Genomic divergence and genetic basis of fruit quality traits in Western and Asian cultivated strawberries

Background Cultivated strawberry displays phenotypic divergence in fruit quality between Western and Asian breeding programs: Asian strawberries are sweeter, Western ones firmer and more acidic. However, the genomic basis of this divergence remains largely unknown. Results Western strawberries were firmer (0.87–0.91) than Asian ones (0.68–0.69), whereas Asian strawberries had higher soluble solids content (SSC) in tips (10.92 vs. 8.81), middle (9.83 vs. 8.03) and shoulders (8.87 vs. 7.42). Population genomics based on 327,432 SNPs clearly separated Western from Asian accessions. Western strawberries showed higher nucleotide diversity (π = 7.75e-5) and longer LD decay (355.51 kb) than Asian ones (π = 7.55e-5; 339.65 kb), with FST = 0.11. Selective sweeps identified 153 regions (3,143 genes) under divergent selection, enriched in organic acid/sugar regulators ( ALMT8 / 9 , ACL , IDH5 , PEPCK , ERDL6 , SUS2.1 , SPS1 , FK7 , WD40 ). GWAS for fruit firmness identified 47 SNPs and 34 candidate genes: cell wall enzymes ( PG1, PL , PME58.1 - 58.3 , XTH2.1/2.2/23.1/23.2/25 , EXPA8 , β-Gal , GATL3 , XYN5 , EGases7 , LAC11 , aCHIT/bCHIT ), transcription factors ( NAC053 , NAC090.1 / 090.2 , WRKY2 4, ERF027.1-027.3 , SCL1 , SCL28 ), and signalling components ( MPK16.1/16.2 , PP2A15 , P2A12 , SCPL , STP1 , SPX ). For SSC, GWAS identified 31 SNPs and 20 candidates: sugar metabolism genes ( FK4 , RBSK , SUS2.2 , SUS3 , SQD 1), transporter UTR4 , ABA catabolic gene CYP707A3 , cell wall-related genes ( EGases6 , B3GALT12 ), and transcription factors ( MYB29 , MYB35 , MYB1R1 , KUA1 , WRKY17/5 1, bHLH79 , NAC090 , ARF31 , AGL15 , HAT4 ). Allelic effect validation confirmed that specific alleles significantly increase firmness or SSC. Conclusions Our findings illuminate the genomic divergence between Western and Asian cultivated strawberries and provide a comprehensive inventory of candidate genes for fruit firmness and soluble solids content. These results offer valuable targets for marker‑assisted breeding to improve strawberry fruit quality.