Chunchao Wang

Transcriptome analysis reveals salt-stress-regulated biological processes and key pathways in roots of cotton (Gossypium hirsutum L.)

High salinity is one of the main factors limiting cotton growth and productivity. The genes that regulate salt stress in TM-1 upland cotton were monitored using microarray and real-time PCR (RT-PCR) with samples taken from roots. Microarray analysis showed that 1503 probe sets were up-regulated and 1490 probe sets were down-regulated in plants exposed for 3h to 100mM NaCl, and RT-PCR analysis validated 42 relevant/related genes. The distribution of enriched gene ontology terms showed such important processes as the response to water stress and pathways of hormone metabolism and signal transduction were induced by the NaCl treatment. Some key regulatory gene families involved in abiotic and biotic sources of stress such as WRKY, ERF, and JAZ were differentially expressed. Our transcriptome analysis might provide some useful insights into salt-mediated signal transduction pathways in cotton and offer a number of candidate genes as potential markers of tolerance to salt stress.

Gene Expression Profiles Deciphering Rice Phenotypic Variation between Nipponbare (Japonica) and 93-11 (Indica) during Oxidative Stress

Rice is a very important food staple that feeds more than half the worlds population. Two major Asian cultivated rice (Oryza sativa L.) subspecies, japonica and indica, show significant phenotypic variation in their stress responses. However, the molecular mechanisms underlying this phenotypic variation are still largely unknown. A common link among different stresses is that they produce an oxidative burst and result in an increase of reactive oxygen species (ROS). In this study, methyl viologen (MV) as a ROS agent was applied to investigate the rice oxidative stress response. We observed that 93-11 (indica) seedlings exhibited leaf senescence with severe lesions under MV treatment compared to Nipponbare (japonica). Whole-genome microarray experiments were conducted, and 1,062 probe sets were identified with gene expression level polymorphisms between the two rice cultivars in addition to differential expression under MV treatment, which were assigned as Core Intersectional Probesets (CIPs). These CIPs were analyzed by gene ontology (GO) and highlighted with enrichment GO terms related to toxin and oxidative stress responses as well as other responses. These GO term-enriched genes of the CIPs include glutathine S-transferases (GSTs), P450, plant defense genes, and secondary metabolism related genes such as chalcone synthase (CHS). Further insertion/deletion (InDel) and regulatory element analyses for these identified CIPs suggested that there may be some eQTL hotspots related to oxidative stress in the rice genome, such as GST genes encoded on chromosome 10. In addition, we identified a group of marker genes individuating the japonica and indica subspecies. In summary, we developed a new strategy combining biological experiments and data mining to study the possible molecular mechanism of phenotypic variation during oxidative stress between Nipponbare and 93-11. This study will aid in the analysis of the molecular basis of quantitative traits.

mRNA-seq Analysis of the Gossypium arboreum transcriptome Reveals Tissue Selective Signaling in Response to Water Stress during Seedling Stage

The cotton diploid species, Gossypium arboreum, shows important properties of stress tolerance and good genetic stability. In this study, through mRNA-seq, we de novo assembled the unigenes of multiple samples with 3h H2O, NaCl, or PEG treatments in leaf, stem and root tissues and successfully obtained 123,579 transcripts of G. arboreum, 89,128 of which were with hits through BLAST against known cotton ESTs and draft genome of G. raimondii. About 36,961 transcripts (including 1,958 possible transcription factor members) were identified with differential expression under water stresses. Principal component analysis of differential expression levels in multiple samples suggested tissue selective signalling responding to water stresses. Venn diagram analysis showed the specificity and intersection of transcripts’ response to NaCl and PEG treatments in different tissues. Self-organized mapping and hierarchical cluster analysis of the data also revealed strong tissue selectivity of transcripts under salt and osmotic stresses. In addition, the enriched gene ontology (GO) terms for the selected tissue groups were differed, including some unique enriched GO terms such as photosynthesis and tetrapyrrole binding only in leaf tissues, while the stem-specific genes showed unique GO terms related to plant-type cell wall biogenesis, and root-specific genes showed unique GO terms such as monooxygenase activity. Furthermore, there were multiple hormone cross-talks in response to osmotic and salt stress. In summary, our multidimensional mRNA sequencing revealed tissue selective signalling and hormone crosstalk in response to salt and osmotic stresses in G. arboreum. To our knowledge, this is the first such report of spatial resolution of transcriptome analysis in G. arboreum. Our study will potentially advance understanding of possible transcriptional networks associated with water stress in cotton and other crop species.

JAZ7 negatively regulates dark-induced leaf senescence in Arabidopsis.

Highlight Under darkness, JAZ7 was up-regulated and the mutant showed a severe leaf senescence phenotype. Genetics and transcriptomic analysis revealed JAZ7 as an important regulator of dark-induced leaf senescence.

Down-Regulation of OsSPX1 Causes High Sensitivity to Cold and Oxidative Stresses in Rice Seedlings

Rice SPX domain gene, OsSPX1, plays an important role in the phosphate (Pi) signaling network. Our previous work showed that constitutive overexpression of OsSPX1 in tobacco and Arabidopsis plants improved cold tolerance while also decreasing total leaf Pi. In the present study, we generated rice antisense and sense transgenic lines of OsSPX1 and found that down-regulation of OsSPX1 caused high sensitivity to cold and oxidative stresses in rice seedlings. Compared to wild-type and OsSPX1-sense transgenic lines, more hydrogen peroxide accumulated in seedling leaves of OsSPX1-antisense transgenic lines for controls, cold and methyl viologen (MV) treatments. Glutathione as a ROS scavenger could protect the antisense transgenic lines from cold and MV stress. Rice whole genome GeneChip analysis showed that some oxidative-stress marker genes (e.g. glutathione S-transferase and P450s) and Pi-signaling pathway related genes (e.g. OsPHO2) were significantly down-regulated by the antisense of OsSPX1. The microarray results were validated by real-time RT-PCR. Our study indicated that OsSPX1 may be involved in cross-talks between oxidative stress, cold stress and phosphate homeostasis in rice seedling leaves.

Differential deposition of H2A.Z in combination with histone modifications within related genes in Oryza sativa callus and seedling.

Summary As a histone variant, H2A.Z is highly conserved among species and plays a significant role in diverse cellular processes. Here, we generated genome‐wide maps of H2A.Z in Oryza sativa (rice) callus and seedling by combining chromatin immunoprecipitation using H2A.Z antibody and high‐throughput sequencing. We found a significantly high peak and a small peak of H2A.Z distributed at the 5′ and 3′ ends of highly expressed genes, respectively. H2A.Z was also associated with inactive genes in both tissues. H3 lysine 4 trimethylation was associated with H2A.Z deposition at the 5′ end of expressed genes, and H3 lysine 27 trimethylation peaks were partially associated with H2A.Z. In summary, our study provides global analysis data for the distribution of H2A.Z in the rice genome. Our results demonstrate that the differential deposition of H2A.Z might play important roles in gene transcription during rice development. Significance Statement Regulation of chromatin structure is important in modulating genome activities. The histone variant H2A.Z is highly conserved between species and plays a significant role, but how H2A.Z nucleosome occupancy mediates differential transcription in plants other than Arabidopsis is still poorly understood. Here, we performed a genome‐wide distribution of H2A.Z in rice seedlings and callus. We conclude that differential deposition of H2A.Z, in combination with other chromatin marks, affects gene transcription during rice development.

Down-regulation of OsSPX1 caused semi-male sterility, resulting in reduction of grain yield in rice.

Summary OsSPX1, a rice SPX domain gene, involved in the phosphate (Pi)‐sensing mechanism plays an essential role in the Pi‐signalling network through interaction with OsPHR2. In this study, we focused on the potential function of OsSPX1 during rice reproductive phase. Based on investigation of OsSPX1 antisense and sense transgenic rice lines in the paddy fields, we discovered that the down‐regulation of OsSPX1 caused reduction of seed‐setting rate and filled grain number. Through examination of anthers and pollens of the transgenic and wild‐type plants by microscopy, we found that the antisense of OsSPX1 gene led to semi‐male sterility, with lacking of mature pollen grains and phenotypes with a disordered surface of anthers and pollens. We further conducted rice whole‐genome GeneChip analysis to elucidate the possible molecular mechanism underlying why the down‐regulation of OsSPX1 caused deficiencies in anthers and pollens and lower seed‐setting rate in rice. The down‐regulation of OsSPX1 significantly affected expression of genes involved in carbohydrate metabolism and sugar transport, anther development, cell cycle, etc. These genes may be related to pollen fertility and male gametophyte development. Our study demonstrated that down‐regulation of OsSPX1 disrupted rice normal anther and pollen development by affecting carbohydrate metabolism and sugar transport, leading to semi‐male sterility, and ultimately resulted in low seed‐setting rate and grain yield.

Evaluation of connectedness between herds for three pig breeds in China.

Using data on age at 100 kg of three pig breeds (Large White, Landrace and Duroc) the connectedness between herds in China was evaluated by the connectedness rating (CR) method. The results show that most herds in China have low average CR (0-3.59%) with other herds. In Large White, of the 36 herds analyzed there are 20 herds, which are connected with at least one other herd. In Landrace and Duroc, of the 27 and 18 herds analyzed, only four and five herds, respectively, were found having connectedness with other herds. Generally, the connectedness exists only among two or few herds in the same region. A certain degree of connectedness between herds is a precondition for cross-herd genetic evaluation. A national or regional cross-herd genetic evaluation is not practicable at the present time in China. More intense efforts are needed to establish and enhance the connectedness between herds by means of extensively using artificial insemination (AI) in the swine industry in China.

Differential deposition of H2A.Z in rice seedling tissue during the day-night cycle

ABSTRACT Chromatin structure has an important role in modulating gene expression. The incorporation of histone variants into the nucleosome leads to important changes in the chromatin structure. The histone variant H2A.Z is highly conserved between different species of fungi, animals, and plants. However, dynamic changes to H2A.Z in rice have not been reported during the day-night cycle. In this study, we generated genome wide maps of H2A.Z for day and night time in harvested seedling tissues by combining chromatin immunoprecipitation and high-throughput sequencing. The analysis results for the H2A.Z data sets detected 7099 genes with higher depositions of H2A.Z in seedling tissues harvested at night compared with seedling tissues harvested during the day, whereas 4597 genes had higher H2A.Z depositions in seedlings harvested during the day. The gene expression profiles data suggested that H2A.Z probably negatively regulated gene expression during the day-night cycle and was involved in many important biologic processes. In general, our results indicated that H2A.Z may play an important role in plant responses to the diurnal oscillation process.

Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation

Polyploidy is a common evolutionary occurrence in plants. Recently, published genomes of allotetraploid G. hirsutum and its donors G. arboreum and G. raimondii make cotton an accessible polyploid model. This study used chromatin immunoprecipitation with high-throughput sequencing (ChIP-Seq) to investigate the genome-wide distribution of H3K4me3 in G. arboreum and G. hirsutum, and explore the conservation and variation of genome structures between diploid and allotetraploid cotton. Our results showed that H3K4me3 modifications were associated with active transcription in both cottons. The H3K4me3 histone markers appeared mainly in genic regions and were enriched around the transcription start sites (TSSs) of genes. We integrated the ChIP-seq data of H3K4me3 with RNA-seq and ESTs data to refine the genic structure annotation. There were 6,773 and 12,773 new transcripts discovered in G. arboreum and G. hirsutum, respectively. Furthermore, co-expression networks were linked with histone modification and modularized in an attempt to explain differential H3K4me3 enrichment correlated with changes in gene transcription during cotton development and evolution. Taken together, we have combined epigenomic and transcriptomic datasets to systematically discover functional genes and compare them between G. arboreum and G. hirsutum, which may be beneficial for studying diploid and allotetraploid plants with large genomes and complicated evolution.