Mango (Mangifera indica L.) has been widely cultivated as a culturally and economically significant fruit tree for roughly 4000 years. Despite its rich history, little is known about the crop’s domestication, genomic variation, and the genetic loci underlying agronomic traits. This study employs the whole-genome re-sequencing of 224 mango accessions sourced from 22 countries, with an average sequencing depth of 16.37×, to explore their genomic variation and diversity. Through phylogenomic analysis, M. himalis J.Y. Liang, a species grown in China, was reclassified into the cultivated mango group known as M. indica. Moreover, our investigation of mango population structure and differentiation revealed that Chinese accessions could be divided into two distinct gene pools, indicating the presence of independent genetic diversity ecotypes. By coupling genome-wide association studies with analyses of genotype variation patterns and expression patterns, we identified several candidate loci and dominant genotypes associated with mango flowering capability, fruit weight, and volatile compound production. In conclusion, our study offers valuable insights into the genetic differentiation of mango populations, paving the way for future agronomic improvements through genomic-assisted breeding.

Background: The dramatic temperature fluctuations spurred by global warming and the accompanying extreme weather events inhibit mango growth and threaten mango productivity. Particularly, mango flowering is highly sensitive to temperature changes. The mango fruit setting rate was significantly positively correlated with pollen activity, and pollen activity was regulated by different metabolites. Methods: In this study, the in vitro pollen of two mango varieties (‘Renong No.1’ and ‘Jinhuang’), in which sensitivity to temperature differed significantly, were subjected to different temperature stresses (15 °C, 25 °C and 35 °C), and their metabolomics were analyzed. Results: The present results showed that 775 differential metabolites were screened by liquid chromatography–mass spectrometry and divided into 12 categories. The two varieties had significant differences in metabolite expression under different temperature stresses and the effect of low temperature on ‘Renong No.1’ mainly focused on amino acid metabolism, while the effect on ‘Jinhuang’ was mainly related to glycolysis. However, under the 35 °C temperature stress, ‘Renong No.1’ responded by redistributing riboflavin and betaine in vivo and the most obvious metabolic pathway of ‘Jinhuang’ enrichment was pyrimidine metabolism, which had undergone complex main body formation and extensive regulatory processes. The changes of metabolites of different varieties under low temperature and high temperature stress were different. Among them, flavonoids or flavonoid derivatives were included in class A (216 metabolites), C (163 metabolites) and D (233 metabolites) metabolites, indicating that flavonoid metabolites had an obvious regulatory effect on mango pollen metabolism under different temperature stress. Conclusions: The present results provide valuable information for reproductive biology studies and breeding in mango, in particular, the selection and breeding of the most suitable varieties for different production areas.

Seasonal drought constitutes a major abiotic stress limiting the growth and yield of pineapple, a globally important Crassulacean acid metabolism (CAM) crop. The sucrose catabolism mediated by cell wall invertase (CWIN) plays a vital role in regulating plant growth and development, as well as adaptive responses to abiotic stresses. Invertase inhibitors (INHs) serve as specific post-translational regulators that modulate CWIN enzymatic activity. However, the INH family has not been systematically characterized in pineapple, and its functional roles in mediating sucrose metabolism and drought resistance remain elusive. In this study, three AcINHs were identified from the pineapple genome, followed by comprehensive analyses of their gene structures, phylogenetic relationships, homology characteristics and protein structures. Structural analysis revealed that all AcINH members harbor conserved motifs 1, 2, 3, 5 and 9, whereas only AcINH3 possesses motif 7. Expression analysis showed that only AcINH3 was significantly transcriptionally induced by drought stress among all family members. Functional validation demonstrated that AcINH3 knockout markedly elevated CWIN activity in pineapple seedling leaves, facilitating hexose accumulation and promoting plant growth and development. Moreover, AcINH3-edited lines exhibited enhanced drought resistance, accompanied by increased accumulation of soluble sugars (sucrose, glucose, fructose), abscisic acid (ABA), and proline (PRO), reduced malondialdehyde (MDA) content, and enhanced peroxidase (POD) activity. Biochemical assays further verified a direct physical interaction between AcINH3 and AcCWIN1, which mediates sucrose metabolism and drought stress responses. Collectively, this study identifies a novel AcINH3–AcCWIN1 post-translational module that modulates sugar metabolism and drought tolerance in pineapple, providing critical mechanistic insights for CAM plants. Our findings highlight AcINH3 as a promising target for genome-editing breeding to enhance drought resistance in CAM crops.

Seedless mangoes are desirable for fresh consumption and processing; however, they frequently exhibit poor fruit development and elevated abscission rates, necessitating applications of fruit regulators, though their physiological and molecular targets remain unclear. In this study, hormonal deficits and regulatory genes associated with mango fruit development were identified. Morphological observations showed that embryo-containing (EC) and embryo-absent (EA) fruits begin to diverge in development between 30 and 45 days after bloom (DAB). During this period, targeted metabolomics of gibberellins (GAs) detected nine GAs; four (GA₂₀, GA₃₄, GA₄, GA₇) behaved consistently across cultivars, with GA₄ and GA₇ showing the largest declines in EA fruit. Applying 50 mg/L GA₃ or GA₄₊₇ at 30 DAB increased fruit growth versus water, with GA₄₊₇ having the greatest effect. Comparative transcriptomic analysis revealed 1476 shared DEGs that were enriched in hormone signaling pathways. Among 13 DEGs involved in GA biosynthesis, KAO (Mi05g23760.1) showed the strongest correlation with GA levels and was markedly downregulated in EA fruits. Together, these results indicate that deficiencies in GA₄/GA₇—potentially resulting from reduced KAO expression—contribute to impaired EA fruit development and that targeted GA₄₊₇ supplementation may more effectively rescue growth than conventional GA₃ treatments. These results provide mechanistic insights and practical guidance for hormone-based strategies to promote consistent development of seedless mangoes, thereby improving yield stability and supporting more sustainable production.