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Identification and bioinformatic characterization of rare variants of Rhododendron canescens architecture genes

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Abstract

Rhododendron canescens (Michaux) Sweet is a deciduous azalea from the southeastern United States that is used as an ornamental landscaping plant. We identified and characterized allelic variation in R. canescens architecture genes as the first step towards breeding a more compact phenotype for urban settings. The transcriptome of R. canescens vegetative and reproductive tissues was sequenced and analyzed using PacBio Iso-Seq methods. The analysis generated 24,244 full-length isoform sequences, of which 16,825 were annotated. Orthologs were identified of genes that have been shown to control height or branching across multiple plant species. These included genes for regulatory factors and components of phytohormone biosynthesis and signaling pathways. Exons of these genes were captured and sequenced from DNA libraries of 216 R. canescens plants, including a dwarf genotype. In this germplasm collection, 40 non-synonymous single-nucleotide polymorphisms (nsSNPs) were identified in R. canescens orthologs of GA INSENSITIVE (GAI), PHOTOPERIOD RESPONSIVE1 (PHOR1), GA-INSENSITIVE DWARF1 (GID1), BRASSINOSTEROID INSENSITIVE1 (BRI1), FLOWERING LOCUS C (FLC), MORE AXILLARY BRANCHING2 (MAX2), and BRANCHED1 (BRC1). The effect of amino acid changes on the primary and tertiary protein structure was examined in silico and several nsSNPs were found to be deleterious to protein function. Missense mutations were identified in RcMAX2 of the dwarf genotype. Discriminant Analysis of Principal Components found that RcMAX2 could be responsible for the difference between the dwarf and other R. canescens accessions. This investigation provides a pathway for breeding R. canescens with architectural traits better suited for urban environments.

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Data availability

All sequence data supporting this work are available in the NCBI SRA database under the project ID PRJNA685847.

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Acknowledgements

The authors thank the Georgia Genomics and Bioinformatics Core (Athens, Georgia, USA) for technical support, Dr. Ron Miller for providing the dwarf R. canescens, and the USDA (Specialty Crop Block Grant 16-SCBGP-GA-0010; Hatch project GEO00755) for financial support.

Funding

This work was supported by USDA Specialty Crop Block Grant 16-SCBGP-GA-0010 and Hatch project GEO00755.

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  1. Horticulture Department, University of Georgia, Athens, GA, USA

    Lav K. Yadav & H. Dayton Wilde

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  1. Lav K. Yadav
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LKY and HDW designed the experiment. LKY performed the experiment and analyzed the results. LKY and HDW wrote the manuscript and both authors read and approved the final version.

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Correspondence to H. Dayton Wilde.

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Yadav, L.K., Wilde, H.D. Identification and bioinformatic characterization of rare variants of Rhododendron canescens architecture genes. Euphytica 218, 66 (2022). https://doi.org/10.1007/s10681-022-03019-7

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