I am not an expert in this field, but I am very interested and have researched to find an answer. I received some assistance from tlooto.com for this response. Could you please review the response below to see if it is correct?

Conducting GWAS (Genome-Wide Association Studies) using clones from the same plant accession is generally not advisable. GWAS relies on genetic variation between individuals to identify associations between genetic markers and phenotypic traits. Clones from the same plant accession are genetically identical or nearly identical, which means there is minimal genetic variation to exploit for association mapping. This lack of genetic diversity would undermine the power and reliability of the GWAS, making it difficult to draw meaningful conclusions [1][2][4]. For effective GWAS, it is essential to use a diverse population with substantial genetic variation among individuals [6][8]. However, if genetic diversity within clones can be artificially introduced or if somaclonal variation is present, it might offer some insights but generally would not suffice for robust GWAS analysis [5]. Therefore, a diverse population is crucial to capture the genetic basis of complex traits effectively [3][7].

Reference

[1] Yano, K., Morinaka, Y., Wang, F., Huang, P., Takehara, S., Hirai, T., Ito, A., Koketsu, E., Kawamura, M., Kotake, K., Yoshida, S., Endo, M., Tamiya, G., Kitano, H., Ueguchi-Tanaka, M., Hirano, K., & Matsuoka, M. (2019). GWAS with principal component analysis identifies a gene comprehensively controlling rice architecture. Proceedings of the National Academy of Sciences of the United States of America, 116, 21262 - 21267.

[2] Khan, S., Saeed, S., Khan, M. H. U., Fan, C., Ahmar, S., Arriagada, O., Shahzad, R., Branca, F., & Mora-Poblete, F. (2021). Advances and Challenges for QTL Analysis and GWAS in the Plant-Breeding of High-Yielding: A Focus on Rapeseed. Biomolecules, 11.

[3] Luo, Z., Szczepanek, A., & Abdel-Haleem, H. (2020). Genome-Wide Association Study (GWAS) Analysis of Camelina Seedling Germination under Salt Stress Condition. Agronomy.

[4] Wang, J., Hu, B., Jing, Y., Hu, X., Guo, Y., Chen, J., Liu, Y., Hao, J., Li, W., & Ning, H. (2022). Detecting QTL and Candidate Genes for Plant Height in Soybean via Linkage Analysis and GWAS. Frontiers in Plant Science, 12.

[5] Wu, X., Jiang, W., Fragoso, C. A., Huang, J., Zhou, G., Zhao, H., & Dellaporta, S. (2022). Prioritized candidate causal haplotype blocks in plant genome-wide association studies. PLOS Genetics, 18.

[6] Ding, W., Zhang, X., Liu, D., Li, C., Wang, C., Sun, R., Jin, X., Guo, N., Zhao, J., & Xing, H. (2022). Genome-Wide Association Studies of Plant Architecture-Related Traits in the Chinese Soybean Mini Core Collection. Agronomy.

[7] Dang, D., Guan, Y., Zheng, H., Zhang, X., Zhang, A., Wang, H., Ruan, Y., & Qin, L. (2023). Genome-Wide Association Study and Genomic Prediction on Plant Architecture Traits in Sweet Corn and Waxy Corn. Plants, 12.

[8] Zhang, Y., Wan, J., He, L., Lan, H., & Li, L. (2019). Genome-Wide Association Analysis of Plant Height Using the Maize F1 Population. Plants, 8.

GWAS is studied in a variable gene pool. But clones have similar genotype,aren't they.! Then why would you use GWAS for such clones.