Long non-coding RNAs (lncRNAs) have been found to play a vital role in several gene regulatory networks involved in the various biological processes in plants related to stress response. However, systematic analyses of lncRNAs expressed in rice Cadmium (Cd) stress are seldom studied. Thus, we presented the characterization and expression of lncRNAs in rice root development at an early stage in response to Cd stress. The lncRNA deep sequencing revealed differentially expressed lncRNAs among Cd stress and normal condition. In the Cd stress group, 69 lncRNAs were up-regulated and 75 lncRNAs were down-regulated. Furthermore, 386 matched lncRNA-mRNA pairs were detected for 120 differentially expressed lncRNAs and 362 differentially expressed genes in cis, and target gene-related pathway analyses exhibited significant variations in cysteine and methionine metabolism pathway-related genes. For the genes in trans, overall, 28,276 interaction relationships for 144 lncRNAs and differentially expressed protein-coding genes were detected. The pathway analyses found that secondary metabolites, such as phenylpropanoids and phenylalanine, and photosynthesis pathway-related genes were significantly altered by Cd stress. All of these results indicate that lncRNAs may regulate genes of cysteine-rich peptide metabolism in cis, as well as secondary metabolites and photosynthesis in trans, to activate various physiological and biochemical reactions to respond to excessive Cd. The present study could provide a valuable resource for lncRNA studies in response to Cd treatment in rice. It also expands our knowledge about lncRNA biological function and contributes to the annotation of the rice genome.

Mapping major quantitative trait loci (QTL) responsible for rice seed germinability under low temperature (GULT) can provide valuable gene sources for cold tolerant rice lines breeding. In this study, 124 rice backcross recombinant inbred lines (BRILs) derived from indica cv. Changhui 891 and japonica cv. 02428 were genotyped through re-sequencing technology, and a bin map including 3057 bins spanning 1266.5 cM with an average resolution of 0.41 cM between markers was generated. Based on the new high-density genetic map, six QTL ranged from 40 kb to 140 kb in Nipponbare genome were fine-mapped. Among these, qCGR8 and qGRR11, whose 02428 alleles could increase GULT and seed germination recovery rate after cold stress, respectively, were detected. qNGR1 and qNGR4 may be two major QTL affecting indica Changhui 891 germination under normal condition. qGRR1 and qGRR8 are two QTL affecting the seed germination recovery rate after cold stress, the Changhui 891 alleles can improve seed germination rate after cold stress dramatically. These QTL would be a highly valuable genetic factor for cold tolerant rice lines breeding. Moreover, the BRILs developed in this study serve as an excellent system for mapping and studying genetic basis of rice complex traits.

N⁶-methyladenosine (m⁶A) is the most prevalent internal modification present in the mRNAs of all higher eukaryotes. However, the role of the m⁶A methylomes in rice is still poorly understood. With the development of the MeRIP-seq technique, the in-depth identification of mRNAs with m⁶A modification has become feasible. A study suggested that m⁶A modification is crucial for posttranscriptional regulation related to Cd²⁺-induced malignant transformation, but the association between m⁶A modification in plants and Cd tolerance has not been reported. We investigated the m⁶A methylomes in the roots of a cadmium (Cd)-treated group and compared them with the roots in the control (CK) group by m⁶A sequencing of cv. 9311 and cv. Nipponbare (NIP) plants. The results indicated that Cd leads to an altered modification profile in 3,406 differential m⁶A peaks in cv. 9311 and 2,065 differential m⁶A peaks in cv. NIP. KEGG pathway analysis of the genes with differentially modified m⁶A peaks indicated that the “phenylalanine”, “tyrosine and tryptophan biosynthesis”, “glycine”, “adherens junctions”, “glycerophospholipid metabolism” and “threonine metabolism” signalling pathways may be associated with the abnormal root development of cv. 9311 rice due to exposure to Cd. The “arginine”, “proline metabolism”, “glycerolipid”, and “protein processing in endoplasmic reticulum” metabolism pathways were significantly enriched in genes with differentially modified m⁶A peaks in cv. NIP. Unlike that in Arabidopsis, the m⁶A-modified nucleotide position on mRNAs (m⁶A peak) distribution in rice exhibited a preference towards both the stop codon and 3′ untranslated regions (3′ UTRs). These findings provide a resource for plant RNA epitranscriptomic studies and further increase our knowledge on the function of m⁶A modification in RNA in plants.

Despite the great contributions of utilizing heterosis to crop productivity worldwide, the molecular mechanism of heterosis remains largely unexplored. Thus, the present research is focused on the grain number heterosis of a widely used late-cropping indica super hybrid rice combination in China using a high-throughput next-generation RNA-seq strategy. Here, we obtained 872 million clean reads, and at least one read could maps 27,917 transcripts out of 35,679 annotations. Transcript differential expression analysis revealed a total of 5910 differentially expressed genes (DGHP) between super-hybrid rice Wufengyou T025 (WFYT025) and its parents were identified in the young panicles. Out of the 5910 DGHP, 63.1% had a genetic action mode of over-dominance, 17.3% had a complete-dominance action, 15.6% had a partial-dominance action and 4.0% had an additive action. DGHP were significantly enriched in carotenoid biosynthesis, diterpenoid biosynthesis and plant hormone signal transduction pathways, with the key genes involved in the three pathways being up-regulated in the hybrid. By comparing the DGHP enriched in the KEGG pathway with QTLs associated with grain number, several DGHP were located on the same chromosomal segment with some of these grain number QTLs. Through young panicle development transcriptome analysis, we conclude that the over-dominant effect is probably the major contributor to the grain number heterosis of WFYT025. The DGHP sharing the same location with grain number QTLs could be considered a candidate gene and provide valuable targets for the cloning and functional analysis of these grain number QTLs.

Background: Rice is a crop that is very sensitive to low temperature, and its morphological development and production are greatly affected by low temperature. Therefore, understanding the genetic basis of cold tolerance in rice is of great significance for mining favorable genes and cultivating excellent rice varieties. However, there have been limited studies focusing on cold tolerance at the bud burst stage; therefore, considerable attention should be given to the genetic basis of cold tolerance at this stage. Results: In this study, a natural population consisting of 211 rice landraces collected from 15 provinces in China and other countries was used for the first time to evaluate cold tolerance at the bud burst stage. Population structure analysis showed that this population was divided into two groups and was rich in genetic diversity. Our evaluation results confirmed that japonica rice was more tolerant to cold at the bud burst stage than indica rice. A genome-wide association study (GWAS) was performed with the phenotypic data of 211 rice landraces and a 36,727 SNP dataset under a mixed linear model. Twelve QTLs (P < 0.0001) were identified for the seedling survival rate (SR) after treatment at 4 °C, in which there were five QTLs (qSR2–2, qSR3–1, qSR3–2, qSR3–3 and qSR9) that were colocalized with those from previous studies and seven QTLs (qSR2–1, qSR3–4, qSR3–5, qSR3–6, qSR3–7, qSR4 and qSR7) that were reported for the first time. Among these QTLs, qSR9, harboring the most significant SNP, explained the most phenotypic variation. Through bioinformatics analysis, five genes (LOC_Os09g12440, LOC_Os09g12470, LOC_Os09g12520, LOC_Os09g12580 and LOC_Os09g12720) were identified as candidates for qSR9. Conclusion: This natural population consisting of 211 rice landraces combined with high-density SNPs will serve as a better choice for identifying rice QTLs/genes in the future, and the detected QTLs associated with cold tolerance at the bud burst stage in rice will be conducive to further mining favorable genes and breeding rice varieties under cold stress.

Rice (Oryza sativa) is one of the most important cereal crops, providing food for more than half of the world’s population. However, grain yields are challenged by various abiotic stresses such as drought, fertilizer, heat, and their interaction. Rice at reproductive stage is much more sensitive to environmental temperatures, and little is known about molecular mechanisms of rice spikelet in response to high temperature interacting with nitrogen (N). Here we reported the transcriptional profiling analysis of rice spikelet at meiosis stage using RNA sequencing (RNA-seq) as an attempt to gain insights into molecular events associated with temperature and nitrogen. This study received four treatments: 1) NN: normal nitrogen level (165 kg ha−1) with natural temperature (30 °C); 2) HH: high nitrogen level (330 kg ha−1) with high temperature (37 °C); 3) NH: normal nitrogen level and high temperature; and 4) HN: high nitrogen level and natural temperature, respectively. The de novo assembly generated 52,553,536 clean reads aligned with 72,667 unigenes. About 10 M reads were identified from each treatment. In these differentially expressed genes (DEGs), we found 151 and 323 temperature-responsive DEGs in NN-vs-NH and HN-vs-HH, and 114 DEGs were co-expressed. Meanwhile, 203 and 144 nitrogen-responsive DEGs were focused in NN-vs-HN and NH-vs-HH, and 111 DEGs were co-expressed. The temperature-responsive genes were principally associated with calcium-dependent protein, cytochrome, flavonoid, heat shock protein, peroxidase, ubiquitin, and transcription factor while the nitrogen-responsive genes were mainly involved in glutamine synthetase, transcription factor, anthocyanin, amino acid transporter, leucine zipper protein, and hormone. It is noted that, rice spikelet fertility was significantly decreased under high temperature, but it was more reduced under higher nitrogen. Accordingly, numerous spikelet genes involved in pollen development, pollen tube growth, pollen germination, especially sporopollenin biosynthetic process, and pollen exine formation were mainly down-regulated under high temperature. Moreover, the expression levels of co-expressed DEGs including 5 sporopollenin biosynthetic process and 7 pollen exine formation genes of NN-vs-NH were lower than that of HN-vs-HH. Therefore, these spikelet genes may play important roles in response to high temperature with high nitrogen and may be good candidates for crop improvement. This RNA-seq study will help elucidate the molecular mechanisms of rice spikelet defense response to high temperature interacting with high nitrogen level.