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Genome-wide association study using an aus Rice panel identifies a Salinity Sensitive Gene on Chromosome 6 at

Shiqin Hu1, Yuetong Chen2, Qing Zhao1

  • 1College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, China; CAAS-IRRI Joint Laboratory for Genomics-assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.

International Journal of Biological Macromolecules
|December 6, 2025
PubMed
Summary

Researchers identified a key gene, OsSS6, that negatively regulates salt tolerance in rice seedlings. OsSS6 mutants show enhanced survival under salinity, offering potential for breeding salt-resistant rice varieties.

Keywords:
AusDUF1645GWASOsSS6RiceSalt tolerance

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Area of Science:

  • Plant Genetics
  • Molecular Biology
  • Agronomy

Background:

  • Rice is a vital global food source, but salinity stress severely impacts its yield.
  • Identifying genetic factors for salt tolerance is crucial for crop improvement.

Purpose of the Study:

  • To identify quantitative trait loci (QTLs) and candidate genes associated with seedling-stage salt tolerance in rice.
  • To characterize the function of a novel salt tolerance gene, OsSS6.

Main Methods:

  • Genome-wide association study (GWAS) on 163 aus rice accessions.
  • CRISPR/Cas9 gene editing to create OsSS6 mutants.
  • Phenotypic evaluation of salt tolerance, including ion content and biomass.

Main Results:

  • Five salt tolerance-related QTLs were identified, with qSES6.1 on chromosome 6 showing the strongest association.
  • OsSS6, identified as a negative regulator of salt tolerance, was localized to the plasma membrane.
  • OsSS6 mutants exhibited significantly enhanced salt tolerance and up-regulation of other tolerance-related genes.

Conclusions:

  • OsSS6 plays a critical role in regulating salt tolerance in rice seedlings.
  • Targeting OsSS6 presents a promising strategy for developing salt-tolerant rice cultivars.
  • Haplotype analysis suggests potential indica-japonica differentiation in salt tolerance traits.