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2025

• Kayikci, H.C., Aydin, S., Adak, A., Dogan, A., Sapkota, M., Feng, Q. and Topcu, Y., 2025. Associatioin mapping of tomato fruit quality for weight, firmness, brix, and color using GWAS. BMC Plant Biology
• 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. and Simko, I., 2025. A major and stable QTL confers impatiens necrotic spot virus resistance in lettuce cv, Eruption. Theoretical and Applied Genetics
• Xia, Z., Yang, M., Huang, Y., Wan, T., Wang, D., Li, Q., Sapkota, M., Yan, S., Cao, B. and Qiu, Z., 2025. A 725 bp quadruple repeat in the promoter of SmMYB113 is associated with light-independent anthocyanin regulation in eggplant. Horticulture Research
• 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. and Beil, C.T., 2025. BIGapp: A user‐friendly genomic tool kit identified quantitative trait loci for creeping rootedness in alfalfa (Medicago sativa L.). The Plant Genome, 18(3), p.e70067.
• Topcu, Y., Yildiz, K., Kayikci, H.C., Aydin, S., Feng, Q. and Sapkota, M., 2025. Deciphering resistance to Tomato brown rugose fruit virus (ToBRFV) using Genome-Wide Association Studies. Scientia Horticulturae, 341, p.113968.
• Medina, C.A., Hansen, J., Crawford, J., Viands, D., Sapkota, M., Xu, Z., Peel, M.D. and Yu, L.X., 2025. Genome-Wide Association and Genomic Prediction of Alfalfa (Medicago sativa L.) Biomass Yield Under Drought Stress. International journal of molecular sciences, 26(2), p.608.
• 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. and Claessens, A., 2025. Pre-breeding in alfalfa germplasm develops highly differentiated populations, as revealed by genome-wide microhaplotype markers. Scientific reports, 15(1), p.1253.

2024

• Thapa D.B., Subedi, M., Sapkota M., Bohora S.K., Pokhrel K.R., Aryal L., Acharya B., Tripathi S., Chaudhary C., Mahato B., Timsena K., Govindan V., and Joshi, A.K. 2024. The first assessment of grain yield and associated traits in durum wheat across a decade in Nepal. Frontiers in Plant Science – Crop and Product Physiology
• Topcu Y., Sapkota M., and Aydin S.2024. QTL-seq rapid, cost-effective, and reliable method for QTL identification, Horticulture Studies
• Zhao D., Sapkota M., Bassil N., Mengist M.F., Iorizzo M., Heller-Uszynska, Molinari M., Beil C., and Sheehan M.J. 2024. A public mid-density genotyping platform for Blueberry (Vaccinium corymbosum L.), Genetic Resources.
• Zhao D., Sapkota M., Lin M., Beil C., Sheehan M.J., Greene S., and Irish B. 2024. Genetic diversity, population structure, and taxonomic confirmation in annual medic (Medicago spp.) collection from Crimea, Ukraine. Frontiers in Plant science.

2023

• Li Q., Luo S., Zhang L., Feng Q., Song L., Sapkota, M., Xuan S., Wang Y., Zhao J., van der Knaap, E., Chen X. and Shen S. 2023. Molecular and genetic regulation of fleshy fruit shape and lessons from Arabidopsis and rice. Horticulture Research.
• Sapkota, M., Pereira, L., Wang, Y., Zhang, L., Topcu, Y., Tieman, D. and van der knaap, E., 2023. Structural variation underlies functional diversity at methyl salicylate loci in tomato. PLOS Genetics.
• Zhang, B., Li, Q., Keyhaninejad, N., Taitano, N., Sapkota, M., Snouffer, A. and van der Knaap, E., 2023. A combinatorial TRM‐OFP module bilaterally fine‐tunes tomato fruit shape. New Phytologist.
• Frick, E.M., Sapkota, M., Pereira Garcia, L., Wang, Y., Hermanns, A., Giovannoni, J.J., van der Knaap, E., Tieman, D.M. and Klee, H.J., 2023. A family of methyl esterases converts methyl salicylate to salicylic acid in ripening tomato fruit. Plant Physiology

2022

• Barnett, J., Buonauro, G., Kuipers, A., Sapkota, M., van der Knaap, E., & Razifard, H. 2022. Genomic characterization of a wild-like tomato accession found in Arizona; a northward migration story. Systematic Botany. In press, accepted in volume 47 issue 4 (October-December 2022)
• 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., and Govindan, V. 2022. Variation in Grain Zinc and Iron Concentrations, Grain Yield and Associated Traits of Biofortified Wheat Genotypes in Nepal. Frontiers in Plant Science, 13:881965. doi:10.3389/fpls.2022.881965

2021

• Pereira, L., Zhang, L., Sapkota, M., Ramos, A., Razifard, H., Caicedo, A.L. and van der Knaap, E., 2021. Unraveling the genetics of tomato fruit weight during crop domestication and diversification. Theoretical and Applied Genetics, 134(10), pp.3363-3378.
• Topcu, Y., Sapkota, M., Illa-Berenguer, E., Nambeesan, S.U. and van der Knaap, E., 2021. Identification of blossom-end rot loci using joint QTL-seq and linkage-based QTL mapping in tomato. Theoretical and Applied Genetics, pp.1-15.
• Pereira, L., Sapkota, M., Alonge, M., Zheng, Y., Zhang, Y., Razifard, H., Taitano, N.K., Schatz, M., Fernie, A., Wang, Y. and Fei, Z., 2021. Natural genetic diversity in tomato flavor genes. Frontiers in plant science, 12, p.914.

2020

• Li Q., Sapkota M., and van der Knaap E. 2020. Perspectives of CRISPR/Cas-mediated cis-engineering in horticulture: unlocking the neglected potential for crop improvement. Horticulture research, 7(1), 1-11.

2018

• Shahi, D., Ghimire, S.K., Ojha, B.R., Bhatta, M.R., Rasaily, S., Rauniyar, D.R. and Sapkota, M., 2018. Evaluation of variability and genetic parameters for yield and yield-attributing traits in spring wheat (Triticum aestivum L.). Nepalese Journal of Agricultural Sciences 2018, volume 17, p.134.

2017

• Poudel A., Thapa D.B., and Sapkota M. 2017. Cluster Analysis of Wheat (Triticum aestivum L.) Genotypes Based Upon Response to Terminal Heat Stress. International Journal of Applied Sciences and Biotechnology, 5(2), 188-193. DOI: 10.3126/ijasbt.v5i2.17614
• Bhattarai R.P., Ojha, B.R., Thapa D.B., Kharel R., Ojha, A., and Sapkota M. 2017. Evaluation of Elite Spring Wheat (Triticum aestivum L.) Genotypes for Yield and Yield Attributing Traits under Irrigated Condition. International Journal of Applied Sciences and Biotechnology, 5(2), 194-202. DOI: 10.3126/ijasbt.v5i2.17615
• Raut, S.K., Ghimire, S.K., Kharel, R., Kuwar, C.B., Sapkota, M. and Kushwaha, U.K.S., 2017. Study of yield and yield attributing traits of maize. American Journal of Food Science and Health, 3(6), pp.123-129.

2016

• Sapkota M., Timilsina D., Yadav M.K., and Ghimire S. 2016. Agromorphological Characterisation of Foxtail millet Setaria italica L. Beuv. at Rampur, Chitwan. Thesis. Himalayan Crops, Official site of the Local Crop Project.
• Sapkota M., Pandey M.P., and Thapa D.B. 2016. Agromorphological Characterisation of Foxtail millet (Setaria italica L. Beauv) at Rampur, Chitwan, Nepal. International Journal of Applied Science and Biotechnology, 4(3), 298-307.
• Sapkota M., Pandey M.P., Thapa D.B., Yadav M.K., Ghimire S. and Timalsina D. 2016. Diversity Assessment of Foxtail millet (Setaria italica L. Beauv) Accessions Collected from Different Locations of Nepal. International Journal of Applied Science and Biotechnology, 4(4), 483-488. DOI: 10.3126/ijasbt.v4i4.16244.
• Vitrakoti D., Aryal S., Rasaily S., Ojha B.R., Kharel R., and M. Sapkota. 2016. Study on Genotypic Response And Correlation Analysis Of The Yield And Yield Attributing Traits Of Different Barley (Hordeum vulgare) Genotypes. International Journal of Applied Science and Biotechnology, 4(4), 529-536, DOI: 10.3126/ijasbt.v4i4.16269.