Analysis of gene expression patterns and levels in maize hybrids and their parents.

Heterosis has greatly contributed to conventional plant breeding and is widely used to increase crop plant productivity. However, although some studies have explored the mechanisms of heterosis at the genomic and transcriptome level, these mechanisms still remain unclear. The growth and development of maize seedlings and immature embryos have an important impact on subsequent production. This study investigated differentially expressed genes (DEGs) between parents and reciprocal hybrids in the seedling leaves, roots, and immature embryo 15 days after pollination using amplified fragment length polymorphism (AFLP)-based transcript profiling (cDNA-AFLP). We isolated 180, 170, and 108 genes from the leaves, roots, and immature embryos, respectively, that were differentially expressed between hybrids and parents. Sequencing and functional analysis revealed that 107 transcript-derived fragments in the roots and leaves and 90 in the immature embryos were involved in known functions, whereas many DEGs had roles in plant growth and development, photosynthesis, signal transduction, and seed germination. Quantitative reverse-transcription polymerase chain reaction analysis of relative expression levels between reciprocal hybrids and both parental genotypes of selected genes produced results that were consistent with cDNA-AFLP. We validated the expression patterns of 15 selected genes related to heterosis formation and revealed that most showed non-additive expression in one or both hybrids, including dominant, underdominant, and overdominant expression. This indicates that gene-regulatory interactions among parental alleles play an important role in heterosis during the early developmental stages of maize.

Analysis of DNA methylation patterns and levels in maize hybrids and their parents.

Heterosis is the superior performance of heterozygous individuals and has been widely exploited in plant breeding, although the underlying regulatory mechanisms still remain largely elusive. To understand the molecular basis of heterosis in maize, in this study, roots and leaves at the seedling stage and embryos and endosperm tissues 15 days after fertilization of 2 elite hybrids and their parental lines were used to estimate the levels and patterns of cytosine methylation by the methylation-sensitive amplification polymorphism method. The relative total methylation levels were lower in all the tissues of all hybrids than their corresponding mid-parent values, and the number of demethylation events was higher in the hybrids. These results implied that the decreasing trend and demethylation in hybrids relative to their parents may enable the derepression and possibly expression of many genes that were associated with the phenotypic variation in hybrids. To further analyze the observed methylation pattern changes, a total of 63 differentially displayed DNA fragments were successfully sequenced. Basic Local Alignment Search Tool analysis showed that 11 fragments shared similarity with known functional proteins in maize or other plant species, including metabolism, transposon/retrotransposon, development, stress response, and signal transduction, which indicated that these genes might play a significant role in maize hybrid vigor.

Analysis of protein-protein interaction network in chronic obstructive pulmonary disease.

Chronic obstructive pulmonary disease (COPD) is a growing cause of morbidity and mortality throughout the world. The purpose of our study was to uncover biomarkers and explore its pathogenic mechanisms at the molecular level. The gene expression profiles of COPD samples and normal controls were downloaded from Gene Expression Omnibus. Matlab was used for data preprocessing and SAM4.0 was applied to determine the differentially expressed genes (DEGs). Furthermore, a protein-protein interaction (PPI) network was constructed by mapping the DEGs into PPI data, and functional analysis of the network was conducted with BiNGO. A total of 348 DEGs and 765 interactive genes were identified. The hub genes were mainly involved in metabolic processes and ribosome biogenesis. Several genes related to COPD in the PPI network were found, including CAMK1D, ALB, KIT, and DDX3Y. In conclusion, CAMK1D, ALB, KIT, and DDX3Y were chosen as candidate genes, which have the potential to be biomarkers or candidate target molecules to apply in clinical diagnosis and treatment of COPD.

Expressed sequence tag-PCR markers for identification of alien barley chromosome 2H in wheat.

We developed EST-PCR markers specific to barley chromosome 2H, for the purpose of effectively tracing alien chromosomes or chromosome parts in the wheat genetic background. The target alien chromosome 2H confers high resistance to pre-harvest sprouting, which is a worldwide natural disaster in wheat. A total of 120 primer pairs were selected by combining the wheat group 2 chromosomes of the EST database and the genome sequences of the new model plant Brachypodium distachyon. Seventy-seven of 120 primer pairs were polymorphic and 31 of 120 primer pairs were monomorphic between a set of wheat-barley chromosome 2H disomic addition/substitution lines and their parents by agarose gel electrophoresis and polyacrylamide gel electrophoresis. Thirty of 77 polymorphic primer pairs including primer pair P120 derived from the basi gene were chromosome 2H-specific. These markers are expected to be valuable in screening of wheat-barley chromosome 2H recombination lines and pre-harvest sprouting resistant varieties.

Cloning and characterization of a ß-amyrin synthase gene from the medicinal tree Aralia elata (Araliaceae).

Aralia elata is an important medicinal plant in China; it produces large amounts of oleanane type triterpene saponins. A full-length cDNA encoding ß-amyrin synthase (designated as AeAS) was isolated from young leaves of A. elata by reverse transcription-PCR. The full-length cDNA of AeAS was found to have a 2292-bp open reading frame, encoding a protein with 763 amino acid residues. The deduced amino acid sequence of AeAS showed the highest identity (97%) to Panax ginseng ß-amyrin synthase. When AeAS cDNA was expressed in Escherichia coli, an 87.8-kDa recombinant protein was detected by SDS-PAGE and Western blotting. The sequence was also heterologously expressed in the yeast Pichia pastoris, and production of ß-amyrin was detected by HPLC. Tissue expression pattern analysis by real-time reverse transcription-PCR revealed that AeAS is strongly expressed in leaves and stems, and weakly expressed in roots and flowers.

Comparative analyses of genetic/epigenetic diversities and structures in a wild barley species (Hordeum brevisubulatum) using MSAP, SSAP and AFLP.

We analyzed genetic diversity and population genetic structure of four artificial populations of wild barley (Hordeum brevisubulatum); 96 plants collected from the Songnen Prairie in northeastern China were analyzed using amplified fragment length polymorphism (AFLP), specific-sequence amplified polymorphism (SSAP) and methylation-sensitive amplified polymorphism (MSAP) markers. Indices of (epi-)genetic diversity, (epi-)genetic distance, gene flow, genotype frequency, cluster analysis, PCA analysis and AMOVA analysis generated from MSAP, AFLP and SSAP markers had the same trend. We found a high level of correlation in the artificial populations between MSAP, SSAP and AFLP markers by the Mantel test (r > 0.8). This is incongruent with previous findings showing that there is virtually no correlation between DNA methylation polymorphism and classical genetic variation; the high level of genetic polymorphism could be a result of epigenetic regulation. We compared our results with data from natural populations. The population diversity of the artificial populations was lower. However, different from what was found using AFLP and SSAP, based on MSAP results the methylation polymorphism of the artificial populations was not significantly reduced. This leads us to suggest that the DNA methylation pattern change in H. brevisubulatum populations is not only related to DNA sequence variation, but is also regulated by other controlling systems.