Cutting through the clones: genomic strategies for core collection development in moso bamboo

Abstract Background Conserving genetic diversity is crucial for effective germplasm use and crop improvement. Developing core collections with minimal redundancy and maximum diversity requires a clear understanding of population structure. However, the nationwide population structure of moso bamboo (Phyllostachys edulis) remains poorly characterized, creating a major gap for developing representative, non-redundant core collections. Results Using whole-genome resequencing data from 432 moso bamboo accessions covering a broad geographic range across the distribution of the species in China, we investigated the population genetic structure and diversity patterns. Principal component analysis and phylogenetic tree analyses identified three distinct genetic clusters together with a hybrid group. To identify the optimal strategy for core collection development, we evaluated two stratification schemes, seven sampling strategies, and five sampling intensities. Across 70 candidate cores, stratified sampling combined with expected heterozygosity optimization at 20% intensity (S-HE20) maximized genetic diversity (He = 0.3665; PIC = 0.2904; I = 0.5302) and captured broad phenotypic variation (CR = 82.32%; MD = 0%), yielding an 84-accession core spanning 15 geographic regions. Conclusions This study revealed the population genetic structure of moso bamboo and identified the S-HE20 strategy as optimal for core collection construction. The resulting core collection offers a representative and genetically diverse resource for future gene discovery and molecular breeding efforts in moso bamboo.