At the Sapkota Lab, we are building a multidisciplinary program that combines plant breeding, genetics, genomics, bioinformatics, and metabolomics to improve horticultural crops. Our overarching goal is to develop better fruits and vegetables with enhanced flavor, nutrition, disease resistance, and stress resilience, while also advancing the science behind the traits that matter most.

We focus on both the improvement of crop varieties and the discovery of genetic mechanisms underlying key traits — from gene mapping and cloning to genome-enabled selection.

Our research areas include:

Vegetable Breeding & Genetics

We develop improved vegetable varieties — including tomatoes, peppers, and leafy greens — using a combination of classical breeding and modern genomics tools. This work is tightly integrated with genetic analyses aimed at mapping and dissecting traits related to yield, disease resistance, flavor, and nutrition.

Fruit Breeding & Genetics

We focus on breeding berries and tree fruits suited to Kentucky’s growing conditions, with superior flavor, nutrient content, and resistance to biotic and abiotic stresses. Our fruit genetics work includes linkage mapping, QTL analysis, and the identification of genes involved in fruit quality traits.

Horticultural Genetics & Genomics

We use next-generation sequencing, fine mapping, QTL-seq, GWAS, and gene cloning approaches to uncover the genetic architecture of important horticultural traits. We are especially interested in understanding the molecular and biochemical basis of flavor and nutrition, and how plants respond to environmental stressors.

Horticulture Bioinformatics

Our lab develops and applies bioinformatic pipelines for analyzing genomic, transcriptomic, and metabolomic data from diverse horticultural crops. These tools enable trait discovery, genomic selection, and integration of multi-omics data for next-gen crop improvement.

As the lab grows, individual project pages will be added under each category. In the meantime, feel free to Contact Us if you're curious about our work or interested in collaboration.