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.)

Roy, Jayanta; Sreedasyam, Avinash; Osborne, Caroline; Lee, Rian; McClean, Phillip E.

doi:10.1186/s12870-025-06282-7

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.)

Journal Article · Wed Mar 05 00:00:00 EST 2025 · BMC Plant Biology

DOI:https://doi.org/10.1186/s12870-025-06282-7· OSTI ID:2564860

^[1]; Sreedasyam, Avinash ^[2]; Osborne, Caroline ^[1]; Lee, Rian ^[1]; McClean, Phillip E. ^[1]

North Dakota State University, Fargo, ND (United States)
HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDA; USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science (BSS)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2564860

Journal Information:: BMC Plant Biology, Journal Name: BMC Plant Biology Journal Issue: 1 Vol. 25; ISSN 1471-2229

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

References (47)

Genetics of Seed Coat Color and Pattern in Common Bean Bassett, Mark J. Plant Breeding Reviews https://doi.org/10.1002/9780470168028.ch8	book	January 2007
Ultrafast one‐pass FASTQ data preprocessing, quality control, and deduplication using fastp Chen, Shifu iMeta, Vol. 2, Issue 2 https://doi.org/10.1002/imt2.107	journal	May 2023
Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method Livak, Kenneth J.; Schmittgen, Thomas D. Methods, Vol. 25, Issue 4 https://doi.org/10.1006/meth.2001.1262	journal	December 2001
Flavonoid diversity and biosynthesis in seed of Arabidopsis thaliana Routaboul, Jean-Marc; Kerhoas, Lucien; Debeaujon, Isabelle Planta, Vol. 224, Issue 1 https://doi.org/10.1007/s00425-005-0197-5	journal	January 2006
Antimutagenic effects of natural phenolic compounds in beans de Mejı́a, Elvira González; Castaño-Tostado, Eduardo; Loarca-Piña, Guadalupe Mutation Research/Genetic Toxicology and Environmental Mutagenesis, Vol. 441, Issue 1 https://doi.org/10.1016/S1383-5718(99)00040-6	journal	April 1999
The polyphenolic profiles of common bean (Phaseolus vulgaris L.) Lin, Long-Ze; Harnly, James M.; Pastor-Corrales, Marcial S. Food Chemistry, Vol. 107, Issue 1 https://doi.org/10.1016/j.foodchem.2007.08.038	journal	March 2008
Characterization of extractable phenolic profile of common bean seeds (Phaseolus vulgaris L.) in a Spanish diversity panel Rodríguez Madrera, Roberto; Campa Negrillo, Ana; Suárez Valles, Belén Food Research International, Vol. 138 https://doi.org/10.1016/j.foodres.2020.109713	journal	December 2020
Molecular components associated with the regulation of flavonoid biosynthesis Naik, Jogindra; Misra, Prashant; Trivedi, Prabodh Kumar Plant Science, Vol. 317 https://doi.org/10.1016/j.plantsci.2022.111196	journal	April 2022
Transcriptomic profiling reveals pigment regulation during peanut testa development Wan, Liyun; Li, Bei; Lei, Yong Plant Physiology and Biochemistry, Vol. 125 https://doi.org/10.1016/j.plaphy.2018.01.029	journal	April 2018
Metabolomics and transcriptomics provide insights into the molecular mechanisms of anthocyanin accumulation in the seed coat of differently colored mung bean (Vigna radiata L.) Ma, Chao; Feng, Yalan; Zhou, Shuang Plant Physiology and Biochemistry, Vol. 200 https://doi.org/10.1016/j.plaphy.2023.107739	journal	July 2023
Hormonal regulation of anthocyanin biosynthesis for improved stress tolerance in plants Li, Zhe; Ahammed, Golam Jalal Plant Physiology and Biochemistry, Vol. 201 https://doi.org/10.1016/j.plaphy.2023.107835	journal	August 2023
Flavonoids: a colorful model for the regulation and evolution of biochemical pathways Koes, Ronald; Verweij, Walter; Quattrocchio, Francesca Trends in Plant Science, Vol. 10, Issue 5 https://doi.org/10.1016/j.tplants.2005.03.002	journal	May 2005
Transcriptional control of flavonoid biosynthesis by MYB–bHLH–WDR complexes Xu, Wenjia; Dubos, Christian; Lepiniec, Loïc Trends in Plant Science, Vol. 20, Issue 3 https://doi.org/10.1016/j.tplants.2014.12.001	journal	March 2015
clusterProfiler 4.0: A universal enrichment tool for interpreting omics data Wu, Tianzhi; Hu, Erqiang; Xu, Shuangbin The Innovation, Vol. 2, Issue 3 https://doi.org/10.1016/j.xinn.2021.100141	journal	August 2021
Antioxidant Activity in Common Beans (Phaseolus vulgaris L.) Cardador-Martínez, Anaberta; Loarca-Piña, Guadalupe; Oomah, B. Dave Journal of Agricultural and Food Chemistry, Vol. 50, Issue 24 https://doi.org/10.1021/jf020296n	journal	October 2002
Antioxidant Activity of Extracts, Condensed Tannin Fractions, and Pure Flavonoids from Phaseolus vulgaris L. Seed Coat Color Genotypes Beninger, Clifford W.; Hosfield, George L. Journal of Agricultural and Food Chemistry, Vol. 51, Issue 27 https://doi.org/10.1021/jf0304324	journal	December 2003
Polyphenols in Wild and Weedy Mexican Common Beans (Phaseolus vulgarisL.) Espinosa-Alonso, L. Gabriela; Lygin, Anatoly; Widholm, Jack M. Journal of Agricultural and Food Chemistry, Vol. 54, Issue 12 https://doi.org/10.1021/jf060185e	journal	May 2006
Flavonol Glycosides from the Seed Coat of a New Manteca-Type Dry Bean (Phaseolus vulgaris L.) Beninger, Clifford W.; Hosfield, George L.; Nair, Muraleedharan G. Journal of Agricultural and Food Chemistry, Vol. 46, Issue 8 https://doi.org/10.1021/jf9801522	journal	July 1998
STAR: ultrafast universal RNA-seq aligner Dobin, Alexander; Davis, Carrie A.; Schlesinger, Felix Bioinformatics, Vol. 29, Issue 1 https://doi.org/10.1093/bioinformatics/bts635	journal	October 2012
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features Liao, Y.; Smyth, G. K.; Shi, W. Bioinformatics, Vol. 30, Issue 7 https://doi.org/10.1093/bioinformatics/btt656	journal	November 2013
T and Z, partial seed coat patterning genes in common bean, provide insight into the structure and protein interactions of a plant MBW complex McClean, Phillip E.; Roy, Jayanta; Colbert, Christopher L. G3: Genes, Genomes, Genetics, Vol. 14, Issue 10 https://doi.org/10.1093/g3journal/jkae184	journal	August 2024
Molecular and Phenotypic Mapping of Genes Controlling Seed Coat Pattern and Color in Common Bean (Phaseolus vulgaris L.) McClean, P. E. Journal of Heredity, Vol. 93, Issue 2 https://doi.org/10.1093/jhered/93.2.148	journal	March 2002
limma powers differential expression analyses for RNA-sequencing and microarray studies Ritchie, Matthew E.; Phipson, Belinda; Wu, Di Nucleic Acids Research, Vol. 43, Issue 7 https://doi.org/10.1093/nar/gkv007	journal	January 2015
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses Huerta-Cepas, Jaime; Szklarczyk, Damian; Heller, Davide Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1085	journal	November 2018
Tight Linkage of Purple Pod Character and the Complex C Locus in Common Bean Bassett, M. J. Journal of Heredity, Vol. 85, Issue 4 https://doi.org/10.1093/oxfordjournals.jhered.a111458	journal	July 1994
Advances in the MYB–bHLH–WD Repeat (MBW) Pigment Regulatory Model: Addition of a WRKY Factor and Co-option of an Anthocyanin MYB for Betalain Regulation Lloyd, Alan; Brockman, Austen; Aguirre, Lyndsey Plant and Cell Physiology, Vol. 58, Issue 9 https://doi.org/10.1093/pcp/pcx075	journal	May 2017
Isolation and Characterization of Mutants Defective in Seed Coat Mucilage Secretory Cell Development in Arabidopsis Western, Tamara L.; Burn, Joanne; Tan, Wei Ling Plant Physiology, Vol. 127, Issue 3 https://doi.org/10.1104/pp.010410	journal	November 2001
Ethylene Suppression of Sugar-Induced Anthocyanin Pigmentation in Arabidopsis Jeong, Seok-Won; Das, Prasanta Kumar; Jeoung, Sae Chae Plant Physiology, Vol. 154, Issue 3 https://doi.org/10.1104/pp.110.161869	journal	September 2010
Flavonoid Biosynthesis. A Colorful Model for Genetics, Biochemistry, Cell Biology, and Biotechnology Winkel-Shirley, Brenda Plant Physiology, Vol. 126, Issue 2 https://doi.org/10.1104/pp.126.2.485	journal	June 2001
Differential regulation of closely related R2R3-MYB transcription factors controls flavonol accumulation in different parts of the Arabidopsis thaliana seedling: TFs of A. thaliana R2R3-MYB subgroup 7 Stracke, Ralf; Ishihara, Hirofumi; Huep, Gunnar The Plant Journal, Vol. 50, Issue 4 https://doi.org/10.1111/j.1365-313X.2007.03078.x	journal	April 2007
MYBL2 is a new regulator of flavonoid biosynthesis in Arabidopsis thaliana Dubos, Christian; Le Gourrierec, José; Baudry, Antoine The Plant Journal, Vol. 55, Issue 6 https://doi.org/10.1111/j.1365-313X.2008.03564.x	journal	September 2008
TRANSPARENT TESTA1 interacts with R2R3‐MYB factors and affects early and late steps of flavonoid biosynthesis in the endothelium of Arabidopsis thaliana seeds Appelhagen, Ingo; Lu, Gui‐Hua; Huep, Gunnar The Plant Journal, Vol. 67, Issue 3 https://doi.org/10.1111/j.1365-313X.2011.04603.x	journal	May 2011
Zur Genetik von Phaseolus Vulgaris Lamprecht, Herbert Hereditas, Vol. 17, Issue 1 https://doi.org/10.1111/j.1601-5223.1932.tb02577.x	journal	July 2010
White seed color in common bean ( Phaseolus vulgaris ) results from convergent evolution in the P ( pigment ) gene McClean, Phillip E.; Bett, Kirstin E.; Stonehouse, Robert New Phytologist, Vol. 219, Issue 3 https://doi.org/10.1111/nph.15259	journal	June 2018
MYBD employed by HY5 increases anthocyanin accumulation via repression of MYBL2 in Arabidopsis Nguyen, Nguyen Hoai; Jeong, Chan Young; Kang, Geun‐Ho The Plant Journal, Vol. 84, Issue 6 https://doi.org/10.1111/tpj.13077	journal	December 2015
Seed color patterns in domesticated common bean are regulated by MYB‐bHLH‐WD40 transcription factors and temperature Parker, Travis; Bolt, Tayah; Williams, Troy The Plant Journal, Vol. 119, Issue 6 https://doi.org/10.1111/tpj.16947	journal	August 2024
Genetics and Biochemistry of seed Flavonoids Lepiniec, Loïc; Debeaujon, Isabelle; Routaboul, Jean-Marc Annual Review of Plant Biology, Vol. 57, Issue 1 https://doi.org/10.1146/annurev.arplant.57.032905.105252	journal	June 2006
Transcriptome analysis reveals biosynthesis and regulation of flavonoid in common bean seeds during grain filling Tapia, Gerardo; Gonzalez, Máximo; Méndez, José BMC Plant Biology, Vol. 24, Issue 1 https://doi.org/10.1186/s12870-024-05593-5	journal	October 2024
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Love, Michael I.; Huber, Wolfgang; Anders, Simon Genome Biology, Vol. 15, Issue 12 https://doi.org/10.1186/s13059-014-0550-8	journal	December 2014
The Phenylpropanoid Pathway in Arabidopsis Fraser, Christopher M.; Chapple, Clint The Arabidopsis Book, Vol. 9 https://doi.org/10.1199/tab.0152	journal	January 2011
Flavonoid Composition of Three Genotypes of Dry Bean (Phaseolus vulgaris) Differing in Seedcoat Color Beninger, Clifford W.; Hosfield, George L.; Bassett, Mark J. Journal of the American Society for Horticultural Science, Vol. 124, Issue 5 https://doi.org/10.21273/JASHS.124.5.514	journal	September 1999
Chemical and Morphological Expression of the B and Asp Seedcoat Genes in Phaseolus vulgaris Beninger, Clifford W.; Hosfield, George L.; Bassett, Mark J. Journal of the American Society for Horticultural Science, Vol. 125, Issue 1 https://doi.org/10.21273/JASHS.125.1.52	journal	January 2000
Classical and Molecular Genetic Studies of the Strong Greenish Yellow Seedcoat Color in `Wagenaar' and `Enola' Common Bean Bassett, Mark J.; Lee, Rian; Otto, Carla Journal of the American Society for Horticultural Science, Vol. 127, Issue 1 https://doi.org/10.21273/JASHS.127.1.50	journal	January 2002
A legume biofortification quandary: variability and genetic control of seed coat micronutrient accumulation in common beans Blair, Matthew W.; Izquierdo, Paulo; Astudillo, Carolina Frontiers in Plant Science, Vol. 4 https://doi.org/10.3389/fpls.2013.00275	journal	January 2013
The Common Bean V Gene Encodes Flavonoid 3′5′ Hydroxylase: A Major Mutational Target for Flavonoid Diversity in Angiosperms McClean, Phillip E.; Lee, Rian; Howe, Kevin Frontiers in Plant Science, Vol. 13 https://doi.org/10.3389/fpls.2022.869582	journal	March 2022
Flaski Iqbal, Ayesha; Duitama, Camila; Metge, Franziska https://doi.org/10.5281/zenodo.4849515	software	November 2022
Comparative transcriptome and flavonoids components analysis reveal the structural genes responsible for the yellow seed coat color of Brassica rapa L. Ren, Yanjing; Zhang, Ning; Li, Ru PeerJ, Vol. 9 https://doi.org/10.7717/peerj.10770	journal	March 2021

Similar Records

Investigation and Expression Analysis of R2R3-MYBs and Anthocyanin Biosynthesis-Related Genes during Seed Color Development of Common Bean (Phaseolus vulgaris)

Journal Article · Sun Dec 04 19:00:00 EST 2022 · Plants · OSTI ID:2471081

Enhancing microRNA 167A expression in seed decreases the α-linolenic acid content and increases seed size in Camelina sativa

Journal Article · Wed Jan 02 19:00:00 EST 2019 · The Plant Journal · OSTI ID:1616082

Related Subjects

60 APPLIED LIFE SCIENCES
Flavonoid biosynthesis
Flavonoids
Phaseolus vulgaris
RNA-Seq
Seed coat color

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.)

Citation Formats

References (47)

Similar Records

Related Subjects