ArticlePloS one2012
Genome-wide haplotype changes produced by artificial selection during modern rice breeding in Japan.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 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
34 citing papers in PubMed.
- GWAS and Candidate Gene Prediction of Elemental Accumulation Traits in Rice Using a Multiparental Population.Rice (New York, N.Y.) · 2026Article
- Introgression among subgroups is an important driving force for genetic improvement and evolution of the Asian cultivated riceFrontiers in plant science · 2025Review
- Development of SNP genotyping assays for heading date in rice.Breeding science · 2024Article
- Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud.G3 (Bethesda, Md.) · 2023Article
- Identification of Novel Quantitative Trait Loci for Culm Thickness of Rice Derived from Strong-Culm Landrace in Japan, Omachi.Rice (New York, N.Y.) · 2023Article
- Article
- SSR marker-based genetic diversity analysis and SNP haplotyping of genes associating abiotic and biotic stress tolerance, rice growth and development and yield across 93 rice landraces.Molecular biology reports · 2021Article
- Translation of continuous artificial selection on phenotype into genotype during rice breeding programs.Breeding science · 2021Article
- Genome-Wide Association Study Reveals Novel Marker-Trait Associations (MTAs) Governing the Localization of Fe and Zn in the Rice Grain.Frontiers in genetics · 2020Article
- Marker-assisted selection in rice breeding programs in Hokkaido.Breeding science · 2019Review
- Haplotype-based genotyping-by-sequencing in oat genome research.Plant biotechnology journal · 2018Article
- Haplotype-based allele mining in the Japan-MAGIC rice population.Scientific reports · 2018Article
- High Levels of Variation Within Gene Sequences ofFrontiers in plant science · 2018Article
- A follow-up study for biomass yield QTLs in rice.PloS one · 2018Article
- Genetic dissection of agronomically important traits in closely related temperateBreeding science · 2017Review
- Article
- Barcode System for Genetic Identification of Soybean [Frontiers in plant science · 2017Article
- Genetic characterization and population structure of Indian rice cultivars and wild genotypes using core set markers.3 Biotech · 2016Article
- Open access resources for genome-wide association mapping in rice.Nature communications · 2016Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
During the last 90 years, the breeding of rice has delivered cultivars with improved agronomic and economic characteristics. Crossing of different lines and successive artificial selection of progeny based on their phenotypes have changed the chromosomal constitution of the ancestors of modern rice; however, the nature of these changes is unclear. The recent accumulation of data for genome-wide single-nucleotide polymorphisms (SNPs) in rice has allowed us to investigate the change in haplotype structure and composition. To assess the impact of these changes during modern breeding, we studied 177 Japanese rice accessions, which were categorized into three groups: landraces, improved cultivars developed from 1931 to 1974 (the early breeding phase), and improved cultivars developed from 1975 to 2005 (the late breeding phase). Phylogenetic tree and structure analysis indicated genetic differentiation between non-irrigated (upland) and irrigated (lowland) rice groups as well as genetic structuring within the irrigated rice group that corresponded to the existence of three subgroups. Pedigree analysis revealed that a limited number of landraces and cultivars was used for breeding at the beginning of the period of systematic breeding and that 11 landraces accounted for 70% of the ancestors of the modern improved cultivars. The values for linkage disequilibrium estimated from SNP alleles and the haplotype diversity determined from consecutive alleles in five-SNP windows indicated that haplotype blocks became less diverse over time as a result of the breeding process. A decrease in haplotype diversity, caused by a reduced number of polymorphisms in the haplotype blocks, was observed in several chromosomal regions. However, our results also indicate that new haplotype polymorphisms have been generated across the genome during the breeding process. These findings will facilitate our understanding of the association between particular haplotypes and desirable phenotypes in modern Japanese rice cultivars.
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.