Identification of Salt Tolerance Related Candidate Genes in ‘Sea Rice 86’ at the Seedling and Reproductive Stages Using QTL-Seq and BSA-Seq

Abstract

Salt stress seriously affects plant growth and development and reduces the yield of rice. Therefore, the development of salt-tolerant high-yielding rice cultivars through quantitative trait locus (QTL) identification and bulked segregant analysis (BSA) is the main focus of molecular breeding projects. In this study, sea rice (SR86) showed greater salt tolerance than conventional rice. Under salt stress, the cell membrane and chlorophyll were more stable and the antioxidant enzyme activity was higher in SR86 than in conventional rice. Thirty extremely salt-tolerant plants and thirty extremely salt-sensitive plants were selected from the F2 progenies of SR86 × Nipponbare (Nip) and SR86 × 9311 crosses during the whole vegetative and reproductive growth period and mixed bulks were generated. Eleven salt tolerance related candidate genes were located using QTL-seq together with BSA. Real time quantitative PCR (RT-qPCR) analysis showed that LOC_Os04g03320.1 and BGIOSGA019540 were expressed at higher levels in the SR86 plants than in Nip and 9311 plants, suggesting that these genes are critical for the salt tolerance of SR86. The QTLs identified using this method could be effectively utilized in future salt tolerance breeding programs, providing important theoretical significance and application value for rice salt tolerance breeding.

OsJRL40, a Jacalin-Related Lectin Gene, Promotes Salt Stress Tolerance in Rice

“…In a previous study, we preliminarily determined that OsJRL40 is involved in regulating salt tolerance in rice [ 38 ]. To investigate the possible function of OsJRL40 in the salt stress response, two OsJRL40 loss-of-function knockout mutant lines (KO1 and KO2) were generated in the Nip background using the CRISPR/Cas9 technology.…”

“…The relative conductivity is as described previously [ 38 ]. Rice leaves are washed with deionized water, and the surface water was soaked dry.…”

“…After cooling to room temperature, the absorbance of the sample was measured at 450, 532, and 600 nm. To determine the chlorophyll content of leaves, chlorophyll was extracted from leaves (100 mg), and the absorbance of the extract was measured at 663 and 645 nm [ 38 , 61 ].…”

“…In our previous work on the identification of salt tolerance-related candidate genes in ‘Sea Rice 86′(SR86) using quantitative trait locus (QTL)-Seq and bulked segregant analysis (BSA)-Seq, we found a JRL family gene may be an important candidate gene and is named OsJRL40 ; RT-qPCR analysis showed that this gene actively responds to salt stress [ 38 ], but its molecular function was unclear. In the present study, we investigated the spatiotemporal expression patterns of OsJRL40 , subcellular localization of the encoded protein, and salt tolerance phenotype of OsJRL40 -overexpressing transgenic plants under salt stress.…”

Optimized extraction technology of glutathione from ‘Haidao 86’ germ rice by response surface methodology

“…In addition, 'Haidao 86' is a natural organic rice with fewer pests and diseases and no need to spray pesticides and chemical fertilizers (Gao et al, 2023).…”