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Published (Version of record)CC BY-NC V4.0, Open Access
Published (Version of record)CC BY-NC V4.0, Open
Journal article
Chromosome-level genome assembly of IR64 near-isogenic line harboring Saltol reveals novel genomic regions associated with salinity tolerance in rice (Oryza sativa L.)
Plant physiology and biochemistry, Vol.229(Part D), pp.1-10
12/2025
PMID: 41145043
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Abstract
Climate change-induced sea level rise significantly exacerbates soil and groundwater salinization, posing a substantial threat to global agriculture, particularly impacting salt-sensitive crops like rice (Oryza sativa L.). Significant advancements have been made in identifying the genetic factors that influence salinity tolerance. A well-studied quantitative trait locus (QTL), known as Saltol, is located on chromosome 1 and provides notable salinity tolerance during the seedling stage by maintaining low ratios of Na+ to K+ in the shoots. Although considerable progress has been made in identifying genetic factors of salinity tolerance, Saltol QTL does not fully account for phenotypic variability under saline conditions. This study aims to comprehensively characterize additional genomic regions associated with salinity tolerance by using a high-quality genome assembly of the IR64 rice variety, a high-yielding and quality. We will also analyze its near-isogenic line (NIL), IR64-Saltol, which harbors Saltol QTL. Comparative genomic analyses identified 228 introgression segments from FL478, prominently on chromosomes 1, 2, 8, and 12, spanning a total of 7.04 Mb. Integrated QTL mapping highlighted 137 previously reported salinity tolerance loci from Pokkali populations, with significant overlaps observed in the introgression segments. Within these genomic regions, we identified 175 candidate genes, including transcription factors (MYB2, MYBY1), ion transporters (CCC2, CNGC17), and stress-responsive regulators (TPS10, IAA10), which implicates complex physiological networks in salinity adaptation. Our findings substantially expand the genetic framework available for breeding salt-tolerant rice varieties, providing critical resources to address agricultural challenges posed by salinization under ongoing climate change.
Details
- Title
- Chromosome-level genome assembly of IR64 near-isogenic line harboring Saltol reveals novel genomic regions associated with salinity tolerance in rice (Oryza sativa L.)
- Creators
- Jae-Hyuk Han - IRRIKJi-Hun Hwang - Myongji UniversityNa-Hyun Shin - Pusan National UniversitySunghan Kim - Sejong UniversityHyun-Sook Lee - Rural Development AdministrationTobias Kretzschmar - Southern Cross UniversityKyung Do Kim - Sejong UniversityIl-Ryong Choi - IRRIKJoong Hyoun Chin - Sejong University
- Publication Details
- Plant physiology and biochemistry, Vol.229(Part D), pp.1-10
- Publisher
- Elsevier Masson SAS; ISSY-LES-MOULINEAUX
- Grant note
- This research was supported by the National Research Foundation of Korea (NRF) grant funded by the Korean government (MSIT) (RS-2024- 00343462). This work was also supported by the Temperate Rice Research Consortium (TRRC) of the International Rice Research Institute (IRRI).
- Identifiers
- 991013325411102368
- Copyright
- © 2025 The Authors.
- Academic Unit
- Faculty of Science and Engineering; Science
- Language
- English
- Resource Type
- Journal article