Gene Reports最新文献

Protein kinase plays important roles in plant growth, development, and responses to various biotic and abiotic stresses. Levels of nucleotide diversity, however, have not been investigated to date in natural populations of wild rice. In this study, the diversity of the MAPK5 gene and its characteristics were analyzed in samples of wild rice collected from natural populations in Thailand and Lao PDR, using a re-sequencing DNA technique. For the entire of 514 nucleotides sequence analyzed, non-synonymous, synonymous substitutions, and frame-shift indels were identified in coding sequence of exon1, but not for exon2. For non-coding sequences, indel mutations were present in the sequenced region of the first intron of the MAPK5 gene. These results suggest that alternative splicing transcripts of the MAPK5 gene are potentially generated in response to various environment factors. There was substantial nucleotide variation with a high estimate of nucleotide diversity (π = 0.18113), number of haplotypes (H = 15), and the number of polymorphic sites (S = 319). The Tajima's D value of the MAPK5 gene was 1.673 (p > 0.10), suggesting that the MAPK5 gene of wild rice evolved neutrally. The high level of nucleotide diversity found in natural populations of wild rice may provide populations with the opportunity to adapt to environmental changes in their natural habitats.

Pulses are important crops for global food security and are highly adaptable to diverse environmental conditions. Despite these merits, pulses often face neglect and undervaluation in production. Conventional breeding has been successful for centuries in improving various traits, based on their superior agronomic performance. However, this is a phenotype-based selection that is laborious, expensive, inefficient, error-prone, and often poorly adaptive. To address these challenges, molecular breeding has emerged as a valuable approach, bridging the gap between phenotype and genotype.

Consequently, we aimed to review recent advances in molecular breeding for major pulse crops, and the introgression of novel genes providing a comprehensive overview of breeding strategies for sustainable food security, particularly in developing countries. Genetic improvement through molecular breeding tools has been used to reliably improve pulse nutritional quality traits (such as taste, aroma, protein digestibility, essential amino acid profile, and the absence of anti-nutritional factors) and resistance to environmental stresses. Accordingly, the integration of next-generation genome sequencing, genome-wide association studies, high-throughput phenotyping, and omics research approaches are accelerating the discovery of the genetic loci underlying these traits and improving pulse research, mainly for key pulses like soybean, chickpea, broad bean, common bean, field pea, grass pea, cowpea, mung bean, and lentil. In general, molecular interventions in pulse breeding hold great promise for improving food and nutrition security, particularly in developing countries.

Purpose

Hepatitis C Virus (HCV) RNA quantification is crucial for diagnosing and monitoring chronic HCV treatment. Cost-effective methods are crucial to ensure accessibility. This study evaluated the Fluorion HCV QNP v3.0 Real-Time PCR assay's effectiveness in EDTA-plasma and serum, comparing it with the COBAS AmpliPrep/COBAS TaqMan HCV v2.0 (CAP/CTM HCV v2.0) test.

Methods

105 matched pairs of EDTA-plasma and serum specimens (91 positive and 14 negative) from HCV infected Moroccan patients were analyzed using the Fluorion HCV QNP v3.0 assay and compared to the CAP/CTM HCV v2.0 test, being the reference method.

Results

The values obtained by the Fluorion HCV QNP v3.0 in plasma were slightly higher than those in serum (3.94 ± 2.23 log₁₀ IU/mL versus 3.91 ± 2.22 log₁₀ IU/mL) and were both significantly lower than those quantified by the CAP/CTM HCV v2.0 assay (4.34 ± 2.28 log₁₀ IU/mL; p < 0.001). High correlations were observed between the Fluorion HCV QNP v3.0 serum and CAP/CTM HCV v2.0 (R² = 0.9433), the Fluorion HCV QNP v3.0 plasma and CAP/CTM HCV v2.0 (R² = 0.949) and the Fluorion HCV QNP v3.0 serum and plasma (R² = 0.9954). HCV RNA was detected in all tested genotypes by both assays.

Conclusion

The Fluorion HCV QNP v3.0 assay demonstrated excellent performance in comparison with the CAP/CTM HCV v2.0 on both plasma and serum samples which can be used interchangeably for HCV quantification. The test was shown to be suitable for disease monitoring including all HCV genotypes.

Sweet sorghum (Sorghum bicolor (L.) Moench) is the only grain and stalk crop that can be used for multipurpose. Despite its global significance and potential, it faced genetic erosion. These are due to low productivity and lower farmers' preferences, which is not considered one of the most important cereal crops in Ethiopia. To utilize and popularize these crops, understanding the genetic diversity and population structure is a pre-request. Therefore, this study was aimed to assess the genetic diversity and population structure of selected 82 Ethiopian sweet sorghum accessions using 10 simple sequence repeat (SSR) markers that represent seven geographic regions of Ethiopia. The study revealed a total of 116 alleles with a mean of 11.6 alleles per locus. All used microsatellite loci were highly polymorphic with polymorphic information content (PIC) ranging from 0.75 to 0.90 with an average of 0.82. They showed high gene diversity ranging from 0.59 to 0.81 with an overall mean of 0.70. There was a moderate genetic differentiation (FST = 0.21) showing the presence of high gene flow (Nm = 5.033) where 91 % of the total variation was accounted for within populations genetic variability. The clustering, principal coordinate analysis (PCoA) and population structure did not cluster the studied populations into a separate group according to their geographical origin. In conclusion, the highest intra-population diversity was observed among populations of North Wollo (He = 0.81) and South Wollo (He = 0.79), and hence these areas can be considered as hot spots for the identification of novel traits. Therefore, the present study has generated baseline information for breeders to improve Ethiopian sweet sorghum through breeding, management, and conservation of the available genetic resources.

Xinjiang is home to three indigenous cattle breeds (Xinjiang Mongolian, Altay white-headed, and Kazakh cattle) and one crossbreed (Xinjiang Brown cattle), each possessing distinct and remarkable characteristics. In this study, we conducted comprehensive genome analyses of these four breeds in comparison with eight representative cattle breeds from around the world. Despite being predominantly Bos taurus, the proportion of Bos indicus ancestry in these indigenous breeds decreases with increasing latitude. This mixed genomic composition contributes to higher nucleotide diversity, lower linkage disequilibrium, and larger effective population sizes. Notably, Xinjiang Brown cattle exhibited higher LD at short distances, faster LD decay, and the largest effective population size, indicative of hybrid characteristics. Furthermore, we identified selective signals for lipids dynamics and coat colour in Altay white-headed cattle, immune resistance to local pathogens in Kazakh cattle, hydro-electrolyte balance and immune response in Xinjiang Mongolian cattle, and rapid growth and large body size in Xinjiang Brown cattle, as well as substance metabolism in three indigenous cattle. Our findings not only deepen the understanding of breed origins and diversity but also provide a foundation for exploring the genetic mechanisms underlying breed characteristics and facilitating further breed improvement.

Background

Retinitis Pigmentosa (RP) as inherited disease of the retina causes vision impairment due to progressive abnormalities of photoreceptors or the retinal pigment epithelial cells. RP as a clinical heterogenous disorder characterized by wide genetic heterogeneity with a broad range of causative genes involved in the genesis of the disease. Pathogenic variants in AGBL5 have been reported in few cases with RP. The aim of this study is to identify the accurate clinical diagnosis of RP in an Iranian family based on the combination of clinical and genetic investigations.

Materials and methods

We used whole exome sequencing (WES) to identify the pathogenic genetic defect responsible for RP in an Iranian family with consanguineous marriage. Using various filtering steps, we filtered out the exome data to narrow down the annotated variants. Variant prioritization was done based on a panel of RP genes.

Results

All the annotated variants from WES analysis were passed through various filtering steps depending upon allelic frequency, genomic position, protein impact, pathogenic effect, previous relevance to the disease phenotype and quality of the variants. Finally, we found the nonsense homozygous change in AGBL5 gene (NM_021831.6; c.1729C>T; p.Arg577Ter). The RP phenotypes of the proband were similar to previous reports.

Conclusion

This study can provide further evidence regarding the relationship of pathogenic variants in AGBL5 as a cause of RP and we believe that it can provide evidences for the relationship between clinical manifestations and pathogenic variants.

Preeclampsia is a pregnancy-associated hypertensive pathology that affects maternal and fetal quality of life. It was linked to several environmental and genetic factors including genetic polymorphisms. This study aimed to study the association, SNP-SNP interactions and haplotypes associations of thrombophilia, folate cycle and hypertension maternal genetic variations with preeclampsia risk in Russian women from Rostov region. 53 pregnant women diagnosed with preeclampsia were compared with 3108 women with relatively healthy pregnancy. DNA was extracted from blood samples and real time allele specific PCR was used for genotyping. MDR analysis was used for SNP-SNP interactions study. According to our data, F5(G1691A) and ITGB3(T1565C) mutant homozygotes were associated with higher risk of preeclampsia. MTRR (A66G) mutant allele (G) was shown as significant preeclampsia risk factor. ADD1 (G1378T) showed significantly higher frequency of mutant allele (T) and mutant homozygote genotype (TT) in preeclampsia patients comparing to control group. MDR showed that this polymorphism has the higher entropy among targeted variations which was confirmed by binary haplotypes association study. We have also examined linkage disequilibrium showing two haploblocks in between the studied genetic variations included MTHFR (C677T) and MTHFR (A1298C) block and AGT (T704C) with AGT (C521T) block. Results suggest several genetic variations and haplotypes as perspective maternal marker for preeclampsia which will contribute to improve prognosis tools and accordingly treatment and prevention possibilities.

We explore the understudied role of Y chromosome genes in modulating mating behaviors and interval timing in male fruit flies. Our findings reveal a significant impact of these genes on mating duration, a critical aspect of sexual selection and reproductive success. Through the use of XO males lacking a Y chromosome and RNA interference (RNAi) techniques to knockdown specific Y chromosome genes, we demonstrate that the Y chromosome and its genes WDY and CCY are essential for the generation of Longer-Mating-Duration (LMD) and Shorter-Mating-Duration (SMD) behaviors. Notably, the neuronal knockdown of Ppr-Y, a gene highly expressed in both neuronal and glial cells, leads to profound disruptions in courtship and mating behaviors without affecting fertility. Utilizing the fly SCope scRNA-seq data platform, we identified that several Y chromosome genes, including kl-3, kl-5, WDY, and PRY, are preferentially expressed in fru-positive neurons, suggesting a role in male-specific neuronal populations. Our work not only advances the understanding of the Y chromosome's contribution to complex mating behaviors but also sets the stage for future investigations into the molecular mechanisms underlying sexual dimorphism and reproductive strategies in Drosophila.

Background

Ohdo syndrome (OMIM≠ 249,620) is a clinically heterogeneous group of genetic disorders mainly characterized by intellectual disability, blepharophimosis and specific facial features. It comprises five distinct subtypes, each exhibiting unique clinical characteristics. Herein, we report a novel case of the Maat-Kievit-Brunner (OSMKB; X-linked recessive) subtype caused by a novel pathogenic MED12 nonsense variant, classically associated with missense variants of the MED12 gene (Xq13.1). Moreover, we conduct a comparative analysis of reported MED12 pathogenic variants in the literature.

Case presentation

Our patient is a five-year-old girl demonstrating a complete OSMKB phenotype. She exhibits all the characteristic features associated to this latter including intellectual disability, developmental delay, indicative dysmorphia featured by blepharophemosis and a triangular face, and hypotonia.

Conclusions

clinical and molecular data of this rare case expands the clinical and genetic landscapes of MED12 gene which is considered important for establishing strong genotype-phenotype correlations as much as for genetic counselling.

Type 2 Diabetes (T2D) as a global health challenge is characterized by insulin resistance and impaired glucose regulation. This condition has a significant impact on both human health and the global economy. Insulin plays a crucial role as a peptide hormone in regulating glucose metabolism throughout the body. Insulin resistance (IR) as one of the common implications of type 2 diabetes occurs when the body's response to insulin is disrupted, leading to dysfunction in various molecular pathways within tissues targeted by insulin. Identifying the genetic factors involved in T2D is a crucial focus of diabetes research to better comprehend its mechanisms and complications, for treatment, and prevention. Progress in genetic research during the 1980s allowed researchers to identify genetic markers associated with this hereditary trait. Genome Wide Association Studies (GWAS) have been instrumental in pinpointing genetic loci associated with various complications of diabetes. Over 300 loci have been linked to T2D, accounting for more than 19 % of the risk.

The present review manuscript aims to examine the complex interplay between genetic factors and T2D development. We review the current knowledge regarding the genetic basis, examining predisposing genetic variants, epigenetic modifications, and gene-environment interactions implicated in the disease pathogenesis. Understanding the underlying genetic mechanisms of T2D opens new avenues for personalized therapies and preventive strategies.