ArticleG3 (Bethesda, Md.)2013
Dissecting genome-wide association signals for loss-of-function phenotypes in sorghum flavonoid pigmentation traits.
Article in G3 (Bethesda, Md.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers, 1 of them a synthesis that pooled it.
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Who cites it
35 citing papers in PubMed, 1 synthesis or guideline pooled it, 87 citations in OpenAlex.
- Meta-analysis identifies pleiotropic loci controlling phenotypic trade-offs in sorghum.Genetics · 2021Pooled it
- The SbTDR gene is required for anther development and male fertility in Sorghum bicolor.Plant reproduction · 2026Article
- The Germination Paradox in Sorghum: A Review.Foods (Basel, Switzerland) · 2026Review
- Genetic dissection of sorghum [Frontiers in plant science · 2026Article
- Loss of Pleiotropic Regulatory Functions inPlant direct · 2025Article
- Genomic resources, opportunities, and prospects for accelerated improvement of millets.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Review
- Major impacts of widespread structural variation on sorghum.Genome research · 2024Article
- Novel allelic variations inMolecular breeding : new strategies in plant improvement · 2024Article
- Article
- Deleterious mutations predicted in the sorghum (Sorghum bicolor) Maturity (Ma) and Dwarf (Dw) genes from whole-genome resequencing.Scientific reports · 2023Article
- Recent advancements in the breeding of sorghum crop: current status and future strategies for marker-assisted breeding.Frontiers in genetics · 2023Review
- Sorghum genetic, genomic, and breeding resources.Planta · 2021Review
- SorGSD: updating and expanding the sorghum genome science database with new contents and tools.Biotechnology for biofuels · 2021Article
- Genetic characterization of a Sorghum bicolor multiparent mapping population emphasizing carbon-partitioning dynamics.G3 (Bethesda, Md.) · 2021Article
- Genome-wide association analysis reveals seed protein loci as determinants of variations in grain mold resistance in sorghum.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Genome-wide variations analysis of sorghum cultivar Hongyingzi for brewing Moutai liquor.Hereditas · 2020Article
- Genomics-assisted breeding in minor and pseudo-cereals.Breeding science · 2020Article
- Genetic Architecture of Chilling Tolerance in Sorghum Dissected with a Nested Association Mapping Population.G3 (Bethesda, Md.) · 2019Article
- Genome-Wide Association Mapping of Anthracnose (G3 (Bethesda, Md.) · 2019Article
- Genome-Wide Association Mapping of Grain Mold Resistance in the US Sorghum Association Panel.The plant genome · 2019Article
Corrections and comments
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Authors and funding
12 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome-wide association studies are a powerful method to dissect the genetic basis of traits, although in practice the effects of complex genetic architecture and population structure remain poorly understood. To compare mapping strategies we dissected the genetic control of flavonoid pigmentation traits in the cereal grass sorghum by using high-resolution genotyping-by-sequencing single-nucleotide polymorphism markers. Studying the grain tannin trait, we find that general linear models (GLMs) are not able to precisely map tan1-a, a known loss-of-function allele of the Tannin1 gene, with either a small panel (n = 142) or large association panel (n = 336), and that indirect associations limit the mapping of the Tannin1 locus to Mb-resolution. A GLM that accounts for population structure (Q) or standard mixed linear model that accounts for kinship (K) can identify tan1-a, whereas a compressed mixed linear model performs worse than the naive GLM. Interestingly, a simple loss-of-function genome scan, for genotype-phenotype covariation only in the putative loss-of-function allele, is able to precisely identify the Tannin1 gene without considering relatedness. We also find that the tan1-a allele can be mapped with gene resolution in a biparental recombinant inbred line family (n = 263) using genotyping-by-sequencing markers but lower precision in the mapping of vegetative pigmentation traits suggest that consistent gene-level resolution will likely require larger families or multiple recombinant inbred lines. These findings highlight that complex association signals can emerge from even the simplest traits given epistasis and structured alleles, but that gene-resolution mapping of these traits is possible with high marker density and appropriate models.
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