Genetic Linkage Research Articles

From genes to phenotype: investigating the link between smad2rs29725537:c>a and high take off in mice

Abstract Funding Acknowledgements Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Junta de Andalucía, Ministerio de Ciencia e Innovación, Gobierno de España. Introduction and Purpose High take off (HTO) is a congenital anomaly with a prevalence of 0.36% that can cause severe ischemia and sudden cardiac death. The C57Bl/6 (B6) mouse strain shows around 60% incidence of HTO, whereas it is absent in the Balb/c (BC) strain. The aim of this study was to identify the genes responsible for the development of HTO. Methods Following an inheritance study, a genetic linkage study was performed in B6C mice using 134 microsatellites (MIT). After selection of Smad2 as a candidate gene, a genotype-phenotype study was performed by PCR-RFLP genotyping of 293 B6C mice. The process of coronariogenesis was examined in E13.5 and E14.5 mouse embryos of B6 (n = 27) and BC (n = 23) strains with specific markers for the vascular plexuses involved in coronariogenesis (PROX1 and ERG 1/2/3) and for SMAD2. Finally, the SMAD2 and pSMAD2 protein expression levels were analyzed by western blot in ventricle, liver, and kidney of B6C mice. Results The incidence of HTO in B6, BC and B6C mice were concordant with an inheritance pattern mediated by a dominant causal allele and dominant modifier in the BC strain that reduces the incidence of HTO. The genetic linkage study revealed the association of a region between markers MIT-49 and 106 on chromosome 18 with the presence of HTO. This region contained a total of 10 genes, of which Smad2 was selected as a candidate gene because of its functions in aortic root formation. Comparative sequence analysis of Smad2 between the B6 and BC mouse strains uncovered an intronic SNP (Smad2rs29725537:C>A or Smad2C>A) that predicts and error in the splicing of intron 10-11. A statistically significant association (p<0.05) between the Smad2C>A allele and the presence of HTO was found. pSMAD2 was detected in embryonic coronary primordia, the subepicardial aortic plexus (SAP) and the primary coronary plexus. Around 60% of B6 examined embryos showed an exacerbated SAP compared to the BC embryos. Additionally, we detected a differential expression of total SMAD2, but not of pSMAD2, in different organs according to the Smad2C>A allele genotype (C/C > A/C > A/A). Conclusions We conclude that: 1) Smad2C>A allelic variant is associated with HTO in mice, suggesting it as a major causal factor. 2) Smad2 altered expression may affect the establishment of the embryonic coronary primordia leading to a mispositioned ostium. 3) the Smad2C>A allele has a systemic effect on total SMAD2 expression without affecting its phosphorylation level, which suggest a compensatory mechanism of expression that maintain the normal activity of pSMAD2 in most tissues.

Recycling carbonated hydrous sediments into the mantle source of carbonatite-associated rare-earth-element deposits

Decoding the petrogenesis of carbonatites is of great importance for our understanding of the Earth’s deep carbon cycling and formation of rare-earth-element (REE) deposits. Among global carbonatites, the Cenozoic Mianning-Dechang (MD) carbonatites in the western Yangtze Craton are unique because of their development in a post-collisional zone and host numerous giant-large REE deposits. However, most of previous studies have focused on the late magmatic to hydrothermal stages, while the nature of the mantle source and early-stage magmatic evolution remain largely unexplored. Here we present a combined petrographic, chemical and Sr-Nd-Pb isotopic study on the MD lamprophyres to address these issues. A genetic linkage is revealed between these lamprophyres and the MD carbonatites and syenites by their geochemical similarities and close spatial and temporal associations. Our data suggest a phlogopite-rich carbonated subcontinental lithospheric mantle (SCLM) source metasomatized by subducted carbonated hydrous sediment-derived melts/fluids. Significant fractional crystallization of olivine, clinopyroxene and biotite (±Ti-Fe oxides) from hydrous, K-rich and carbonated primary melts caused the carbonate–silicate liquid immiscibility in the highly evolved melts and thus formation of the MD carbonatites and syenites at shallow depths. Melting of subducted carbonated hydrous sediments not only provides carbonatitic liquids for the SCLM carbonation, but also supplies sufficient water and alkalis that are critical for accumulating and transporting REE in carbonatitic fluids. Post-collisional lithospheric thinning also played a critical role in the formation of carbonatites via triggering the melting of the carbonated SCLM. This study provides new insights into the deep processes during the formation of carbonatites and associated REE deposits in post-collisional zones.

Identification and expression of gene loci underlying the quantitative trait loci of starch content in cassava

ABSTRACT In this study, a genetic linkage map was developed based on simple sequence repeat (SSR) markers to aid in the identification and expression analysis of gene loci underlying the quantitative trait loci (QTL) of starch content (SC) in cassava (Manihot esculenta). A total of 912 polymorphic loci from 4,515 tested SSRs were mapped into 18 linkage groups. QTL analysis revealed four loci with highly significant associations with starch. Gene annotation was performed, and potential genes related to starch synthesis were identified. Of these, expression of four genes related to starch synthesis (Raffinose synthase [RS], Phosphoenolpyruvate kinase [PK], Glucose-6-phosphate [G6P], and Glycogen synthase kinase 3 [GSK-3]) was investigated by real-time PCR assays. The results found a statistically significant difference (p < 0.05) at 3 months after planting (MAP) in all the tested genes, whereas a higher expression was detected in the low-SC group with specific genotypes of linked markers. A higher level of expression was observed in the RS, PK, and G6P genes at six and nine MAP, indicating that starch accumulation mainly occurs after 3 MAP, during which the root system begins to form. The potential genes identified in this study could provide a better understanding of the starch biosynthesis mechanism, and could be useful for applications in marker-assisted selection to facilitate cassava breeding programs in the future.

Seedling root system adaptation to water availability during maize domestication and global expansion.

The maize root system has been reshaped by indirect selection during global adaptation to new agricultural environments. In this study, we characterized the root systems of more than 9,000 global maize accessions and its wild relatives, defining the geographical signature and genomic basis of variation in seminal root number. We demonstrate that seminal root number has increased during maize domestication followed by a decrease in response to limited water availability in locally adapted varieties. By combining environmental and phenotypic association analyses with linkage mapping, we identified genes linking environmental variation and seminal root number. Functional characterization of the transcription factor ZmHb77 and in silico root modeling provides evidence that reshaping root system architecture by reducing the number of seminal roots and promoting lateral root density is beneficial for the resilience of maize seedlings to drought.

Low-level viremia episodes appear to affect the provirus composition of the circulating cellular HIV reservoir during antiretroviral therapy.

Low-level viremia (LLV) ranging from 50 to 1,000 copies/ml is common in most HIV-1-infected patients receiving antiretroviral therapy (ART). However, the source of LLV and the impact of LLV on the HIV-1 reservoir during ART remain uncertain. We hypothesized that LLV may arise from the HIV reservoir and its occurrence affect the composition of the reservoir after LLV episodes. Accordingly, we investigated the genetic linkage of sequences obtained from plasma at LLV and pre-ART time points and from peripheral blood mononuclear cells (PBMCs) at pre-ART, pre-LLV, LLV, and post-LLV time points. We found that LLV sequences were populated with a predominant viral quasispecies that accounted for 67.29%∼100% of all sequences. Two episodes of LLV in subject 1, spaced 6 months apart, appeared to have originated from the stochastic reactivation of latently HIV-1-infected cells. Moreover, 3.77% of pre-ART plasma sequences were identical to 67.29% of LLV-3 plasma sequences in subject 1, suggesting that LLV may have arisen from a subset of cells that were infected before ART was initiated. No direct evidence of sequence linkage was found between LLV viruses and circulating cellular reservoirs in all subjects. The reservoir size, diversity, and divergence of the PBMC DNA did not differ significantly between the pre- and post-LLV sampling points (P > 0.05), but the composition of viral reservoir quasispecies shifted markedly before and after LLV episodes. Indeed, subjects with LLV had a higher total PBMC DNA level, greater viral diversity, a lower proportion of variants with identical sequences detected at two or more time points, and a shorter variant duration during ART compared with subjects without LLV. Overall, our findings suggested that LLV viruses may stem from an unidentified source other than circulating cellular reservoirs. LLV episodes may introduce great complexity into the HIV reservoir, which brings challenges to the development of treatment strategies.

An evaluation of a Stenotrophomonas maltophilia outbreak due to commercial arterial blood gas collection kit

BackgroundStenotrophomonas maltophilia is a gram-negative bacterium that can cause hospital infections and outbreaks within hospitals. This study aimed to evaluate an outbreak of Stenotrophomonas maltophilia, caused by ready-to-use commercial syringes containing liquid lithium and heparin for arterial blood gas collection in a university hospital.MethodsUpon detecting an increase in Stenotrophomonas maltophilia growth in blood cultures between 15.09.2021 and 19.11.2021, an outbreak analysis and a case-control study (52 patients for the case group, 56 patients for the control group) were performed considering risk factors for bacteremia. Samples from possible foci for bacteremia were also cultured. Growing bacteria were identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The genetic linkage and clonal relationship isolates were investigated with pulsed-field gel electrophoresis (PFGE) in the reference laboratory.ResultsIn the case-control study, the odds ratio for the central venous catheter [3.38 (95% confidence interval [CI]: 1.444, 8.705 ; p = 0.006)], for surgery [3.387 (95% confidence interval [CI]: 1.370, 8.373 ; p = 0.008)] and for arterial blood gas collection history [18.584 (95% confidence interval [CI]:4.086, 84.197; p < 0.001)] were identified as significant risk factors. Stenotrophomonas maltophilia growth was found in ready-to-use commercial syringes used for arterial blood gas collection. Molecular analysis showed that the growths in the samples taken from commercial syringes and the growths from blood cultures were the same. It was decided that the epidemic occurred because the method for sterilization of heparinized liquid preparations were not suitable. After discontinuing the use of the kits with this lot number, the outbreak was brought under control.ConclusionsAccording to our results, disposable or sterile medical equipment should be included as a risk factor in outbreak analyses. The method by which injectors containing liquids, such as heparin, are sterilized should be reviewed. Our study also revealed the importance of the cooperation of the infection control team with the microbiology laboratory.

Genetic Mapping for Leaf Shape and Leaf Size in Non-Heading Chinese Cabbage by a RIL Population

Leaves are the predominant photosynthetic and edible organs in non-heading Chinese cabbage (Brassica campestris ssp. chinensis, NHCC), contributing significantly to yield, appearance, and desirability to consumers. However, the genetic basis of leaf shape and size in non-heading Chinese cabbage remains unclear. In this study, we developed a RIL population using ‘Maertou’, with slender leaves and narrow petioles, and ‘Suzhouqing’, with oval leaves and wide petioles, to construct a genetic linkage map and detect QTLs. To obtain stable and reliable QTLs, the 11 leaf-related traits, including the leaf length, leaf width, and fresh weight of the lamina and petiole and the thickness of petiole was observed on two locations—while the leaf shape, petiole shape, index of lamina/petiole length, and index of petiole fresh weight were calculated based on 7 leaf-related traits. QTL mapping illustrated that a total of 27 QTLs for leaf-related traits were preliminarily detected. The candidate genes were annotated and several genes involved in leaf development and leaf shape appeared in the overlapping regions of multiple loci, such as KRP2, GRF4, ARGOS, and SAUR9. This study lays the foundation for further exploration of the genetic mechanisms and development of effective molecular markers for leaf shape and size in NHCC.

Selective allele stacking of a novel quantitative trait locus facilitates the enhancement of seed epicatechin content in soybean (Glycine max (L.) Merr.)

(-)-Epicatechin (EC), a primary form of flavan-3ol and a building block of proanthocyanidins, has health benefits as it is a potent antioxidant. So far, no quantitative trait loci (QTLs) associated with EC have yet been identified in soybean. In this study, QTLs for EC and hilum color were identified in recombinant inbred lines (RILs) derived from the varieties Jinpung and IT109098 using high-resolution single nucleotide polymorphism linkage mapping. This revealed two major QTLs for EC content, qEC06 and qEC08. qEC06 spanned the Tawny (T) locus encoding flavonoid 3′-hydroxylase. qEC08, located near the Inhibitor (I) locus on Chr08, was also a major QTL for hilum color; however, allelic stacking of qEC08 and I revealed no relationship between I and EC content. RILs with IT109098 alleles at both qEC06 and qEC08 had higher EC content than other lines. These results will enable the production of soybean varieties with high EC content via marker-assisted selection.

Understanding genome structure facilitates the use of wild lentil germplasm for breeding: A case study with shattering loci.

Plant breeders are generally reluctant to cross elite crop cultivars with their wild relatives to introgress novel desirable traits due to associated negative traits such as pod shattering. This results in a genetic bottleneck that could be reduced through better understanding of the genomic locations of the gene(s) controlling this trait. We integrated information on parental genomes, pod shattering data from multiple environments, and high-density genetic linkage maps to identify pod shattering quantitative trait loci (QTLs) in three lentil interspecific recombinant inbred line populations. The broad-sense heritability on a multi-environment basis varied from 0.46 (in LR-70, Lens culinaris × Lens odemensis) to 0.77 (in LR-68, Lens orientalis × L. culinaris). Genetic linkage maps of the interspecific populations revealed reciprocal translocations of chromosomal segments that differed among the populations, and which were associated with reduced recombination. LR-68 had a 2-5 translocation, LR-70 had 1-5, 2-6, and 2-7 translocations, and LR-86 had a 2-7 translocation in one parent relative to the other. Segregation distortion was also observed for clusters of single nucleotide polymorphisms on multiple chromosomes per population, further affecting introgression. Two major QTL, on chromosomes 4 and 7, were repeatedly detected in the three populations and contain several candidate genes. These findings will be of significant value for lentil breeders to strategically access novel superior alleles while minimizing the genetic impact of pod shattering from wild parents.

Genomic loci associated with grain yield under well-watered and water-stressed conditions in multiple bi-parental maize populations

Smallholder maize farming systems in sub-Saharan Africa (SSA) are vulnerable to drought-induced yield losses, which significantly impact food security and livelihoods within these communities. Mapping and characterizing genomic regions associated with water stress tolerance in tropical maize is essential for future breeding initiatives targeting this region. In this study, three biparental F3 populations composed of 753 families were evaluated in Kenya and Zimbabwe and genotyped with high-density single nucleotide polymorphism (SNP) markers. Quantitative trait loci maping was performed on these genotypes to dissect the genetic architecture for grain yield (GY), plant height (PH), ear height (EH) and anthesis-silking interval (ASI) under well-watered (WW) and water-stressed (WS) conditions. Across the studied maize populations, mean GY exhibited a range of 4.55–8.55 t/ha under WW and 1.29–5.59 t/ha under WS, reflecting a 31–59% reduction range under WS conditions. Genotypic and genotype-by-environment (G × E) variances were significant for all traits except ASI. Overall broad sense heritabilities for GY were low to high (0.25–0.60). For GY, these genetic parameters were decreased under WS conditions. Linkage mapping revealed a significant difference in the number of QTLs detected, with 93 identified under WW conditions and 41 under WS conditions. These QTLs were distributed across all maize chromosomes. For GY, eight and two major effect QTLs (&amp;gt;10% phenotypic variation explained) were detected under WW and WS conditions, respectively. Under WS conditions, Joint Linkage Association Mapping (JLAM) identified several QTLs with minor effects for GY and revealed genomic region overlaps in the studied populations. Across the studied water regimes, five-fold cross-validation showed moderate to high prediction accuracies (−0.15–0.90) for GY and other agronomic traits. Our findings demonstrate the polygenic nature of WS tolerance and highlights the immense potential of using genomic selection in improving genetic gain in maize breeding.

Advances in Breeding for Oil Quality Enhancement in Indian Mustard (Brassica spp. L.): Achievements, Challenges, and Research Opportunities

Major objectives in oil crop improvement are enhancement of seed and oil yield, quality of oil according to its use, i.e. edible or industrial uses, breeding of varieties that fit in different cropping systems and breeding biotic and abiotic stress resistant/tolerant varieties. Despite traditional breeding approaches, including pure line breeding, yielding only modest gains in productivity, recent advancements in mustard breeding have led to significant breakthroughs in both productivity and oil quality. This review discusses the innovative breeding strategies that have contributed to these advancements, with a focus on hybrid development, oil quality enhancement, and biotechnological approaches. To enhance productivity, researchers at the University of Delhi have developed hybrid seed production techniques using transgenic Barnase-barstar systems and cytoplasmic male sterility (CMS) systems. These systems enable large-scale hybrid seed production, with field trials demonstrating significant yield heterosis ranging from 31% to 55% compared to national check varieties. In addition to productivity, improving oil and meal quality has been a key objective. By integrating genes from canola-quality mustard lines, breeders have achieved reductions in erucic acid and glucosinolates, enhancing the health profile and industrial applicability of mustard oil. A high-density linkage map developed using an F1 double haploid mapping population has facilitated the marker-assisted backcross breeding of desirable traits, enabling precise transfer of key quality traits. Transgenic approaches, such as antisense RNA technology, have led to the development of high-oleic, low-linoleic mustard lines with improved fatty acid profiles. These advancements reflect a strategic combination of conventional and biotechnological methods, demonstrating a clear pathway for boosting mustard yields while enhancing oil quality. Molecular markers reported for genetic diversity assessment, mapping and tagging genes/QTLs for different qualitative and quantitative traits and their use in marker-assisted selection have been presented. This progress not only addresses current challenges but also sets the stage for future research aimed at further optimizing productivity, oil quality, and resistance to pests and diseases in mustard cultivation.

Unraveling the genetic basis of superior traits in Gossypium barbadense: From phenotype to genotype

G. barbadense is renowned for its high-quality fiber and is highly regarded as a natural material in the textile industry. However, research on cotton has mainly focused on G. hirsutum, and progress in sea island cotton has been relatively slow. There was limited understanding of the genetic loci and transcriptional regulatory mechanisms of important traits, and the genetic basis for the development of superior traits remains unclear. In this study, a recombinant inbred line (RIL) population was constructed using two sea island cotton parents from different cotton regions. The phenotypic characteristics of the two parents and the RIL population, as well as the phenotypic correlations, heritability, and genetic models of the RIL population, were comprehensively analyzed. The RIL population was genotyped using whole-genome resequencing technology, and a high-density intraspecific linkage map was constructed, consisting of 5295 bin markers and a total genetic map distance of 2721.79 centimorgans (cM). Phenotypic data collected from five different environments were used to detect 169 quantitative trait loci (QTLs) using the composite interval mapping method. Among these QTLs, 30 were related to agronomic traits, 61 were related to yield traits, and 78 were related to fiber quality traits. Additionally, 17 QTL clusters were detected, and the additive effects of these clusters explained the correlation between different phenotypic traits. Candidate genes for stable QTLs related to agronomic and yield traits were identified through variant annotation and functional prediction. Two bin markers associated with lint percentage (LP) were validated as potential breeding markers. Furthermore, using RNA-seq data of cotton fiber from the RIL population parents, the dynamic changes in gene expression during different developmental stages of cotton fiber were revealed, and important differentially expressed genes in the secondary cell wall development and metabolism network of fibers were identified. Importantly, through the combined analysis of fiber trait QTLs and transcriptomes, eight candidate genes involved in regulating fiber quality traits were predicted, and the genetic basis of the excellent allele site qFL_D04_1 in the breeding history of Chinese sea island cotton was elucidated. In summary, this study provides new genetic resources and potential breeding markers for cotton variety improvement, valuable theoretical information for understanding the genetic basis of important traits in sea island cotton, and effectively promotes the development of cotton biotechnology breeding.

Genetic Diversity, Linkage Disequilibrium, and Population Structure in a Common Bean Reference Collection

An in-depth understanding of the extent and pattern of genetic diversity and population structure in crop populations is of paramount importance for any crop improvement program to efficiently promote the translation of genetic diversity into genetic gain. A reference collection of 150 common bean genotypes selected from the International Center for Tropical Agriculture’s global core collection was evaluated using single-nucleotide polymorphism (SNP) markers to quantify the amount of genetic diversity, linkage disequilibrium, and population structure. The cultivars and landraces of the collection were diverse and originated from 14 countries, and wild accessions were used as controls for each gene pool. The collection was genotyped using an SNP array, generating a total of 5398 locus calls distributed across the entire bean genome. The SNP data quality was checked, and two datasets were generated. The first dataset (Dataset_1) comprised a set of 5108 SNPs and 150 genotypes after filtering for 10% missing alleles and an MAF &lt; 0.05. The second dataset (Dataset_2) comprised a set of 2300 SNPs that remained after removing any null-allele SNPs and LD pruning for a criterion of r2 &lt; 0.2. Dataset_1 was used for a principal coordinate analysis (PCoA), phylogenetic relationship determination, an analysis of molecular variance (AMOVA), and a discriminant analysis of principal components. Dataset_2 was used for a population structure analysis using STRUCTURE software and is proposed for a genome-wide association study (GWAS). The population structure analysis split the reference collection into two subpopulations according to an Andean or Mesoamerican gene pool. The Mesoamerican populations displayed higher genetic differentiation and tended to split into more groups that were somewhat aligned with common bean races. Andean beans were characterized by a larger average LD but lower LD percentage, a small average genetic distance between members of the population, and a higher major allele frequency, which suggested narrower genetic diversity compared to the Mesoamerican gene pool. In conclusion, the results indicated the presence of high genetic diversity, which is useful for a GWAS. However, the presence of significant linkage disequilibrium requires that genetic distance be considered as a co-factor for any further genetic studies. Overall, the molecular variation observed in the genotypes shows that this reference collection is valuable as a genebank-derived diversity panel which is useful for marker trait association studies.

Mapping QTLs for adult-plant resistance to powdery mildew and stripe rust using a recombinant inbred line population derived from cross Qingxinmai × 041133.

A recombinant inbred line (RIL) population derived from wheat landrace Qingxinmai and breeding line 041133 exhibited segregation in resistance to powdery mildew and stripe rust in five and three field tests, respectively. A 16K genotyping by target sequencing (GBTS) single-nucleotide polymorphism (SNP) array-based genetic linkage map was used to dissect the quantitative trait loci (QTLs) for disease resistance. Four and seven QTLs were identified for adult-plant resistance (APR) against powdery mildew and stripe rust. QPm.caas-1B and QPm.caas-5A on chromosomes 1B and 5A were responsible for the APR against powdery mildew in line 041133. QYr.caas-1B, QYr.caas-3B, QYr.caas-4B, QYr.caas-6B.1, QYr.caas-6B.2, and QYr.caas-7B detected on the five B-genome chromosomes of line 041133 conferred its APR to stripe rust. QPm.caas-1B and QYr.caas.1B were co-localized with the pleiotropic locus Lr46/Yr29/Sr58/Pm39/Ltn2. A Kompetitive Allele Specific Polymorphic (KASP) marker KASP_1B_668028290 was developed to trace QPm/Yr.caas.1B. Four lines pyramiding six major disease resistance loci, PmQ, Yr041133, QPm/Yr.caas-1B, QPm.caas-2B.1, QYr.caas-3B, and QPm.caas-6B, were developed. They displayed effective resistance against both powdery mildew and stripe rust at the seedling and adult-plant stages.

The impact of maternal smoking during pregnancy and the age of smoking initiation on incident dementia: A prospective cohort study.

The impact of early-life tobacco exposure on dementia has remained unknown. Using the UK Biobank, the associations of maternal smoking during pregnancy (MSDP) and age of smoking initiation (ASI) with the onset time of all-cause dementia were estimated with accelerated failure time models. The effects of MSDP and ASI on brain structure and their genetic correlation to Alzheimer's disease (AD) were analyzed. A Mendelian randomization (MR) analysis was conducted. The time ratios for smokers starting in childhood, adolescence, and adulthood (vs never smokers) were 0.87 (0.76 to 0.99), 0.92 (0.88 to 0.96), and 0.95 (0.89 to 1.01). MSDP and smoking in adolescence altered many brain regions, including the hippocampus. In genetic analysis, MSDP was genetically and causally linked to AD, and a younger ASI was genetically correlated to a higher AD risk. Early-life smoking accelerated dementia onset and was genetically correlated to AD. MSDP demonstrated genetic and causal linkage to AD risks. Unlike the commonly used Cox proportional hazards model, this article uses a parametric survival analysis method - the accelerated failure model - to explore the relationship between exposure to onset time. It can be used as an alternative method when the proportional hazards assumption is not met. Genetic analyses including genetic correlation study and MR analysis and brain structure analyses were conducted to support our findings and explore the potential mechanisms. The study reveals the relationship between different smoking initiation periods and the onset time of dementia and shows that earlier smoking exposure has a more significant impact on dementia. It emphasizes the importance of preventing early smoking. In the future, more research focusing on the relationship between early exposure and dementia is called for to provide more detailed prevention measures for dementia that cover all age groups.

Prevalence and molecular characterization of colistin resistance in Pseudomonas aeruginosa isolates: insights from a study in Ardabil hospitals

BackgroundPseudomonas aeruginosa is a common cause of nosocomial infections. However, the emergence of multidrug-resistant strains has complicated the treatment of P. aeruginosa infections. While polymyxins have been the mainstay for treatment, there is a global increase in resistance to these antibiotics. Therefore, our study aimed to determine the prevalence and molecular details of colistin resistance in P. aeruginosa clinical isolates collected between June 2019 and May 2023, as well as the genetic linkage of colistin-resistant P. aeruginosa isolates.ResultsThe resistance rate to colistin was 9% (n = 18) among P. aeruginosa isolates. All 18 colistin-resistant isolates were biofilm producers and carried genes associated with biofilm formation. Furthermore, the presence of genes encoding efflux pumps, TCSs, and outer membrane porin was observed in all colistin-resistant P. aeruginosa strains, while the mcr-1 gene was not detected. Amino acid substitutions were identified only in the PmrB protein of multidrug- and colistin-resistant strains. The expression levels of mexA, mexC, mexE, mexY, phoP, and pmrA genes in the 18 colistin-resistant P. aeruginosa strains were as follows: 88.8%, 94.4%, 11.1%, 83.3%, 83.3%, and 38.8%, respectively. Additionally, down-regulation of the oprD gene was observed in 44.4% of colistin-resistant P. aeruginosa strains.ConclusionThis study reports the emergence of colistin resistance with various mechanisms among P. aeruginosa strains in Ardabil hospitals. We recommend avoiding unnecessary use of colistin to prevent potential future increases in colistin resistance.

Leaf morphology related genes revealed by integrating Pan-transcriptome, GWAS and eQTL analyses in a Liriodendron population.

Leaf plays an indispensable role in plant development and growth. Although many known genes related to leaf morphology development have been identified, elucidating the complex genetic basis of leaf morphological traits remains a challenge. Liriodendron plants are common ornamental trees due to their unique leaf shapes, while the molecular mechanism underlying Liriodendron leaf morphogenesis has remained unknown. Herein, we firstly constructed a population-level pan-transcriptome of Liriodendron from 81 accessions to explore the expression presence or absence variations (ePAVs), global expression differences at the population level, as well as differentially expressed genes (DEGs) between the Liriodendron chinense and Liriodendron tulipifera accessions. Subsequently, we integrated a genome-wide association study (GWAS), expression quantitative trait loci (eQTL), and transcriptome-wide association study (TWAS) to identify candidate genes related to leaf morphology. Through GWAS analysis, we identified 18 and 17 significant allelic loci in the leaf size and leaf shape modules, respectively. In addition, we discerned 16 candidate genes in relation to leaf morphological traits via TWAS. Further, integrating the co-localization results of GWAS and eQTL, we determined two regulatory hotspot regions, hot88 and hot758, related to leaf size and leaf shape, respectively. Finally, co-expression analysis, eQTL, and linkage mapping together demonstrated that Lchi_4g10795 regulate their own expression levels through cis-eQTL to affect the expression of downstream genes and cooperatively participate in the development of Liriodendron leaf morphology. These findings will improve our understanding of the molecular regulatory mechanism of Liriodendron leaf morphogenesis and will also accelerate molecular breeding of Liriodendron.

Identification of novel SNPs and candidate genes significantly affecting growth in grass carp (Ctenopharyngodon idella) through GWAS analysis

Grass carp (Ctenopharyngodon idella) is one of the most important cultivated fish species in the global freshwater aquaculture with fast growth, low cost of production and delicious meat. A breeding program to improve economically important growth traits in grass carp would benefit from effective molecular markers. Although a genetic linkage map of grass carp has been constructed, and quantitative trait loci (QTL) mapping and a genome-wide association study (GWAS) have been conducted, the effective number of SNP markers and genes currently available for breeding is still very limited. In this study, we conducted a GWAS based on re-sequencing of individuals to identify genomic regions and candidate genes potentially associated with various growth traits of grass carp, including body weight (BW), body length (BL) and body height (BH). A total of 4,854,366 high-quality SNPs were identified and located on 24 chromosomes. Among them, 31 SNPs were identified as being associated with growth traits, including 8 SNPs on chromosomes 1, 2, 10, 13, 14, 17 and 22 associated with BW, 21 SNPs on chromosomes 2, 4, 5, 8, 10, 13, 14, 15, 17, 23 and 24 correlated with BL, and 18 SNPs on chromosomes 2, 9, 10, 13, 14, 17, 23 and 24 related to BH. In addition, 13 of these SNPs were simultaneously associated with two or three growth traits. Within a 48 kb range upstream and downstream of these significant SNPs, 120 candidate genes were identified to be associated with the QTLs. Most of these genes were related to growth and development, fat metabolism, bone mineralization and differentiation, vascular development, and feeding regulation. Notably, the genes pwp1, cers5, chrebp, lsr, ctnnbip1, smoc2, ano6 and cckrb were specifically associated with growth, fat, bone formation and feeding. Our findings would provide a foundation for molecular marker-assisted selection, genomic selection, and functional analysis of growth traits in grass carp.

Co-localization and analysis of miR477b with fiber length quantitative trait loci in cotton.

Cotton is an important cash crop for the textile industry. However, the understanding of natural genetic variation of fiber elongation in relation to miRNA is lacking. A miRNA gene (miR477b) was found to co-localize with a previously mapped fiber length (FL) quantitative trait locus (QTL). The miR477b was differentially expressed during fiber elongation between two backcross inbred lines (BILs) differing in FL and its precursor sequences. Bioinformatics and qRT-PCR analysis were further used to analyse the miRNA genes, which could produce mature miR477b. Cotton plants with virus-induced gene silencing (VIGS) constructs to over-express the allele of miR477b from the BIL with longer fibers had significantly longer fibers as compared with negative control plants, while the VIGS plants with suppressed miRNA expression had significantly shorter fibers. The expression level of the target gene (DELLA) and related genes (RDL1 and EXPA1 for DELLA through HOX3 protein) in the two BILs and/or the VIGS plants were generally congruent, as expected. This report represents one of the first comprehensive studies to integrate QTL linkage mapping and physical mapping of small RNAs with both small and mRNA transcriptome analysis, followed by VIGS, to identify candidate small RNA genes affecting the natural variation of fiber elongation in cotton.

The role of dietary preferences in osteoarthritis: a Mendelian randomization study using genome-wide association analysis data from the UK Biobank.

To understand the impact of individual preferences for specific dietary items on OA, and to help inform the development of effective and targeted OA prevention and management strategies, we performed a Mendelian randomization analysis between dietary preferences and osteoarthritis. This study utilized genetic data from the UK Biobank to investigate the association between OA and 21 different common dietary items. Instrumental variables representing European populations were carefully selected based on their genetic significance and linkage disequilibrium. In cases where a dietary item had few relevant genetic markers, a more lenient selection threshold was applied. To prevent bias, the analysis excluded single nucleotide polymorphisms (SNPs) associated with factors such as body mass index (BMI) and cholesterol. Using inverse-variance weighting (IVW) and Mendelian randomization, significant associations were detected between certain dietary items and OA. Using Mendelian randomization to examine the relationship between 21 different dietary items and OA, significant associations were found for coffee, peas, watercress, and cheese, where the first two had a promoting effect and the last two an inhibiting effect on OA. Due to heterogeneity in the test results for cheese, a random IVW representation was used. The results of sensitivity analysis showed no significant heterogeneity or horizontal pleiotropy in the selected SNPS, demonstrating the reliability of Mendelian randomization analysis. This study identified coffee, peas, watercress, and cheese as food items that may have significant dietary effects on osteoarthritis. This information may be useful to consider in the development of OA management strategies.