F2 bulk segregant analysis reveals salt-tolerant QTLs related to the ubiquitination process

Abstract

The growth and yield of rice, a major global food crop, are impaired by salt stress. This study aimed to identify quantitative trait loci (QTLs) associated with salt tolerance at the seedling stage. Bulk segregant analysis (BSA) of an F2 population from a cross between ‘Jao Khao’ (salt-tolerant) and IR29 (salt-susceptible) identified four QTLs on chromosomes 2, 3, 6, and 12. Four markers linked to these QTLs were validated in an F3 population, showing strong correlations (r = 0.7–0.8) with membrane stability, relative water content, and salt injury scores. Single nucleotide polymorphism (SNP)-by-SNP interactions across parental lines and four additional salt-tolerant and four salt-susceptible varieties revealed significant enrichment of the “plant hormone signal transduction” pathway, identifying LOC_OS03G49990 (OsSLR1) encoding DELLA, as a key gene. Comparative analysis of BSA-predicted QTLs with weighted gene co-expression network analysis-based key genes suggested LOC_Os02g02830 (ubiquitin-conjugating enzyme E2 28) and LOC_Os06g06170 (RING-type E3 ubiquitin transferase) as potential candidate genes. SNP association analysis across ten cultivars identified significant quantitative trait nucleotides on chromosomes 1, 2, 3, and 9, notably involving OsFBOX72 (F-box-type E3 ubiquitin ligase L7). These findings highlight the role of ubiquitination and hormone signalling in salt tolerance, providing potential targets for marker-assisted breeding. © The Author(s) 2025.