GWAS
Soybean GWAS for protein and oil
Open access · cc by · source: Europe PMC
Genome-wide SNPs in 298 soybean accessions associate with seed protein and oil content.
How this study connects
Role on claims
Each row is a claim on a concept or method page where this paper supports, challenges, or qualifies the statement. Roles are hand-checked — not a model guess.
Large dairy GWAS recover many additive SNP effects, some in genes and some elsewhere.
Large GWAS of Holstein dairy traits recovered thousands of genome-wide significant additive effects, with many top SNPs in genes and some SNPs associated with multiple traits (pleiotropy).
Scope note — different traits — soybean protein/oil, not cattle production health
Limits the claim's scope: a different population, assay, or outcome.
Crop and livestock GWAS in this set return many significant markers, LD that stretches for hundreds of kilobases, and networks rather than single genes. A soybean protein/oil scan used 31,954 QC SNPs covering about 86% of the genome, with euchromatic LD (r²) falling to 0.2 by about 360 kbp and protein ranging roughly 35–50% across accessions; a later 809-accession soybean scan tied GWAS loci into agronomic networks; a Holstein scan of ~46k SNPs across 31 PTA traits found thousands of genome-wide significant additive effects and pleiotropic SNPs.
Evidence for the claim as stated.
Phenotype quality differs. Holstein analyses use processed predicted transmitting abilities, not raw farm records; soybean protein/oil was measured in limited field environments; liver eQTLs are expression, not disease. Hits inherit those phenotype choices.
Evidence for the claim as stated.
Open questions
Tensions this paper is part of
From concept pages' “where studies disagree.” Disagreement means the same question; scope means different assays, populations, or outcomes.
Phenotype quality differs. Holstein analyses use processed predicted transmitting abilities, not raw farm records; soybean protein/oil was measured in limited field environments; liver eQTLs are expression, not disease. Hits inherit those phenotype choices.
- Supports · Holstein GWAS across 31 dairy traits
- Supports · Genetics of gene expression in human liver
History
When this study was placed
Dated entries from the concept change log — when this paper was added or removed as support, challenge, or qualifier on a claim.
Placed as a scope qualifier on GWAS
Large GWAS of Holstein dairy traits recovered thousands of genome-wide significant additive effects, with many top SNPs in genes and some SNPs associated with multiple traits (pleiotropy).
Study at a glance
- Design
- Computational / modelling — GWAS of soybean germplasm SNPs for seed protein and oil with LD/structure estimation
- N
- N=298 · 298 germplasm accessions; 31,954 QC SNPs
- Population
- Soybean germplasm accessions
- Outcome
- SNP associations with seed protein and oil content
Structured fields used in claim comparison tables when every cited study has a complete layer.
Inspect source passages
Soybean GWAS for protein and oil
These passages occur verbatim in the stored paper text. They support the points listed below; they do not verify every statement in the explanation.
31,954 SNPs used after QC.
A total of 31,954 SNPs distributed across the soybean genome with minor allele frequency >0.10 and missing data of less than 25% was used for the estimation of LD level in the 298 soybean germplasm accessions.
QC SNP count?
A total of 31,954 SNPs distributed across the soybean genome
Key findings
31,954 QC SNPs across ~86% of the genome; euchromatic LD (r²) fell to 0.2 by ~360 Kbp; protein content varied ~35–50% across accessions.
Methodology
Genotyped soybean germplasm with tens of thousands of SNPs, estimated LD and population structure, and ran GWAS for seed protein and oil.
Limitations
Does not prove causal genes without functional follow-up; field environments were limited.
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