ArticleThe plant genome2020
Choosing the optimal population for a genome-wide association study: A simulation of whole-genome sequences from rice.
Article in The plant genome, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 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
12 citing papers in PubMed.
- Feasibility and pitfalls of combining small subpopulations for genome-wide association analysis of maize (Zea mays L.) kernel traits.The plant genome · 2026Article
- Assembly of Silphium interspecific hybrid genomes opens the genus to phylogenomics, ecogenomics, and molecular breeding.Nature communications · 2026Article
- Multi-population GWAS detects robust marker associations in a newly established six-rowed winter barley breeding program.Heredity · 2025Article
- Studies of genetic diversity and genome-wide association for vitamin C content in lettuce (Lactuca sativa L.) using high-throughput SNP arrays.The plant genome · 2024Article
- Genome-Wide Association Study as an Efficacious Approach to Discover Candidate Genes Associated with Body Linear Type Traits in Dairy Cattle.Animals : an open access journal from MDPI · 2024Review
- Genomic determinants, architecture, and constraints in drought-related traits in Corymbia calophylla.BMC genomics · 2024Article
- Advancements and Prospects of Genome-Wide Association Studies (GWAS) in Maize.International journal of molecular sciences · 2024Review
- Genome-wide association study of salt tolerance at the seed germination stage in lettuce.PloS one · 2024Article
- Upcycling rice yield trial data using a weather-driven crop growth model.Communications biology · 2023Article
- Preparation and Curation of Omics Data for Genome-Wide Association Studies.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Landraces of temperate japonica rice have superior alleles for improving culm strength associated with lodging resistance.Scientific reports · 2020Article
- Choosing the optimal population for a genome-wide association study: A simulation of whole-genome sequences from rice.The plant genome · 2020Article
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
A genome-wide association study (GWAS) needs to have a suitable population. The factors that affect a GWAS (e.g. population structure, sample size, and sequence analysis and field testing costs) need to be considered. Mixed populations containing subpopulations of different genetic backgrounds may be suitable populations. We conducted simulation experiments to see if a population with high genetic diversity, such as a diversity panel, should be added to a target population, especially when the target population harbors small genetic diversity. The target population was 112 accessions of Oryza sativa L. subsp. japonica, mainly developed in Japan. We combined the target population with three populations that had higher genetic diversity. These were 100 indica accessions, 100 japonica accessions, and 100 accessions with various genetic backgrounds. The results showed that the GWAS's power with a mixed population was generally higher than with a separate population. Also, the optimal GWAS populations varied depending on the fixation index (F
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.