Quantitative trait locus mapping and candidate gene analysis for salt tolerance at bud stage in rice

Abstract

Soil salinization has a serious influence on rice yield and quality. How to enhance salt tolerance in rice is a topical issue. In this study, 120 recombinant inbred line populations were generated through nonstop multi-generation selfing using a male indica rice variety Huazhan (Oryza sativa L. subsp. indica cv. ‘HZ’) and a female variety of Nekken2 (Oryza sativa L. subsp. japonica cv. ‘Nekken2’) as the parents. Germination under 80 mM NaCl conditions was measured and analyzed, and quantitative trait locus (QTL) mapping was completed using a genetic map. A total of 16 salt-tolerance QTL ranges were detected at bud stage in rice, which were situated on chromosomes 3, 4, 6, 8, 9, 10, 11, and 12. The maximum limit of detection was 4.69. Moreover, the qST12.3 was narrowed to a 192 kb region on chromosome 12 using map-based cloning strategy. Statistical analysis of the expression levels of these candidate genes under different NaCl concentrations by qRT-PCR revealed that qST12.3 (LOC_Os12g25200) was significantly down-regulated with increasing NaCl concentration, and the expression level of the chlorine-transporter-encoding gene LOC_Os12g25200 in HZ was significantly higher than that of Nekken2 under 0 mM NaCl. Sequencing analysis of LOC_Os12g25200 promoter region indicated that the gene expression difference between parents may be due to eight base differences in the promoter region. Through QTL mining and analysis, a plurality of candidate genes related to salt tolerance in rice was obtained, and the results showed that LOC_Os12g25200 might negatively regulate salt tolerance in rice. The results provide the basis for further screening and cultivation of salt-tolerant rice varieties and have laid the foundation for elucidating further molecular regulation mechanisms of salt tolerance in rice.

Discovering New QTNs and Candidate Genes Associated with Rice-Grain-Related Traits within a Collection of Northeast Core Set and Rice Landraces

“…qGW-12-1 , identified by two ML-GWAS methods, corresponds to LOC_Os12g25200 , which is a chloride transporter. The chloride channel family negatively regulate salt tolerance in rice [ 88 ]. However, a member of the chloride efflux transporter is involved in mediating grain size as well [ 89 ].…”

Characterization of an Excellent Hybrid Rice Restorer Line R382 with Enhanced Lodging Resistance

“…indica cv.) is a kind of super rice variety with high and stable yield, which has strong adaptability, better resistance to adversity and stress than ordinary varieties, and better resistance to diseases and pests [37]. Huazhan have been widely popularized in hybrid rice breeding in China (www.ricedata.cn (accessed on 10 June 2024)).…”

Haplotype analysis and marker development of five salt-tolerant–related genes in rice (Oryza sativa L.)

“…Up to now, large quantities of genetic studies on mining quantitative trait loci (QTL) and genes related to salt tolerance have been conducted, and hundreds of related QTL have been identified ( Lin et al., 2004 ; Quan et al., 2018 ; Ju et al., 2022 ; Li et al., 2022 ; Lv et al., 2022 ; Yin et al., 2022 ; Yuan et al., 2022 ; Geng et al., 2023 ). However, only five genes with natural variations have been cloned ( Table 1 ).…”