Cytogenetic analyses have revealed that complex karyotypes with numerous and highly variable genomic aberrations including single-nucleotide polymorphisms (SNPs) and copy number variants (CNVs), are observed in most of the conventional osteosarcomas (OSs). Several genome-wide studies have reported that the dysregulated expression of many genes is correlated with genomic aberrations in OS. We first compared OS gene expression in Gene Expression Omnibus (GEO) data sets and genomic aberrations in International Cancer Genome Consortium (ICGC) database to identify differentially expressed genes (DEGs) associated with SNPs or CNVs in OS. Then the function annotation of SNP- or CNV-associated DEGs was performed in terms of gene ontology analysis, pathway analysis and protein-protein interactions (PPIs). Finally, the expression of genes correlated with both SNPs and CNVs were confirmed by quantitative reverse-transcription PCR. Eight publicly available GEO data sets were obtained, and a set of 979 DEGs were identified (472 upregulated and 507 downregulated DEGs). Moreover, we obtained 1039 SNPs mapped in 938 genes, and 583 CNV sites mapped in 2915 genes. Comparing genomic aberrations and DGEs, we found 41 SNP-associated DEGs and 124 CNV-associated DEGs, in which 7 DGEs were associated with both SNPs and CNVs, including WWP1, EXT1, LDHB, C8orf59, PLEKHA5, CCT3 and VWF. The result of function annotation showed that ossification, bone development and skeletal system development were the significantly enriched terms of biological processes for DEGs. PPI network analysis showed that CCT3, COPS3 and WWP1 were the significant hub proteins. We conclude that these genes, including CCT3, COPS3 and WWP1 are candidate driver genes of importance in OS tumorigenesis.

Germination is a common practice for nutrition improvement in many crops. In soybean, the nutrient value and genome-wide gene expression pattern of whole seeds germinated for short-time has not been fully investigated. In this study, protein content (PC), water soluble protein content (WSPC), isoflavone compositions were evaluated at 0 and 36 h after germination (HAG), respectively. The results showed that at 36HAG, PC was slightly decreased (P > 0.05) in ZD41, J58 and JHD, WSPC and free isoflavone (aglycones: daidzein, genistein, and glycitein) were significantly increased (P < 0.05), while total isoflavone content was unchanged. Transcriptomic analysis identified 5240, 6840 and 15,766 DEGs in different time point comparisons, respectively. GO and KEGG analysis showed that photosynthesis process was significantly activated from 18HAG, and alternative splicing might play an important role during germination in a complex manner. Response to hydrogen peroxide (H2O2) was found to be down regulated significantly from 18 to 36HAG, suggesting that H2O2 might play an important role in germination. Expression pattern analysis showed the synthesis of storage proteins was slowing down, while the genes coding for protein degradation (peptidase and protease) were up regulated as time went by during germination. For genes involved in isoflavone metabolism pathway, UGT (7-O-glucosyltransferase) coding genes were significantly up regulated (40 up-DEGs vs 27 down-DEGs), while MAT (7-O-glucoside-6′′-O-malonyltransferase) coding genes were down regulated, which might explain the increase of aglycones after germination. This study provided a universal transcriptomic atlas for whole soybean seeds germination in terms of nutrition and gene regulation mechanism.

The N absorption and assimilation is critical for the rice (Oryza sativa L.) yield increase when overdose N was applied in rice production. Three different rice genotypes, 'Quanliangyou 1' (Q1), 'Quanliangyou 681' (Q681) and 'Huanghuazhan' (HHZ), were selected to investigate the effects of elevated N input on the N partitioning, plant growth, grain quality and key genes involved in glutamate biosynthesis. Under increasing N inputs (0, 120, 180, 250 kg ha-1), N content in leaf, culm, seed and root were increased significantly. The increased N was preferentially deposited in leaf and culm. Tiller number, panicle number and length were also proved to be significantly promoted, but plant height and 1000-grain weight were nonsignificantly affected under elevated N input. Under high N input, seed protein content was elevated, while fatty acid and amylose content remained unchanged in comparison to low N input, but amylopectin content decreased. For the key genes in N assimilation, glutamine synthetase (OsGS1;1) could be induced by increasing N input (0 to 180 kg ha-1) but higher N input (250 kg ha-1) inhibit its expression, which showed similar response pattern with the glutamine synthetase activity. Although different rice genotypes showed similar response pattern to elevated N input, each genotype varied a lot in certain phenotypic indexes. And the response pattern of all these phenotypic characteristics to elevated N input was independent of rice genotype. These findings suggest that elevated N input could promote rice growth, reallocate N content in different tissues, and have negative impact on grain quality. This study provided physiological and molecular foundation for rice breeding and cultivation under high N input.