COVID-19 inhibits spermatogenesis in the testes by inducing cellular senescence
Conclusion: These results give us a new understanding of how COVID-19 inhibits spermatogenesis and provide a possible solution to alleviate this damage. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 5, 2023 Category: Genetics & Stem Cells Source Type: research

Multi-functional gene ZNF281 identified as a molecular biomarker in soft tissue regeneration and pan-cancer progression
Regeneration and tumorigenesis are indicated as related processes, while regeneration leads to life and the outcome of tumorigenesis is death. Here, we show the upregulation of zfp281 (zinc finger 281) in our adipose de novo regeneration model through RNA-seq analysis. Then, we validated the upregulation of zfp281 in adipose regeneration via immunofluorescence. Following that, we found that ZNF281 (the human homolog of Zfp281) was upregulated in most types of cancer and related to worse prognosis in 10 tumors. We further investigated the role of ZNF281 in cervical squamous cell carcinoma and endocervical adenocarcinoma (CE...
Source: Frontiers in Genetics - January 5, 2023 Category: Genetics & Stem Cells Source Type: research

Functional impact of multi-omic interactions in breast cancer subtypes
Multi-omic approaches are expected to deliver a broader molecular view of cancer. However, the promised mechanistic explanations have not quite settled yet. Here, we propose a theoretical and computational analysis framework to semi-automatically produce network models of the regulatory constraints influencing a biological function. This way, we identified functions significantly enriched on the analyzed omics and described associated features, for each of the four breast cancer molecular subtypes. For instance, we identified functions sustaining over-representation of invasion-related processes in the basal subtype and DN...
Source: Frontiers in Genetics - January 5, 2023 Category: Genetics & Stem Cells Source Type: research

Analysis of genotype × environment interactions for agronomic traits of soybean (Glycine max [L.] Merr.) using association mapping
The soybean yield is a complex quantitative trait that is significantly influenced by environmental factors. G × E interaction (GEI), which derives the performance of soybean genotypes differentially in various environmental conditions, is one of the main obstacles to increasing the net production. The primary goal of this study is to identify the outperforming genotypes in different latitudes, which can then be used in future breeding programs. A total of 96 soybean genotypes were examined in two different ecological regions: Faisalabad and Tando Jam in Pakistan. The evaluation of genotypes in different environmental con...
Source: Frontiers in Genetics - January 5, 2023 Category: Genetics & Stem Cells Source Type: research

Survival association of XRCC1 for patients with head and neck squamous cell carcinoma: A systematic review and meta-analysis
ConclusionThis meta-analysis demonstrated that XRCC1 Arg399Gln and XRCC1 high protein expression increase the risk of poor survival for HNSCC patients. XRCC1 is a potential therapeutic target for HNSCC. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 5, 2023 Category: Genetics & Stem Cells Source Type: research

Supervised learning techniques for dairy cattle body weight prediction from 3D digital images
In this study, various supervised learning techniques representing different families of methods in the machine learning space were implemented and compared for performance in the prediction of body weight from 3D image data in dairy cows. A total of 83,011 records of contour data from 3D images and body weight measurements taken from a total of 914 Danish Holstein and Jersey cows from 3 different herds were used for the predictions. Various metrics including Pearson’s correlation coefficient (r), the root mean squared error (RMSE), and the mean absolute percentage error (MAPE) were used for robust evaluation of the vari...
Source: Frontiers in Genetics - January 5, 2023 Category: Genetics & Stem Cells Source Type: research

Editorial: Application of fishes as biological models in genetic studies
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 5, 2023 Category: Genetics & Stem Cells Source Type: research

Genetic parameters estimation and genome molecular marker identification for gestation length in pigs
This study provided effective molecular information for the genetic improvement of GL in pigs. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 5, 2023 Category: Genetics & Stem Cells Source Type: research

Metabolite profiling and transcriptome analyses provide insight into the regulatory network of graft incompatibility in litchi
This study characterized the abundance of metabolites and genes in graft incompatible combinations and further discussed the genetic mechanism of graft incompatibility in litchi. Our results provide a platform to dissect the molecular mechanisms of graft incompatibility in the litchi fruit. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 5, 2023 Category: Genetics & Stem Cells Source Type: research

Whole genome sequencing of Clarireedia aff. paspali reveals potential pathogenesis factors in Clarireedia species, causal agents of dollar spot in turfgrass
Dollar spot is one of the most damaging diseases in turfgrass, reducing its quality and playability. Two species, Clarireedia monteithiana and C. jacksonii (formerly Sclerotinia homoeocarpa) have been reported so far in the United States To study the Clarireedia genome, two isolates H2 and H3, sampled from seashore paspalum in Hawaii in 2019 were sequenced via Illumina paired-end sequencing by synthesis technology and PacBio SMRT sequencing. Both isolates were identified as C. aff. paspali, a novel species in the United States Using short and long reads, C. aff. paspali H3 contained 193 contigs with 48.6 Mbp and presented...
Source: Frontiers in Genetics - January 5, 2023 Category: Genetics & Stem Cells Source Type: research

Genomic diversity and relationship analyses of endangered German Black Pied cattle (DSN) to 68 other taurine breeds based on whole-genome sequencing
German Black Pied cattle (Deutsches Schwarzbuntes Niederungsrind, DSN) are an endangered dual-purpose cattle breed originating from the North Sea region. The population comprises about 2,500 cattle and is considered one of the ancestral populations of the modern Holstein breed. The current study aimed at defining the breeds closest related to DSN cattle, characterizing their genomic diversity and inbreeding. In addition, the detection of selection signatures between DSN and Holstein was a goal. Relationship analyses using fixation index (FST), phylogenetic, and admixture analyses were performed between DSN and 68 other bre...
Source: Frontiers in Genetics - January 4, 2023 Category: Genetics & Stem Cells Source Type: research

Growth performance, survivability and profitability of improved smallholder chicken genetics in Nigeria: A COVID-19 intervention study
This study provided a total of 150 smallholder poultry farmers, randomly selected from three states (Kebbi, Nasarawa, and Imo) in Nigeria, with ten 5-week-old chickens (mixed sexes) each, of either FUNAAB Alpha or Noiler chicken genetics. The improved, dual-purpose chickens were evaluated for growth performance (GP), survivability and profitability. The birds were managed under semi-scavenging production system. Body weight, mortality, and cost of production (COP) were recorded every 4 weeks until 21 weeks of age. Profitability was a function of the COP, and the selling price for live-birds (cocks). Body weight of Noiler...
Source: Frontiers in Genetics - January 4, 2023 Category: Genetics & Stem Cells Source Type: research

Identification of rare thalassemia variants using third-generation sequencing
In this study, we evaluated a new third-generation sequencing-based approach termed comprehensive analysis of thalassemia alleles (CATSA) in subjects with no variants identified by routine PCR, Sanger sequencing, and specially designed GAP-PCR. Hemoglobin testing and routine PCR tests for 23 common variants were performed for 3,033 subjects. Then, Sanger sequencing and specially designed GAP-PCR were performed for a subject with no variants identified by routine PCR, no iron deficiency, and positive hemoglobin testing. Finally, the new CATSA method was conducted for the subjects with no variants identified by Sanger sequen...
Source: Frontiers in Genetics - January 4, 2023 Category: Genetics & Stem Cells Source Type: research

Mapping of a QTL associated with sucrose content in peanut kernels using BSA-seq
In this study, an F2 segregating population and a recombinant inbred line (RIL) population, derived from a cross between the high sucrose content variety Jihuatian 1 and the low sucrose content line PI478819, were used as materials to map a quantitative trait locus (QTL) associated with sucrose content in peanut kernels. Four QTLs were initially located on chromosomes A03 and A06 based on BSA-seq technology, and multiple kompetitive allele-specific PCR markers were developed based on single-nucleotide polymorphisms (SNPs) in the intervals. The markers were genotyped in the RIL population and finely mapped to a stable QTL, ...
Source: Frontiers in Genetics - January 4, 2023 Category: Genetics & Stem Cells Source Type: research

Maternal body condition and season influence RNA deposition in the oocytes of alfalfa leafcutting bees (Megachile rotundata)
Maternal effects are an important source of phenotypic variance, whereby females influence offspring developmental trajectory beyond direct genetic contributions, often in response to changing environmental conditions. However, relatively little is known about the mechanisms by which maternal experience is translated into molecular signals that shape offspring development. One such signal may be maternal RNA transcripts (mRNAs and miRNAs) deposited into maturing oocytes. These regulate the earliest stages of development of all animals, but are understudied in most insects. Here we investigated the effects of female interna...
Source: Frontiers in Genetics - January 4, 2023 Category: Genetics & Stem Cells Source Type: research