Thirty SNPs and eight InDels were identified using a transcriptomic approach (RNA-Seq). We used an integrative analysis based on RNA-Seq, SNP/InDel search and validation on table grape segregants and varieties with different genetic backgrounds. The aim of this work was to perform marker discovery using a transcriptomic approach, in order to identify and characterize SNP and InDel markers associated with berry size in table grapes. However, berry size is a complex quantitive trait under polygenic control, and its genetic determination of berry weight is not yet fully understood. Here, the authors develop a workflow to deliver robust cWGTS analyses and reports within clinically-relevant timeframes for paediatric, adolescent and young adult solid tumour patients.īerry size is considered as one of the main selection criteria in table grapes breeding programs, due to the consumer preferences. Cancer whole-genome and transcriptome sequencing (cWGTS) has been challenging to implement in clinical settings. These results establish key technical considerations for the implementation of cWGTS as an integrated test in clinical oncology. Integration of germline, somatic DNA and RNA-seq data enable data-driven variant prioritization and reporting, with oncogenic findings reported in 54% more patients than standard of care. Benchmarking identifies a minimum of 80× as optimal depth for clinical WGS sequencing. Comparison of cWGTS to diagnostic panel assays demonstrates the potential of cWGTS to capture all clinically reported mutations with comparable sensitivity in a single workflow. In a prospective research study we develop a workflow that reports comprehensive cWGTS results in 9 days. However, implementation of cWGTS is challenged by the need to deliver results within clinically relevant timeframes, concerns about assay sensitivity, reporting and prioritization of findings. The utility of cancer whole genome and transcriptome sequencing (cWGTS) in oncology is increasingly recognized. Ultimately, these SNPs could serve as a powerful marker for accelerating wheat breeding programs. The allele-specific polymerase chain reaction results revealed that Gemmeiza-9 was heterozygous (C/G), whereas the Sakha-93 was homozygous (C/C), indicating that these SNPs might affect positively the response of wheat cultivars to tolerate the salinity. For SNP in vitro validation, we used two Egyptian cultivars with opposite salinity responses (tolerant: Sakha-93 and sensitive: Gemmeiza-9). The expression of the WRKY-1 gene was consistent between salt-tolerant and salt-sensitive wheat cultivars, indicating that the WRKY-1 had no influence on the MIOX-1 gene expression and these SNP might positively affect the salinity tolerance. The results revealed that the occurrence of this sSNP is irreplaceable and positioned in the WRKY-1 binding site. Therefore, the SNP located in the promotor area of the MIOX-1 gene was further analyzed to predict the transcription factor binding sites. Interestingly, the expression of the MIOX-1 gene was significantly down-regulated in the tolerant compared to the sensitive. For in silico validation of MIOX-1 expression, we compared transcriptomes of salt-tolerant and sensitive wheat cultivars. Interestingly, six shared SNPs (sSNPs) were identified across four genes including the MIOX-1 gene. The identified shared DEGs (31 sDEGs) were extracted and compared to available wheat reference genomes to obtain all single-nucleotide polymorphisms (SNPs). First, we analyzed multi-transcriptomic datasets for salt-tolerant cultivars to identify the shared differentially expressed genes (DEGs). Here, we utilize the available next-generation sequencing (NGS) data to develop robust markers differentiating between salt-tolerant and sensitive wheat cultivars.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |