I am Manoj Sapkota, a Genomics Postdoctoral Associate at Breeding Insight at Cornell University. My passion lies in plant breeding, genetics, genomics, and bioinformatics. I consider myself a practical, solution-oriented plant scientist with a broad range of research experiences. With over six years of expertise in bioinformatics, statistics, plant breeding, traditional gene cloning, QTL mapping, molecular cloning, and gene editing, I excel in motivating both myself and others. I am highly organized, detail-oriented, and adept at taking on leadership roles to drive projects forward. As an excellent team player, I firmly believe that collaborative efforts lead to significant success. Among my colleagues, I am known for being helpful and versatile.

In my current role, I collaborate with USDA breeders working on a variety of specialty crops, ranging from diploids to polyploids, such as alfalfa, lettuce, hops, blackberry, blueberry, and cucumber. My work focuses on exploring genetic diversity, QTL mapping, GWAS, and genomic selection, assisting breeders in developing efficient breeding strategies. I also contribute to the development of marker panels for these crops. I prepare reports, manuscripts, and presentations to share research findings, ensuring that our work is effectively communicated. My skill set encompasses marker-assisted selection, gene editing, molecular cloning, and other cutting-edge techniques, advancing the field of plant breeding.

I earned my PhD from the Institute of Plant Breeding, Genetics, and Genomics at the University of Georgia, where I worked under the guidance of Dr. Esther van der Knaap in the van der Knaap lab. My doctoral research focused on uncovering the genetic basis of fruit weight and flavor volatiles in tomatoes. I also hold a B.S. in Agriculture from Tribhuvan University, Nepal, where I specialized in Plant Breeding.

Originally from Nepal, I completed my undergraduate studies at the Institute of Agriculture and Animal Sciences, Tribhuvan University, Rampur, Chitwan, Nepal. Before pursuing my PhD, I worked as a Research Technician at the International Maize and Wheat Improvement Centre (CIMMYT) in Nepal.

In addition to my research, I am actively involved in campus and community activities. I served as President of the Nepalese Students Association at UGA and currently participate in the Postdoctoral Association at Cornell University. My leadership roles reflect my commitment to fostering a vibrant and collaborative academic community.

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

Genomics Postdoc Breeding Insight, Cornell University, Ithaca, New York US; July 2023 to present Supervisor: Dr. Dongyan Zhao

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 lab

Currently, I am Genomics Postdoc at Breeding Insight at Cornell University working with an amazing team. I am 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 integrate 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!!).

About me