Comparative transcriptome analysis of Portlandia species provides clues to genetic variations in the genes involved in flower color and fragrance

Authors: GANDHAM, PRASAS - Louisiana State University Agcenter; Nageswara Rao, Madhugiri; Singh, Sukhwinder; BAISAKH, NIRANJAN - Louisiana State University Agcenter

Submitted to: Tropical Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/3/2025
Publication Date: 7/16/2025
Citation: Gandham, P., Nageswara Rao, M., Singh, S., Baisakh, N. 2025. Comparative transcriptome analysis of Portlandia species provides clues to genetic variations in the genes involved in flower color and fragrance. Tropical Plant Biology. https://doi.org/10.1007/s12042-025-09434-z.
DOI: https://doi.org/10.1007/s12042-025-09434-z

Interpretive Summary: Portlandia species, part of the Rubiaceae family, are prized for their fragrant flowers and ornamental use in landscaping. Native to Jamaica, these woody plants thrive in rich, calcicole environments. A transcriptome analysis of P. grandiflora, P. coccinea, and their hybrid revealed 4,896 differentially expressed genes, shedding light on genetic factors influencing floral traits. Key genes responsible for flower color, including BCH2, CHS, DFR, and others, showed significant differences in expression. Additionally, genes involved in producing volatile organic compounds that attract pollinators were also differentially expressed. Several transcription factors, such as bHLH, ERF, MYB, and WD40, exhibited varied expression patterns related to flower color and scent. Among 60,269 identified single nucleotide polymorphisms in 15,747 transcripts, nine were linked to flower color and three to fragrance. The study also identified 7,042 simple sequence repeats from 5,353 unigenes. This research provides important insights into the genetic basis of flower color and fragrance in Portlandia species, serving as a valuable resource for future genetic studies.

Technical Abstract: Portlandia species, members of the Rubiaceae family, are valued for their fragrant flowers and ornamental use in the landscape industry. Native to Jamaica, these woody plants thrive in rich, calcicole environments. A comparative transcriptome analysis of P. grandiflora, P. coccinea, and their hybrid identified 4,896 differentially expressed unigenes, shedding light on key genetic factors influencing floral traits. Notably, genes such as BCH2, CHS, DFR, F3H, F3GalTase, and LCY-ß, which are responsible for flower color, were significantly differentially expressed among the Portlandias. Genes associated with the biosynthesis of volatile organic compounds (VOCs) including amyrin synthase, geraniol synthase, terpene synthase, vinorine synthase, and viridiflorene synthase, which are crucial for flower scents that attract pollinators and support ecological interactions, were also differentially expressed. Several transcription factors such as bHLH, ERF, MYB, and WD40, known to regulate both flower color and scent, exhibited differential expression patterns among the Portlandias. Of the total 60,269 single nucleotide polymorphisms (SNPs) identified in 15,747 transcripts, nine SNPs were identified in four transcripts associated with flower color and three on one transcript related to flower fragrance. The analysis also identified 7,042 simple sequence repeats (SSRs) from 5,353 unigenes with dinucleotide being the most abundant (51.35%) followed by trinucleotide repeats 43.77%) and. AG/CT (1,792) being the most prevalent motif followed by AT/AT (1,212). The current investigation provided first-hand information on gene expression differences underlying flower color and fragrance in Portlandia species. The study also generated valuable sequence variant resources (SSRs and SNPs) for their utilization in future genetic studies.