Auxin is a phytohormone essential for plant development. However, our understanding of auxin-regulated endosperm development remains limited. Here, we described rice YUCCA (YUC) flavin-containing monooxygenase encoding gene OsYUC11 as a key contributor to auxin biosynthesis in rice (Oryza sativa) endosperm. Grain filling or storage product accumulation was halted by mutation of OsYUC11, but the deficiencies could be recovered by the exogenous application of auxin. A rice transcription factor (TF) yeast library was screened, and 41 TFs that potentially bind to the OsYUC11 promoter were identified, of which OsNF-YB1, a member of the nuclear factor Y family, is predominantly expressed in the endosperm. Both osyuc11 and osnf-yb1 mutants exhibited reduced seed size and increased chalkiness, accompanied by a reduction in indole-3-acetic acid biosynthesis. OsNF-YB1 can bind the OsYUC11 promoter to induce gene expression in vivo. We also found that OsYUC11 was a dynamically imprinted gene that predominantly expressed the paternal allele in the endosperm up to 10 d after fertilization (DAF) but then became a non-imprinted gene at 15 DAF. A functional maternal allele of OsYUC11 was able to recover the paternal defects of this gene. Overall, the findings indicate that OsYUC11-mediated auxin biosynthesis is essential for endosperm development in rice.

Cold stress is a major factor limiting rice (Oryza sativa L.) production worldwide, especially at the seedling and booting stages. Identification of genes associated with cold tolerance (CT) in rice is important for sustainable food production. Here, we report the results of a genome-wide association study (GWAS) to identify the genetic loci associated with CT by using a 1,033-accession diversity panel. We identified five CT-related genetic loci at the booting stage. Accessions carrying multiple cold-tolerant alleles displayed a higher seed setting rate than did accessions that had no cold-tolerant alleles or carried a single allele. At the seedling stage, eight genetic loci related to CT have been identified. Among these, LOC_Os10g34840 was identified as the candidate gene for the qPSR10 genetic locus that is associated with CT in rice seedlings. A single-nucleotide polymorphism (SNP), SNP2G, at position 343 in LOC_Os10g34840 is responsible for conferring cold tolerance at the seedling stage in rice. Further analysis of the haplotype network revealed that SNP2G was present in 80.08% of the temperate japonica accessions but only 3.8% of the indica ones. We used marker-assisted selection to construct a series of BC4F3 near-isogenic lines possessing the cold-tolerance allele SNP2G. When subjected to cold stress, plants carrying SNP2G survived better as seedlings and showed higher grain weight than plants with carrying the SNP2A allele. The CT-related loci identified here and the functional verification of LOC_Os10g34840 will provide genetic resources for breeding cold-tolerant varieties and for studying the molecular basis of cold tolerance in rice.

Stomata are crucial valves coordinating the fixation of carbon dioxide by photosynthesis and water loss through leaf transpiration. Phytochrome interacting factors (PIFs) are negative regulators of red light responses that belong to the basic helix–loop–helix family of transcription factors. Here, we show that the rice (Oryza sativa) PIF family gene OsPIL15 acts as a negative regulator of stomatal aperture to control transpiration in rice. OsPIL15 reduces stomatal aperture by activating rice ABSCISIC ACID INSENSITIVE 5 (OsABI5), which encodes a critical positive regulator of ABSCISIC ACID (ABA) signaling in rice. Moreover, OsPIL15 interacts with the NIGT1/HRS1/HHO family transcription factor rice HRS1 HOMOLOG 3 (OsHHO3) to possibly enhance the regulation of stomatal aperture. Notably, we discovered that the maize (Zea mays) PIF family genes ZmPIF1 and ZmPIF3, which are homologous to OsPIL15, are also involved in the regulation of stomatal aperture in maize, indicating that PIF-mediated regulation of stomatal aperture may be conserved in the plant lineage. Our findings explain the molecular mechanism by which PIFs play a role in red-light-mediated stomatal opening, and demonstrate that PIFs regulate stomatal aperture by coordinating the red light and ABA signaling pathways.

The NIGT1/HRS1/HHO transcription factor (TF) family is a new subfamily of the G2-like TF family in the GARP superfamily and contains two conserved domains: the Myb-DNA binding domain and the hydrophobic and globular domain. Some studies showed that NIGT1/HRS1/HHO TFs are involved in coordinating the absorption and utilization of nitrogen and phosphorus. NIGT1/HRS1/HHO TFs also play an important role in plant growth and development and in the responses to abiotic stresses. This review focuses on recent advances in the structural characteristics of the NIGT1/HRS1/HHO TF family and discusses how the roles and functions of the NIGT1/HRS1/HHO TFs operate in terms of in plant growth, development, and stress responses.

Abscisic acid (ABA) plays an important regulatory role in the grain filling process, which in turn will affect the final yield and quality of rice. The ABA biosynthesis genes of OsNCED3 and degradation gene OsABA8ox3 affect the ABA content, and then further regulate the ABA signaling. During the development of rice panicle, compared with primary grains (superior grains) growing on primary branches, secondary grains (inferior grains) growing on secondary branches exhibit characteristics. However, little is reported on the physicochemical characteristics of starch between superior and inferior grains in ABA related transgenic lines. In this study, OsNCED3 and OsABA8ox3 transgenic plants were used as materials. The results showed that compared with the WT, the OsNCED3-RNAi lines on grain weight was consistent with the trend of superior and inferior grains, while the OsABA8ox3-RNAi lines affected superior or inferior grains. The total starch and soluble sugar content of grains decreased in both OsNCED3-RNAi and OsABA8ox3-RNAi lines, and the total starch content of superior and inferior grains in OsABA8ox3-RNAi lines decreased. The starch granule size distribution of all samples showed a bimodal and increased proportion of starch grains with large granule size, in which the influence on inferior grains was greater than that of superior grains, which eventually led to a significant increase in their average granule size. The apparent amylose content of inferior grains increased significantly in most lines. The swelling power of the superior grains decreased significantly, while that of the inferior grains increased significantly. Fourier analysis showed that the order degree of starch granule surface decreased in the superior grains of the RNAi line, while it increased in the inferior grains of the OsABA8ox3-RNAi line but decreased in the OsNCED3-RNAi lines. In the superior grains, the relative crystallinity of starch decreased in the OsNCED3-RNAi lines, but remained unchanged or increased in the OsABA8ox3-RNAi line. In inferior grains, the relative crystallinity of starch decreased in the ABA synthesis RNAi line, but increased in the OsABA8ox3-RNAi line. In summary, the influence of ABA on the physicochemical properties of inferior grains is greater than that of superior grains.