Improving rice yield is one of the most important food issues internationally. It is an undeniable goal of rice breeding, and the effective panicle number (EPN) is a key factor determining rice yield. Increasing the EPN in rice is a major way to increase rice yield. Currently, the main quantitative trait locus (QTL) for EPN in rice is limited, and there is also limited research on the gene for EPN in rice. Therefore, the excavation and analysis of major genes related to EPN in rice is of great significance for molecular breeding and yield improvement. This study used japonica rice varieties Dongfu 114 and Longyang 11 to construct an F₅ population consisting of 309 individual plants. Two extreme phenotypic pools were constructed by identifying the EPN of the population, and QTL-seq analysis was performed to obtain three main effective QTL intervals for EPN. This analysis also helped to screen out 34 candidate genes. Then, EPN time expression pattern analysis was performed on these 34 genes to screen out six candidate genes with higher expression levels. Using a 3K database to perform haplotype analysis on these six genes, we selected haplotypes with significant differences in EPN. Finally, five candidate genes related to EPN were obtained.

Salinity stress is one of the major abiotic stresses affecting crop growth and production. Rice is an important food crop in the world, but also a salt-sensitive crop, and the rice seedling stage is the most sensitive to salt stress, which directly affects the final yield formation. In this study, two RIL populations derived from the crosses of CD (salt-sensitive)/WD (salt-tolerant) and KY131 (salt-sensitive)/XBJZ (salt-tolerant) were used as experimental materials, and the score of salinity toxicity (SST), the relative shoot length (RSL), the relative shoot fresh weight (RSFW), and the relative shoot dry weight (RSDW) were used for evaluating the degree of tolerance under salt stress in different lines. The genetic linkage map containing 978 and 527 bin markers were constructed in two RIL populations. A total of 14 QTLs were detected on chromosomes 1, 2, 3, 4, 7, 9, 10, 11, and 12. Among them, qSST12-1, qSST12-2, and qRSL12 were co-localized in a 140-kb overlap interval on chromosome 12, which containing 16 candidate genes. Furthermore, transcriptome sequencing and qRT-PCR were analyzed in CD and WD under normal and 120 mM NaCl stress. LOC_Os12g29330, LOC_Os12g29350, LOC_Os12g29390, and LOC_Os12g29400 were significantly induced by salt stress in both CD and WD. Sequence analysis showed that LOC_Os12g29400 in the salt-sensitive parents CD and KY131 was consistent with the reference sequence (Nipponbare), whereas the salt-tolerant parents WD and XBJZ differed significantly from the reference sequence both in the promoter and exon regions. The salt-tolerant phenotype was identified by using two T₃ homozygous mutant plants of LOC_Os12g29400; the results showed that the score of salinity toxicity (SST) of the mutant plants (CR-3 and CR-5) was significantly lower than that of the wild type, and the seedling survival rate (SSR) was significantly higher than that of the wild type, which indicated that LOC_Os12g29400 could negatively regulate the salinity tolerance of rice at the seedling stage. The results lay a foundation for the analysis of the molecular mechanism of rice salinity tolerance and the cultivation of new rice varieties.

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.