Somatic mutations during rapid clonal domestication of Populus alba var. pyramidalis

Abstract

For many clonally propagated species, the accumulation of somatic mutations is the principal driver of declines in yield and quality. However, somatic mutations may also promote genetic diversification. Thus, elucidating somatic mutation rates and patterns is important to understand the genetic basis undergirding the emergence of commercially valuable traits and developmental processes. In this study, we studied the effect of short-time clonal domestication of Populus alba var. pyramidalis, a species that has been propagated by cutting for the last 67 years. We found that: (1) the somatic mutation rate for P. alba var. pyramidalis is 9.24 × 10^-9, which is higher than rates observed in related species; (2) there were more mutations near heterozygous regions, and a larger proportion of CpG and CHG sites were associated with somatic mutations, which may be related to the blocking of DNA repair by methylation; and (3) deleterious mutations were not shared by multiple individuals, and all occurred in heterozygous states, demonstrating the strong selective pressures that act against deleterious mutations. Taken together, the results of our study provide a global view of somatic mutation that will aid efforts to understand the genetic basis of commercially valuable traits and to improve clonally breeding species.

Keywords: Populus alba var. pyramidalis; clonal; deleterious; heterozygous; somatic mutation.

FIGURE 1

Sample location and relatedness. (a) Sampling locations for P. alba var. pyramidalis (pay, in blue points) and P. alba (Palb, in red points). (b) Phylogenetic relationship between P. alba var. pyramidalis, P. alba and six other species that are distributed across Xinjiang province. (c) Heterozygosity for P. alba and P. alba var. pyramidalis. (d) Kinship between each sample of P. alba var. pyramidalis, P. alba and P. trichocarpa.

FIGURE 2

Derived mutation network tree (a) and spectrum (b, c). (a) Derived mutation network tree based on the SNP dataset. Spectrum for SNPs (b) and indels (c). The ancestral state was identified using P. alba and P. tremula as outgroup.

FIGURE 3

Somatic mutation tendentiousness. (a) Spectrum of somatic mutations. (b) Proportion of base content for distance from somatic mutations. The gray dashed line represents genome‐wide averages for A/T (upper) and C/G (lower).

FIGURE 4

Relationship between nucleotide diversity and the distance to somatic mutations for intergenic, intron, exon, deleterious and artificial mutations.

FIGURE 5

Selection of somatic alleles in P. alba. (a) For each somatic mutation in P. alba var. pyramidalis, corresponding premutation and postmutation allele frequency in P. alba. (b) Distribution of SNPs under selection in P. alba.