Quantitative Trait Locus Mapping of Salt Tolerance in Wild Rice Oryza longistaminata

Rice has been reported to be highly sensitive to salt stress at the seedling stage. However, the lack of target genes that can be used for improving salt tolerance has resulted in several saline soils unsuitable for cultivation and planting. To characterize new salt-tolerant genes, we used 1,002 F2:3 populations derived from Teng-Xi144 and Long-Dao19 crosses as the phenotypic source to systematically characterize seedlings’ survival days and ion concentration under salt stress. Utilizing QTL-seq resequencing technology and a high-density linkage map based on 4,326 SNP markers, we identified qSTS4 as a major QTL influencing seedling salt tolerance, which accounted for 33.14% of the phenotypic variation. Through functional annotation, variation detection and qRT-PCR analysis of genes within 46.9 Kb of qSTS4, it was revealed that there was one SNP in the promoter region of OsBBX11, which resulted in a significant response difference between the two parents to salt stress. Transgenic plants using knockout-based technology and demonstrated that Na+ and K+ in the roots of the functional-loss-type OsBBX11 were translocated largely to the leaves under 120 mmol/L NaCl compared with the wild-type, causing osbbx11 leaves to die after 12 days of salt stress due to an imbalance in osmotic pressure. In conclusion, this study identified OsBBX11 as a salt-tolerance gene, and one SNPs in the OsBBX11 promoter region can be used to identify its interacting transcription factors. This provides a theoretical basis for finding the molecular mechanism of OsBBX11 upstream and downstream regulation of salt tolerance and molecular design breeding in the future.

Section: Discussionmentioning

confidence: 99%

OsBBX11 on qSTS4 links to salt tolerance at the seeding stage in Oryza sativa L. ssp. Japonica

Lei

Cao²,

Ding³

et al. 2023

“…To increase the rice yield under salinity stress, it is imperative to unfold the essential mechanisms involved in rice response to salinity stress ( Reddy et al, 2017 ; Prakash et al, 2022 ). Studies recommended that multiple genes mainly control salinity tolerance in rice through a complex and interacting network ( Chinnusamy et al, 2005 ; Wang et al, 2022 ; Yuan et al, 2022 ). Rice has been categorized in the list of salt-sensitive crops ( Lutts et al, 1995 ; Sangwongchai et al, 2022 ), and salinity limits production at the maturity stage ( Todaka et al, 2012 ; Kumar et al, 2022 ).…”

Section: Mechanisms Of Salinity Tolerance In Ricementioning

confidence: 99%

“…For this reason, identifying hotspot regions associated with salinity tolerance is critical to be used in salt breeding programs. Hence, it has been proven that salt breeding programs cannot be successful without the interference of molecular tools ( Fan et al, 2021 ; Yuan et al, 2022 ). Salinity stress affects the rice reproductive stage and undermines its yield and quality.…”

Section: Molecular Factors Contributing To Salinity Tolerance In Ricementioning

confidence: 99%

“…The key indicators were salt injury score (SIC) and water content of seedling (WCS). QTL, qSIS2 , and qWCSST2 for these two traits were located on chromosome 2 ( Yuan et al, 2022 ). Likewise, Le et al (2021) studied QTL mapping for salt tolerance in Vietnamese rice landraces genotyped with 21,623 SNP markers.…”

Section: Quantitative Trait Loci Mapping and Genome-wide Association ...mentioning

confidence: 99%

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Molecular tools, potential frontiers for enhancing salinity tolerance in rice: A critical review and future prospective

Rasheed

Nawaz

et al. 2022

Improvement of salinity tolerance in rice can minimize the stress-induced yield losses. Rice (Oryza sativa) is one of Asia’s most widely consumed crops, native to the subtropical regions, and is generally associated with sensitivity to salinity stress episodes. Salt-tolerant rice genotypes have been developed using conventional breeding methods; however, the success ratio is limited because of the complex nature of the trait and the high cost of development. The narrow genetic base of rice limited the success of conventional breeding methods. Hence, it is critical to launch the molecular tools for screening rice novel germplasm for salt-tolerant genes. In this regard, the latest molecular techniques like quantitative trait loci (QTL) mapping, genetic engineering (GE), transcription factors (TFs) analysis, and clustered regularly interspaced short palindromic repeats (CRISPR) are reliable for incorporating the salt tolerance in rice at the molecular level. Large-scale use of these potent genetic approaches leads to identifying and editing several genes/alleles, and QTL/genes are accountable for holding the genetic mechanism of salinity tolerance in rice. Continuous breeding practices resulted in a huge decline in rice genetic diversity, which is a great worry for global food security. However, molecular breeding tools are the only way to conserve genetic diversity by exploring wild germplasm for desired genes in salt tolerance breeding programs. In this review, we have compiled the logical evidences of successful applications of potent molecular tools for boosting salinity tolerance in rice, their limitations, and future prospects. This well-organized information would assist future researchers in understanding the genetic improvement of salinity tolerance in rice.

“…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 ).…”

Section: Introductionmentioning

confidence: 99%

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

Li,

Liu

et al. 2023

Salinity stress is a great threat to the growth and productivity of crops, and development of salt-tolerant crops is of great necessity to ensure food security. Although a few genes with natural variations that confer salt tolerance at germination and seedling stage in rice have been cloned, effective intragenic markers for these genes are awaited to be developed, which hinder the use of these genes in genetic improvement of salt tolerance in rice. In this study, we first performed haplotype analysis of five rice salt-tolerant–related genes using 38 rice accessions with reference genome and 4,726 rice germplasm accessions with imputed genotypes and classified main haplotype groups and haplotypes. Subsequently, we identified unique variations for elite haplotypes reported in previous studies and developed 11 effective intragenic makers. Finally, we conducted genotyping of 533 of the 4,726 rice accessions from worldwide and 70 approved temperate geng/japonica cultivars in China using the developed markers. These results could provide effective donors and markers of salt-tolerant–related genes and thus could be of great use in genetic improvement of salt tolerance in rice.