Integrative genome-wide association study and transcriptomic analyses unveil key candidate genes regulating fruit shape diversity in mango

• Generated a high-quality genome assembly of spherical-fruited mango 'JPM'. • Identified 467 genes via transcriptome sequencing of two contrasting fruit shape cultivars ('HXY' vs. 'JPM'). • Three-dimensional scanning was employed to measure mango fruit morphology and yielded nine key traits, enabling the analysis and classification of its diversity. • GWAS uncovered 99 loci (linked to 59 annotated genes) as candidate regulators of mango fruit shape. • Eight key genes—LOC123222869 (TCP4-like), LOC123213947 (bZIP61-like), LOC123210819 (ABC-G10), LOC123200572 (ARF3), LOC123228419 (TTL1), LOC123214860 (PLAZT), and LOC123222890 (ACO1)—were identified as key candidates underlying fruit shape variation. Fruit shape is a key horticultural trait affecting the market value and consumer preference of mango ( Mangifera indica L.), but the genetic and molecular mechanisms underlying its variation remain unclear. In this study, a high-quality genome of 'Jinpingmang' (‘JPM’), a cultivar with spherical fruits, was obtained. The assembled genome size is 350.66 Mb, containing 34,035 protein-coding genes, with repetitive sequences accounting for 39.28% of the genome. Two cultivars with significantly different fruit shapes, 'Hongxiangya' (‘HXY’) and 'JPM', were selected for fruit development observation and transcriptome sequencing. It was found that DAP3, DAP5, and DAP10 are critical stages for fruit shape development, and a total of 467 fruit shape-related genes were identified. Seventy-five mango germplasms with different fruit shapes were resequenced to obtain 26,285,317 single-nucleotide polymorphisms (SNPs), based on which the 75 accessions were clustered into 4 groups with significant differences in fruit shape. Combined with 9 fruit-related traits from three-dimensional scanning, a genome-wide association study (GWAS) of 72 accessions on 6 key fruit shape traits identified 99 genetic loci (linked to 59 annotated genes) as well as fruit volume and fruit shape index. Integration of GWAS and transcriptome data identified 44 key candidate genes with significant differential expression during development, among which 8 genes including LOC123222869 ( TCP4-like ), LOC123213947 (bZIP61-like ), LOC123210819 ( ABC-G10 ), LOC123200572 ( ARF3 ) and LOC123228419 ( TTL1 ) were proposed as key candidates underlying fruit shape variation. This study provides high-quality resources for dissecting key genetic loci associated with mango fruit shape differences and can inform future genome-based breeding for improved fruit shape in mango.