Rapid growth is an innovative trait of woody bamboos that has been widely studied. However, the genetic basis and evolution of this trait are poorly understood. Taking advantage of genomic resources of 11 representative bamboos at different ploidal levels, we integrated morphological, physiological, and transcriptomic datasets to investigate rapid growth. In particular, these bamboos include two large-sized and a small-sized woody species, compared with a diploid herbaceous species. Our results showed that gibberellin A1 was important for the rapid shoot growth of the world's largest bamboo, Dendrocalamus sinicus, and indicated that two gibberellins (GAs)-related genes, KAO and SLRL1, were key to the rapid shoot growth and culm size in woody bamboos. The expression of GAs-related genes exhibited significant subgenome asymmetry with subgenomes A and C demonstrating expression dominance in the large-sized woody bamboos while the generally submissive subgenomes B and D dominating in the small-sized species. The subgenome asymmetry was found to be correlated with the subgenome-specific gene structure, particularly UTRs and core promoters. Our study provides novel insights into the molecular mechanism and evolution of rapid shoot growth following allopolyploidization in woody bamboos, particularly via subgenome asymmetry. These findings are helpful for understanding of how polyploidization in general and subgenome asymmetry in particular contributed to the origin of innovative traits in plants.

Woody bamboo (Bambusoideae) is renowned for its polyploidy and rare flowering. Bambusa odashimae is one of the bamboo species with the highest chromosome count (104) in the subfamily and has the highest heterozygosity of all sequenced bamboo genomes so far. Compared with other bamboo species, it can efficiently utilize exogenous hormones to regulate in vitro flowering, providing valuable insights into the hormonal regulation of bamboo flowering. Here, we generated the haplotype-resolved genome assembly of B. odashimae, despite the complexity and high chromosome number, supplemented by thirty-three transcriptomes from eleven developmental periods using a tissue culture system. The assembled genome can be divided into Haplotype I, Haplotype II, and Haplotype III, each containing A, B, and C subgenomes. Haplotype I may be derived from Dendrocalamus whereas Haplotypes II and III are closely related to Bambusa, indicating that B. odashimae has an origin involving both intergeneric and interspecific hybridizations. The high heterozygosity renders the possibility to detect abundant allele-specific expression (ASE), with ASE genes enriched in cytokinin-related pathways, likely associated with efficient cytokinin-promoted flowering. Notably, we found that the CONSTANS (CO) genes were potentially key regulators of in vitro flowering in B. odashimae. Overall, our study, based on the in vitro system combined with a high-quality reference genome, provides critical insights into the origin of this nonaploid bamboo and links hybridization and in vitro flowering in bamboo.

Most woody bamboos bloom only once after long vegetative growth phases and die immediately afterwards. It is difficult, however, to determine the timing of the floral transition, as little information is available on the molecular mechanism of plant maturity in bamboos. To uncover the bamboo floral transition mechanism, its morpho-physiological characteristics, transcriptomes and large-scale quantitative proteomes were investigated in leaves which were collected at different stages during floral transition in a woody bamboo, Dendrocalamus latiflorus. We identified many flowering time-associated genes and the continued increase and decrease genes were screened as flowering biomarker genes (e.g., the MADS14 and bHLH13 genes). These different genes were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes (KEGG). And the photoperiod pathways depending on the circadian rhythm may play an essential role in the bamboo floral transition. In addition, a total of 721 differently expressed proteins of leaves from the vegetative-to-reproductive stages were identified. Fifty-five genes were specifically differentially expressed at both the transcriptomic and proteomic levels, including genes related to photosynthesis and nucleotide sugar, which may be involved in the floral transition. This work provides insights into bamboo flowers and the management of forest breeding.

Background Most woody bamboos flower only once after long vegetable growth phases and die immediately afterward. It is difficult to know the timing of the floral transition, as little information is available on the molecular mechanism of plant maturity in bamboos. Results In this study, through RNA sequencing of leaves of D. latiflorus during floral transition and de novo assembly, a final set of 155,494 unigenes were obtained with N50 of 2,069 bp. We identified a lot of flowering time-associated and flowering integration genes and the continued increase and decrease genes were screened as flowering biomarker genes, such as MADS14, bHLH13, ABA-related genes. The different genes were assigned to specific metabolic pathways by Kyoto Encyclopedia of Genes and Genomes (KEGG) and the photoperiod pathways depending on the circadian rhythm may play an essential role in the bamboo floral transition. In addition, a total of 721 different expressed proteins of leaves from the vegetable-to-reproductive stages in the same flowering clumps were identified using iTRAQ technique. The correlations between the expression levels of a transcript and the abundance of its corresponding protein were observed infrequently, but the very strong correlation in the specific metabolic process was observed, such as carbon metabolism, sugar metabolism, and photosynthesis, underlining the importance of these metabolic pathways during floral transition. Conclusions In this report, we combined transcriptome with large-scale quantitative proteomes to investigate the flower transition of D. latiflorus. This work will provide insights into mechanism of floral transition for bamboos, and management of forest breeding.