Search Results (365)

A distinct form of chronic kidney disease of unknown etiology (CKDu) has emerged in tropical regions of Sri Lanka, predominantly affecting individuals aged 30–60 years in the North Central Province. Unlike conventional chronic kidney disease (CKD), CKDu occurs independently of diabetes or hypertension and is characterized by tubulointerstitial damage, including tubular atrophy, interstitial inflammation, and fibrosis. Epidemiological studies showed familial clustering, suggesting an underlying genetic predisposition. This study aimed to identify genetic variants associated with CKDu in Sri Lankan populations using whole-exome sequencing (WES). Eighty-six individuals (47 CKDu patients and 39 controls) were recruited from endemic and non-endemic regions. Physiological, biochemical, and geographic parameters were recorded. DNA extracted from blood was subjected to WES to identify variants associated with CKDu. Results: A total of 171 unique variants across 121 genes were identified. Among the most prevalent genes were ATXN3, LFNG, PNLDC1, LINC02456, and HLA-DRB1. In the case–control comparison, only LFNG showed statistically significant enrichment in affected individuals, whereas signals in ATXN3, PNLDC1, and LINC02456 were not statistically significant, but have an association with renal dysfunction, and thus are included as hypothesis-generating variant observations. HLA-DRB1 variants showed trends toward a protective haplotype. LFNG showed the greatest prevalence in affected individuals (71.7%), followed by PNLDC1 (63%), ATXN3 (56%), FIP1L1 (41%), and HLA-DRB1 (32%). Conclusion: Findings suggest genetic variants in combination with environmental factors may contribute to CKDu susceptibility in the Sri Lankan population. We underscore the multi-factorial nature of CKDu and highlight the need for integrative genomic and environmental research to elucidate disease mechanisms and inform targeted prevention strategies. Full article

Seed size-related traits are pivotal determinants of yield and appearance quality in peanut breeding programs. This study aimed to (1) investigate the genetic diversity and population structure of 120 peanut accessions (including landraces, cultivated varieties, and introduced germplasm) through genome-wide resequencing, and (2) identify key genomic regions and candidate genes associated with seed size-related traits using Genome-wide association studies (GWAS) and haplotype analysis. The population relationship and the evolution of peanuts using a large-scale single nucleotide polymorphism (SNP) dataset generated from the genome-wide resequencing of 120 peanut accessions was explored. GWAS and haplotype analysis were employed to identify regions and candidate genes associated with seed size-related traits. GWAS and haplotype analysis identified a novel region associated with HSW and SW on chr14, and a haplotype that was more dominant in HSW and SW. Two candidate genes were screened by combining LD decay distance, SNP variation information and gene function annotations. Full article

Background/Objectives: Non-indigenous species are increasingly reshaping Mediterranean marine ecosystems, particularly under ongoing climate warming. The rayed pearl oyster Pinctada radiata, a thermophilic species originating from the Indo-Pacific region, is one of the earliest and most successful invaders in the Mediterranean Sea and has recently established populations in the Adriatic Sea. Methods: This study integrates preliminary shell morphometric data with molecular genetic analyses based on mitochondrial cytochrome c oxidase subunit I (COI) and nuclear internal transcribed spacer 2 (ITS2) markers to confirm species identity and examine patterns of genetic variation in comparison with other Mediterranean Sea regions and the Persian Gulf. Results: Phylogenetic analyses based on COI confirmed P. radiata as a distinct and well-supported monophyletic lineage, whereas the nuclear ITS2 marker showed limited resolution and interspecific overlap. Mediterranean and Adriatic populations showed low COI haplotype and nucleotide diversity and weak genetic structuring, consistent with recent colonization and secondary expansion, whereas Persian Gulf populations were more genetically diverse. Conclusions: Future studies should employ larger sample sizes and broader geographic sampling across both the Mediterranean Sea and the full native range of P. radiata, combined with high-resolution genome-wide nuclear markers, to better resolve connectivity and invasion dynamics. Full article

Soybean (Glycine max L. Merr.) is a globally significant oilseed crop. The number of four-seeded pods in the lower part (FSPL) serves as a critical yield component under high-density planting. To date, numerous crop-specific traits have been investigated in multiple breeding studies of soybean; however, little attention has been paid to studies on FSPL. Hence, in this study, we investigated the genetic basis of FSPL using a recombinant inbred line population (RIL3613) across four environments. The segregated genetic mapping population was cultivated during the field experiments, and the collected phenotypic dataset of FSPL exhibited quantitative genetics and high broad-sense heritability (0.724), indicating stable genetic control. Further, we performed quantitative trait locus (QTL) mapping using raw means in each environment and identified 10 QTL, explaining phenotypic variations (PVE) ranging from 0.10% to 2.94%. Among the identified environmentally stable QTL, qFSPL-15-1 was consistently detected across all environments. Two candidate genes [Glyma.15G034100 (encoding lysophosphatidic acid acyltransferase 2) and Glyma.15G034200 (encoding an RNA-binding protein)] were predicted within the flanking genomic interval. The allele frequencies of haplotype combinations of Hap1: Pro2 + CDS1 for Glyma.15G034100 and Hap3: Pro3 + CDS1 for Glyma.15G034200 in wild soybeans (26.6–30.0%) were larger than improved cultivars (52.6–53.4%). We believe that our current findings elucidate the molecular mechanisms regulating lower-pod formation and provide precise genetic targets for marker-assisted selection in high-yield soybean breeding. Full article

Background: Gametophytic self-incompatibility (GSI) controlled by a multi-allelic S-locus, is inferred to have evolved before the spilt of the Rosidae and Asteridae. In Rosaceae, molecular characterisation of the genera Prunus and Malus reveals that different numbers of genes determine GSI specificity. In Prunus, one pistil-expressed (female) gene and one pollen (male) gene encode a series of stylar RNase (S-RNase) alleles and series of S-haplotype-specific F-box (SFB) alleles, respectively, thereby determining the female and male specificity. In contrast, in Malus, GSI specificity is controlled by one pistil gene and multiple pollen genes, known as SFB-brothers (SFBBs), which encode a series of S-RNase and SFBB alleles, respectively, within the S-locus, to determine female and male specificity. Despite these advances, the molecular mechanisms of these two genera remain largely unknown, and it is still uncertain how GSI originated or which factors shape the orientation, evolution, and function of the S-locus. Methods: Therefore, in this study, we applied a holistic integrative approach combining analyses of gene distribution, phylogenetic inference, biogeographic history, selective pressures, co-evolution, and protein interaction networks across three Prunus genomes (P. dulcis, P. persica, and P. avium) to elucidate the evolutionary forces driving sexual diversity and molecular specificity of GSI within the Rosaceae. Results: Our results indicated that rapid diversification of the Prunus S-locus was due to the repeated duplication events in the SFB, SLF, and S-RNase genes producing both functional and non-functional duplicates. Conclusions: In Rosaceae, diversity of S-locus mechanisms is shaped by lineage-specific selection, functional divergence, co-evolution of pistil- and pollen-expressed components, dynamic protein-interaction networks, geological history and climatic change. Full article

Background/Objectives: Ischemic sudden cardiac death (SCD) is a devastating event that often occurs in apparently healthy individuals. Genetic susceptibility may play a key role in the pathogenesis of such ischemic events. This study aimed to investigate the correlations between Human Leukocyte Antigen (HLA) alleles, genotypes, and haplotypes and SCD to identify potential risk factors. This study also investigated three Single-Nucleotide Polymorphisms (SNPs) in the MYBPC3 gene and their association with SCD. Methods: We conducted an exploratory study between 2022 and 2024 in North-Western Transylvania (Romania) on 81 autopsy-confirmed SCD cases, compared with 162 controls for HLA typing, and with 96 controls for SNPs. HLA analysis of the HLA-DRB1 and HLA-DQB1 genes was performed using low-resolution SSP-PCR. The three SNPs in the MYBPC3 gene: rs142317339 (C > T), rs148808089 (G > A), and rs11570076 (G > A) were performed using a Real-Time PCR System. Results: The HLA-DRB1*07 allele has reduced odds of SCD, after adjustment for age and sex, and the HLA-DRB1*08 allele showed a trend toward increased odds. No statistically significant associations were detected at the allele or genotype level for HLA-DQB1. Haplotype-based analyses further revealed that genetic susceptibility is driven predominantly by low-frequency protective haplotypes rather than by common risk haplotypes, with several combinations conferring strong or moderate protection (HLA-DRB1*07~HLA-DQB1*03, HLA-DRB1*07~HLA-DQB1*02, and HLA-DRB1*15~HLA-DQB1*05). No statistically significant association was found between the three SNPs studied in the two groups, and their frequencies were very low. Conclusions: Specific HLA-DRB1 and HLA-DQB1 alleles and haplotypes may be associated with protection against SCD, supporting a possible immunogenetic role in SCD and the identification of genetic risk markers. Full article

Fruit size and weight are valuable characteristics for cherry breeders, mainly because of their higher market price. Several molecular markers have been developed in recent years and have been correlated with fruit weight. In cherries, FW_G2a was identified as a promising hotspot for fruit size and weight characteristics. Two markers flanking that region were taken into consideration in this study. The local sweet and sour cherry collection in Érd, Hungary, was analyzed using molecular markers to identify possible correlations between the markers and phenotypes. The duration of phenotypic observations varied from 3 years in sour cherry to 5 years in sweet cherry. In our study, we observed correlations between fruit size and weight and the molecular markers of our germplasm collection. We confirmed the previously published association of haplotypes 190–255 and 192–233 with large and small fruit size, respectively, in sweet cherry. Individual alleles of both markers were identified, showing moderate to strong correlations with large and small fruit size in sweet cherry. In tetraploid sour cherry, a higher number of unique allelic combinations were found due to the higher level of ploidy compared to sweet cherry. Individual alleles were detected with moderate positive correlations with fruit size, while one allele showed a strong negative correlation with fruit dimension-related traits. These markers were found to be useful for the characterization of fruit size characteristics, for population selection and for the differentiation of the Hungarian germplasm collection. Full article

The Skewed5 Similar (SKS) genes play a crucial role in plant growth and development, as well as in responding to abiotic stress, by regulating cell wall remodeling and maintaining reactive oxygen species (ROS) homeostasis. The SKS gene family has not yet been thoroughly studied in soybean. We conducted a comprehensive genome-wide analysis of 88 GmSKS genes, systematically elucidating their gene structures, conserved protein domains, collinearity relationships, and phylogenetic relationships, to identify potential candidate genes associated with soybean tolerance to salt stress. The GmSKS genes are distributed across 18 chromosomes, and the expansion of this gene family is primarily attributed to the combined effects of tandem duplications and segmental duplications. Different tissue-specific expression patterns among GmSKS members were identified using expression profiling. Analysis of cis-regulatory elements further revealed that the promoter region may be involved in plant hormone signaling pathways and responses to abiotic stress. Furthermore, quantitative reverse transcription PCR (qRT-PCR) analysis showed that 21 of the 22 examined GmSKS genes were significantly upregulated under salt stress, while one was significantly downregulated. This expression pattern may be linked to salt tolerance mechanisms in soybean under stress conditions. Haplotype and selection trend analyses of GmSKSs revealed that varieties carrying GmSKS5^1123G, GmSKS22^1727G, GmSKS43^50T and GmSKS71^1213T are highly enriched in cultivated soybeans and have undergone artificial selection. This study provides basic information for the identification of salt stress-responsive gene resources of GmSKS family genes, and provides novel theoretical insights for the functional identification and cloning of soybean salt tolerance-related genes. Full article

Pepper (Capsicum annuum L.) is a significant vegetable crop, and its fruits tend to accumulate cadmium (Cd). The background value of soil Cd in the main pepper-producing area (southwest China) is relatively high, which results in a high risk of Cd contamination in pepper and its products in this area. Therefore, the cultivation of pepper varieties with low Cd accumulation is vital for ensuring food safety and the development of the pepper industry. A prior genome-wide association study (GWAS) identified the heavy-metal-transporting ATPase gene (CaHMA1) as a crucial gene that facilitates Cd accumulation in pepper fruits. Herein, three semi-thermal asymmetric reverse PCR (STARP) molecular markers (STARP1, STARP2, and STARP3) were designed according to three single-nucleotide polymorphism (SNP) loci (Chr02_154361710, Chr02_154362005, and Chr02_154367255) identified in the intronic region of CaHMA1. Subsequently, these STARP molecular markers were validated using 70 pepper core germplasms with known genotypes. The results indicated that the STARP markers exhibited an identity of over 95% with the corresponding SNP markers. By utilizing the aforementioned STARP markers, the pepper population was divided into two haplotypes (Hap) (Hap1 and Hap2). Under Cd stress, the average Cd content in the fruits of Hap2 pepper was 27.01% lower than that of Hap1. Collectively, these three STARP markers can rapidly and accurately identify the Cd accumulation capacity of pepper varieties with different haplotypes. Furthermore, 24 SNPs were additionally screened from 150 core SNPs according to the criteria of minor allele frequency (MAF) > 0.40, polymorphism information content (PIC) > 0.35, observed heterozygosity (OH) < 0.6, and uniform distribution across 12 chromosomes. These 24 SNPs were combined with the 3 SNPs from the STARP marker developed in the intron region of CaHMA1, and a pepper DNA fingerprinting map was successfully constructed. This DNA fingerprinting map achieved a 100% identification efficiency for 216 pepper germplasm accessions and was able to distinguish the Cd accumulation capacities among different pepper germplasm accessions. In conclusion, this study provides reliable STARP markers for the marker-assisted selection (MAS) breeding of pepper varieties with low Cd accumulation. Moreover, the constructed DNA fingerprinting map possesses dual functions, identifying varieties and evaluating Cd accumulation traits that have high practical value in pepper breeding. Full article

The black carp (Mylopharyngodon piceus) is an ecologically and economically important freshwater fish native to China and neighbouring regions, but its wild stocks have declined sharply in recent decades. We analysed mitochondrial cytochrome b (Cyt b) sequences from 100 individuals collected in 2008–2009 from four Yangtze River, two Pearl River and one Red River populations to assess genetic diversity and structure as a pre-ban baseline for maternal lineages. Sixteen polymorphic sites defined 17 haplotypes, with a single dominant haplotype (Hap2) shared across all populations. Haplotype diversity was high but nucleotide diversity low, and neutrality tests together with mismatch-distribution analyses were consistent with a recent Late Pleistocene demographic expansion. Pairwise FST values ranged from negligible differentiation among middle–lower Yangtze populations to pronounced differentiation between the upstream Yangtze population (SS) and middle–lower populations and between the Yangtze and the combined Pearl–Red basins, whereas Pearl and Red River populations showed no significant divergence and high mitochondrial homogeneity, consistent with substantial historical connectivity. Overall, the Cyt b data indicate low mitochondrial diversity and shallow but significant inter-basin structuring, providing preliminary mtDNA-based evidence that Yangtze and Pearl–Red populations represent candidate conservation and management units, and highlighting the need for nuclear genomic markers and contemporary sampling to refine drainage-scale units and evaluate recent management effects. Full article

Objective: To analyze the association between the IRF5 gene variants rs3807135, rs3757385, and rs3778754 and mRNA expression levels in patients from western Mexico diagnosed with melanoma. Methods: An analytical cross-sectional study was conducted including 374 individuals (153 patients with newly diagnosed melanoma and no previous treatment, and 221 controls). The melanoma group was matched to the reference group. Genotyping of the rs3807135 (T>C), rs3757385 (T>G), and rs3778754 (C>G) variants was performed using the allelic discrimination method with TaqMan^® probes. Relative mRNA expression was quantified by qPCR using the 2^–ΔΔCT method, comparing IRF5 expression levels with those of the housekeeping gene GAPDH. Statistical analyses were performed in R, and allelic and genotypic frequencies were compared between patients and controls using the Chi-square test. Results: No statistically significant associations were identified between IRF5 SNVs rs3807135, rs3757385, and rs3778754 and melanoma risk. The haplotypic pattern comprised TTC, CGG, and CGC, with CGG showing a non-significant protective tendency. The mean relative expression of IRF5 was lower in melanoma patients compared with controls (≈0.39 vs. 1.0; Δ = 0.61), although this difference did not reach statistical significance (U = 1725; p = 0.841). These findings suggest a modest modulatory effect of IRF5 at the haplotypic level, likely driven by combined variant effects. Conclusions: In conclusion, the present study did not identify statistically significant associations between the IRF5 single-nucleotide variants rs3807135, rs3757385, and rs3778754 and melanoma risk in the analyzed population from western Mexico. Likewise, no significant differences in allele or genotype distributions were observed between melanoma patients and control individuals. These findings suggest that the evaluated IRF5 genetic variants do not constitute major susceptibility factors for melanoma in this cohort. Full article

Background: 22q11.2 deletion syndrome (DiGeorge Syndrome) is a rare disorder that involves a de novo hemizygous microdeletion within the 22q11.2 chromosomal locus. Individuals affected by this condition display a wide array of clinical phenotypes as well as haplotype sequences, which render understanding the genotype–phenotype relationship quite difficult. Additionally, the complex structure of the 22q11.2 low-copy repeats (LCRs), which usually inhibits sequencing efforts, has complicated the study of possible breakpoints that instigate the deletion events. In this study, 22q11.2 deletion syndrome is investigated on a genomic and phenotypic level for the purpose of determining the impact of each deletion type and identifying possible candidate breakpoints. Methods: In the present study, a systematic review combined with a secondary genomic analysis has been executed following PRISMA guidelines using PubMed and Scopus publications in order to estimate its holistic genomic map, genomic functional elements, and key genomic regions such as LCRs. A statistical content analysis of the affected chromosomal regions was also performed. Groups of functional elements with common traits were composed, and their contribution to the deletion events was investigated. Finally, the 22q11.2 repeat regions were screened for palindromic AT-rich repeats. Results: Of the 8202 unique publications studied in this work, only 65 met the inclusion criteria. The estimated genomic map of 22q11.2 deletion syndrome in the secondary genomic analysis revealed 11 distinct microdeletions occurring between eight LCRs, and a new repeat region within the CES region (CESRR), of which the LCR22A-LCR22D deletion was the most frequently reported. Last but not least, the palindromic analyses indicated eight critical groups as candidate breakpoints that potentially form four distinct patterns, and ten palindromic AT-rich repeat (PATRR) regions were identified amongst LCR22A, LCR22B, LCR22D, LCR22F and LCR22H. Conclusions: The study results validate the differentiating clinical contribution between the proximal and the distal segments. Eight novel candidate breakpoints and five new PATRRs were identified that require further study to establish their involvement in 22q11.2 microdeletion events. Full article

Malaria in pregnancy remains a major driver of poor maternal and neonatal health outcomes in sub-Saharan Africa. For decades, intermittent preventive treatment in pregnancy (IPTp), with sulphadoxine-pyrimethamine (SP), has mitigated malaria-associated health risks, but concerns have been raised regarding accumulated Plasmodium falciparum dihydrofolate reductase (dhfr) and dihydropteroate synthase (dhps) mutations on the efficacy of SP. Western Kenya, including Busia County, is a high malaria transmission setting where molecular surveillance of dhfr and dhps mutations remains limited. This study assessed the prevalence and haplotype structure of dhfr and dhps mutations in P. falciparum isolates from Busia County, Kenya. A total of 66 samples of P. falciparum isolates collected from patients attending Matayos Sub-County Hospital between November 2024 and January 2025 were analysed. PCR amplification and Sanger sequencing targeted dhfr codons C50R, N51I, C59R, S108N/T, I164L, and dhps codons I431V, S436A/F, A437G, K540E, A581G, and A613S/T to determine mutation frequencies, haplotypes, and combined dhps and dhfr haplotype profiles. High frequencies of dhfr and dhps mutations were observed across the parasite isolates. The most common dhfr substitutions included N51I (85.2%) and C59R (75.4%), while S108N (32.8%) and S108T (19.7%) were detected at lower frequencies. Dhfr haplotypes identified included N51I + C59R, N51I + C59R + S108N, and a N51I + C59R + S108T + I164L variant. The I164L mutation was detected at a frequency of 18.0% and was observed exclusively on a non-canonical S108T background (19.7%). Dhps haplotypes were dominated by A437G (92.3%), K540E (40%) alone, and the A437G + K540E double mutant. Combined dhfr and dhps haplotype analyses revealed circulation of classical dhfr triple-mutant (N51I + C59R + S108N) backgrounds with dhps A437G. Quintuple haplotypes (dhfr N51I + C59R + S108T + I164L with dhps A437G) and rare complex haplotypes incorporating both I164L and K540E or I164L and S436F were also detected. These findings indicate the persistence and circulation of both canonical and non-canonical dhfr and dhps haplotypes in P. falciparum isolates from Busia County. This study highlights the need for continuous molecular and phenotypic surveillance to clarify the functional and epidemiological significance of parasites carrying S108T and I164L mutations, and to inform IPT policy. Full article

Background/Objectives: Arctic foxes (Vulpes lagopus) exemplify the vulnerability of Arctic species to global warming and anthropogenic impacts, including habitat loss, interspecific competition with temperate species, pollution (chemical and biological), and declining prey abundance. Despite their ecological importance, the evolutionary and demographic history of the species is still incompletely understood, and the colonization history of isolated island populations, such as the one on Iceland, remains unresolved. Methods: We analyzed 80 mitochondrial genomes from across the Holarctic, including 22 Icelandic individuals. We combined phylogenetic reconstruction, coalescence-dating, haplotype network analysis, and diversity metrics to infer matrilineal relationships and colonization history. Results: Seven distinct haplogroups (Hg.1–Hg.7) were identified, which diverged ≥65 thousand years ago (kya). Two haplogroups were broadly distributed across Fennoscandia, Russia, Iceland, and Canada, while others were region-specific: two in eastern Russia (respectively diverging ~171 kya and ~89 kya), one in central Russia (~66 kya), and two in Iceland (~95 kya and ~66 kya). Three haplogroups were detected in Iceland, and at least four unrelated founding females are required to explain the current matrilineal diversity. One haplogroup contained sufficient representatives for molecular dating, yielding a minimum colonization age of ~5600 years, assuming in situ diversification. Observed matrilineal diversity in Iceland does not uniquely identify a single geographic source. Conclusions: Arctic foxes’ distribution and diversity reflect repeated cycles of isolation and expansion as circumpolar environments shifted. Broader sampling across the Nearctic is critical to clarify the timing, sources, and routes of Iceland’s colonization, as Nearctic sampling was limited to a single Canadian mitogenome. Full article

The grapevine (Vitis vinifera L.) is one of the most important horticultural crops, with thousands of varieties cultivated worldwide. In this study, we analyzed chloroplast SNV markers using a whole-genome shotgun sequencing approach to investigate the genetic diversity and phylogeny of 409 cultivated V. vinifera accessions originating from nine countries across Southeast and Central Europe, as well as a heterogeneous set of additional accessions maintained by INRAE. Shotgun sequencing allowed high coverage, enabling the detection of 93 SNVs across 24 chloroplast genes, including 11 non-synonymous variants. The ycf1 gene showed the highest variability, consistent with its role in species differentiation. Haplotype analysis revealed 102 distinct haplotypes, with clear geographic structuring: ATT predominated in the eastern Mediterranean, ATA in western Europe, and GTA mainly in a heterogeneous group of varieties from a French collection. To validate the shotgun approach, seven SNV markers were analyzed using target capture sequencing, confirming the accuracy of detected variants with only minimal discrepancies, which is mostly attributable to homopolymeric regions and low-frequency alleles. Phylogenetic analyses using both trees and networks delineated three major haplotype clusters, reflecting human-mediated dispersal of grapevine cultivars through historical viticultural practices. This study represents the largest chloroplast genome analysis of cultivated V. vinifera to date, providing a large cpDNA resource for assessing chloroplast diversity and maternal haplotype structure in cultivated grapevine. The results highlight the power of combining high-throughput sequencing and chloroplast genomics for population-level studies in perennial crops. Full article