Abstract
Abstract Seed color is a complex phenotype linked to both the impact of grains on human health and consumer acceptance of new crop varieties. Today, seed color is often quantified via qualitative human assessment or biochemical assays for specific colored metabolites. Imaging‐based approaches have the potential to be more quantitative than human scoring while being lower cost than biochemical assays. We assessed the feasibility of employing image analysis tools trained on rice ( Oryza sativa ) or wheat ( Triticum aestivum ) seeds to quantify seed color in sorghum ( Sorghum bicolor ) using a dataset of 1,500 images. Quantitative measurements of seed color from images were substantially more consistent across biological replicates than human assessment. Genome‐wide association studies conducted using color phenotypes for 682 sorghum genotypes identified more signals near known seed color genes in sorghum with stronger support than manually scored seed color for the same experiment. Previously unreported genomic intervals linked to variation in seed color in our study co‐localized with a gene encoding an enzyme in the biosynthetic pathway leading to anthocyanins, tannins, and phlobaphenes—colored metabolites in sorghum seeds—and with the sorghum ortholog of a transcription factor shown to regulate several enzymes in the same pathway in rice. The cross‐species transferability of image analysis tools, without the retraining, may aid efforts to develop higher value and health‐promoting crop varieties in sorghum and other specialty and orphan grain crops.
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Claims 5
Claim · model-written summary
Image-based seed color measurements were more consistent across biological replicates than human assessment.
SorghumOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“seed color variation in sorghum”
e1“Quantitative measurements of seed color from images were substantially more consistent across biological replicates than human assessment”
Claim · model-written summary
Image-based GWAS identified more signals near known seed color genes than manually scored seed color, with stronger support.
- Outcome
- signals near known seed color genese2
- Qualifier
- with stronger supporte2
- Comparator
- manually scored seed colore2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“seed color variation in sorghum”
e2“identified more signals near known seed color genes in sorghum with stronger support than manually scored seed color for the same experiment”
Claim · model-written summary
Previously unreported genomic intervals linked to seed color co-localized with a gene encoding an enzyme in the anthocyanin, tannin and phlobaphene biosynthesis pathway.
- Gene
- a gene encoding an enzymee4
- Compound
- anthocyanins, tannins, and phlobaphenese4
- Outcome
- genomic intervals linked to variation in seed colore3
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“seed color variation in sorghum”
e3“Previously unreported genomic intervals linked to variation in seed color in our study”
e4“with a gene encoding an enzyme in the biosynthetic pathway leading to anthocyanins, tannins, and phlobaphenes”
Claim · model-written summary
Previously unreported genomic intervals linked to seed color co-localized with the sorghum ortholog of a transcription factor that regulates pathway enzymes in rice.
- Gene
- sorghum ortholog of a transcription factore5
- Outcome
- genomic intervals linked to variation in seed colore3
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“seed color variation in sorghum”
e3“Previously unreported genomic intervals linked to variation in seed color in our study”
e5“with the sorghum ortholog of a transcription factor shown to regulate several enzymes in the same pathway in rice”
Claim · model-written summary
Image analysis tools trained on rice or wheat seeds, used without retraining, may aid efforts to develop higher value sorghum varieties.
- Outcome
- efforts to develop higher valuee6
- Comparator
- trained on rice ( Oryza sativa ) or wheat ( Triticum aestivum ) seedse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“seed color variation in sorghum”
e0“image analysis tools trained on rice ( Oryza sativa ) or wheat ( Triticum aestivum ) seeds”
e6“image analysis tools, without the retraining, may aid efforts to develop higher value”