Pineapple color yellowing and quality promotion gradually manifest as pineapple fruit ripening progresses. To understand the molecular mechanism underlying yellowing in pineapples during ripening, coupled with alterations in fruit quality, comprehensive metabolome and transcriptome investigations were carried out. These investigations were conducted using pulp samples collected at three distinct stages of maturity: young fruit (YF), mature fruit (MF), and fully mature fruit (FMF). This study revealed a noteworthy increase in the levels of total phenols and flavones, coupled with a concurrent decline in lignin and total acid contents as the fruit transitioned from YF to FMF. Furthermore, the analysis yielded 167 differentially accumulated metabolites (DAMs) and 2194 differentially expressed genes (DEGs). Integration analysis based on DAMs and DEGs revealed that the biosynthesis of plant secondary metabolites, particularly the flavonol, flavonoid, and phenypropanoid pathways, plays a pivotal role in fruit yellowing. Additionally, RNA-seq analysis showed that structural genes, such as FLS, FNS, F3H, DFR, ANR, and GST, in the flavonoid biosynthetic pathway were upregulated, whereas the COMT, CCR, and CAD genes involved in lignin metabolism were downregulated as fruit ripening progressed. APX as well as PPO, and ACO genes related to the organic acid accumulations were upregulated and downregulated, respectively. Importantly, a comprehensive regulatory network encompassing genes that contribute to the metabolism of flavones, flavonols, lignin, and organic acids was proposed. This network sheds light on the intricate processes that underlie fruit yellowing and quality alterations. These findings enhance our understanding of the regulatory pathways governing pineapple ripening and offer valuable scientific insight into the molecular breeding of pineapples.

Introduction: Banana is a globally essential staple and industrial crop whose sustainable production is frequently challenged by excessive plant height and susceptibility to wind-induced lodging. Managing plant architecture is therefore critical for improving lodging resistance, yet the underlying genetic mechanisms governing plant height in banana remain poorly understood. Methods: To elucidate the genetic basis of plant height, we performed a systematic pan-genome analysis of the AP2/ERF gene family across 18 diverse banana genomes. The identified genes were characterized for their duplication mechanisms and selective pressures. Furthermore, we integrated the pan-genomic dataset with published phenotypic data using a haplotype-based association study to uncover key candidate genes and analyze the geographic distribution of their associated alleles across accessions. Results: A total of 4,732 MaAP2ERF genes were identified, yielding 468 non-redundant representative members. Dispersed duplication was the primary driver of family expansion (43.38%), whereas whole-genome duplication (WGD) established the conserved core foundation, accounting for all 42 core genes shared across all genomes. In contrast, dispersed duplication drove all 157 private genes, while the remaining 269 dispensable members arose from a combination of five duplication mechanisms. Evolutionary analysis indicated strong purifying selection on most members (K _a /K _s ratios between 0.2 and 0.5). Haplotype-based association identified MaAP2ERF144 and MaAP2ERF407 as key candidates for plant height, with MaAP2ERF407 demonstrating a dual association with stem elongation and lignin content for mechanical strength. Geographic analysis revealed that height-increasing alleles are mainly concentrated in Southeast Asia, Oceania, and East Africa, whereas dwarf alleles predominate in East Asian accessions. Discussion: These findings provide a comprehensive genomic framework for the banana AP2/ERF gene family and elucidate the evolutionary mechanisms shaping its diversity. The identified functional candidate genes and key haplotype loci offer valuable genetic targets for precision molecular breeding to develop high-yielding, lodging-resistant banana cultivars with optimized plant architecture.

To understand the molecular mechanism underlying yellowing in pineapples during ripening, coupled with alterations in fruit quality, comprehensive metabolome and transcriptome investigations were carried out. These investigations were conducted using the pulp samples collected at three distinct stages of maturity: young fruit (YF), mature fruit (MF), and fully mature fruit (FMF). This study revealed a noteworthy increase in the levels of total phenols and flavones, coupled with a concurrent decline in lignin and total acid content, as the fruit transitioned from YF to FMF. Furthermore, the analysis yielded 167 differentially accumulated metabolites (DAMs) and 2194 differentially expressed genes (DEGs). Kyoto Encyclopedia of Genes and Genomes enrichment analysis based on DAMs and DEGs revealed that the biosynthesis of plant secondary metabolites, particularly the flavonol, flavonoid, and phenypropanoid pathways, plays a pivotal role in fruit yellowing. Additionally, a comprehensive regulatory network encompassing genes that contribute to metabolisms of flavones, flavonols, lignin, and organic acids was proposed. This network sheds light on the intricate processes that underlies fruit yellowing and quality alterations. These findings enhance our understanding of the regulatory pathways governing pineapple ripening and offer valuable scientific insight into the molecular breeding of pineapples.