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ARS Home » Southeast Area » Poplarville, Mississippi » Southern Horticultural Research Unit » Research » Research Project #440629

Research Project: New Molecular and Genetic Tools to Select Trees and Plants Better Adapted to Changing Environmental Conditions in the Southeastern United States

Location: Southern Horticultural Research Unit

Project Number: 6062-21000-011-003-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Aug 1, 2021
End Date: Aug 1, 2026

Objective 1. Develop genomics tools and resources (e.g., assembled genome, genetic markers, transcriptome, microbiome) of select ornamental species of high value and interest. Objective 2. Utilize genomics tools and resources to identify the genomic architecture of important phenotypic traits of interest (e.g., leaf color and architecture, disease resistance, phenology), to study how trees respond to local environmental variation (stress, dormancy, microbiome) and how trees adapt to new or changing environments (e.g., heat, drought, disease pressure). Objective 3. Establish a unique long-term common garden experiment to facilitate future research of genotype by environment interactions.

We will employ next generation sequencing technologies (e.g., Illumina massively parallel sequencing, PacBio SMRT sequencing) to construct chromosome-scale reference genome assemblies of Helianthus verticillatus and Cercis canadensis and a reference transcriptome for Weigela florida. We also will develop SSRs and/or SNPs for these species and others of interest for population genetics and genome-wide association studies. We will use both quantitative trait loci (QTL) linkage mapping and association or linkage disequilibrium (LD) mapping (genome-wide association study or GWAS) to unravel the molecular genetic basis underlying natural variation of phenotypic traits of interest. QTL and GWAS are complementary, and using these combined approaches increase the potential to identify causative alleles. We also will conduct phytobiome (host-environment-microbial communities) based research using meta-omics approaches. Host-soil-microbe interactions are particularly under-researched in tree species although they play an important role in host stress tolerance, nutrient acquisition, and pathogen defense. The impacts of this research could be significant with downstream applications being translated into new tools for agroecosystem management, as well as the development of customized varieties for different soil types and novel management strategies (e.g., soil inoculation to promote beneficial microbe colonization). This basic research will be translated into industry-relevant outcomes by developing new accessions or cultivars. For example, with preferred stem color and powdery mildew resistance in sunflowers, and desirable color and disease resistance in redbuds, as well as other traits of interest. Cooperator will clonally propagate dogwoods and supply the USDA ARS Southern Horticultural Research Station in Poplarville, MS, and re-propagate them at UT on genetically similar rootstock. We will seek 1-2 other locations for propagation across the southeast and mid-Atlantic as well. Over the next 5-10 years, these trees will act as a unique resource to study genotype by environment interactions. This could include phenotypic plasticity across southern climates, genetic and epigenetic mechanisms of environmental sensing in perennial trees, core and functional microbiomes, health decline in southern environments, genetic and environmental cues for phenology, and more. This long-term experimental approach could be extended to other ornamental species of interest.