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

• Published in: Euphytica Vol. 218; no. 6
• Main Authors: Yadav, Lav K., Wilde, H. Dayton
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01.06.2022; Springer; Springer Nature B.V
• Subjects: Amino acid sequence; Amino acids; Architecture; Biomedical and Life Sciences; Biosynthesis; Biotechnology; Breeding; Discriminant analysis; Exons; Flowering; Genes; Genomic libraries; Germplasm; Landscaping; Life Sciences; Missense mutation; Mutation; Nucleotide sequence; Nucleotides; Ornamental plants; Phenotypes; Physiological aspects; Plant Genetics and Genomics; Plant Pathology; Plant Physiology; Plant Sciences; Plant species; Protein structure; Proteins; Rhododendron canescens; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Transcriptomes; Urban areas; Urban environments; Exon sequencing; Architecture; Nonsynonymous SNPs; Transcriptome; Azalea
• ISSN: 0014-2336; 1573-5060
• DOI: 10.1007/s10681-022-03019-7

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.