A combination of two approaches, namely QTL analysis and gene enrichment analysis were used to identify candidate genes in the "QTL-hotspot" region for drought tolerance present on the Ca4 pseudomolecule in chickpea. In the first approach, a high-density bin map was developed using 53,223 single nucleotide polymorphisms (SNPs) identified in the recombinant inbred line (RIL) population of ICC 4958 (drought tolerant) and ICC 1882 (drought sensitive) cross. QTL analysis using recombination bins as markers along with the phenotyping data for 17 drought tolerance related traits obtained over 1-5 seasons and 1-5 locations split the "QTL-hotspot" region into two subregions namely "QTL-hotspot_a" (15 genes) and "QTL-hotspot_b" (11 genes). In the second approach, gene enrichment analysis using significant marker trait associations based on SNPs from the Ca4 pseudomolecule with the above mentioned phenotyping data, and the candidate genes from the refined "QTL-hotspot" region showed enrichment for 23 genes. Twelve genes were found common in both approaches. Functional validation using quantitative real-time PCR (qRT-PCR) indicated four promising candidate genes having functional implications on the effect of "QTL-hotspot" for drought tolerance in chickpea.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4609953 | PMC |
| http://dx.doi.org/10.1038/srep15296 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Evaluation of Reference Gene Stability for Investigations of Intracellular Signalling in Human Cancer and Non-Malignant Mesenchymal Stromal Cells.
Front Biosci (Schol Ed)
December 2024
Laboratory of Intracellular Membranes Dynamics, Institute of Cytology of the Russian Academy of Sciences, 194064 Saint Petersburg, Russia.
Background: Real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR) is a powerful tool for analysing target gene expression in biological samples. To achieve reliable results by RT-qPCR, the most stable reference genes must be selected for proper data normalisation, particularly when comparing cells of different types. We aimed to choose the least variable candidate reference genes among eight housekeeping genes tested within a set of human cancer cell lines (HeLa, MCF-7, SK-UT-1B, A549, A431, SK-BR-3), as well as four lines of normal, non-malignant mesenchymal stromal cells (MSCs) of different origins.
View Article and Find Full Text PDFSingle-Cell Sequencing and Machine Learning Integration to Identify Candidate Biomarkers in Psoriasis: .
J Inflamm Res
December 2024
Department of Dermatology, China-Japan Friendship Hospital, National Center for Integrative Medicine, Beijing, 100029, People's Republic of China.
Background: Psoriasis represents a persistent, immune-driven inflammatory condition affecting the skin, characterized by a lack of well-established biologic treatments without adverse events. Consequently, the identification of novel targets and therapeutic agents remains a pressing priority in the field of psoriasis research.
Methods: We collected single-cell RNA sequencing (scRNA-seq) datasets and inferred T cell differentiation trajectories through pseudotime analysis.
Insights into targeting LKB1 in tumorigenesis.
Genes Dis
March 2025
The Mary & John Knight Translational Ovarian Cancer Research Unit, London Regional Cancer Program, London, ON N6A 4L6, Canada.
Genetic alterations to serine-threonine kinase 11 () have been implicated in Peutz-Jeghers syndrome and tumorigenesis. Further exploration of the context-specific roles of liver kinase B1 (LKB1; encoded by ) observed that it regulates AMP-activated protein kinase (AMPK) and AMPK-related kinases. Given that both migration and proliferation are enhanced with the loss of LKB1 activity combined with the prevalence of genetic alterations in cancer biopsies, LKB1 was marked as a tumor suppressor.
View Article and Find Full Text PDFCharacterization and functionality of 1003 isolated from chicken cecum against .
Front Cell Infect Microbiol
December 2024
Postdoctoral Research Workstation, Heilongjiang Academy of Agricultural Sciences, Harbin, China.
Lactic acid bacteria are widely regarded as safe alternatives to antibiotics in livestock and poultry farming and have probiotic potential. () is a prominent component of pigeon crop microbiota; however, its function is unknown. In this study, a strain of 1003 from pigeon cecum was identified by combining whole genome sequencing and phenotypic analysis, and its safety and probiotic properties were studied.
View Article and Find Full Text PDFInvestigating the biomarker potential and molecular targets of TIGD1 in lung cancer using bioinformatics.
Turk J Med Sci
December 2024
Department of Medical Biology, Faculty of Medicine, Kocaeli University, Kocaeli, Turkiye.
Background/aim: Lung cancer, a predominant contributor to cancer mortality, is characterized by diverse etiological factors, including tobacco smoking and genetic susceptibilities. Despite advancements, particularly in nonsmall-cell lung cancer (NSCLC), therapeutic options for lung squamous cell carcinoma (LUSC) are limited. Transposable elements (TEs) and their regulatory proteins, such as tigger transposable element derived (TIGD) family proteins, have been implicated in cancer development.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!