Legume Genomics and Genetics 2026, Vol.17, No.1, 1-13 http://cropscipublisher.com/index.php/lgg 1 Research Report Open Access Uncovering Intracultivar Genetic Variability in Soybean Applying Phenotypic and Genomic Approaches Ewerton Lélys Resende 1,2, Adriano Teodoro Bruzi 2 , Bruna Stephani de Paula 2, Mateus Ribeiro Piza 2,3, Danyllo Amaral de Oliveira 3, Vitório Antônio Pereira de Souza 2, Taine Teotônio Teixeira da Rocha 2, Afrânio Gabriel da Silva Godinho Santiago 2, Carlos Henrique de Souza 2 1 Syngenta Seeds Ltda., Uberlândia-MG, 38402-128, Brazil 2 Universidade Federal de Lavras, Lavras-MG, 37200-900, Brazil 3 GDM Genetica do Brasil S.A., Cambé-PR, 86183-751, Brazil Corresponding email: adrianobruzi@ufla.br Legume Genomics and Genetics, 2026 Vol.17, No.1 doi: 10.5376/lgg.2026.17.0001 Received: 09 Feb., 2026 Accepted: 28 Feb., 2026 Published: 11 Mar., 2026 Copyright © 2026 Resende et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Resende E.L., Bruzi A.T., Paula B.S., Piza M.R., Oliveira D.A., Souza V.A.P., Rocha T.T.T., Santiago A.G.S.G., and Souza C.H, 2026, Uncovering intracultivar genetic variability in soybean applying phenotypic and genomic approaches, Legume Genomics and Genetics, 17(1): 1-13 (doi: 10.5376/lgg.2026.17.0001) Abstract We aimed to understand and explore the intracultivar variability of soybean lines by conducting both phenotypic and genotypic analyses. During the 2017/2018 crop season, plants from six soybean cultivars (SYN1359S IPRO, P98Y11, BMX6160, 97R73 RR, NS7000 IPRO, and NA5909) were used to establish the genetic treatments. For each of these six cultivars, 47 plants were selected to generate progenies and, along with the controls, were subjected to trials across two subsequent crop seasons, 2018/2019 and 2019/2020. Phenotypic traits such as Grain Yield (YIELD), Full Maturity (FM), Days to Flowering (DF), and Plant Height (PH) were measured. Additionally, 288 samples (progenies and controls) were genotyped using a chip containing 1329 SNPs using the Ion S5™ XL System. Phenotypic data were analyzed using mixed models. The genotypic analysis included measures such as observed and expected heterozygosity, hierarchical clustering (UPGMA), and principal component analysis (PCA). The study reveals the existence of both phenotypic and genotypic intracultivar variation among the assessed cultivars. The degree of variation observed differs, with cultivars P98Y11 and NA5909 exhibiting higher levels of diversity, while NS7000 presents a lower level of variation. Given the found variations selection can be employed for soybean breeding to achieve fast and directed gains, as well as to identify genotypes adaptable to specific environments. Keywords Glycine max L. Merrill.; Plant breeding; Genetic diversity; Genetic stability 1 Background Soybean (Glycine max [Merr.] L.) is the most important oilseed crop worldwide, valued for its oil (18%) and protein (36%) content (Duan et al., 2023). Since 2020, Brazil has been the world’s leading producer, and in the 2024/2025 crop season it accounted for 169 million tons (USDA, 2025). This achievement results from several factors, including improved crop management, greater investment in research and technology, and advances in breeding (Medina, et al., 2016). To meet market demands, the ultimate goal of breeding programs is the selection of superior genotypes, and the programs may follow different methods, such as hybridization, pure-line selection, and germplasm introduction. Pure line selection isolates the best genotypes from a heterogeneous population by selecting individual plants and evaluating their progenies. In this process, no new genotype is created, as the goal is simply to identify and preserve superior genotypes within the existing population (Reynolds and Braun, 2016). This breeding strategy has been studied in several self-pollinated species, such as soybean (Amaral et al., 2019), common bean (Santos et al., 2002), wheat (Agorastos and Goulas, 2005), and rice (Roy et al., 2016). Selection of pure and highly homozygous lines is a fundamental objective in plant breeding programs. In soybean, lines are typically developed to serve as cultivars; however, their long-term genetic stability may be affected by intracultivar variability, which can arise through genomic and structural modifications over time (Tokatlidis, 2015). Intracultivar variation has been increasingly documented in autogamous crops, including soybean (Amaral et al.,
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