Location: Southern Horticultural Research Unit
Project Number: 6062-21000-011-008-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Sep 1, 2024
End Date: Sep 30, 2025
Objective:
Develop genomic and genetic resources for molecular and conventional breeding of hydrangea, including determining conserved recurrent flowering loci in smooth hydrangea (Hydrangea arborescens) via whole-genome sequencing and identifying candidate genes for hydrangea powdery mildew (PM) resistance via comparative genomic and transcriptomic analyses of Dichroa febrifuga.
Approach:
The first goal of this agreement is to develop genomic and genetic resources for molecular and conventional breeding of hydrangea. Specific goals include determining conserved recurrent flowering loci in smooth hydrangea (Hydrangea arborescens) via whole-genome sequencing and identifying candidate genes for hydrangea powdery mildew (PM) resistance via comparative genomic and transcriptomic analyses of Dichroa febrifuga. For each species, reference genomes will be developed using previously sequenced genomic DNA libraries using PacBio circular consensus sequencing (CCS) and scaffolded with Hi-C sequencing reads. Each of the reference genomes will be annotated using transcripts generated from diverse plant tissue types. For comparative genomic analysis, all available hydrangea genomes (H. macrophylla, H. arborescens and H. quercifolia) will be aligned at genome scale to identify the genome evolution events responsible for speciation. The second goal of this agreement is to develop genomic and genetic resources for molecular and conventional breeding of hibiscus. Reference genome of tropical hibiscus (H. rosa-sinensis) will be developed using a de novo approach. High-molecular weight genomic DNA libraries will be sequenced on the PacBio circular consensus sequencing (CCS) platform and assembled to a draft genome. Hi-C sequencing will be used to develop the chromosome-level genome. Plant samples representing different tissues will be sequenced on the Illumina platform to capture tissue-specific transcripts. The Illumina reads will be used to annotate the assembled chromosome-level reference genome. Genomic landscape and gene analysis will be performed to understand the evolution and speciation of hibiscus. Putative genes associated with economically important traits such as flowering habit, flower color and disease resistance will be mined and compared to verify their function using a molecular biology approach. Genotyping by sequencing (GBS) will be performed to study the genetic relationship of current tropical hibiscus cultivars for molecular marker development and phylogenetic studies to assist future breeding efforts. The third objective is to identify candidate genes and genetic mechanism related to salt tolerance of induced polyploid Hibiscus hamabo using transcriptomic approach. Polyploid plants tend to be more tolerant to abiotic stresses than their mother plants. We have already induced polyploidy in H. hamabo. Experiment will be conducted to implement salt treatment to induced polyploid and control plants of H. hamabo. Leaf and root samples will be collected from the replicated individual plants at various time points after the salt treatment. High quality RNA will be extracted from the collected samples and sequenced on Illumina platform. Transcriptome assembly will be performed to generate full-length transcripts. Different databases (NCBI, Swiss-Prot and TrEMBL etc.) will be used for annotation purposes. Differentially expressed genes (DEGs) between the polyploid and control plants will be identified with edgeR packages. Gene ontology and KEGG pathway studies of the candidate genes will be performed.
