ArticlePloS one2019
Re-sequencing and transcriptome analysis reveal rich DNA variations and differential expressions of fertility-related genes in neo-tetraploid rice.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 40 citations in OpenAlex.
- Prioritization of candidate genes regulating the dwarfness in rice by integration of whole-genome and transcriptome analyses.Functional & integrative genomics · 2025Article
- Genome Resequencing for Autotetraploid Rice and Its Closest Relatives Reveals Abundant Variation and High Potential in Rice Breeding.International journal of molecular sciences · 2024Article
- Lectin Receptor-Like Protein Kinase OsNRFG6 is Required for Embryo Sac Development and Fertilization in Neo-Tetraploid Rice.Rice (New York, N.Y.) · 2024Article
- Cytological observation and RNA-seq analysis reveal novel miRNAs high expression associated with the pollen fertility of neo-tetraploid rice.BMC plant biology · 2023Article
- Data of germination ability of tetraploid rice lines under multiple stress factors.Data in brief · 2023Article
- Comparative cytological and transcriptome analyses ofFrontiers in plant science · 2023Article
- Thermo-Sensitive Genic Male Sterile Lines of Neo-Tetraploid Rice Developed through Gene Editing Technology Revealed High Levels of Hybrid Vigor.Plants (Basel, Switzerland) · 2022Article
- Article
- A New Way of Rice Breeding: Polyploid Rice Breeding.Plants (Basel, Switzerland) · 2021Review
- Genomics Analyses Reveal Unique Classification, Population Structure and Novel Allele of Neo-Tetraploid Rice.Rice (New York, N.Y.) · 2021Article
- Cytological Observations and Bulked-Segregant Analysis Coupled Global Genome Sequencing Reveal Two Genes Associated with Pollen Fertility in Tetraploid Rice.International journal of molecular sciences · 2021Article
- Transcriptome and Gene Editing Analyses RevealInternational journal of molecular sciences · 2020Article
- Comparative Cytological and Transcriptome Analysis Revealed the Normal Pollen Development Process and Up-Regulation of Fertility-Related Genes in Newly Developed Tetraploid Rice.International journal of molecular sciences · 2020Article
- Production Assessment and Genome Comparison Revealed High Yield Potential and Novel Specific Alleles Associated with Fertility and Yield in Neo-Tetraploid Rice.Rice (New York, N.Y.) · 2020Article
- Heterosis analysis and underlying molecular regulatory mechanism in a wide-compatible neo-tetraploid rice line with long panicles.BMC plant biology · 2020Article
- Profiling of Chemical and Structural Composition of Lignocellulosic Biomasses in Tetraploid Rice Straw.Polymers · 2020Article
- Fertile Tetraploids: New Resources for Future Rice Breeding?Frontiers in plant science · 2020Review
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Autotetraploid rice is a useful germplasm for polyploid rice breeding, however, low seed setting is the major barrier in commercial utilization of autotetraploid rice. Our research group has developed neo-tetraploid rice lines, which have the characteristics of high fertility and heterosis when crossed with autotetraploid rice. In the present study, re-sequencing and RNA-seq were employed to detect global DNA variations and differentially expressed genes (DEGs) during meiosis stage in three neo-tetraploid rice lines compared to their parents, respectively. Here, a total of 4109881 SNPs and 640592 InDels were detected in neo-tetraploid lines compared to the reference genome, and 1805 specific presence/absence variations (PAVs) were detected in three lines. Approximately 12% and 0.5% of the total SNPs and InDels identified in three lines were located in genic regions, respectively. A total of 28 genes, harboring at least one of the large-effect SNP and/or InDel which affect the integrity of the encoded protein, were identified in the three lines. Together, 324 specific mutation genes, including 52 meiosis-related genes and 8 epigenetics-related genes were detected in neo-tetraploid rice compared to their parents. Of these 324 genes, five meiosis-related and three epigenetics-related genes displayed differential expressions during meiosis stage. Notably, 498 specific transcripts, 48 differentially expressed transposons and 245 differentially expressed ncRNAs were also detected in neo-tetraploid rice. Our results suggested that genomic structural reprogramming, DNA variations and differential expressions of some important meiosis and epigenetics related genes might be associated with high fertility in neo-tetraploid rice.
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