Background Plant height is a key factor in the determination of rice yield since excessive height can easily cause lodging and reduce yield. Therefore, the identification and analysis of plant height-related genes to elucidate their physiological, biochemical, and molecular mechanisms have significant implications for rice breeding and production. Results High-throughput quantitative trait locus (QTL) sequencing analysis of a 638-individual F2:3 mapping population resulted in the identification of a novel height-related QTL (qPH9), which was mapped to a 2.02-Mb region of Chromosome 9. Local QTL mapping, which was conducted using 13 single nucleotide polymorphism (SNP)-based Kompetitive allele-specific PCR (KASP) markers for the qPH9 region, and traditional linkage analysis, facilitated the localization of qPH9 to a 126-kb region that contained 15 genes. Subsequent haplotype and sequence analyses indicated that OsPH9 was the most probable candidate gene for plant height at this locus, and functional analysis of osph9 CRISPR/Cas9-generated OsPH9 knockout mutants supported this conclusion. Conclusion OsPH9 was identified as a novel regulatory gene associated with plant height in rice, along with a height-reducing allele in ‘Dongfu-114’ rice, thereby representing an important molecular target for rice improvement. The findings of the present study are expected to spur the investigation of genetic mechanisms underlying rice plant height and further the improvement of rice plant height through marker-assisted selection.
Nitrogen-based nutrients are the main factors affecting rice growth and development. As the nitrogen (N) application rate increased, the nitrogen use efficiency (NUE) of rice decreased. Therefore, it is important to understand the molecular mechanism of rice plant morphological, physiological, and yield formation under low N conditions to improve NUE. In this study, changes in the rice morphological, physiological, and yield-related traits under low N (13.33 ppm) and control N (40.00 ppm) conditions were performed. These results show that, compared with control N conditions, photosynthesis and growth were inhibited and the carbon (C)/N and photosynthetic nitrogen use efficiency (PNUE) were enhanced under low N conditions. To understand the post-translational modification mechanism underlying the rice response to low N conditions, comparative phosphoproteomic analysis was performed, and differentially modified proteins (DMPs) were further characterized. Compared with control N conditions, a total of 258 DMPs were identified under low N conditions. The modification of proteins involved in chloroplast development, chlorophyll synthesis, photosynthesis, carbon metabolism, phytohormones, and morphology-related proteins were differentially altered, which was an important reason for changes in rice morphological, physiological, and yield-related traits. Additionally, inconsistent changes in level of transcription and protein modification, indicates that the study of phosphoproteomics under low N conditions is also important for us to better understand the adaptation mechanism of rice to low N stress. These results provide insights into global changes in the response of rice to low N stress and may facilitate the development of rice cultivars with high NUE by regulating the phosphorylation level of carbon metabolism and rice morphology-related proteins.
BackgroundSalinity tolerance plays a vital role in rice cultivation because the strength of salinity tolerance at the seedling stage directly affects seedling survival and final crop yield in saline soils. Here, we combined a genome-wide association study (GWAS) and linkage mapping to analyze the candidate intervals for salinity tolerance in Japonica rice at the seedling stage.ResultsWe used the Na+ concentration in shoots (SNC), K+ concentration in shoots (SKC), Na+/K+ ratio in shoots (SNK), and seedling survival rate (SSR) as indices to assess the salinity tolerance at the seedling stage in rice. The GWAS identified the lead SNP (Chr12_20864157), associated with an SNK, which the linkage mapping detected as being in qSK12. A 195-kb region on chromosome 12 was selected based on the overlapping regions in the GWAS and the linkage mapping. Based on haplotype analysis, qRT-PCR, and sequence analysis, we obtained LOC_Os12g34450 as a candidate gene.ConclusionBased on these results, LOC_Os12g34450 was identified as a candidate gene contributing to salinity tolerance in Japonica rice. This study provides valuable guidance for plant breeders to improve the response of Japonica rice to salt stress.
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