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Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways
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Document Title
Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways
Author
Phosuwan S. Nounjan N. Theerakulpisut P. Siangliw M. Charoensawan V.
Affiliations
Doctor of Philosophy Program in Biochemistry (International Program) Faculty of Science Mahidol University Bangkok Thailand; Department of Biochemistry Faculty of Science Mahidol University Bangkok Thailand; Biodiversity and Environmental Management Division International College Khon Kaen University Khon Kaen Thailand; Salt-tolerant Rice Research Group Department of Biology Faculty of Science Khon Kaen University Khon Kaen Thailand; National Center for Genetic Engineering and Biotechnology (BIOTEC) National Science and Technology Development Agency (NSTDA) Khlong Luang Thailand; Integrative Computational BioScience (ICBS) Center Mahidol University Nakhon Pathom Thailand; Division of Medical Bioinformatics Research Department Faculty of Medicine Siriraj Hospital Mahidol University Bangkok Thailand; Department of Biochemistry Faculty of Medicine Siriraj Hospital Mahidol University Bangkok Thailand; Siriraj Genomics Faculty of Medicine Siriraj Hospital Mahidol University Bangkok Thailand; School of Chemistry Institute of Science Suranaree University of Technology Nakhon Ratchasima Thailand
Type
Article
Source Title
Frontiers in Plant Science
ISSN
1664462X
Year
2024
Volume
15
Open Access
All Open Access Gold
Publisher
Frontiers Media SA
DOI
10.3389/fpls.2024.1264909
Abstract
Soil salinity is a complex abiotic stress that involves several biological pathways. Hence focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple stress-related traits obtained by different studies. Making use of a combined set of 46 salinity-related traits from three independent studies that were based on the same chromosome segment substitution line (CSSL) population of rice (Oryza sativa) we demonstrate how our approach can address technical biases and limitations from different QTL studies and calling methods. This allows us to compile a comprehensive list of trait-specific and multi-trait QTLs as well as salinity-related candidate genes. In doing so we discover several novel relationships between traits that demonstrate similar trends of phenotype scores across the CSSLs as well as the similarities between genomic locations that the traits were mapped to. Finally we experimentally validate our findings by expression analyses and functional validations of several selected candidate genes from multiple pathways in rice and Arabidopsis orthologous genes including OsKS7 (ENT-KAURENE SYNTHASE 7) OsNUC1 (NUCLEOLIN 1) and OsFRO1 (FERRIC REDUCTASE OXIDASE 1) to name a few. This work not only introduces a novel approach for conducting comparative analyses of multiple QTLs but also provides a list of candidate genes and testable hypotheses for salinity-related mechanisms across several biological pathways. Copyright ? 2024 Phosuwan Nounjan Theerakulpisut Siangliw and Charoensawan.
Industrial Classification
Knowledge Taxonomy Level 1
Knowledge Taxonomy Level 2
Knowledge Taxonomy Level 3
License
CC BY
Rights
Authors
Publication Source
WOS