Browse
Submit Data
Databases
API
Help

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of a Candidate Gene for the Novel Cytoplasmic Male Sterility Derived from Inter-Subspecific Crosses in Rice (Oryza sativa L.).

ABSTRACT: Tetep-cytoplasmic male sterility (CMS) was developed through successive backcrosses between subspecies indica and japonica in rice (Oryza sativa L.), which showed abnormal anther dehiscence phenotypes. Whole genome sequencing and de novo assembly of the mitochondrial genome identified the chimeric gene orf312, which possesses a transmembrane domain and overlaps with two mitotype-specific sequences (MSSs) that are unique to the Tetep-CMS line. The encoded peptide of orf312 was toxic to Escherichia coli and inhibited cell growth compared to the control under isopropyl-β-D-1-thiogalactopyranoside (IPTG) induction. The peptide of orf312 contains COX11-interaction domains, which are thought to be a main functional domain for WA352c in the wild abortive (WA-CMS) line of rice. A QTL for Rf-Tetep (restorer-of-fertility gene(s) originating from Tetep) was identified on chromosome 10. In this region, several restorer genes, Rf1a, Rf1b, and Rf4, have previously been reported. Collectively, the interactions of orf312, a candidate gene for Tetep-CMS, and Rf-Tetep, a restorer QTL, confer male sterility and fertility restoration, respectively, which enables a hybrid rice breeding system. Further studies on orf312 and isolation of Rf-Tetep will help to identify the underlying molecular mechanism of mitochondrial ORFs with the COX11-interaction domains.

SUBMITTER: Jin Z

PROVIDER: S-EPMC8073397 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Cytoplasmic Male Sterility-Associated Mitochondrial Gene orf312 Derived from Rice (Oryza sativa L.) Cultivar Tadukan.

Project description:BackgroundCytoplasmic male sterility (CMS) is a trait associated with non-functional pollen or anthers, caused by the interaction between mitochondrial and nuclear genes.FindingsA Tadukan-type CMS line (TAA) and a restorer line (TAR) were obtained by successive backcrossing between the Oryza sativa cultivars Tadukan (a cytoplasmic donor) and Taichung 65 (a recurrent pollen parent). Using Illumina HiSeq, we determined whole-genome sequences of the mitochondria of TAA and screened the mitochondrial genome for the presence of open reading frame (orf) genes specific to this genome. One of these orf genes, orf312, showed differential expression patterns in TAA and TAR anthers at the meiotic and mature stages, with transcript amounts in TAR being less than those in TAA. The orf312 gene is similar to the previously described orf288, a part of which is among the components comprising WA352, a chimeric CMS-associated gene of wild-abortive-type CMS.ConclusionsThe orf312 gene is a promising candidate for CMS-associated gene in TAA.

| S-EPMC8141088 | biostudies-literature

The underlying pathway involved in inter-subspecific hybrid male sterility in rice

Project description:Asian cultivated rice (Oryza sativa L.) consists of two major subspecies, indica and japonica. Inter-subspecific hybrids between indica and japonica, usually accompanying hybrid sterility, exhibit much more vigorous heterosis than intra-subspecific hybrids. f5 locus, also called S24 or Sb, confers significant effects on hybrid male sterility and segregation distortion. BC14F2 plants with f5-i/i, f5-j/j and f5-i/j genotype respectively, were used to dissect the underlying pathway of f5-caused hybrid male sterility via comparative transcriptome analysis. 350, 421, and 480 differentially expressed genes (DEGs) were identified from f5-i/j vs. f5-j/j, f5-j/j vs. f5-i/i, and f5-i/j vs. f5-i/i respectively. 145 DEGs demonstrated simultaneously differential expression in both f5-i/j vs. f5-j/j and f5-i/j vs. f5-i/i. Enrichment analysis with MapMan and AgriGO indicated that protein and DNA metabolism, and cell control related processes were enriched in the 145 DEGs. Stress and cell control related processes were enriched in the DEGs of f5-i/j vs. f5-j/j and f5-i/j vs. f5-i/i, whereas, these two processes were not enriched in the DEGs of f5-j/j vs. f5-i/i. Biotic and abiotic stress resistance genes were suppressed, which may result in pollen cell more sensitive to various stresses. The down regulation of ascorbate peroxidase (APX) may break the dynamic homeostasis of ROS (reactive oxygen species) and cause oxidative stress, which can damage cellular components. The expression of most of the heat shock protein (HSP) genes, which can protect proteins and cells from been destroyed, were also decreased. Based on these results, a model was proposed to summarize the underlying process for f5-caused rice hybrid male sterility. These results provide significant clues to further dissecting the molecular mechanism of f5-caused intersubspecific reproductive barrier.

2021-02-12 | GSE110483 | GEO

Characterization of the Common <i>Japonica</i>-Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice (<i>Oryza sativa</i> L.).

Project description:The inter-subspecific crossing between indica and japonica subspecies in rice have been utilized to improve the yield potential of temperate rice. In this study, a comparative study of the genomic regions in the eight high-yielding varieties (HYVs) was conducted with those of the four non-HYVs. The Next-Generation Sequencing (NGS) mapping on the Nipponbare reference genome identified a total of 14 common genomic regions of japonica-originated alleles. Interestingly, the HYVs shared japonica-originated genomic regions on nine chromosomes, although they were developed through different breeding programs. A panel of 94 varieties was classified into four varietal groups with 38 single nucleotide polymorphism (SNP) markers from 38 genes residing in the japonica-originated genomic regions and 16 additional trait-specific SNPs. As expected, the japonica-originated genomic regions were only present in the japonica (JAP) and HYV groups, except for Chr4-1 and Chr4-2. The Wx gene, located within Chr6-1, was present in the HYV and JAP variety groups, while the yield-related genes were conserved as indica alleles in HYVs. The japonica-originated genomic regions and alleles shared by HYVs can be employed in molecular breeding programs to further develop the HYVs in temperate rice.

| S-EPMC7290844 | biostudies-literature

Overcoming inter-subspecific hybrid sterility in rice by developing indica-compatible japonica lines.

Project description:Rice (Oryza sativa L.) is an important staple crop. The exploitation of the great heterosis that exists in the inter-subspecific crosses between the indica and japonica rice has long been considered as a promising way to increase the yield potential. However, the male and female sterility frequently occurred in the inter-subspecific hybrids hampered the utilization of the heterosis. Here we report that the inter-subspecific hybrid sterility in rice is mainly affected by the genes at Sb, Sc, Sd and Se loci for F1 male sterility and the gene at S5 locus for F1 female sterility. The indica-compatible japonica lines (ICJLs) developed by pyramiding the indica allele (S-i) at Sb, Sc, Sd and Se loci and the neutral allele (S-n) at S5 locus in japonica genetic background through marker-assisted selection are compatible with indica rice in pollen fertility and in spikelet fertility. These results showed a great promise of overcoming the inter-subspecific hybrid sterility and exploiting the heterosis by developing ICJLs.

| S-EPMC4887987 | biostudies-literature

Inactivation of the UGPase1 gene causes genic male sterility and endosperm chalkiness in rice (Oryza sativa L.).

Project description:A rice genic male-sterility gene ms-h is recessive and has a pleiotropic effect on the chalky endosperm. After fine mapping, nucleotide sequencing analysis of the ms-h gene revealed a single nucleotide substitution at the 3'-splice junction of the 14th intron of the UDP-glucose pyrophosphorylase 1 (UGPase1; EC2.7.7.9) gene, which causes the expression of two mature transcripts with abnormal sizes caused by the aberrant splicing. An in vitro functional assay showed that both proteins encoded by the two abnormal transcripts have no UGPase activity. The suppression of UGPase by the introduction of a UGPase1-RNAi construct in wild-type plants nearly eliminated seed set because of the male defect, with developmental retardation similar to the ms-h mutant phenotype, whereas overexpression of UGPase1 in ms-h mutant plants restored male fertility and the transformants produced T(1) seeds that segregated into normal and chalky endosperms. In addition, both phenotypes were co-segregated with the UGPase1 transgene in segregating T(1) plants, which demonstrates that UGPase1 has functional roles in both male sterility and the development of a chalky endosperm. Our results suggest that UGPase1 plays a key role in pollen development as well as seed carbohydrate metabolism.

| S-EPMC2327258 | biostudies-literature

A candidate factor that interacts with RF2, a restorer of fertility of Lead rice-type cytoplasmic male sterility in rice.

Project description:BackgroundThe pollen function of cytoplasmic male sterile (CMS) plants is often recovered by the Restorer of fertility (Rf) gene encoded by the nuclear genome. An Rf gene of Lead rice type CMS, Rf2, encodes a small mitochondrial glycine-rich protein. RF2 is expected to function by interacting with other proteins, because RF2 has no motifs except for glycine-rich domain.FindingsTo elucidate the protein that interacts with RF2, we performed yeast two-hybrid screening. We identified four genes and named RF2-interacting candidate factors (RIF1 to RIF4). A study of subcellular localization demonstrated that only RIF2 was targeted to mitochondria. A pull-down assay using E. coli-produced recombinant GST-tagged RF2 and His-tagged RIF2 confirmed that RF2 interacted with RIF2. RIF2 encodes ubiquitin domain-containing protein.ConclusionsThese results suggest that RIF2 is a candidate factor of a fertility restoration complex of RF2.

| S-EPMC4884035 | biostudies-literature

Molecular basis of cytoplasmic male sterility and fertility restoration in rice

Project description:Cytoplasmic male sterility (CMS) is a maternally inherited trait that causes dysfunctions in pollen and anther development. CMS is caused by the interaction between nuclear and mitochondrial genomes. A product of a CMS-causing gene encoded by the mitochondrial genome affects mitochondrial function and the regulation of nuclear genes, leading to male sterility. In contrast, the RESTORER OF FERTILITY gene (Rf gene) in the nuclear genome suppresses the expression of the CMS-causing gene and restores male fertility. An alloplasmic CMS line is often bred as a result of nuclear substitution, which causes the removal of functional Rf genes and allows the expression of a CMS-causing gene in mitochondria. The CMS/Rf system is an excellent model for understanding the genetic interactions and cooperative functions of mitochondrial and nuclear genomes in plants, and is also an agronomically important trait for hybrid seed production. In this review article, pollen and anther phenotypes of CMS, CMS-associated mitochondrial genes, Rf genes, and the mechanism that causes pollen abortion and its agronomical application for rice are described.

| S-EPMC8562580 | biostudies-literature

Oryza sativa Argonaute 18 is a regulator of male sterility (RNA-Seq)

Project description:Artificial miRNA mediated knock-down ago18 transgenic lines [ago18(1), ago18(2)] showed developmentally compromised phenotype in both vegetative and reproductive tissues compared to wild-type control. We have performed RNA seq to investigate underlying molecular mechanism and to reveal functional role of AGO18 in rice.

2018-01-15 | GSE107903 | GEO

Oryza sativa Argonaute 18 is a regulator of male sterility (sRNA-Seq)

Project description:Artificial miRNA mediated knock-down ago18 transgenic lines [ago18(1), ago18(2)] showed developmentally compromised phenotype in both vegetative and reproductive tissues compared to wild-type control. We have performed small RNA seq to investigate underlying molecular mechanism and to reveal functional role of AGO18 in rice.

2018-01-15 | GSE107904 | GEO

The underlying pathway involved in inter-subspecific hybrid male sterility in rice

Project description:The underlying pathway involved in inter-subspecific hybrid male sterility in rice

| PRJNA433849 | ENA