Genomic Signatures of Somatic Mutation and Selection in a Bud Sport Population of Bougainvillea × buttiana ‘Miss Manila’

Abstract Background In bougainvillea breeding, bud sports (somatic mutations) offer a rapid method for developing new varieties by altering specific traits while preserving the elite genetic background of the original cultivar. However, a comprehensive understanding of their genomic architecture, genetic differentiation from conventional varieties, and the molecular mechanisms underlying their formation remains limited. This study aims to elucidate the population genomic characteristics of bud sports derived from the commercial variety Bougainvillea ×buttiana 'Miss Manila'. Results Using genotyping-by-sequencing (GBS) on 39 accessions (27 bud sports and 12conventional varieties), we identified 64,810 high-quality SNPs. Population genomic analyses revealed significantly reduced genetic diversity (nucleotide diversity π and expected heterozygosity He) in the bud sports compared to conventional varieties, consistent with their clonal origin. Principal component, phylogenetic, and ADMIXTURE analyses (optimal K=4) demonstrated clear genetic differentiation and distinct population structures between the two groups. The bud sport population possessed far fewer private alleles and exhibited a less negative Tajima's D value. Genome scans identified regions with high genetic differentiation (FST) and signals of selective sweeps (XP-CLR) in bud sports. Functional analysis highlighted differentially mutated genes between the groups, involving pathways such as ubiquitin-mediated proteolysis and RNA transport, with genes like Bou_119143 (UDP-rhamnose rhamnosyltransferase 1) showing high mutation frequency specifically in bud sports. Conclusions Our results demonstrate that bud sports of 'Miss Manila' are genetically distinct, clonal lineages with a narrow genetic base shaped by somatic mutation and selection. This study provides the first population-genomic evidence for the genetic essence of bougainvillea bud sports, confirming them as efficient sources for germplasm innovation. The identified genomic regions and candidate genes lay a foundation for marker-assisted selection and future molecular breeding in bougainvillea .