Identification of QTLs for Morpho-Physiological Traits under Saline Stress in <i>Indica</i> MAGIC Rice Population

Abstract

Rice is sensitive to salinity at both the seedling and reproductive stages, and it reduces the grain yield from 50 to 100%. In this study, 27 SNP markers significantly associated with 15 QTLs were identified. Three major QTLs were associated with shoot length (Sal_SL 7.1), shoot sodium content (Sal_Na 1.1) and shoot magnesium content (Sal_Mg 2.1). Five QTLs for root length (Sal_RL 1.1, Sal_RL 3.1, Sal_RL 6.1 Sal_RL 8.1 and Sal_RL 12.1), shoot K+/Na+ homeostasis (Sal_K/Na 1.1, Sal_K/Na 4.1, Sal_K/Na 5.1, Sal_K/Na 7.1 and Sal_K/Na 10.1) and single QTLs for shoot potassium (Sal_K 6.1) and calcium content (Sal_Ca 5.1) were also detected. QTL Sal_K/Na 1.1 was found responsible for the ionic ratio associated with the Saltol region, and Sal_K/Na 10.1 was associated with the gene OSCA1;4, which is a hyperosmolality-gated calcium-permeable channel that acts as an osmosensor under salt stress condition. A candidate gene haplotype analysis revealed ten significant genes, LOC_Os06g03940, LOC_Os10g42820, LOC_Os07g36230, LOC_Os02g06410, LOC_Os06g48610, LOC_Os12g12950, LOC_Os03g12050, LOC_Os08g02690, LOC_Os07g47560, and LOC_Os05g08840, responsible for abiotic stress tolerance. The identified potential candidate genes can be used for functional characterization to understand the complex mechanism of salinity tolerance in rice.

Keywords

• rice
• salinity
• SNP
• QTL
• GWAS
• haplotype