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Abstract
Rhododendron canescens (Michaux) Sweet (Piedmont azalea) is a native azalea with potential in landscaping because of its adaptability, early flowering, and lace bug resistance. But use of R. canescens in urban settings is limited, however, because of its sparse branching and other architectural traits. The goal of this project was to determine whether genetic variation can be identified for the development of a more compact phenotype. Genotyping-by-sequencing was used to examine the genetic diversity and population structure of a R. canescens collection from across Georgia. Single nucleotide polymorphisms (SNPs) were identified. The SNP data supported the presence of three populations. Statistical results indicated that there was low genetic differentiation between the populations, but relatively high genetic diversity within populations. Next, the transcriptome of vegetative and reproductive tissues was sequenced to identify orthologs of genes known to control height and branching in multiple plant species. Long-read sequencing using PacBio Iso-Seq methods generated 24,244 full-length isoform sequences, of which 16,825 were annotated. We successfully identified orthologs of thirteen genes regulating plant architecture through regulatory factors and phytohormone biosynthesis and signaling. Sequence data for these genes enabled RNA probes to be designed to capture the coding sequences from 216 R. canescens genotypes including one dwarf genotype. Variation in these genes among individuals was identified using capture sequencing. The structural and functional effect of these variants in protein function were predicted. Of the 69 variants, 16 SNPs were predicted to lead to deleterious missense mutations. These genetic variations could potentially be used to breed R. canescens with shorter stature or increased branching. The data analyzed using Discriminant Analysis of Principle Component (DAPC) helped us group azalea genotypes based on the variants. We found that for genes MAX2, PHOR1 and FLC, the dwarf genotype was significantly different from the other genotypes. Our findings further support that the suspected dwarf genotype has unique mutations in the plant architecture related genes. In addition, transcriptome analysis identified 2,871 long non-coding RNA and 13,116 simple sequence repeats. The genetic resources developed in this study have applications in molecular breeding, comparative genomics, and evolutionary studies.Keywords: Genotyping-by-sequencing, Single nucleotide polymorphisms, isoform, transcriptome, gibberellins, dwarf genotype.