Comparative transcript profiling of alloplasmic male-sterile lines revealed altered gene expression related to pollen development in rice (Oryza sativa L.)

Abstract

BackgroundCytoplasmic male sterility (CMS) is an ideal model for investigating the mitochondrial-nuclear interaction and down-regulated genes in CMS lines which might be the candidate genes for pollen development in rice. In this study, a set of rice alloplasmic sporophytic CMS lines was obtained by successive backcrossing of Meixiang B, with three different cytoplasmic types: D62A (D type), ZS97A (WA type) and XQZ-A (DA type).ResultsUsing microarray, the anther transcript profiles of the three indica rice CMS lines revealed 622 differentially expressed genes (DEGs) in each of the three CMS lines compared with the maintainer line Meixiang B. GO and MapMan analysis indicated that these DEGs were mainly involved in lipid metabolism and cell wall organization. Compared with the gene expression of sporophytic and gametophytic CMS lines, 303 DEGs were identified and 56 of them were down-regulated in all the CMS lines of rice. These down-regulated DEGs in the CMS lines were found to be involved in tapetum or cell wall formation and their suppressed expression might be related to male sterility. Weighted gene co-expression network analysis (WGCNA) revealed that two modules were significantly associated with male sterility and many hub genes that were differentially expressed in the CMS lines.ConclusionA large set of putative genes involved in anther development was identified in the present study. The results will give some information for the nuclear gene regulation by different cytoplasmic genotypes and provide a rich resource for further functional research on the pollen development in rice.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0864-7) contains supplementary material, which is available to authorized users.

Comparative Transcriptome Analysis of Different Dendrobium Species Reveals Active Ingredients-Related Genes and Pathways

“…[37]. Analysis of the pollen transcriptome of three male sterile lines using weighted gene co-expression network analysis revealed that two modules were significantly associated with male sterility and many hub genes that were differentially expressed in the sterile lines [38]. Farcuh et al used WGCNA to investigate sugar metabolism during leaf and fruit development of two Japanese plum varieties, and identified 11 key sugar metabolism-related genes, the results showed that sugar metabolism was reprogrammed in a non-climacteric bud mutant of a climacteric plum fruit and showed an increase in sorbitol synthesis [39].…”

Tapetal-Delayed Programmed Cell Death (PCD) and Oxidative Stress-Induced Male Sterility of Aegilops uniaristata Cytoplasm in Wheat

“…Samples were analyzed with a fluorescence confocal scanner microscope (Nikon, Tokyo, Japan) using a 450/515 nm excitation/emission spectrum for TUNEL fluorescein and a 358/461 nm excitation/emission spectrum for DAPI as described in [ 15 ]. For DNA laddering analysis, total DNA was isolated from the anthers in different developmental stages [ 50 ]. Then, the total DNA was redissolved in Tris-EDTA (10 mmol L −1 Tris-HCl (pH 8.0), 5 mmol L −1 EDTA) and incubated at 37 °C for 60 min in the presence of RNase A (100 g mL −1 ).…”

Oxidative Stress and Aberrant Programmed Cell Death Are Associated With Pollen Abortion in Isonuclear Alloplasmic Male-Sterile Wheat

“…Total DNA was isolated from the anthers in different developmental stages using the cetyl trimethylammonium bromide extraction procedure ( Hu et al, 2016 ). Next, the total DNA was redissolved in Tris-EDTA buffer solution (10 mmol L -1 Tris-HCl (pH 8.0), 5 mmol L -1 EDTA) and incubated at 37°C for 60 min in the presence of RNase A (100 g mL -1 ).…”