ArticleBMC plant biology2016
SNP-based analysis of genetic diversity reveals important alleles associated with seed size in rice.
Article in BMC plant biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 63 citations in OpenAlex.
- Key Genomic Regions of Rice Cultivar GuiHeFeng and Its Derivatives Revealed by Genome-Wide Analysis.Plants (Basel, Switzerland) · 2026Article
- A comprehensive catalog of single nucleotide polymorphisms (SNPs) from the black pepper (Piper nigrum L.) genome.BMC genomics · 2025Article
- UDP-glucosyltransferase 71C4 controls the flux of phenylpropanoid metabolism to shape cotton seed development.Plant communications · 2024Article
- Genetic diversity and population structure of Piper nigrum (black pepper) accessions based on next-generation SNP markers.PloS one · 2024Article
- Genetic Basis of Grain Size and Weight in Rice, Wheat, and Barley.International journal of molecular sciences · 2023Review
- Genome-Wide Association Study ofPlants (Basel, Switzerland) · 2023Article
- Mapping of QTLs and Screening Candidate Genes Associated with the Ability of Sugarcane Tillering and Ratooning.International journal of molecular sciences · 2023Article
- Molecular dissection of connected rice populations revealed important genomic regions for agronomic and biofortification traits.Frontiers in plant science · 2023Article
- Conventional and Omics Approaches for Understanding the Abiotic Stress Response in Cereal Crops-An Updated Overview.Plants (Basel, Switzerland) · 2022Review
- Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.).Rice (New York, N.Y.) · 2022Article
- Prediction and expression analysis of deleterious nonsynonymous SNPs of Arabidopsis ACD11 gene by combining computational algorithms and molecular docking approach.PLoS computational biology · 2022Article
- Whole-genome resequencing of Coffea arabica L. (Rubiaceae) genotypes identify SNP and unravels distinct groups showing a strong geographical pattern.BMC plant biology · 2022Article
- Fruit shape lociFrontiers in plant science · 2022Article
- Analysis of genome variants in dwarf soybean lines obtained in F6 derived from cross of normal parents (cultivated and wild soybean).Genomics & informatics · 2021Article
- The Sorghum (Frontiers in plant science · 2021Article
- Heterosis-associated genes confer high yield in super hybrid rice.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Genome- wide structural and functional variant discovery of rice landraces using genotyping by sequencing.Molecular biology reports · 2020Article
- Genome-Wide Association Study of Grain Size Traits inFrontiers in plant science · 2020Article
- Article
- Discovery of Functional SNPs via Genome-Wide Exploration of Malaysian Pigmented Rice Varieties.International journal of genomics · 2019Article
Corrections and comments
- Erratum issued
Authors and funding
10 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSingle-nucleotide polymorphisms (SNPs) have become the genetic markers of choice in various genetic, ecological, and evolutionary studies. Genotyping-by-sequencing (GBS) is a next-generation-sequencing based method that takes advantage of reduced representation to enable high-throughput genotyping using a large number of SNP markers.
resultsIn the present study, the distribution of non-redundant SNPs in the parents of 12 rice recombination line populations was evaluated through GBS. A total of 45 Gigabites of nucleotide sequences conservatively provided satisfactory genotyping of rice SNPs. By assembling to the genomes of reference genomes of japonica Nipponbare, we detected 22,682 polymorphic SNPs that may be utilized for QTL/gene mapping with the Recombinant Inbred Lines (RIL) populations derived from these parental lines. Meanwhile, we identified polymorphic SNPs with large effects on protein-coding and miRNA genes. To validate the effect of the polymorphic SNPs, we further investigated a SNP (chr4:28,894,757) at the miRNA binding site in the 3'-UTR region of the locus Os4g48460, which is associated with rice seed size. Os4g48460 encodes a putative cytochrome P450, CYP704A3. Direct degradation of the 3'-UTR of the CYP704A3 gene by a miRNA (osa-miRf10422-akr) was validated by in planta mRNA degradation assay. We also showed that rice seeds of longer lengths may be produced by downregulating CYP704A3 via RNAi.
conclusionsOur study has identified the genome-wide SNPs by GBS of the parental varieties of RIL populations and identified CYP704A3, a miRNA-regulated gene that is responsible for rice seed length.
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