Abbott, Albert G

Research information updated September 8, 2016

Research Overview

Dr. Abbott's lab, which is part of the Forest Health Research and Education Center (University of Kentucky, Department of Forestry), is focused on using molecular biology to increase our understanding of tree resistance and better prepare for a rapid response to future forest threats. Additional research focuses are on the fundamental mechanisms of resistance to biotic and abiotic stress in trees, especially invasive diseases and insects. We are interested in developing new genetic tools for improving trees and introducing resistant genotypes to tree breeding programs.

Genetic analysis of bloom date in Apricot

We are conducting a GWAS (genome wide association mapping) research using next generation sequencing data of more than 100 apricot germplasms. Peach 2nd version genome assembly will be used as reference for haplotype based association analysis. RNAseq data from peach genotypes with different bloom dates will also be used to identify candidate genes.

Personnal

Shenghua Fan, Postdoc
Tyler J Dreaden, Adjunct Faculty
Darryl W Cremeans, Staff
Jolanta Jaromczyk, Research scientist
Albert Abbott, Research scientist

Software:

Tassel, Freebayes

Genetic analysis of disease resistance genes in American chestnut

The goal of this project is to identify the disease resistance QTLs (loci) in chestnut genome. This knowledge will be used to develop disease resistant chestnut variety and new management technique to restore the chestnut production in US. We will be analyzing whole genome SNP and SSR marker data of a complex collection of genetic materials derived from several Chinese/American ancestors.

Personnel:

Shenghua Fan, Postdoc
Dana Nelson, Research scientist

Software:

R program, Tassel

Development of a rapid cycle breeding technique for tree species

Rapid cycle breeding refers to a new school of accelerated plant breeding programs that can trim the generation time of trees to a fraction of their normal pace. Our approach involves a mix of biotechnology (genetic engineering) and conventional breeding (repeated sexual reproduction and selection) to develop trees faster in a research setting. While this new approach involves cutting edge genetic techniques, the end result is the same as what would be produced by traditional breeding programs. No “GMO”, only faster.

Students:

Shenghua Fan, Research Associate
Anna Conrad, Research Associate
Albert Abbott, Research Scientist

Software:

This project will involve limited bioinformatics analysis and tools like NCBI blast, mutiple sequence alignment, etc.

All software listed above are publicly available.

Genome-wide association study of Oak

We are interested in assessing the impact of forest management strategies, including thinning regimes, on white oak (Quercus alba) genetic diversity and heritability in Kentucky forests. This project will also include building reference oak genomes and transcriptomes using reference-based and de novo assembly approaches for use in this and other studies.

Students

Anna Conrad, Postdoc
Rachel Landham, Grad

Software

Proposed software:
CLC Genomics Workbench, SNAP, FastGC CoGE SynMap, cutadapt, trimmer, Trinity, Bowtie2, Rsem, Edger, EbSeq, DESeq, and others.

HPC Language

Proposed computational methods:
Read Processing, genome assembly, read mapping, genome annotation, SNP detection, transcriptome assembly, differential expression analysis (currently and commercially available)

Collaborators

Association genetics study of apricot

We are interested in identifying makers and putative genes associated with apricot bloom time. To do this we are using an association genetics approach.

Students

Shenghua Fan, Postdoc

Software

TestAsso, EMMAX, Tassel, and others

All software listed above are publically available, except for CLC Genomics Workbench which are laboratory has a license.

Grants: 

Publications