Legume Genomics and Genetics 2026, Vol.17, No.1, 1-13 http://cropscipublisher.com/index.php/lgg 7 findings. Notably, the PCA provided a visualization of the high level of variation within the P98Y11 and NA5909 populations, as evidenced by the larger ellipses representing these groups. Conversely, the progenies derived from NS7000 exhibited the smallest variation. This intra-cultivar variation for P98Y11 and NA5909 can be explained by various mechanisms such as residual heterozygosity, mutations, transposable elements, epigenetic modifications, non-homologous recombination, and chromosomal mutations (Tokatlidis, 2015), and may also be influenced by genetic drift, especially in populations with reduced effective size. In addition, mechanical admixture may have occurred during seed production, and although with low probability, cross-fertilization can also take place, leading to the formation of hybrid seeds (Ahrent and Cavivess, 1994). In this context, the study of Mihelich et al. (2020), detected residual heterozygosity in all evaluated accessions of soybean, although at varying levels depending on the accession type. Landraces exhibited the highest level (5.2%), followed by North American cultivars (4.8%), whereas G.soja, showed the lowest level (0.6%). Studies by Du et al. (2010), through SoyTEdb, identified that approximately 42% of the genome corresponds to class I transposable elements (retrotransposons) and 16% to class II transposable elements (DNA transposons). Moreover, epigenetic modifications have proven to be fundamental, contributing to the adaptive responses of soybean under different environmental stresses (Fang et al., 2025). The genetic variation among soybean progenies derived from six cultivars was assessed by calculating expected heterozygosity (He) values for each population. These He values ranged from 0.047725 in NS7000 to 0.124485 in P98Y11. Additionally, observed heterozygosity (Ho) values were determined for each population to assess the genetic variation within the soybean progenies. The Ho values varied from 0.032058 in NS7000 to 0.112448 in P98Y11, as shown in (Table 2). These findings are consistent with the PCA results, which indicated significant variation in cultivars P98Y11 and NA5909, as reflected by high He and Ho values, indicating a broad genetic base, which suggests potential for intracultivar selection. Conversely, the NS7000 population exhibited the lowest genetic diversity with an He value of 0.047725 and an Ho value of 0.032058 also evidenced by the low dispersion of data points in the PCA. This suggests a more uniform genetic structure within this population (Lu et al., 2022). Remaining heterozygosity (HR) has been identified as an important source of intracultivar variation. In bulk breeding, segregating populations are advanced through successive generations of selfing, with the expectation that heterozygosity will be reduced by half each cycle until reaching near fixation. However, studies have shown that natural selection may preserve heterozygous loci when they confer adaptive advantages, as observed by Hockett et al. (1983) even in advanced generations. This indicates that, despite the inbreeding process inherent to the bulk method, HR can persist within families and contribute to phenotypic variability, which may be exploited during selection in later generations. A study carried out by Fasoula, Yates, and Boerma (2012) using SSR markers in soybean cultivars found 82% to 93% variation attributable to HR. However, even in 100% homogeneous lines, variation can be found, resulted from mutation, intragenic recombination, unequal crossing over, DNA methylation, excision or insertion of transposable elements, and gene duplication (Morgante et al., 2005; Sandhu et al., 2017; Salgotra and Chauhan, 2023). Another hypothesis is that the genome is dynamic and that new genotypic and phenotypic variation arises in each generation. One source of variation is genetic change leading to alleles with modified effects, that is, de novo generated variation. A second, complementary source of variation could come from interaction or epistatic effects, involving both de novo diversity and the original genetic diversity (Rasmusson and Phillips, 1997). Given that phenotypic and genotypic variations have been observed across all populations, selection can be employed for soybean breeding to archive fast and directed gains, as well as to identify plants adaptable to specific environments. 4 Materials and Methods 4.1 Plant material and field trials The experiments were carried out at the Muquém Farm of the Federal University of Lavras (UFLA) (21°14' S; 45°00' W), Lavras, MG, Brazil, in the 2017/2018 crop season, with the selection of plants from the SYN1359S
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