A later heading date generally leads to higher grain yield in favorable ecological regions; however, grain yield reaches a limit as the heading date exceeds a certain threshold. Ghd7 is the first cloned major gene that regulates heading date, plant height and grain number. Here, we investigated the relationship between Ghd7 and florigen genes Hd3a and RFT1, to determine their roles in regulating heading date and grain number under different photoperiods. Our results revealed that under long-day (LD) conditions, Hd3a acts prior to RFT1 to promote heading while negatively regulating plant height and grain number. In contrast, Ghd7 positively regulates heading date, plant height, and grain number by inhibiting both Hd3a and RFT1. Under short-day (SD) conditions, the functions of Hd3a and RFT1 remain consistent with those under LD conditions, but Ghd7 does not inhibit their expression, resulting in a weaker phenotypic effect compared to Hd3a. Additionally, under both LD and SD conditions, increased Ghd7 expression enhances its inhibitory effect on Hd3a and RFT1, leading to later heading and increased grain number; however, once the heading date exceeds 94 d, grain number no longer increases. Moreover, the gn1a allele increased grain number by 16.5% to 42.5%, while combinations of the elite alleles from Ghd7, Hd3a, RFT1, and Gn1a significantly increased grain number by up to 240.9%. Therefore, we propose a new breeding strategy to optimize the heading date and grain number using the Ghd7Hd3aRFT1gn1a combination of Ghd7, Hd3a, RFT1, and Gn1a under LD conditions, and the Ghd7hd3aRFT1gn1a combination under SD conditions. This strategy improved the yield of the high-quality Northeast variety Kongyu 131 (KY131) by 69.1% in Beijing and 93.7% in Hainan. This strategy will greatly improve the efficiency of north-to-south adaptation in rice, providing theoretical guidance for expanding the geographical adaptability of rice varieties.
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Rice panicle apical abortion affects yield. Identification and cloning of genes related to rice panicle apical abortion can enrich the molecular mechanism of rice panicle development regulation, and provide theoretical basis and genetic resources for rice high-yield molecular design breeding.
Here, a stably inherited panicle apical abortion 21 (paa21) mutant was screened from EMS mutant library of the japonica rice variety "Wuyunjing 30". Agronomic traits, such as ratio of degraded primary branches, degraded apical spikelets, grains per panicle, plant height, panicle length, and grain yield per plant, were statistically analyzed. Trypan blue and Evans blue staining were used to detect whether programmed cell death occurred in the apical spikelets. H2O2 content in young panicles at different development stages and different panicle parts of WT and paa21 was determined. Genetic analysis was carried out by reciprocal cross of paa21 with indica rice II-32B and 9311 respectively. The F2 population constructed by crossing paa21 with indica rice II-32B was used for gene mapping and cloning. The three-dimensional structure of wild-type and paa21 proteins were predicted using SWISS-MODEL website. The expression levels of ROS response marker genes, programmed cell death related genes and catalase related genes were analyzed by RT-qPCR.
paa21 produced panicle apical abortion phenotype and the degenerated spikelets were mainly located on the primary branches at the apical panicle. The plant height, grain number per panicle, panicle length and grain yield per plant of paa21 were lower than those of WT. After observing the young panicles at different development stages, we found that the paa21 mutant had a panicle apical abortion phenotype when panicle developed to 12 cm. Trypan blue and Evans blue staining results showed that the apical spikelets of the paa21 mutant had programmed cell death. Stronger DAB staining was observed in the degenerated apical spikelets of paa21 than WT. The results of H2O2 content determination showed that higher level of ROS was accumulated in panicle of paa21 compared with WT. Genetic analysis suggested that paa21 mutant phenotype is controlled by a pair of recessive nuclear genes. The results of map-based cloning showed that a C to T mutation occurred in the second exon of Os02g0673100 in paa21, resulting in the mutation of alanine to valine. This gene encodes an aluminum activated malate transporter, ALMT7. The mutation site was located at the fourth transmembrane helix. SWISS-MODEL prediction results showed that the mutation site did not significantly affect the three-dimensional structure of the mutant protein. The expression level of ROS response marker genes Os01g0826400, Os05g0474800 and Os02g0181300 in paa21 was significantly higher than that in WT when the young spike developed to 10 cm. Compared with WT, the expression level of programmed cell death related genes VPE2 and VPE3 increased significantly in paa21. The expression level of CATA, CATB and CATC which encode catalase in 10 cm young panicle of paa21 was significantly higher than that of WT. The activity of CAT in paa21 10 cm young spikelet was significantly lower than that of WT.
paa21 accumulate excess ROS in the apical spikelet at late stage of panicle development, resulting in programmed cell death, which eventually leads to the degeneration of the apical spikelet. These results lay a good foundation for further enriching the genetic regulatory network of panicle development.
Pentatricopeptide repeat (PPR) proteins perform essential functions in post-transcriptional regulation of gene expression, particularly RNA editing and RNA splicing, in plant organelles. Although research on chloroplast biogenesis and development has been extensive, the functions of most PPR genes in this process in rice (Oryza sativa) remain incompletely understood. This study identifies a novel P-type PPR protein, YELLOW-GREEN LEAF AND SEEDLING LETHALITY (YGS), which localizes to rice chloroplasts. YGS shows predominant expression in leaves. The ygs mutants, generated through CRISPR/Cas9-mediated genome editing of the YGS gene, displayed yellow-green leaves and seedling lethality. These phenotypes corresponded with reduced pigment levels and disrupted chloroplast ultrastructure compared to wild-type plants. Furthermore, the expression of genes associated with chloroplast development and chlorophyll biosynthesis showed significant alterations in the ygs mutants. The absence of YGS function affected RNA editing of rpl2 and intron splicing of ycf3-1 in the plastid genome. Additionally, YGS demonstrated interaction with the chloroplast signal recognition particle protein OscpSRP54b in yeast two-hybrid and bimolecular fluorescence complementation analyses. These results indicate that YGS participates in RNA editing and RNA splicing in chloroplasts, thus serving a vital role in rice chloroplast development
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Research Article
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The development of rice cultivars with improved nitrogen use efficiency (NUE) is desirable for sustainable agriculture. Achieving this goal depends in part on understanding how rice responds to low soil nitrogen (N) and identifying causative genes underlying this trait. To identify quantitative trait loci (QTL) or genes associated with low N response, we conducted a genome-wide association study (GWAS) using a diverse panel of 230 rice accessions and performed a transcriptomic investigation of rice accessions with differential responses to low N stress at two N levels. We detected 411 GWAS-associated genes in 5 QTL and 2722 differentially expressed genes in response to low N, of which 24 were identified by both methods and ranked according to gene annotations, literature queries, gene expression, and genetic diversity analysis. The large-scale datasets obtained from this study reveal low N-responsive characteristics and provide insights towards understanding the regulatory mechanisms of N-deficiency tolerance in rice, and the candidate genes or QTL would be valuable resources for increasing rice NUE via molecular biotechnology.
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