Frontiers in Plant Science (May 2023)

Identification of candidate genes for salinity tolerance in Japonica rice at the seedling stage based on genome-wide association study and linkage mapping

  • Shanbin Xu,
  • Jingnan Cui,
  • Hu Cao,
  • Shaoming Liang,
  • Tianze Ma,
  • Hualong Liu,
  • Jingguo Wang,
  • Luomiao Yang,
  • Wei Xin,
  • Yan Jia,
  • Detang Zou,
  • Hongliang Zheng

DOI
https://doi.org/10.3389/fpls.2023.1184416
Journal volume & issue
Vol. 14

Abstract

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BackgroundSalinity tolerance plays a vital role in rice cultivation because the strength of salinity tolerance at the seedling stage directly affects seedling survival and final crop yield in saline soils. Here, we combined a genome-wide association study (GWAS) and linkage mapping to analyze the candidate intervals for salinity tolerance in Japonica rice at the seedling stage.ResultsWe used the Na+ concentration in shoots (SNC), K+ concentration in shoots (SKC), Na+/K+ ratio in shoots (SNK), and seedling survival rate (SSR) as indices to assess the salinity tolerance at the seedling stage in rice. The GWAS identified the lead SNP (Chr12_20864157), associated with an SNK, which the linkage mapping detected as being in qSK12. A 195-kb region on chromosome 12 was selected based on the overlapping regions in the GWAS and the linkage mapping. Based on haplotype analysis, qRT-PCR, and sequence analysis, we obtained LOC_Os12g34450 as a candidate gene.ConclusionBased on these results, LOC_Os12g34450 was identified as a candidate gene contributing to salinity tolerance in Japonica rice. This study provides valuable guidance for plant breeders to improve the response of Japonica rice to salt stress.

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