Journal of Applied Genetics最新文献

This study aimed to improve the restorer line IR 42266-29-3R (A42) for multiple stress tolerance using integrated marker-assisted backcross breeding (MABB) and the doubled haploid (DH) approach. The primary objective was to introduce the abiotic stress tolerant QTL (qDTY1.1 and qHTSF4.1) into the background IR 42266-29-3R, which already harbors three bacterial blight (BB) resistance genes (xa5, xa13, and Xa21). The BC₁F₁ population was derived from crosses between IR 42266-29-3R and N22, leading to the development of 113 true DHs. Efficient callus induction (29.64%) was achieved using N6 medium supplemented with 2.0 mg/l 2,4-D, 0.5 mg/l BAP, and 3% maltose. Green plant regeneration rates were notably high on the MS medium supplemented with 0.5 mg/l NAA, 0.5 mg/l Kn, 2.0 mg/l BAP, and 3% sucrose, reaching 68.6% and 61.9% on the 2nd and 7th days, respectively. From the 113 DHs, 24 were selected based on superior morpho-agronomic traits and maximum gene combinations. These DHs underwent phenotypic evaluation during the reproductive stage for drought and heat stress responses, alongside assessment for BB resistance. Among them, CS65 showed a genetic profile encompassing xa13, Xa21, qDTY1.1, and qHTSF4.1, while six others exhibited xa5, Xa21, qDTY1.1, and qHTSF4.1. Notably, CS1, CS3, CS37, CS64, and CS65 demonstrated low susceptibility to heat and drought stresses, coupled with yields comparable to the recurrent parent and moderate to high resistance against bacterial blight. CS65 emerged as the most promising genotype due to its robust tolerance to multiple stresses and improved yield potential. Moreover, eight out of the 24 DHs tested positive for both Rf3 and Rf4 genes, displaying spikelet fertility rates exceeding 75%. These selected restorer lines will serve as foundational material for developing superior hybrid rice lines, while the non-restorer lines will contribute to the broader pool of rice varieties in future breeding programs.

Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited renal disorder, primarily caused by mutations in the PKD1 and PKD2. Genetic testing is valuable for the diagnosis, prognosis, and clinical management of ADPKD. Next-generation sequencing (NGS) techniques can overcome the limitations of traditional Sanger sequencing for the genetic diagnosis of ADPKD. This study included 18 Iranian ADPKD families. Long-range PCR and Sanger sequencing were used to analyze PKD1 and PKD2. Subsequently, NGS-based gene panel testing and whole-exome sequencing (WES) were also performed in selected families. Pathogenic/likely pathogenic variants were identified in 13/18 families (72.2%), including 9 in PKD1 and 4 in PKD2. Five novel variants were discovered (c.10016C > A, c.2096_2097 + 4del, c.12138 + 5G > C in PKD1; c.2359-8_2373del, c.180_181delGC in PKD2). Additionally, WES revealed a pathogenic PKD1 frameshift deletion (c.11376delG) in one genetically unresolved family, likely missed by initial Sanger sequencing due to allelic dropout. This study expands the mutational spectrum of PKD1/PKD2 with five novel variants. The findings demonstrate the advantages of NGS over conventional Sanger sequencing methods. The genetically unresolved cases suggest the potential involvement of variants within non-coding regions, large copy number variations, or novel genes in ADPKD pathogenesis. Whole-genome sequencing is warranted to investigate these unresolved cases further.

The antibiotic resistance of pathogenic bacteria is currently one of the major problems in medicine, and finding novel antibacterial agents is one of the most difficult tasks in the field of biomedical sciences. Studies on such tasks can be successful only if genetic and molecular mechanisms leading to antibiotic resistance/sensitivity are understood. Previous reports indicated that the bacterial protein Hfq, discovered as an RNA chaperone but subsequently demonstrated to play also other functions in cells, is involved in the mechanisms of the response of bacterial cells to antibiotics. Recently, it was found that Hfq dysfunction resulted in more effective accumulation of an antibiotic ciprofloxacin in Escherichia coli cells irrespective of the presence or absence of the AcrB efflux pump. However, small RNA-mediated impairment of expression of the ompF gene, which encodes a porin involved in antibiotics influx, reversed the effects of the absence of Hfq on the antibiotic accumulation. This led to the hypothesis that Hfq might influence ciprofloxacin accumulation in the manner independent on its RNA chaperone function, as this protein might also influence cellular membrane structure and functions. Here, we demonstrate that in ompC and ompF mutants of E. coli, accumulation of ciprofloxacin is significantly impaired in the absence of Hfq or its C-terminal domain. These results corroborate the above-mentioned hypothesis on a sRNA-independent mechanism of Hfq-mediated modulation of the antibiotic transmembrane transport. Since fluoroquinolones use both protein- and lipid-mediated pathways to cross the outer membrane, Hfq may influence both processes. This possibility will be discussed herein.

Hip dysplasia (HD) is a major welfare problem, and in the present work, we investigated a sample of Bernese Mountain Dog breed bred in Brazil to estimate the genetic parameters for HD and to determine the best model for the estimation of breeding values (EBV) of dogs. The pedigree database consisted of 2218 dogs, of which 1202 had the hip phenotype available, corresponding to the X-ray (XR) classification according to the Fédération Cynologique Intenationale. Comparisons were made between seven different threshold models considering the HD phenotype with five classifications (reports from A to E) according to the XR (PHD1) and the binary phenotype with joints considered normal (report A) and abnormal (reports B to E) (PHD2). The threshold animal model was used to estimate the variance components and predict the genetic values. Fourteen models were evaluated, seven using variable PHD1 and another seven considering variable PHD2. Evaluated fixed effects were sex, birth year, or country of birth, which differed between models. The best fit model for the PHD1 phenotype estimated a heritability value of 0.30, while the best fit model for PHD2 estimated a value of 0.36. EBVs ranged from - 0.736 to 1.040 for PHD1 and from - 1.050 to 1.459 for PHD2, showing a wide diversity in the genetic merit of dogs. Approximately 40% of the animals had an EBV accuracy value greater than 50%. Considering the best two fit models for the tested phenotypes, we opted for the indication and use of the model working with PHD1, because of the direct correspondence of the PHD1 phenotype with the five possibilities of hip XR reports, once this facilitates understanding by both veterinarians and breeders. This model is used as the only fixed effect of the birth year. The present study is one of the first on canine genetic improvement approach in Brazil, and our results indicate the importance and potential of the use of EBV in the selection of sires for the improvement of HD in the national breeding of the breed.

Fusarium ear rot (FER) is a global disease caused by the fungal pathogen Fusarium verticillioides. Maize FER resistance is a quantitative trait controlled by polygenes. In this study, a doubled haploid (DH) population involving 159 lines, developed from the inbred lines B73 (susceptible) and CXS161 (highly resistant), was inoculated with Fusarium verticillioides across 4-year-location environment combinations in China during 2021 and 2022. The lines were genotyped using target sequencing with a 10 K SNP array. The results showed that the estimated broad-sense heritability (H²) in each environment ranged from 0.659 to 0.871, with an overall H² of 0.805. The average genetic length between adjacent markers in the genetic map constructed using multiple single-nucleotide polymorphisms (mSNP) was smaller than that constructed using SNP, whereas the maximal genetic length was almost the same. Using a genetic map constructed with a SNP, two quantitative trait loci (QTL) were identified on chromosomes 2 and 5, which explained 7.65% and 9.58% of the phenotypic variation, respectively. Using the genetic map constructed by mSNP, four QTL were identified, explaining 6.04-12.60% of the phenotypic variation. Moreover, two kompetitive allele-specific PCR (KASP) markers were developed using single-marker analysis methods, with one KASP marker validated across a backcross population that can be effectively used to identify FER resistance. In conclusion, using mSNP for genetic map construction does not confer advantages when the population size is limited and the marker density is high. However, the mSNP-constructed map identified more minor-effect QTL despite possessing a lower likelihood of the odds (LOD) values.

Strigolactones (SLs) are plant hormones that play a crucial role in regulating various aspects of plant architecture, such as shoot and root branching. However, the knowledge of SL-responsive genes and transcription factors (TFs) that control the shaping of plant architecture remains elusive. Here, transcriptomic analysis was conducted using the SL-insensitive barley mutant hvd14.d (carried mutation in SL receptor DWARF14, HvD14) and its wild-type (WT) to unravel the differences in gene expression separately in root and shoot tissues. This approach enabled us to select more than six thousand SL-dependent genes that were exclusive to each studied organ or not tissue-specific. The data obtained, along with in silico analyses, found several TFs that exhibited changed expression between the analyzed genotypes and that recognized binding sites in promoters of other identified differentially expressed genes (DEGs). In total, 28 TFs that recognize motifs over-represented in DEG promoters were identified. Moreover, nearly half of the identified TFs were connected in a single network of known and predicted interactions, highlighting the complexity and multidimensionality of SL-related signalling in barley. Finally, the SL control on the expression of one of the identified TFs in HvD14- and dose-dependent manners was proved. Obtained results bring us closer to understanding the signalling pathways regulating SL-dependent plant development.

Pedigree indices (PI) and genomically enhanced breeding values (GBV) of Polish Holstein-Friesian heifers were compared with their future performance. Phenotypes of 15,794 cows from 294 herds were analyzed. The traits evaluated included milk, fat and protein yield, somatic cell score (SCC), stature, overall udder and feet and legs score, heifer conception rate, and longevity. PI and GBV were from official evaluation systems, and performance records were adjusted for non-genetic effects. Correlations between breeding values and adjusted phenotypes were analyzed. Additionally, cows within each herd were divided into quartiles based on their breeding values, and the performance of cows from the top and bottom quartiles was compared. For production traits, similar analyses were conducted separately for high and low milk-producing herds to check for possible genotype by environment interaction. The analyses confirmed the significant correlation between breeding values and cow performance. Incorporating genomic information into PI significantly improved the predictive accuracy for milk, fat, and protein yields, as well as for SCC and stature, with increases ranging from 34 to 64%. Comparisons of cows' performance from the top and bottom quartiles supported these observations for all these traits except protein yield, with differences in performance being 43-92% greater when cows were ranked by GBV instead of PI. In a more productive environment, greater differences in performance were found between the top and bottom quartiles. These findings suggest that Polish breeders can enhance the outcomes of their breeding decisions by using GBV instead of PI. This change offers particular benefits in improving the predictability of future performance for the most economically important traits such as milk yield, fat yield, protein yield, somatic cell score, and stature.

Europe is highly dependent on soybean meal imports and anticipates an increase of domestic plant protein production. Ongoing climate change resulted in northward shift of plant hardiness zones, enabling spring-sowing of freezing-sensitive crops, including soybean. However, it requires efficient reselection of germplasm adapted to relatively short growing season and long-day photoperiod. In the present study, a PCR array has been implemented, targeting early maturity (E1-E4, E7, E9, and E10), pod shattering (qPHD1), and growth determination (Dt1) genes. This array was optimized for routine screening of soybean diversity panel (204 accessions), subjected to the 2018-2020 survey of phenology, morphology, and yield-related traits in a potential cultivation region in Poland. High broad-sense heritability (0.84-0.88) was observed for plant height, thousand grain weight, maturity date, and the first pod height. Significant positive correlations were identified between the number of seeds and pods per plant, between these two traits and seed yield per plant as well as between flowering, maturity, plant height, and first pod height. PCR array genotyping revealed high genetic diversity, yielding 98 allelic combinations. The most remarkable correlations were identified between flowering and E7 or E1, between maturity and E4 or E7 and between plant height and Dt1 or E4. The study demonstrated high applicability of this PCR array for molecular selection of soybean towards adaptation to Central Europe, designating recessive qPHD1 and dominant Dt1, E3, and E4 alleles as major targets to align soybean growth season requirements with the length of the frost-free period, improve plant performance, and increase yield.

Background: The activation of TGF-β pathway can facilitate tumorigenesis. Understanding the TGF-related genes (TRGs) in oral cancer and determining their prognostic value is of utmost importance.

Methods: The TRGs were selected to develop a prognostic model based on lasso regression. Oral cancer patients were classified into high-risk and low-risk groups based on the risk model. Subsequently, multivariate COX regression was employed to identify the prognostic marker. Additionally, the expression of SMURF2 was validated using quantitative real-time polymerase chain reaction (qRT-PCR) and the Human Protein Atlas (HPA) database. To investigate the relationship between SMURF2 expression and immune cell infiltrations, we conducted single-sample Gene Set Enrichment Analysis (ssGSEA) analyses.

Results: We identified 16 differentially expressed TRGs in oral cancer, all of which showed upregulation. From these, we selected eight TRGs as prognostic signatures. Furthermore, the high-risk group demonstrated lower infiltration levels of immune cells, immune score, and higher tumor purity. Interestingly, we also found that SMURF2 serves as an independent prognostic biomarker. SMURF2 was upregulated in oral cancer, as confirmed by public databases and qRT-PCR analysis. Importantly, our results indicate a close association between SMURF2 expression and the immune microenvironment.

Conclusion: The 8-TRG signature prognosis model that we constructed has the ability to predict the survival rate and immune activity of oral cancer patients. SMURF2 could be effective in recognizing prognosis and evaluating immune efficacy for oral cancer.

Several rivers that are tributaries of the Oder estuary are inhabited by Salmo trutta L, the most important of which are Ina, Gowienica, and Wołczenica. Both forms of the species, sea trout and resident brown trout, are present. All rivers are traditionally stocked with either sea trout from the neighboring Pomeranian river Rega basin or resident brown trout from various locations. To examine populations in these rivers in terms of genetic structure, genetic diversity, and origin, they were analyzed using 13 microsatellite loci. Relatedness was also assessed for fish stocked in the same year. The obtained genotypes were compared with breeding stocks used for stocking in Poland. The analyses revealed a significant genetic distance between adult individuals from Ina and Rega Rivers and fish caught during electrofishing. Strong kinship relationships were identified in the sampled areas, with high proportions of fish originating from stocking and their dominance in numbers over wild juveniles, primarily in smaller tributaries. Additionally, clear separation in the origin of stocked individuals was observed. Adult trout from Ina and Rega are genetically closer to northern brown trout lineages, providing crucial information for the management and biodiversity conservation of Polish Salmo trutta populations.