During rice domestication and improvement, increasing grain yield to meet human needs was the primary objective. Rice grain yield is a quantitative trait determined by multiple genes, but the molecular basis for increased grain yield is still unclear. Here, we show that NUMBER OF GRAINS 1 (NOG1), which encodes an enoyl-CoA hydratase/isomerase, increases the grain yield of rice by enhancing grain number per panicle without a negative effect on the number of panicles per plant or grain weight. NOG1 can significantly increase the grain yield of commercial high-yield varieties: introduction of NOG1 increases the grain yield by 25.8% in the NOG1-deficient rice cultivar Zhonghua 17, and overexpression of NOG1 can further increase the grain yield by 19.5% in the NOG1-containing variety Teqing. Interestingly, NOG1 plays a prominent role in increasing grain number, but does not change heading date or seed-setting rate. Our findings suggest that NOG1 could be used to increase rice production.
Some plant-specific resistance genes could affect rhizosphere microorganisms by regulating the release of root exudates. In a previous study, the SST (seedling salt tolerant) gene in rice (Oryza sativa) was identified, and loss of SST function resulted in better plant adaptation to salt stress. However, whether the rice SST variation could alleviate salt stress via regulating soil metabolites and microbiota in the rhizosphere is still unknown. Here, we used transgenic plants with SST edited in the Huanghuazhan (HHZ) and Zhonghua 11 (ZH11) cultivars by the CRISPR/Cas9 system and found that loss of SST function increased the accumulation of potassium and reduced the accumulation of sodium ions in rice plants. Using 16S rRNA gene amplicon high-throughput sequencing, we found that the mutant material shifted the rhizobacterial assembly under salt-free stress. Importantly, under salt stress, the sst, HHZcas, and ZH11cas plants significantly changed the assembly of the rhizobacteria. Furthermore, the rice SST gene also affected the soil metabolites, which were closely related to the dynamics of rhizosphere microbial communities, and we further determined the relationship between the rhizosphere microbiota and soil metabolites. Overall, our results show the effects of the rice SST gene on the response to salt stress associated with the soil microbiota and metabolites in the rhizosphere. This study reveals a helpful linkage among the rice SST gene, soil metabolites, and rhizobacterial community assembly and also provides a theoretical basis for improving crop adaptation through soil microbial management practices. IMPORTANCE Soil salinization is one of the major environmental stresses limiting crop productivity. Crops in agricultural ecosystems have developed various strategies to adapt to salt stress. We used rice mutant and CRISPR-edited lines to investigate the relationships among the Squamosa promoter Binding Protein box (SBP box) family gene (SST/OsSPL10), soil metabolites, and the rhizosphere bacterial community. We found that during salt stress, there are significant differences in the rhizosphere bacterial community and soil metabolites between the plants with the SST gene and those without it. Our findings provide a useful paradigm for revealing the roles of key genes of plants in shaping rhizosphere microbiomes and their relationships with soil metabolites and offer new insights into strategies to enhance rice tolerance to high salt levels from microbial and ecological perspectives.
Grain chalkiness is the main factor determining the market value of rice. Reducing chalkiness is an important breeding goal for genetic improvement of high quality rice. Identification of QTLs or genes controlling chalkiness is the prerequisite for molecular breeding in rice. Here, we conducted a genome-wide association study to identify QTLs associated with grain chalkiness including percentage of grains with chalkiness (PGWC) and degree of endosperm chalkiness (DEC) in 450 rice accessions consisting of 300 indica and 150 japonica rice in two environments. A total of 34 QTLs were identified, including 14 QTLs for PGWC and 20 QTLs for DEC. Among them, seven QTLs were commonly identified in two environments, and eight QTLs were simultaneously related to two traits. Based on the haplotype analysis, LD decay analysis, RNA-sequencing, qRT-PCR confirmation and haplotype comparisons, four genes (LOC_Os10g36170, LOC_Os10g36260, LOC_Os10g36340 and LOC_Os10g36610) were considered as the candidate genes for qDEC-10c1w,2wj, which could be identified in both environments and had the most significant p-value among the newly identified QTLs. These results provided new insight into the genetic basis of grain chalkiness and gene resources for improving quality by molecular breeding in rice.
A semidwarf gene iga-1 of rice (Oryza sativa L.) by mutagenesis of outer space treatment from Texianzhan 13 was identified. The dwarf lines CHA-2 and CHA-2N which carried iga-1 showed great variation in agronomic traits. On the basis of the internode length of CHA-2 and CHA-2N, the mutant belongs to the dn type of dwarfing. GA 3 treatment, endo-GA 3 measurement and α-amylase activity analysis in endosperm showed that iga-1 is independent of gibberellin acid. Using a large F 2 population derived from a cross between the CHA-2 and an japonica rice variety, 02428, the iga-1 gene was fine mapped into a 32.01 kb physical distance between two InDel markers, DL18 and DL19 on chromosome 5, where five open reading frames were predicted, one of which was the rice gibberellin-insensitive dwarf mutant gene D1. Sequence analysis showed that no variation in D1 locus was detected among CHA-2, CHA-2N and Texianzhan 13. Thus, D1 can not be the candidate gene of iga-1. Comparing the other dwarf genes on chromosome 5 showed that iga-1 is possibly allelic to the semidwarf gene sd-7.
Rice originated in tropical and subtropical regions and is distributed worldwide. Low temperature is one of the most critical abiotic stresses affecting grain yield and geographical distribution of rice. It is vital to elucidate the molecular mechanism of chilling tolerance in rice for ensuring cereals production. Previously we isolated the domestication-related gene NOG1 which affects rice grain number and yield. In this study, we specified that rice varieties harboring high-yielding NOG1 allele are more distributed in low-latitude regions. Additionally, we observed NOG1 influences the chilling tolerance of rice. Through genome-wide transcriptional analysis after cold treatment at 10°C, there were 717 differentially expressed genes (DEGs) in nog1 near-isogenic lines compared with the control Guichao 2, including 432 up-regulated DEGs and 284 down-regulated DEGs. Gene ontology annotations and KEGG enrichment analysis of DEGs showed that various biological processes and signaling pathways were related to cold stress, such as lipid metabolism and genetic information processing. These results provide new insights into the mechanism of chilling tolerance in rice and the molecular basis of environmental adaptation during rice domestication.
In order to cultivate new upland rice varieties with high yield and wide adaptability, which is suitable for Yunnan, Hainan and other tropical and subtropical areas, a new temperature sensitive upland rice variety 'Zhongkexilu 2' was cultivated by hybridization and backcrossing between rice variety 'Minhui 63' and upland rice variety 'Lu 46'. The upland adaptive QTLs were introduced through the molecular marker assisted selection technology and pedigree method. The variety participated in evaluation trial at 3 sites in two years in Hainan. The average yield of multi-point regional trial in two years were 4 914 kg/hm 2 , which increased by more than 25.5% compared with the contrast variety 'Yunlu 201'. This shows that it has a strong potential for increasing production. The plant height was 105 cm, with panicle length of 22 cm. Effective panicles number per plant were 7, and grain number per panicle was 144. Seed setting rate was 89.2%, and the thousand grain weight was 24.1 g, showing the moderate plant type and panicle traits. The drought resistance of 'Zhongkexilu 2' was identified. The result showed that its drought resistance was basically the same as that of the upland parent 'Luyin 46', and it was significantly stronger than that of the parent 'Minghui 63'. It was approved by Hainan Variety Certification Committee in 2019 (Qiongshen Rice 2018033). New varieties with high yield and drought resistant were cultivated through the molecular marker assisted selection technology and pedigree method, which was of great significance to promote the regeneration of upland rice varieties and the development of upland rice industry.
Background Although the role of the basic leucine zipper (bZIP) family of transcription factors in response to various abiotic stresses has been investigated, few studies have been conducted on their function in submergence stress. Results In this study, we localized a bZIP gene GmbZIP71-4 in the nucleus of soybean and constructed a GmbZIP71-4overexpressing tabocco line, which showed reduced submergence resistance due to the decreased abscisic acid (ABA) content. GO and KEGG pathway enrichment analysis based on chromatin immunoprecipitation assay sequencing (ChIP-seq) indicated that the most significant differences were the expression levels of the factors in plant hormone signal transduction, especially those in response to ABA. Electrophoretic Mobility Shift Assays (EMSA) demonstrated that GmbZIP71-4 bound to the promoter of GmABF2, which is consistent with the ChIP-qPCR result. Conclusions Our study showed that GmbZIP71-4 was a negative regulator of submergence stress tolerance. The findings in this work will set a solid foundation for the understanding of submergence resistance in plants.
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