolomic analysis results, low-temperature stress induced the differential expression of relevant genes, leading to the differential accumulation of metabolites such as L-glutamic acid, 4-aminobutyric acid, and Lysophosphatidylcholine (LPC). These results enrich the information for molecular marker-assisted selection of maize tolerance to low-temperature stress and provide genetic resources for the maize varieties breeding. Full article

Nickel (Ni) pollution poses significant threats to human health and crop development through the food chain. This study aimed to identify the novel genomic regions and superior alleles associated with Ni accumulation in wheat (Triticum aestivum L.) grains using genome-wide association analysis (GWAS) with a diversity panel of 207 bread wheat varieties. In total, five unique genetic loci associated with Ni accumulation were identified and they explained, on average, 8.20–11.29% of the phenotypic variation. Among them, three unique genetic loci were mutually verified by different statistical models in at least two environments, indicating their stability across different environments. Moreover, the highest effect quantitative trait nucleotide (QTN) AX-111126872 with a quantitative trait locus (QTL) hotspot on chromosome 6B identified in this study was not reported previously. Three putative candidate genes linked to Ni accumulation were revealed from the stable genetic loci. Among them, one gene associated with the stable genetic locus on chromosome 6B (AX-111126872) encodes the glycine-rich proteins (GRPs) as a critical factor influencing Ni accumulation in wheat grains. This study increases our understanding of the genetic architecture of Ni accumulation in wheat grains, which is potentially helpful for breeding wheat varieties without Ni toxicity. Full article

In spite of the increasing industrial cultivation of lavender (Lavandula angustifolia Mill.), no genetic linkage map and mapping of QTLs (quantitative trait locus) has been reported for Lavandula species. We present the development of a set of SSR (simple sequence repeat) markers and the first genetic linkage map of lavender following the genotyping of a segregating population obtained by the self-pollination of the industrial lavender variety Hemus. The resulting genetic map comprises 25 linkage groups (LGs) corresponding to the chromosome number of the lavender reference genome. The map includes 375 loci covering a total of 2631.57 centimorgan (cM). The average marker distance in the established map is 7.01 cM. The comparison of the map and reference genome sequence shows that LG maps cover an average of 82.6% of the chromosome sequences. The PCR amplification tests suggest that the developed SSR marker set possesses high intra-species (>93%) and inter-species (>78%) transferability. The QTL analysis employing the constructed map and gas chromatography/mass spectrometry (GC/MS) dataset of flower extracted volatiles resulted in the mapping of a total of 43 QTLs for the accumulation of 25 different floral volatiles. The comparison of the genome location of the QTLs and known biosynthetic genes suggests candidate genes for some QTLs. Full article

Sunflower Verticillium Wilt and Leaf Mottle (SVW), caused by Verticillium dahliae Kleb., is a globally prevalent disease affecting sunflower production. In this study, we identified a major quantitative trait locus (QTL) on chromosome 10 and other genomic regions associated with SVW resistance by integrating biparental and association mapping in sunflower populations from the National Institute of Agricultural Technology. Nine replicated field trials were conducted in highly infested V. dahliae reservoirs to assess disease incidence and severity. Both mapping populations were genotyped using double-digest restriction-site-associated DNA sequencing (ddRADseq). Association mapping with 18,161 SNPs and biparental QTL mapping with 1769 SNPs identified a major QTL on chromosome 10 explaining up to 30% of phenotypic variation for disease incidence at flowering and for the area under the disease progress curve for disease incidence, and which contributes to a lesser extent to disease severity reduction. Additional QTLs on chromosomes 17, 8, 9, 14, 13, and 11 were associated with reduced disease incidence, severity, or both. Candidate genes were identified within these associated regions, 39 of which are in the major QTL on Chromosome 10. These findings demonstrate the value of integrating complementary QTL mapping strategies for validating resistance loci and advancing sunflower breeding for SVW resistance. Full article

Background: The German Black Pied Dairy (DSN) cattle is an endangered dual-purpose breed considered an ancestor of the modern Holstein population. DSN is known for its high milk yield, favorable milk composition, and good meat quality. Maintaining a functional body structure is essential for ensuring sustained performance across multiple lactations in dual-purpose breeds like DSN. This study aims to identify candidate genes and genetic regions associated with conformation traits in DSN cattle through genome-wide association studies (GWAS). Methods: The analysis utilized imputed whole-genome sequencing data of 1852 DSN cows with conformation data for 19 linear traits and four composite scores derived from these traits. GWAS was performed using linear mixed models. Results: In total, we identified 118 sequence variants distributed across 24 quantitative trait locus (QTL) regions comprising 74 positional candidate genes. Among the most significant findings were variants associated with “Rump width” on chromosome 21 and “Teat length” on chromosome 22, with AGBL1 and SRGAP3 identified as the most likely candidate genes. Additionally, a QTL region on chromosome 15 linked to “Central ligament” contained 39 olfactory receptor genes, and a QTL region on chromosome 23 associated with “Hock quality” included eight immune-related genes, notably, BOLA and TRIM family members. Conclusions: Selective breeding for favorable alleles of the investigated conformation traits may contribute to DSN’s longevity, robustness, and overall resilience. Hence, continuous focus on healthy udders, feet, and legs in herd management contributes to preserving DSN’s positive traits while improving conformation. Full article

Improving wheat yield is essential to meet the increasing demand for food production. This study aims to identify quantitative trait loci (QTL) associated with grain traits and plant height (PH) in winter wheat, using a recombinant inbred line (RIL) population derived from a cross between Zhongke 331 and Nongda 399. The RIL population was genotyped using the 16K GenoBaits Wheat single nucleotide polymorphism (SNP) array. A genetic linkage map was established, comprising 14,868 SNPs and spanning 3846.91 cM, with an average interval of 1.11 cM between markers. These SNPs were categorized into 3463 SNP bin markers, with 1653, 1508, and 302 located in the A, B, and D sub-genomes, respectively. QTL analysis for thousand-grain weight (TGW), grain length (GL), grain width (GW), and PH revealed 61 QTL influencing these traits across six environments. Loci qPH-4B.1 and qPH-4D.1 were consistently detected in five environments. QTL clusters with pleiotropic effects that regulate multiple grain traits were identified on chromosomes 4B and 4D. Furthermore, the combination of qPH-4B.1 and qPH-4D.1 resulted in a reduced plant height compared to the presence of either locus alone, indicating an additive effect between these loci. Full article