ArticleBMC genomics2016
Genome-wide resequencing of KRICE_CORE reveals their potential for future breeding, as well as functional and evolutionary studies in the post-genomic era.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
35 citing papers in PubMed.
- Genome-wide association analysis identifies natural allelic variants associated with leaf rolling in rice (Oryza sativa L.).Annals of botany · 2025Article
- Genome-Wide Identification and Functional Characterization of Brown Spot Resistance Genes in Rice (Journal of agricultural and food chemistry · 2025Article
- Integrative transcriptogenomic analyses reveal the regulatory network underlying rice eating and cooking quality and identify a role for alpha-globulin in modulating starch and sucrose metabolism.Plant communications · 2025Article
- A combination of upstream alleles involved in rice heading hastens natural long-day responses.Genes & genomics · 2025Article
- Article
- Genomic landscape of theFrontiers in plant science · 2023Article
- Multi-omics analysis reveals the genetic basis of rice fragrance mediated by betaine aldehyde dehydrogenase 2.Journal of advanced research · 2022Article
- Characterization of Domestication Loci Associated with Awn Development in Rice.Rice (New York, N.Y.) · 2022Article
- Global Identification and Characterization of C2 Domain-Containing Proteins Associated with Abiotic Stress Response in Rice (International journal of molecular sciences · 2022Article
- Brassinosteroid biosynthesis geneFrontiers in plant science · 2022Article
- Functional Haplotypes and Evolutionary Insight into the Granule-Bound Starch Synthase II (Foods (Basel, Switzerland) · 2021Article
- Genome-Wide Association Study Reveals the Genetic Basis of Chilling Tolerance in Rice at the Reproductive Stage.Plants (Basel, Switzerland) · 2021Article
- Haplotype Analysis ofInternational journal of molecular sciences · 2021Article
- Genome-Wide Identification and Genetic Variations of the Starch Synthase Gene Family in Rice.Plants (Basel, Switzerland) · 2021Article
- Natural variation in rice ascorbate peroxidase gene APX9 is associated with a yield-enhancing QTL cluster.Journal of experimental botany · 2021Article
- OsGATA16, a GATA Transcription Factor, Confers Cold Tolerance by Repressing OsWRKY45-1 at the Seedling Stage in Rice.Rice (New York, N.Y.) · 2021Article
- Genomic resources in plant breeding for sustainable agriculture.Journal of plant physiology · 2021Review
- A Novel Embryo Phenotype Associated With Interspecific Hybrid Weakness in Rice Is Controlled by the MADS-Domain Transcription FactorFrontiers in plant science · 2021Article
- Haplotype Variations and Evolutionary Analysis of the Granule-Bound Starch Synthase I Gene in the Korean World Rice Collection.Frontiers in plant science · 2021Article
- Genomic interventions for sustainable agriculture.Plant biotechnology journal · 2020Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
18 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRice germplasm collections continue to grow in number and size around the world. Since maintaining and screening such massive resources remains challenging, it is important to establish practical methods to manage them. A core collection, by definition, refers to a subset of the entire population that preserves the majority of genetic diversity, enhancing the efficiency of germplasm utilization.
resultsHere, we report whole-genome resequencing of the 137 rice mini core collection or Korean rice core set (KRICE_CORE) that represents 25,604 rice germplasms deposited in the Korean genebank of the Rural Development Administration (RDA). We implemented the Illumina HiSeq 2000 and 2500 platform to produce short reads and then assembled those with 9.8 depths using Nipponbare as a reference. Comparisons of the sequences with the reference genome yielded more than 15 million (M) single nucleotide polymorphisms (SNPs) and 1.3 M INDELs. Phylogenetic and population analyses using 2,046,529 high-quality SNPs successfully assigned rice accessions to the relevant rice subgroups, suggesting that these SNPs capture evolutionary signatures that have accumulated in rice subpopulations. Furthermore, genome-wide association studies (GWAS) for four exemplary agronomic traits in the KRIC_CORE manifest the utility of KRICE_CORE; that is, identifying previously defined genes or novel genetic factors that potentially regulate important phenotypes.
conclusionThis study provides strong evidence that the size of KRICE_CORE is small but contains high genetic and functional diversity across the genome. Thus, our resequencing results will be useful for future breeding, as well as functional and evolutionary studies, in the post-genomic era.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.