Global Transcriptome and Co-Expression Network Analysis Reveal Contrasting Response of Japonica and Indica Rice Cultivar to γ Radiation

Abstract

Japonica and indica are two important subspecies in cultivated Asian rice. Irradiation is a classical approach to induce mutations and create novel germplasm. However, little is known about the differential response between japonica and indica rice after γ radiation. Here, we utilized the RNA sequencing and Weighted Gene Co-expression Network Analysis (WGCNA) to compare the transcriptome differences between japonica Nipponbare (NPB) and indica Yangdao6 (YD6) in response to irradiation. Japonica subspecies are more sensitive to irradiation than the indica subspecies. Indica showed a higher seedling survival rate than japonica. Irradiation caused more extensive DNA damage in shoots than in roots, and the severity was higher in NPB than in YD6. GO and KEGG pathway analyses indicate that the core genes related to DNA repair and replication and cell proliferation are similarly regulated between the varieties, however the universal stress responsive genes show contrasting differential response patterns in japonica and indica. WGCNA identifies 37 co-expressing gene modules and ten candidate hub genes for each module. This provides novel evidence indicating that certain peripheral pathways may dominate the molecular networks in irradiation survival and suggests more potential target genes in breeding for universal stress tolerance in rice.

Transcriptomic and Co-Expression Network Profiling of Shoot Apical Meristem Reveal Contrasting Response to Nitrogen Rate between Indica and Japonica Rice Subspecies

“…WGCNA (v1.29) package in R was performed to construct the gene co-expression regulation network [20]. Detailed analysis procedures and methods were followed in accordance with Zhang et al [51]. Among the 37,824 genes, 21,700 genes with an averaged FPKM from three replicates > 1 were used for the WGCNA unsigned co-expression network analysis.…”

Transcriptome Analysis of Nitrogen-Deficiency-Responsive Genes in Two Potato Cultivars

“…A total of 20,832 and 21,061 genes with an average FPKM > 1 from the seedling and tuber formation stages were selected for the WGCNA network analysis. The WGCNA (v1.29) package in R was used, as in previous studies [34,35]. The module similarity threshold was 0.25, and the minimum number of genes for the module was 30.…”

“…Nitrogen is a component of various cellular components and enzymes and plays an important role in the growth and development of plants. Nitrogen affects plant roots [36][37][38] and leaves [39], according to previous studies, and crop photosynthesis is also affected by nitrogen [30][31][32][33][34][35][36][37][38][39][40][41][42]. In this study, we first investigated the dry matter accumulation of two potato cultivars, DN322 and DN314, at the seedling and tuber formation stages under normal-nitrogen fertilizer (N1) and low-nitrogen conditions (N0), and we found that under low-nitrogen conditions, the dry matter weight of the roots, stems, leaves, and tubers of these two potato cultivars decreased significantly (Figure 1, Supplementary Figure S1, and Supplementary Table S1), indicating that nitrogen has an important effect on potato dry matter accumulation, which are the same findings as those of our previous study.…”

Efficient mutation induction using carbon-ion beams irradiation and simple genomic screening with SSR and RAPD in japonica rice

“…100 seeds of 'Tonghe 899' (M1 generation) were used for morphological observations. Germination vigor and germination rate of seeds were determined at 2 and 7 days, respectively, together with the measurement of the survival rate of seedlings at 15 days [29]. Meanwhile, the treated 'Tonghe 899' seeds were planted and the materials of each generation (M1-M5) and recorded the characters of the progeny plants to screen stable mutant materials.…”