Comparative Transcriptome Analysis between the Cytoplasmic Male Sterile Line NJCMS1A and Its Maintainer NJCMS1B in Soybean (Glycine max (L.) Merr.)

Abstract

BackgroundThe utilization of soybean heterosis is probably one of the potential approaches in future yield breakthrough as was the situation in rice breeding in China. Cytoplasmic male sterility (CMS) plays an important role in the production of hybrid seeds. However, the molecular mechanism of CMS in soybean remains unclear.ResultsThe comparative transcriptome analysis between cytoplasmic male sterile line NJCMS1A and its near-isogenic maintainer NJCMS1B in soybean was conducted using Illumina sequencing technology. A total of 88,643 transcripts were produced in Illumina sequencing. Then 56,044 genes were obtained matching soybean reference genome. Three hundred and sixty five differentially expressed genes (DEGs) between NJCMS1A and NJCMS1B were screened by threshold, among which, 339 down-regulated and 26 up-regulated in NJCMS1A compared to in NJCMS1B. Gene Ontology (GO) annotation showed that 242 DEGs were annotated to 19 functional categories. Clusters of Orthologous Groups of proteins (COG) annotation showed that 265 DEGs were classified into 19 categories. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that 46 DEGs were assigned to 33 metabolic pathways. According to functional and metabolic pathway analysis combined with reported literatures, the relations between some key DEGs and the male sterility of NJCMS1A were discussed. qRT-PCR analysis validated that the gene expression pattern in RNA-Seq was reliable. Finally, enzyme activity assay showed that energy supply was decreased in NJCMS1A compared to in NJCMS1B.ConclusionsWe concluded that the male sterility of NJCMS1A might be related to the disturbed functions and metabolism pathways of some key DEGs, such as DEGs involved in carbohydrate and energy metabolism, transcription factors, regulation of pollen development, elimination of reactive oxygen species (ROS), cellular signal transduction, and programmed cell death (PCD) etc. Future research will focus on cloning and transgenic function validation of possible candidate genes associated with soybean CMS.

Genetic and Biochemical Mechanisms of Pollen Wall Development

“…Unfortunately, currently-available microarray and RNA-seq data are mainly for flowers, anthers, or pollen grains [37][38][39][40]. However, these studies indicated that functions of pollen-enriched genes and differentially expressed genes in the male-sterile mutants are mainly relative to two pathways: cell wall and cytoskeletal remodeling [37,40], highlighting possible roles for these genes in pollen wall development. Furthermore, our recent genome-wide coexpression analysis revealed that 98 candidate genes with specific expression in the anther are likely involved in pollen wall formation.…”

“…Furthemore, mutation in genes encoding other polysaccharide-associated enzymes also causes abnormal pollen wall development [31,32,36]. Recent transcriptomic analyses also indicated that the expression of polysaccharide metabolism-associated genes in a male-sterile soybean line was significantly downregulated compared to the male-fertile line; these genes encode invertases, hexokinases, and pectin lyases [37]. However, little is known about the biochemical mechanism.…”

Transcription Factors and MicroRNA Interplay: A New Strategy for Crop Improvement

“…Mainly, TFs act by binding the cis element present inside the transcription initiation (promoter) region of their target gene [15]. Recent studies have shown that changes in gene expression are closely related with changes in expression of TFs [16] affecting growth and development in plants [17]. Manipulation of desired traits in plants by engineering TF genes is considered as a major future outlook [18].…”

Comparative transcriptome profiling of the fertile and sterile flower buds of a dominant genic male sterile line in sesame (Sesamum indicum L.)

“…To elucidate the mechanism of MS more comprehensively, the transcriptomes of many higher plants have been sequenced, including Arabidopsis [21], buckwheat [22], cotton [23–25], watermelon [26], soybean [27], Brassica napus [28–30] and Brassica oleracea [31]. In this study, fertile and sterile flower buds from DGMS line with a length of ~2.5 mm were sampled for RNA-seq, representing the first study of the sesame DGMS transcriptome.…”