I’m an Assistant Professor of Horticultural Crop Breeding for Nutrition in the Department of Horticulture at the University of Kentucky. My research group—The Sapkota Lab—is dedicated to blending the best of traditional plant breeding with the latest innovations in molecular biology, genomics, metabolomics, bioinformatics, machine learning, and AI. Our mission is to develop improved horticultural crop varieties that are not only high-yielding and disease-resistant but also packed with better flavor and enhanced nutritional value—helping to meet the evolving needs of Kentucky growers and consumers while contributing to food security on a global scale.

Before joining UK, I worked as a Genomics Postdoctoral Associate at Breeding Insight, Cornell University, where I collaborated with USDA breeders on a range of specialty crops. My work focused on developing marker panels, exploring genetic diversity, QTL mapping, genome-wide association studies, genomic selection, and bioinformatics-driven breeding strategies. I earned my Ph.D. in Plant Breeding, Genetics, and Genomics from the University of Georgia, where I was part of the van der Knaap lab, studying the genetic and molecular basis of fruit weight, shape, size, and flavor volatiles in tomatoes. Prior to that, I served as a research technician at CIMMYT-Nepal and completed my undergraduate degree in Agriculture (Plant Breeding) at the Institute of Agriculture and Animal Sciences, Tribhuvan University in Nepal.

With several years of experience in plant breeding, genetics, bioinformatics, statistics, and molecular breeding, I’m passionate about harnessing cutting-edge science to create crops that are better for farmers, consumers, and the planet.

Education

University of Georgia (UGA), Athens, GA, USA

Ph.D., Plant Breeding, Genetics and Genomics, Institute of Plant Breeding, Genetics and Genomics (IPBGG); 2023

Thesis title: Elucidating the genetic basis of flavor volatiles in tomato

Tribhuvan University (TU), Nepal

B.S., Agriculture, Institute of Agriculture and Animal Sciences, Rampur, Nepal Major in Plant Breeding, 2016

Thesis title: Agromorphological characterization of foxtail millet (Setaria italica L. Beauv) at Rampur, Chitwan

Awards

• The Roger and Cindy Boerma Plant Breeding Excellence Scholarship Award 2022.
• The John Ingle Innovation in Plant Breeding Award 2021.
• Awarded research grant for B.S. thesis research by Local Initiatives for Biodiversity, Research and Development (Li-BIRD), Nepal, 2016
• Full scholarship to study B.S. Agriculture in Rampur Campus, Institute of Agriculture and Animal Sciences by Tribhuvan University in competition basis, 2012-2016

Computational skills

• Linux shell script programming
• Bulk segregant and QTLseq analysis
• RNAseq, WGCNA, differential expression and GO term analysis
• Genetic map construction and QTL mapping of diploid and polyploid crop species
• Genome-wide Association Study (GWAS)
• Genotyping by Sequencing (GBS)
• Genetic diversity and haplotype analysis
• Big data and whole genome sequencing analysis
• Graphic designing: Adobe Illustrator and Photoshop
• Programming: R, bash, Python, Perl, Matlab
• Cloud computing: Globus, Cyverse
• Website designing and management
• Gas Chromatography chromatograms analysis
• Proficient in using Microsoft Office package (Word, Excel and PowerPoint)

Molecular Biology skills

• Marker assisted selection and assays
• Developing and using molecular markers (CAPS, dCAPS, KASP)
• PCR, RT-qPCR, KASP-PCR
• DNA and RNA extraction
• Gene editing and cloning
• CRIPSR/Cas9 gRNA designing
• Plasmid preparation, transformation, and cloning
• Tissue culture (tomato)
• Microscopy, imaging and image analysis

Research Experience

Assistant Professor, Horticulture Crop Breeding for Nutrition

Department of Horticulture, University of Kentucky, Lexington, KY; July 2025 to present

Genomics Postdoc

Breeding Insight, Cornell University, Ithaca, New York US; July 2023 to June 2025 Supervisor: Dr. Dongyan Zhao & Dr. Moira Sheehan

Graduate Research Assistant

Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, Georgia, US; August 2017 - June 2023; Supervisor: Dr. Esther van der Knaap

Research Technician

International Maize and Wheat Improvement Centre (CIMMYT), Nepal; November 2016-June 2017; Supervisor: Dr. Ajanahalli Ramaiah Sadananda

Research Intern

Wheat Breeding Unit, Agriculture and Botany Division, Nepal Agriculture Research Council, Nepal; April 2016 – November 2016; Supervisor: Dr. Dhruba Bahadur Thapa

You can find more information in my CV here.

Here are some other things about me:

My family

My postdoc lab

I was Genomics Postdoc at Breeding Insight at Cornell University working with an amazing team. I was supervised by Dr. Dongyan Zhao and Dr. Moira Sheehan. At Breeding Insight, we level the playing field for routine use of genomics insights, creating new opportunities for specialty breeders to adopt tools, technologies and methods from basic research. We integrated phenomics (trait analysis), genomics (genotypic data), data management, and software tools to help breeders increase rates of genetic gain, which results in more healthy, nutritious, and sustainable food for consumers.

My previous lab

Previously, I was a member of van der Knaap lab at the UGA. I am supervised by Dr. Esther van der Knaap. The lab works on exploring the genetics behind fruit and floral organ development. My research work focused on identifying and characterizing novel loci associated with tomato fruit size and flavor volatiles.

Science communication

I like to communicate my science whenever I get an opportunity. I believe science is nothing without communication. I have participated in several conferences, events and competitions and presented my work (both virtual and in person). You can go through some of my posters and my recorded research talks here in my science blog.

My Hobbies

While I don’t do science, I do these:

Photography

You will always find me with a camera in my hand while I am travelling. I like capturing memories. I like to take potrait images and since I am around plants most of the time you can see plenty of plant potraits in my collection. Here are some of my collections.

Aquascaping

I am a beginner aquascaper and love aquariums. I own fresh water aquariums and will soon set up a salt water tank. You can see some snapshots of my aquascaping hobbies here.

Travelling and exploring new places

I like travelling, hiking and visiting new places. I aim to visit all the states in the US. This was somethine I had from back home where I visited a lot of hilly areas in Nepal and travel almost the width of the country. Besides travelling, I like exploring new activities like kayaking, ice skaiting, river tubing and so on.

Foods (Eating and cooking)

When I am doing nothing, I like to try making new dishes following online recipes. I love cooking and making people try my dises (I cook good ;p). I also like eating outside and trying new cuisines. I am a level 6 google guide and love to explore new food places and give reviews and take pretty food pictures. You can check my google guide profile and see all my reviews and contributions.

Sports

I love playing soccer, cricket and other outdoor sports. In soccer, I follow Arsenal and I am a UGA football fan (Go Dawgs!!).