Dominant early heading (DEH) in rice (Oryza sativa L.) is of interest in both breeding and genetics. The genetic mechanisms underlying DEH have remained largely unclear. We have developed a near-isogenic DEH line without yield drag named DEH_229 by sister-line backcross (BC) breeding with MH63, a restorer, as the genetic background. We conducted a pilot genetic investigation under both short-day (SD) and long-day (LD) conditions. The DEH line harbored only 1.06% variation in the genome sequence relative to MH63. The variants were distributed throughout the genome. Using QTL mapping by sequencing (QTL-seq) on an F₂ population derived from a cross of MH63 × DEH_229, 57 loci were detected under the SD condition. Joint mapping employing a genome-wide association study with accessions from the 3000 rice genome sequencing project (3K-RG), reduced the number of QTL by 43.9%. Using Rice Functional Genomics & Breeding (RFGB) database, the number of SNP cluster regions within the QTL regions reduced by 27.3%. Further comparison of the genome variation between DEH_229 and MH63 in addition to gene annotation information revealed a new DEH allele of DTH3 with multiple variable sites as a possible major factor underlying the early-heading phenotype of DEH_229. An InDel marker, ZMEH_1, was designed based on the variation between DEH_229 and MH63 within this region. It accounted for 86.0% of heading date variation under both SD and LD conditions in 109 randomly chosen progeny derived from extreme lines of the MH63 × DEH_229 population. This study reveals the genetic complexity of DEH in the near-isogenic line and may provide useful material and marker information for plant molecular breeding.

Identification of metabolites responsible for tolerance to low nitrogen availability (low-N) will aid in the genetic improvement of rice yield under nitrogen deficiency. In this study, a backcross introgression line (G9) and its recurrent parent Shuhui 527 (SH527), which show differential responses to low-N stress, were used to identify metabolites associated with low-N tolerance in rice. Differences in metabolite contents in the leaves of G9 and SH527 at three growth stages under low-N stress were assessed by gas chromatography–mass spectrometry. Many metabolites, including amino acids and derivatives, were highly enriched in G9 compared with SH527 under the control condition, suggesting that the two genotypes had basal metabolite differences. Low-N stress induced genotype-specific as well as growth stage-dependent metabolite changes. Metabolites induced specifically in G9 that were involved in glycolysis and tricarboxylic acid metabolism were enriched at the tillering and grain filling stages, and metabolites involved in nitrogen and proline metabolism were enriched at the booting stage. Enrichment of pyroglutamate, glutamate, 2-oxoglutarate, sorbose, glycerate-2-P, and phosphoenolpyruvic acid in G9 suggests that these metabolites could be involved in low-N stress tolerance. The results presented here provide valuable information for further elucidation of the molecular mechanisms of low-N tolerance in crops.

Plant microRNAs (miRNAs) play important roles in biological processes such as development and stress responses. Although the diverse functions of miRNAs in model organisms have been well studied, their function in wild rice is poorly understood. In this study, high-throughput small RNA sequencing was performed to characterize tissue-specific transcriptomes in Oryza longistaminata. A total of 603 miRNAs, 380 known rice miRNAs, 72 conserved plant miRNAs, and 151 predicted novel miRNAs were identified as being expressed in aerial shoots and rhizomes. Additionally, 99 and 79 miRNAs were expressed exclusively or differentially, respectively, in the two tissues, and 144 potential targets were predicted for the differentially expressed miRNAs in the rhizomes. Functional annotation of these targets suggested that transcription factors, including squamosa promoter binding proteins and auxin response factors, function in rhizome growth and development. The expression levels of several miRNAs and target genes in the rhizomes were quantified by RT-PCR, and the results indicated the existence of complex regulatory mechanisms between the miRNAs and their targets. Eight target cleavage sites were verified by RNA ligase-mediated rapid 5′ end amplification. These results provide valuable information on the composition, expression and function of miRNAs in O. longistaminata, and will aid in understanding the molecular mechanisms of rhizome development.