ArticleBMC plant biology2025
Seed coat transcriptomic profiling of 5-593, a genotype important for genetic studies of seed coat color and patterning in common bean (Phaseolus vulgaris L.).
Article in BMC plant biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed.
- Genomic resources to advance seed coat color and patterning genetics and breeding in common bean (Phaseolus vulgaris L.).The plant genome · 2026Article
- Association of Qualitative Characters With Agronomic Traits, and Their Breeding Importance in Lentil (Plant-environment interactions (Hoboken, N.J.) · 2026Article
- Integrative genomic analyses reveal candidate genes for the Ur-3 and Ur-7 rust resistance loci in common bean.The plant genome · 2026Article
- A candidate gene marker at the red kidney color locus (Rk) enables the development of slow-darkening pink beans.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- GWAS identifies regulators of seed and leaf morphology in common bean, revealing OFP5 as a major seed size determinant.The Plant journal : for cell and molecular biology · 2026Article
- Fine mapping and identification of the geneFrontiers in plant science · 2025Article
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Abstract
Common bean (Phaseolus vulgaris L.) market classes have distinct seed coat colors, which are directly related to the diverse flavonoids found in the mature seed coat. To understand and elucidate the molecular mechanisms underlying the regulation of seed coat color, RNA-Seq data was collected from the black bean 5-593 and used for a differential gene expression and enrichment analysis from four different seed coat color development stages. 5-593 carries dominant alleles for 10 of the 11 major genes that control seed coat color and expression and has historically been used to develop introgression lines used for seed coat genetic analysis. Pairwise comparison among the four stages identified 6,294 differentially expressed genes (DEGs) varying from 508 to 5,780 DEGs depending on the compared stages. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that phenylpropanoid biosynthesis, flavonoid biosynthesis, and plant hormone signal transduction comprised the principal pathways expressed during bean seed coat pigment development. Transcriptome analysis suggested that most structural genes for flavonoid biosynthesis and some potential regulatory genes were significantly differentially expressed. Further studies detected 29 DEGs as important candidate genes governing the key enzymatic flavonoid biosynthetic pathways for common bean seed coat color development. Additionally, four gene models, Pv5-593.02G016100, 593.02G078700, Pv5-593.02G090900, and Pv5-593.06G121300, encode MYB-like transcription factor family protein were identified as strong candidate regulatory genes in anthocyanin biosynthesis which could regulate the expression levels of some important structural genes in flavonoid biosynthesis pathway. These findings provide a framework to draw new insights into the molecular networks underlying common bean seed coat pigment development.
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