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.

Drought seriously curtails growth, physiology and productivity in rapeseed (Brassica napus). Although drought tolerance is a complex trait, efficient phenotyping and genotyping has led to the identification of novel marker-trait associations underlying drought tolerance. A diverse panel of 228 Brassica accessions was phenotyped under normal (without stress) and water-stress conditions, simulated by polyethylene glycol (PEG-6000) (15% PEG stress) at the seedling stage; stress tolerance index (STI) and stress susceptibility index (SSI) values were acquired. Genome-wide association studies (GWAS) using 201 817 high quality SNPs identified 314 marker-trait associations strongly linked with drought indices and distributed across all nineteen chromosomes in both the A and C genomes. None of these quantitative trait loci (QTL) had been previously identified by other studies. We identified 85 genes underlying these QTL (most within 100 kb of associated SNPs) which were orthologous to Arabidopsis genes known to be associated with drought tolerance. Our study provides a novel resource for breeding drought-tolerant Brassica crops.

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.

Fe is a trace element considered to be essential for rice, and it drives several metabolic processes. Fe toxicity occurs due to excessive Fe ions (Fe2+) and which, disturb cellular homeostasis and dramatically reduces the rice yield. A set of 118 BRILs made from a cross of japonica cv.’02428’ and indica ‘Changhui 891’ was used with high density bin map constructed by using high quality SNP to identify the QTL for Fe toxicity tolerance. As a whole total of 23 QTL were identified for various seedling traits, 3 under control with phenotypic difference ranging from 14.21% to 62.46%, 11 QTL under stress with phenotypic difference ranging from 7.89% to 47.39% and 9 under stressed/control ratio with phenotypic variance ranging from 9.17% to 183.50%. LOD values of QTL ranging from 4.05 to 17.04 in control, 3.41 to 8.09 in stress and 2.84 to131.63 in stress/control ratio. Shoot length (SL), root length (RL), shoot fresh weight (SFW), root fresh weight (RFW), shoot dry weight (SDW), and root dry weight (RDW), were used to estimate the degree of Fe tolerance. Many stable QTL, qSSDW-4, qSSDW-6, qRSDW-4 and qRSDW-6 affecting SDW were detected and beside this some new QTL, qRSFW-1, qRRFW-10 and qRRDW-1 were successfully identified significantly contributing to Fe toxicity tolerance in rice. The results of current study indicated that these novel regions could be transferred via markers assisted section and QTL pyramiding to develop Fe resistant lines in rice.