Comparative transcriptome analysis reveals that tricarboxylic acid cycle-related genes are associated with maize CMS-C fertility restoration

Abstract

BackgroundC-type cytoplasmic male sterility (CMS-C) is one of the three major types of cytoplasmic male sterility (CMS) in maize. Rf4 is a dominant restorer gene for CMS-C and has great value in hybrid maize breeding, but little information concerning its functional mechanism is known.ResultsTo reveal the functional mechanism of Rf4, we developed a pair of maize near-isogenic lines (NILs) for the Rf4 locus, which included a NIL_rf4 male-sterile line and a NIL_Rf4 male fertility-restored line. Genetic analysis and molecular marker detection indicated that the male fertility of NIL_Rf4 was controlled by Rf4. Whole-genome sequencing demonstrated genomic differences between the two NILs was clustered in the Rf4 mapping region. Unmapped reads of NILs were further assembled to uncover Rf4 candidates. RNA-Seq was then performed for the developing anthers of the NILs to identify critical genes and pathways associated with fertility restoration. A total of 7125 differentially expressed genes (DEGs) were identified. These DEGs were significantly enriched in 242 Gene Ontology (GO) categories, wherein 100 DEGs were involved in pollen tube development, pollen tube growth, pollen development, and gametophyte development. Homology analysis revealed 198 male fertility-related DEGs, and pathway enrichment analysis revealed that 58 DEGs were enriched in cell energy metabolism processes involved in glycolysis, the pentose phosphate pathway, and pyruvate metabolism. By querying the Plant Reactome Pathway database, we found that 14 of the DEGs were involved in the mitochondrial tricarboxylic acid (TCA) cycle and that most of them belonged to the isocitrate dehydrogenase (IDH) and oxoglutarate dehydrogenase (OGDH) enzyme complexes. Transcriptome sequencing and real-time quantitative PCR (qPCR) showed that all the above TCA cycle-related genes were up-regulated in NIL_Rf4. The results of our subsequent enzyme-linked immunosorbent assay (ELISA) experiments pointed out that the contents of both the IDH and OGDH enzymes accumulated more in the spikelets of NIL_Rf4 than in those of NIL_rf4.ConclusionThe present research provides valuable genomic resources for deep insight into the molecular mechanism underlying CMS-C male fertility restoration. Importantly, our results indicated that genes involved in energy metabolism, especially some mitochondrial TCA cycle-related genes, were associated with maize CMS-C male fertility restoration.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1409-z) contains supplementary material, which is available to authorized users.

Comparative Transcriptome Analysis of Waterlogging-Sensitive and Tolerant Zombi Pea (Vigna vexillata) Reveals Energy Conservation and Root Plasticity Controlling Waterlogging Tolerance

“…Functional characterization of the WS-induced candidate genes is required to further identify candidate genes controlling waterlogging-tolerant traits. Additionally, recent studies demonstrated that differentially-regulated genes controlling for the traits of interest could be accurately identified using comparative transcriptome RNA-seq analysis of near-isogenic lines (NILs) [66,67]. Clearly, this method could help to narrow down the list of candidate genes responsible for waterlogging tolerance in zombi pea by removing genetic background effects.…”

Identification and characterization of the TCA cycle genes in maize

“…The expression data of each gene were obtained from three biological replicates, each of which was measured at least three times. In addition, part of the expression data was retrieved from our previous report [67].…”

Comparative proteomic analysis of mitochondrial proteins from maize CMS‐C sterile, maintainer and restorer anthers

“…The CMS system is an efficient, economical tool for exploitation of heterosis by maize breeders. Although maize CMS‐C has been widely used in hybrid seed production, and extensive research involving segregating population (Kohls et al., 2011; Tang et al., 2001), genomics (Allen et al., 2007), epigenetics (Chen et al., 2016; Li et al., 2017a), transcriptomics (Li et al., 2017b; Liu et al., 2018; Xue et al., 2019), has been conducted, the molecular mechanism of sterility and restoration in CMS‐C maize remains to be further explored.…”