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To enhance the sensitivity of an ongoing Genome Wide Association Study (GWAS) for in vitro shoot regeneration and genetic transformation, a wide range of factors that can affect regeneration rate and, therefore, expression of genetic diversity were studied. Included were explant types and sources; direct versus indirect regeneration; nitrogen salts and micronutrient levels in basal medium; sucrose, auxin, and cytokinin types and levels; light intensity and quality; melatonin and serotonin; antibiotics (to exogenously control contaminants); antioxidants; and the ethylene-mitigating agent silver nitrate. Genotype was a statistically significant source of variance in response to nearly every treatment and for every measure of regeneration noted in shoots and roots, and initial generation of callus. Nonetheless, broad-sense heritability estimates varied widely as a result of variable degrees of environmental modification and statistical interactions with genotype. Compared to leaves, stem and petiole explants were highly correlated in their expression of genetic variation in response to treatments, a likely result of their functional similarity. Based on literature review, this study appears to be the most intensive analysis of plant natural genetic variation in response to in vitro manipulations published. It should help to guide development of improved and highly heritable treatments in other plant species that employ organogenic regeneration systems.

In preparation for a major GWAS (Genome Wide Association Study) of plant regeneration and transformation, a large number of factors were examined for their effects on indirect regeneration rate in diverse wild genotypes—seeking a high rate of regeneration, but also highly genetically variable and heritable treatments. Many of the factors examined have never before been reported on for their effects on callus, shoot, or root organogenesis in poplar (Populus). Stems had the highest regeneration potential, followed by petioles and leaves, with greenhouse grown explant sources superior to in vitro growth explant sources. Changes of ± 50% to Murashige and Skoog (MS) basal medium salts and micronutrients had a minor effect on regeneration. Many popular treatments that were evaluated also had little to no useful effect at the levels studied, including activated charcoal, ascorbic acid, silver nitrate, melatonin, serotonin, sucrose concentration, and lipoic acid. As a result of this wide exploration, treatment combinations that substantially elevated regeneration in diverse genotypes were identified, enabling GWAS.