Dr. Honglian Ye

Young woman in bright yellow outfit, smiling, with sunglasses, against a green, outdoor background.

Position Title
Postdoctoral Scholar (2024 June - present)

Bio

Current position

Postdoctoral Researcher Associate
-University of California, Davis at the Department of Plant Science 2022-pres.
Visiting Postdoctoral Researcher
-United States of the Department Agriculture 2022-2025

Education
Postdoc Research, genomics, 2022-pres.
University of California, Davis (UCD)
United States of the Department Agriculture (USDA; 2022-2025)
Ph.D. Silviculture 2016-2021
Beijing Forestry University (BJFU)
M.S., Forest Genetics and Tree Breeding 2013-2016
Southwest Forestry University (SWFU)
B.S., Forestry 2007-2012
Jiangxi Agricultural University (JAU)

RESEARCH EXPERIENCE
Genome assembly of wild wheat relative Aegilops caudata
Led a research project on the wild wheat relative Aegilops caudata to develop genomic resources and facilitate the discovery and utilization of resistance genes for wheat improvement.
● Collected plant materials and prepared high-molecular-weight DNA for long-read sequencing and optical mapping.
● Coordinated PacBio HiFi sequencing, Bionano optical mapping, and RNA-seq data generation for genome assembly.
● Led the development of genomic resources for Aegilops caudata using integrated sequencing and optical mapping approaches.

● Conducted comparative genomic analyses between Aegilops caudata and wheatgenomes to investigate chromosomal rearrangements and genome evolution.
● Performed population genomic analyses of multiple A. caudata accessions tocharacterize genetic diversity and structural variation.
● Performed virus-induced gene silencing (VIGS) experiments to functionally validatecandidate resistance genes.
● Led interpretation of results and manuscript preparation

Identification of resistance loci for insect pests and fungal diseases in synthetic hexaploid wheat
Investigated genetic resistance to major insect pests and fungal diseases in synthetic wheat populations to identify genomic loci useful for wheat breeding.
● Evaluated resistance of synthetic hexaploid wheat populations against greenbug, Hessian fly, tan spot, and Stagonospora nodorum blotch (SNB).
● Integrated phenotypic resistance data from multiple experiments and environments with genotyping-by-sequencing (GBS) markers for genetic analysis.
● Conducted genome-wide association studies (GWAS) to identify genomic regions associated with resistance traits.
● Identified candidate genomic regions contributing to insect and disease resistance in wheat.

Wide hybridization and genetic population development
Utilized wild relatives of wheat to introduce novel genetic variation for gene discovery and wheat improvement.
● Utilized wild relatives of wheat to introduce novel genetic variation and develop populations for gene discovery.
● Performed wide hybridization between Aegilops caudata and durum wheat to introgress resistance-related chromosomal segments into wheat backgrounds.
● Generated and evaluated introgression lines carrying alien chromosomal fragments.
● Analyzed chromosomal rearrangements and alien introgressions using molecular and genomic approaches.
● Conducted intraspecific hybridization within Aegilops caudata to generate mapping populations.
● Developed linkage mapping populations for identifying genes controlling agronomic and resistance traits.

Water management for oil of woody plants
Studied the effects of mulching strategies on yield and oil quality of Camellia oleifera under seasonal drought conditions.
● Conducted field experiments with various mulching treatments including ecological pads, straw, gravel, sawdust, and camellia shells.
● Evaluated the effects of organic mulches on fruit yield, oil quality, and plant growth.
● Performed plant and soil sample collection, preparation, and analysis

Plant metabolomics and soil microorganisms (16S rRNA)
Characterized metabolic and microbial responses of Camellia oleifera to mulching treatments.
● Applied LC-MS and GC-MS metabolomics to analyze metabolic changes in oilproducing fruits.
● Investigated soil microbial community structure using 16S rRNA sequencing.
● Identified metabolic biomarkers associated with mulching treatments.
● Conducted batch identification of unknown metabolites using CANOPUS.
● Assisted the West Coast Metabolomics Center in metadata collection and data processing for the Longevity Project.
● Contributed to development of an accurate mass spectral and retention index library using quadrupole time-of-flight GC/MS in collaboration with Agilent.

Selection of plus tree
Evaluated germplasm resources of Camellia saluenensis and Sapindus mukorossi.
● Evaluated multiple morphological and productivity traits to identify superior individuals.
● Applied multi-index evaluation methods for germplasm selection. 

Cuttings propagation and tissue culture  Conducted propagation experiments for woody plant species.
● Performed cutting and tissue culture experiments for Camellia oleifera, Euscaphis konishii, and Ternstroemia gymnanthera.
● Evaluated the effects of different auxin concentrations on rooting efficiency and survival rate.