Evolutionary relationship of moso bamboo forms and a multihormone regulatory cascade involving culm shape variation

Moso bamboo (Phyllostachys edulis) known as Mao Zhu (MZ) in Chinese exhibits various forms with distinct morphological characteristics. However, the evolutionary relationship among MZ forms and the mechanisms of culm shape variation are still lacking. Here, the main differences among MZ forms were identified as culm shape variation, which were confirmed by analysing MZ forms (799 bamboo culms) and MZ (458 bamboo culms) populations. To unravel the genetic basis underlying the morphological variations, 20 MZ forms were subjected to whole-genome resequencing. Further analysis yielded 3 230 107 high-quality SNPs and uncovered low genetic diversity and high genotype heterozygosity associated with MZ forms' formation. By integrating the SNP data of 427 MZ individuals representing 15 geographic regions, the origins of eight MZ forms were successfully traced using the phylogenetic tree and the identified common heterozygous loci. Meanwhile, transcriptomic analysis was performed using shoots from MZ and its two forms with culm shape variation. The results, combined with genomic analyses, demonstrated that hormone signalling related genes played crucial roles in culm variation. Co-expression network analysis uncovered genes associated with multiple plant hormone signal transduction, especially auxin and cytokinin were involved in culm shape variation. Furthermore, the regulatory relationships of a specific transcription factor and their target genes associated with auxin and ethylene signalling were validated by yeast one-hybrid, electrophoretic mobility shift assays, and dual-luciferase reporter. Overall, this study provides important insights into the culm shape variation formation in bamboo, which facilitates to breed new varieties with novel culms.