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Marker-assisted selection (MAS) refers to the use of molecular markers to assist phenotypic selections in crop improvement. Several types of molecular markers, such as single nucleotide polymorphism (SNP), have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS) technologies has led to remarkable advances in whole genome sequencing, which provides ultra-throughput sequences to revolutionize plant genotyping and breeding. To further broaden NGS usages to large crop genomes such as maize and wheat, genotyping-by-sequencing (GBS) has been developed and applied in sequencing multiplexed samples that combine molecular marker discovery and genotyping. GBS is a novel application of NGS protocols for discovering and genotyping SNPs in crop genomes and populations. The GBS approach includes the digestion of genomic DNA with restriction enzymes followed by the ligation of barcode adapter, PCR amplification and sequencing of the amplified DNA pool on a single lane of flow cells. Bioinformatic pipelines are needed to analyze and interpret GBS datasets. As an ultimate MAS tool and a cost-effective technique, GBS has been successfully used in implementing genome-wide association study (GWAS), genomic diversity study, genetic linkage analysis, molecular marker discovery and genomic selection under a large scale of plant breeding programs.

Yeast culture is widely used in ruminants to improve gut health, immunity, and productivity; however, its impact on meat quality remains unclear. This study aimed to investigate the effects of yeast culture supplementation in the basic diet on meat quality of Small-tail Han sheep. A total of 40 Small-tail Han sheep (17.5 ± 1.2 kg) were randomly assigned to two treatment groups, with 20 sheep in each group. The sheep were fed either a basic diet (CON) or the basic diet supplemented with 1% yeast culture (YSD) for 90 days. At the end of the trial, the Longissimus dorsi muscle (LOD) of the sheep was collected for meat quality evaluation, as well as transcriptome and metabolome analyses. Meat quality data were analyzed using t-tests, while transcriptome and metabolome data were analyzed using bioinformatics tools. The results showed that YSD supplementation significantly reduced carcass fat content (p < 0.05) and increased the pH values (p < 0.05) of LOD compared to the CON group. Multi-omics analysis revealed significant changes in the levels of 349 transcripts and 149 metabolites (p < 0.05) in the YSD group relative to the CON group. These changes were primarily associated with immune response pathways and purine metabolism. Further integrated transcriptomics and metabolomics analysis identified significant alterations in the expression of adenylate kinase 4 (AK4) and ribonucleotide reductase M2 (RRM2), which influenced purine metabolites, such as ADP, GMP, 3′-AMP, 3′-GMP, dGDP, adenine, guanosine, and guanine. These metabolites were markedly upregulated in the LOD of the sheep supplemented with yeast culture. In conclusion, yeast culture supplementation improved the meat quality of Small-tail Han sheep, potentially through the enhancement of immune response and purine metabolism. These findings offer valuable insights into the molecular mechanisms underlying the effects of yeast culture on animal health and meat quality.

Normal proliferation of ovarian granulosa cells is essential for follicular development. The results of this study showed that ADAMTS1 was primarily localized in the cytoplasm of granulosa cells in sheep ovarian follicles, as revealed by immunohistochemistry and immunofluorescence staining. Knockdown and overexpression experiments of ADAMTS1 in granulosa cells demonstrated that the number of EdU-positive cells significantly decreased in the knockdown group (p < 0.05), while the expression levels of Bax (p < 0.05), Bax/Bcl2 (p < 0.01), and caspase3 (p < 0.05) were significantly upregulated, indicating that knockdown of ADAMTS1 markedly inhibited granulosa cell proliferation. In contrast, overexpression of ADAMTS1 significantly promoted cell proliferation. Transcriptome sequencing revealed that PSAT1 and SLC6A9 were significantly downregulated in the knockdown group and significantly upregulated in the overexpression group, which was confirmed by Quantitative Polymerase Chain Reaction (Q-PCR) (p < 0.05). KEGG enrichment analysis showed that PSAT1 was significantly enriched in the glycine, serine and threonine metabolism and vitamin B6 metabolism pathways. Molecular docking analysis indicated a stable binding interface between ADAMTS1 and PSAT1. Based on these findings, we speculate that ADAMTS1 may regulate amino acid metabolism in ovarian granulosa cells by modulating the expression of SLC6A9, which in turn affects PSAT1 in the glycine, serine, and threonine metabolism and vitamin B6 metabolism pathways, thereby influencing granulosa cell proliferation.

Background Periodontitis is the most common oral disease and is closely related to immune infiltration in the periodontal microenvironment and its poor prognosis is related to the complex immune response. The progression of periodontitis is closely related to necroptosis, but there is still no systematic study of long non-coding RNA (lncRNA) associated with necroptosis for diagnosis and treatment of periodontitis. Material and methods Transcriptome data and clinical data of periodontitis and healthy populations were obtained from the Gene Expression Omnibus (GEO) database, and necroptosis-related genes were obtained from previously published literature. FactoMineR package in R was used to perform principal component analysis (PCA) for obtaining the necroptosis-related lncRNAs. The core necroptosis-related lncRNAs were screened by the Linear Models for Microarray Data (limma) package in R, PCA principal component analysis and lasso algorithm. These lncRNAs were then used to construct a classifier for periodontitis with logistic regression. The receiver operating characteristic (ROC) curve was used to evaluate the sensitivity and specificity of the model. The CIBERSORT method and ssGSEA algorithm were used to estimate the immune infiltration and immune pathway activation of periodontitis. Spearman’s correlation analysis was used to further verify the correlation between core genes and periodontitis immune microenvironment. The expression level of core genes in human periodontal ligament cells (hPDLCs) was detected by RT-qPCR. Results A total of 10 core necroptosis-related lncRNAs (10-lncRNAs) were identified, including EPB41L4A-AS1, FAM30A, LINC01004, MALAT1, MIAT, OSER1-DT, PCOLCE-AS1, RNF144A-AS1, CARMN, and LINC00582. The classifier for periodontitis was successfully constructed. The Area Under the Curve (AUC) was 0.952, which suggested that the model had good predictive performance. The correlation analysis of 10-lncRNAs and periodontitis immune microenvironment showed that 10-lncRNAs had an impact on the immune infiltration of periodontitis. Notably, the RT-qPCR results showed that the expression level of the 10-lncRNAs obtained was consistent with the chip analysis results. Conclusions The 10-lncRNAs identified from the GEO dataset had a significant impact on the immune infiltration of periodontitis and the classifier based on 10-lncRNAs had good detection efficiency for periodontitis, which provided a new target for diagnosis and treatment of periodontitis.

Background This study was carried out to investigate the individual and combined contamination of aflatoxin B 1 (AFB 1 ), deoxynivalenol (DON), and zearalenone (ZEN) in feeds in China between 2021 and 2024. A total of 23,003 feed samples, including 17,489 feedstuff samples and 5,514 complete feed samples, were collected from different provinces of China for mycotoxin analysis. Results The analyzed mycotoxins displayed considerably high contamination in the feed samples, with the individual contamination of AFB 1 , DON, and ZEN were 20.0%–100%, 33.3%–100%, and 85.0%–100%, respectively. The average concentrations of AFB 1 , DON, and ZEN were 1.2–728.7 μg/kg, 106–8,634.8 μg/kg, and 18.1–3,341.6 μg/kg, respectively. Notably, the rates over China’s safety standards for AFB 1 , DON, and ZEN in raw ingredients were 9.7%, 2.7%, and 15.7%, respectively. Meanwhile, 3.5%, 1.1%, and 8.7% of analyzed complete feeds exceeded China’s safety standards for AFB 1 , DON, and ZEN, respectively. Moreover, the co-contamination rates of AFB 1 , DON, and ZEN in more than 70% of raw ingredients and 87.5% of complete feed products were 60.0%–100% and 61.5%–100%, respectively. Conclusion This study reveals that the feeds in China have commonly been contaminated with AFB 1 , DON, and ZEN alone and their combination during the past four years. These findings highlight the significance of monitoring mycotoxin contaminant levels in domestic animal feed and the importance of carrying out feed administration and remediation strategies for mycotoxin control.

Sugar beet ( Beta vulgaris L.) is an important sugar-producing and energy crop worldwide. The sugar beet pure line IMA1 independently bred by Chinese scientists is a standard diploid parent material that is widely used in hybrid-breeding programs. In this study, a high-quality, chromosome-level genome assembly for IMA1was conducted, and 99.1% of genome sequences were assigned to nine chromosomes. A total of 35,003 protein-coding genes were annotated, with 91.56% functionally annotated by public databases. Compared with previously released sugar beet assemblies, the new genome was larger with at least 1.6 times larger N50 size, thereby substantially improving the completeness and continuity of the sugar beet genome. A Genome-Wide Association Studies analysis identified 10 disease-resistance genes associated with three important beet diseases and five genes associated with sugar yield per hectare, which could be key targets to improve sugar productivity. Nine highly expressed genes associated with pollen fertility of sugar beet were also identified. The results of this study provide valuable information to identify and dissect functional genes affecting sugar beet agronomic traits, which can increase sugar beet production and help screen for excellent sugar beet breeding materials. In addition, information is provided that can precisely incorporate biotechnology tools into breeding efforts.

Background Radiotherapy (RT) is frequently adopted to control cancer cell proliferation, which is achieved by altering the tumor microenvironment (TME) and immunogenicity. Apoptosis of cancer cells is the major effect of radiation on tumor tissues. Fas/APO-1(CD95) receptors on the cell membrane are death receptors that can be activated by diverse factors, including radiation and integration with CD95L on CD8 + T cells. The abscopal effect is defined as tumor regression out of the local RT field, and it is produced through anti-tumor immunity. The immune response against the radiated tumor is characterized by the cross-presentation between antigen-presenting cells (APCs), which includes cytotoxic T cells (CTLs) and dendritic cells (DCs). Methods The effect of activation and radiation of CD95 receptors on melanoma cell lines was examined in vivo and in vitro. In vivo, bilateral lower limbs were given a subcutaneous injection of a dual-tumor. Tumors in the right limb were radiated with a single dose of 10 Gy (primary tumor), while tumors in the left limb (secondary tumor) were spared. Results The anti-CD95 treatment plus radiation (combination treatment) reduced growth rates of both primary and secondary tumors relative to the control or radiation groups. In addition, higher degrees of infiltrating CTLs and DCs were detected in the combination treatment compared to the other groups, but the immune response responsible for secondary tumor rejection was not proven to be tumor specific. In vitro, combination treatment combined with radiation resulted in further apoptosis of melanoma cells relative to controls or cells treated with radiation. Conclusions Targeting CD95 on cancer cells will induce tumor control and the abscopal effect.

Advancements in sequencing have enabled the assembly of numerous sheep genomes, significantly advancing our understanding of the link between genetic variation and phenotypic traits. However, the genome of East Friesian sheep ( Ostfriesisches Milchschaf ), a key high-yield milk breed, remains to be fully assembled. Here, we constructed a near-complete and gap-free East Friesian genome assembly using PacBio HiFi, ultra-long ONT and Hi-C sequencing. The resulting genome assembly spans approximately 2.96 Gb, with a contig N50 length of 104.1 Mb and only 164 unplaced sequences. Remarkably, our assembly has captured 41 telomeres and 24 centromeres. The assembled sequence is of high quality on completeness (BUSCO score: 97.1%) and correctness (QV: 69.1). In addition, a total of 24,580 protein-coding genes were predicted, of which 97.2% (23,891) carried at least one conserved functional domain. Collectively, this assembly provides not only a near T2T gap-free genome, but also provides a valuable genetic resource for comparative genome studies of sheep and will serve as an important tool for the sheep research community.