Dissecting fruit weight and quality traits in Australian passion fruit through genetic linkage mapping and QTL analysis

Introduction Passion fruit ( Passiflora edulis ) is a commercially significant horticultural crop in tropical and subtropical regions. However, the development of high-yielding cultivars with superior fruit quality is currently hindered by limited understanding of the genetic architecture of complex fruit traits. This study aimed to construct a high-density genetic linkage map and elucidate the genomic regions underlying fruit weight and key quality traits, including total soluble solids and pH. Methods A bi-parental mapping population was developed from a cross between the Australian elite cultivars ‘Tom’s Special’ and ‘Lacey’ and high-throughput genotyping was performed on the parents and 184 full-sib progeny to identify single-nucleotide polymorphisms (SNPs). Results and discussion The genomic best linear unbiased prediction (GBLUP) analysis indicated low genomic heritability estimates ranging from 16.7% to 38.1%. Significant positive correlations were detected between fruit weight and total soluble solids for both observed and predicted values. The linkage map constructed with the Cross-Pollination (CP) model comprised 8223 SNP markers distributed across 9 chromosomes, spanning a total length of 706.35 cM. Using the interval mapping algorithm, five quantitative trait loci (QTLs) were identified based on observed phenotypic data. These QTLs were located on three linkage groups, accounting for 11.51% to 19.40% of the phenotypic variation, with the highest LOD score of 5.48. Functional gene annotations of significant QTLs revealed bHLH68 , NHX1 , AGP4 , and IAA18 as putative candidates, suggesting carbohydrate allocation, vacuolar pH regulation, cell wall dynamics, and Auxin-mediated growth as potential mechanisms underlying the observed trait variation. Collectively, these findings provide a robust foundation for future fine-mapping and the implementation of marker-assisted selection to accelerate genetic gain in passion fruit.