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I am Manoj Sapkota, Genomics Postdoc at Breeding Insight in Cornell University. I am passionate about plant breeding, genetics and bioinformatics. I call myself a grounded and solution-oriented plant scientist with wide variety of research experiences. I possess 5 plus years of experience in bioinformatics, statistics, plant breeding, traditional gene cloning, QTL mapping, molecular cloning, and gene editing. I am adept at motivating self and others. I am also highly organized, detail oriented and capable of taking leadership role to carry out assigned projects. I call myself an excellent team player and believe that we can achieve huge success working together. I am known as being very helpful and versatile among my colleagues.

In my current role, I collaborate with USDA breeders working on specialty crops like alfalfa, lettuce, blueberry, and cucumber in projects related to exploring genetic diversity, QTL mapping, GWAS and Genomic selections. Additionally, I perform genomic and bioinformatics analysis to help breeders develop breeding strategies and prepare reports, manuscripts, and presentations to share research results and findings.

Previously, I was a PhD student in the Institute of Plant Breeding, Genetics, and Genomics at the University of Georgia, Athens, GA, US and a member of van der Knaap lab working under the supervision of Dr. Esther van der Knaap. I am originally from Nepal. I did my undergrad in the Institute of Agriculture and Animal Sciences at the Tribhuvan University, Rampur, Chitwan, Nepal. I had also worked as a Reserch Technician at International Maize and Wheat Improvement Centre (CIMMYT), Nepal before I came to UGA to pursue my PhD.

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, differential expression and GO term analysis
  • Genetic map construction and QTL mapping
  • 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

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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

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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.

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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.

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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.

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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.

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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.

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Sports

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

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