Although many horticulturists and botanists are familiar with the economic aspects and heritability of somatic mutation, the role somatic mutation plays as a mechanism for evolutionary change is unknown. The modular and layered nature of plant tissues provides the basis for mutations to occur and then be perpetuated through cell division and differentiation, potentially creating heterogeneity within an individual plant. The commercially important tree species black cottonwood, Populus trichocarpa, is a long-lived organism which provides an ideal system to survey the level of somatic mosaicism within an individual and between parent and clonal-offspring. We sampled reproductive bud tissue (from the highest possible branch) and stem tissue (from the lowest branch) from both the parent and clonal-offspring. We also sampled the root tissue between parent and clonal offspring for a total of 5 tissues, replicated among 11 trees. Genomic DNA was extracted from each tissue and re-sequenced on the Illumina platform, after which a SNP analysis was completed for each tissue against the reference genome. Results from the SNP analysis were exported to a 150 million record database which allowed for comparisons between and within trees, tissues and parent-offspring pairings for similarities/differences in heterozygosity and amino acid changes within exons.
Populus trichocarpa’s genome (chromosomes 1-19) and transcriptome is approximately 379 and 65 mbp, respectively, consequently, we averaged 16x coverage in our samples. 1 in 164 bp results in a SNP for an average of 2.77 million SNPs per tissue sampled. On average, 53% of all SNPs were heterozygous, 5.6% were exonic, and 57.3% of the exonic SNPs resulted in an amino acid change. Of these, 188,406 SNPs are unique to a tissue, even from within the same individual, 8,629 are exonic and 5,529 result in an amino acid change; consequently, 2,800 genes are affected per tissue. These results clearly demonstrate a change in gene frequency from parent to clonally derived offspring. Ultimately, these results provide empirical evidence for and take a step toward resolving a long-standing debate over the importance of somatic mutations in nature. Understanding the level of mosaicism within an individual plant, challenges our assumptions in a diverse range of fields, from pharmacology to agriculture to conservation. Overall, this study represents the first genome-wide assessment of somatic variation within an individual plant with important implications for understanding ways in which plants can cope with changing environmental conditions on short and long term scales from an evolutionary perspective.