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.

Scholars@UK

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A major and stable QTL confers impatiens necrotic spot virus resistance in lettuce cv. Eruption

Nayak, S., Richardson, K. L., Eriksen, R. L., Hasegawa, D. K., Wintermantel, W. M., Sapkota, M., Tang, X., Chen, S., Lin, M., Zhao, D., Beil, C. T., Sheehan, M. J. & Simko, I., Dec 2025, In: Theoretical And Applied Genetics. 138, 12, 312.

Research output: Contribution to journalArticlepeer-review

Unraveling the genetics of tomato fruit weight during crop domestication and diversification

Pereira, L., Zhang, L., Sapkota, M., Ramos, A., Razifard, H., Caicedo, A. L. & van der Knaap, E., Oct 2021, In: Theoretical And Applied Genetics. 134, 10, p. 3363-3378 16 p.

Research output: Contribution to journalArticlepeer-review

A family of methyl esterases converts methyl salicylate to salicylic acid in ripening tomato fruit

Frick, E. M., Sapkota, M., Pereira, L., Wang, Y., Hermanns, A., Giovannoni, J. J., van der Knaap, E., Tieman, D. M. & Klee, H. J., Jan 2023, In: Plant Physiology. 191, 1, p. 110-124 15 p.

Research output: Contribution to journalArticlepeer-review

BIGapp: A user-friendly genomic tool kit identified quantitative trait loci for creeping rootedness in alfalfa (Medicago sativa L.)

Sandercock, A. M., Peel, M. D., Taniguti, C. H., Chinchilla-Vargas, J., Chen, S., Sapkota, M., Lin, M., Zhao, D., Ackerman, A. J., Basnet, B. R., Beil, C. T. & Sheehan, M. J., Sep 2025, In: Plant Genome. 18, 3, e70067.

Research output: Contribution to journalArticlepeer-review

Genomic Characterization of a Wild-Like Tomato Accession from Arizona

Barnett, J., Buonauro, G., Kuipers, A., Sapkota, M., Van Der Knaap, E. & Razifard, H., Dec 12 2022, In: Systematic Botany. 47, 4, p. 1100-1106 7 p.

Research output: Contribution to journalArticlepeer-review

Natural Genetic Diversity in Tomato Flavor Genes

Pereira, L., Sapkota, M., Alonge, M., Zheng, Y., Zhang, Y., Razifard, H., Taitano, N. K., Schatz, M. C., Fernie, A. R., Wang, Y., Fei, Z., Caicedo, A. L., Tieman, D. M. & van der Knaap, E., Jun 4 2021, In: Frontiers in Plant Science. 12, 642828.

Research output: Contribution to journalArticlepeer-review

The first assessment of grain yield and associated traits in durum wheat across a decade in Nepal

Thapa, D. B., Subedi, M., Sapkota, M., Bohara, S., Pokhrel, K. R., Aryal, L., Acharya, B., Tripathi, S., Chaudhary, C., Mahato, B., Timsina, K., Govindan, V. & Joshi, A. K., 2024, In: Frontiers in Plant Science. 15, 1456062.

Research output: Contribution to journalArticlepeer-review

Variation in Grain Zinc and Iron Concentrations, Grain Yield and Associated Traits of Biofortified Bread Wheat Genotypes in Nepal

Thapa, D. B., Subedi, M., Yadav, R. P., Joshi, B. P., Adhikari, B. N., Shrestha, K. P., Magar, P. B., Pant, K. R., Gurung, S. B., Ghimire, S., Gautam, N. R., Acharya, N. R., Sapkota, M., Mishra, V. K., Joshi, A. K., Singh, R. P. & Govindan, V., Jun 13 2022, In: Frontiers in Plant Science. 13, 881965.

Research output: Contribution to journalArticlepeer-review

Perspectives of CRISPR/Cas-mediated cis-engineering in horticulture: unlocking the neglected potential for crop improvement

Li, Q., Sapkota, M. & van der Knaap, E., Dec 1 2020, In: Horticulture Research. 7, 1, 36.

Research output: Contribution to journalReview articlepeer-review

Pre-breeding in alfalfa germplasm develops highly differentiated populations, as revealed by genome-wide microhaplotype markers

Medina, C. A., Zhao, D., Lin, M., Sapkota, M., Sandercock, A. M., Beil, C. T., Sheehan, M. J., Irish, B. M., Yu, L. X., Poudel, H., Claessens, A., Moore, V., Crawford, J., Hansen, J., Viands, D., Peel, M. D., Tilhou, N., Riday, H., Brummer, E. C. & Xu, Z., Dec 2025, In: Scientific Reports. 15, 1, 1253.

Research output: Contribution to journalArticlepeer-review

Molecular and genetic regulations of fleshy fruit shape and lessons from Arabidopsis and rice

Li, Q., Luo, S., Zhang, L., Feng, Q., Song, L., Sapkota, M., Xuan, S., Wang, Y., Zhao, J., Van Der Knaap, E., Chen, X. & Shen, S., Jul 1 2023, In: Horticulture Research. 10, 7, uhad108.

Research output: Contribution to journalReview articlepeer-review

Correction to: Pre-breeding in alfalfa germplasm develops highly differentiated populations, as revealed by genome-wide microhaplotype markers (Scientific Reports, (2025), 15, 1, (1253), 10.1038/s41598-024-84262-x)

Medina, C. A., Zhao, D., Lin, M., Sapkota, M., Sandercock, A. M., Beil, C. T., Sheehan, M. J., Irish, B. M., Yu, L. X., Poudel, H., Claessens, A., Moore, V., Crawford, J., Hansen, J., Viands, D., Peel, M. D., Tilhou, N., Riday, H., Brummer, E. C. & Xu, Z., Dec 2025, In: Scientific Reports. 15, 1, 12001.

Research output: Contribution to journalComment/debate

Genetic diversity, population structure, and taxonomic confirmation in annual medic (Medicago spp.) collections from Crimea, Ukraine

Zhao, D., Sapkota, M., Lin, M., Beil, C., Sheehan, M., Greene, S. & Irish, B. M., 2024, In: Frontiers in Plant Science. 15, 1339298.

Research output: Contribution to journalArticlepeer-review

A combinatorial TRM-OFP module bilaterally fine-tunes tomato fruit shape

Zhang, B., Li, Q., Keyhaninejad, N., Taitano, N., Sapkota, M., Snouffer, A. & van der Knaap, E., Jun 2023, In: New Phytologist. 238, 6, p. 2393-2409 17 p.

Research output: Contribution to journalArticlepeer-review

Genome-Wide Association and Genomic Prediction of Alfalfa (Medicago sativa L.) Biomass Yield Under Drought Stress

Medina, C. A., Hansen, J., Crawford, J., Viands, D., Sapkota, M., Xu, Z., Peel, M. D. & Yu, L. X., Jan 2025, In: International Journal of Molecular Sciences. 26, 2, 608.

Research output: Contribution to journalArticlepeer-review

A public mid-density genotyping platform for cultivated blueberry (Vaccinium spp.)

Zhao, D., Sapkota, M., Glaubitz, J., Bassil, N., Mengist, M. F., Iorizzo, M., Heller-Uszynska, K., Mollinari, M., Beil, C. T. & Sheehan, M. J., 2024, In: Genetic Resources. 5, 9, p. 36-44 9 p.

Research output: Contribution to journalArticlepeer-review

Identification of blossom-end rot loci using joint QTL-seq and linkage-based QTL mapping in tomato

Topcu, Y., Sapkota, M., Illa-Berenguer, E., Nambeesan, S. U. & van der Knaap, E., Sep 2021, In: Theoretical And Applied Genetics. 134, 9, p. 2931-2945 15 p.

Research output: Contribution to journalArticlepeer-review

Deciphering resistance to Tomato brown rugose fruit virus (ToBRFV) using Genome-Wide Association Studies

Topcu, Y., Yildiz, K., Kayikci, H. C., Aydin, S., Feng, Q. & Sapkota, M., Feb 1 2025, In: Scientia Horticulturae. 341, 113968.

Research output: Contribution to journalArticlepeer-review

Structural variation underlies functional diversity at methyl salicylate loci in tomato

Sapkota, M., Pereira, L., Wang, Y., Zhang, L., Topcu, Y., Tieman, D. & van der Knaap, E., May 4 2023, In: PLoS Genetics. 19, 5 May, e1010751.

Research output: Contribution to journalArticlepeer-review

Education

  • Ph.D., Plant Breeding, Genetics, & Genomics, University of Georgia, 2023
  • B.S., Agriculture (Plant Breeding), Tribhuvan University, 2016

Associated Departments

Horticulture