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Soil salinity is an environmental stress severely impacting on rice grain yield. However, limited information is available on how salinity affects expression levels of genes determining grain yield. In this study, we investigated agronomic traits associated with grain yield among three japonica rice cultivars grown either under moderate salinity with an electrical conductivity of 4 dS/m or under non-saline conditions in a paddy field in Dongying, Shandong, China. Moderate salinity affected rice yield predominantly by reducing grain number and grain filling. We compared expression levels of genes determining grain number in young panicles (0.5–1 cm in length) of plants grown under salinity or non-saline conditions. Transcription of Lax panicle 1, Lax panicle 2, Ideal plant architecture (IPA1), Dense and erect panicle 1, Tawawa 1, and OsMADS1 was significantly repressed, whereas that of Cytokinin oxidase/dehydrogenase, Grain number per panicle 1, and Narrow leaf 1 was not significantly influenced by salinity. OsmicroRNA156, the posttranscriptional regulator of IPA1, was induced by salinity in the panicle and seedlings and complemented the expression patterns of IPA1. This result implied that the OsmicroRNA156–IPA1 pathway was involved in rice salinity responses. The grain filling-associated genes Grain incomplete filling 1, Grain incomplete filling 2, and Nuclear factor Y were down-regulated by salinity in the spikelet at 5 or 10 days after fertilization, which contributed to the salinity-triggered reduction in grain weight. These findings suggest some targets that may be utilized to improve the grain yield under salinity stress conditions via breeding and gene-pyramiding approaches.

Grain filling is an extremely important process in rice growth and development. This process which involves complex genetic regulatory networks and environmental interaction, is directly related to the formation of rice yield and quality. A stable inherited mutant with grain extended filling ( gef1 ) was identified from an EMS mutagenized population of Yixiang 1B. The investigation of agronomic traits, measurement of physiological and biochemical characteristics, histology observation, gene expression analysis and gene mapping were performed in this study. Compared with the wild type plants, the grain filling rate of gef1 was significantly lower than that of Yixiang 1B, resulting in the grain filling time of gef1 was about 30 days delay. Meanwhile, the 1000-grain weight of gef1 became bigger and seed setting rate decreased by 22%. During the development of caryopsis, we found that the soluble sugar content in wild type showed a single peak curve, and the content maintained at a low level throughout the grain filling stage. However, the soluble sugar content of the gef1 was significantly higher than that of the wild type, and showing a bimodal curve. It revealed that the transportation and distribution of photosynthate, and starch synthesis were inefficiency in gef1 . In addition, histocytological analysis showed that the number of big vascular bundles in the same transection parts of rachis, the first top internodes and the second top internodes were all decreased in gef1 , and indicated that the transport efficiency of photosynthate was one of the limiting factors in the rate of grain filling. The scanning electron microscope showed that the glume of gef1 had smooth surface and slender cells. Scanning of grain transection showed that gef1 had spherical amyloplasts and arranged loosely, but the wild type had unregular polygon amyloplasts and packed closely. These results suggested that the changes of grain size associated with the cell number and shape of glume, and gef1 had impact on rice quality. Additionally, by analyzing the expression of the glycometabolism-related genes in developing caryopsis, we found that all of them were keeping at a low level in gef1 compared with the wild type. By analyzing the three crosses gef1 /Yixiang 1B, gef1 /02428 and gef1 /Kitaake, we found that the F1 plants of these three crosses were all normal and indicated that the mutant trait was controlled by a recessive gene. The ratio of normal plants to mutant plants in the three F2 populations was 3:1 and indicating that the mutant trait was controlled by a single recessive nuclear gene. gef1 was preliminarily mapped on the short arm of rice chromosome 3, and was narrowed to a 198 kb region between InDel3-1 and InDel3-2. This region has 21 open reading frames and there was no homologous gene had been reported within it, and the further identification work of candidate genes is ongoing.

Panicle apical abortion (PAA) causes severe yield losses in rice production, but details about its development and molecular basis remain elusive. Herein, a PAA mutant, paa1019, was identified among the progeny of an elite indica maintainer rice line Yixiang 1B (YXB) mutagenized population obtained using ethyl methyl sulfonate. The abortion rate of spikelets in paa1019 was observed up to 60%. Genetic mapping combined with Mutmap analysis revealed that LOC_Os03g20380 harbored a single-bp substitution (C to T) that altered its transcript length. This gene encodes calcineurin B-like protein-interacting protein kinase 31 (OsCIPK31) localized into the cytoplasm, and is preferentially expressed in transport tissues of rice. Complementation of paa1019 by transferring the open reading frame of LOC_Os03g20380 from YXB reversed the mutant phenotype, and conversely, gene editing by knocking out of OsCIPK31 in YXB results in PAA phenotype. Our results support that OsCIPK31 plays an important role in panicle development. We found that dysregulation is caused by the disruption of OsCIPK31 function due to excessive accumulation of ROS, which ultimately leads to cell death in rice panicle. OsCIPK31 and MAPK pathway might have a synergistic effect to lead ROS accumulation in response to stresses. Meanwhile the PAA distribution is related to IAA hormone accumulation in the panicle. Our study provides an understanding of the role of OsCIPK31 in panicle development by responding to various stresses and phytohormones.

Lesion mimic mutants display spontaneous cell death, and thus are valuable for understanding the molecular mechanism of cell death and disease resistance. Although a lot of such mutants have been characterized in rice, the relationship between lesion formation and abscisic acid (ABA) synthesis pathway is not reported. In the present study, we identified a rice mutant, lesion mimic mutant 9150 (lmm9150), exhibiting spontaneous cell death, pre-harvest sprouting, enhanced growth, and resistance to rice bacterial and blast diseases. Cell death in the mutant was accompanied with excessive accumulation of H2O2. Enhanced disease resistance was associated with cell death and upregulation of defense-related genes. Map-based cloning identified a G-to-A point mutation resulting in a D-to-N substitution at the amino acid position 110 of OsABA2 (LOC_Os03g59610) in lmm9150. Knock-out of OsABA2 through CRISPR/Cas9 led to phenotypes similar to those of lmm9150. Consistent with the function of OsABA2 in ABA biosynthesis, ABA level in the lmm9150 mutant was significantly reduced. Moreover, exogenous application of ABA could rescue all the mutant phenotypes of lmm9150. Taken together, our data linked ABA deficiency to cell death and provided insight into the role of ABA in rice disease resistance.