Development of NBS-LRR gene-specific microsatellite markers for passion fruit Passiflora edulis Sims

Abstract

The chromosome-level genome assembly of passion fruit (Passiflora edulis Sims) has facilitated computational analyses in developing novel informative SSR markers for genetics and breeding research. In this study, in-silico analysis was conducted to discover potential microsatellite loci and to design specific primers from the sequences of the characterised nucleotide-binding site - leucine-rich repeats (NBS-LRR) gene family of passion fruit, and a genotyping experiment was performed to validate the novel simple sequence repeat (SSR) markers.In total, 497 microsatellite loci were detected from 161 passion fruit NBS-LRR genes, of which 383 loci were qualified for primer generation. Forty-six SSR markers were selected for polymorphism verification, targeting 35 NBS-LRR genes that showed potential gene expression in response to biotic and abiotic stresses. From that, 25 SSR markers showed consistent polymorphic alleles among different passion fruit genotypes via PCR-PAGE analysis. These novel NBS-LRR-specific SSR markers might provide valuable tools for fortifying research on germplasm evaluation, genetic mapping, and molecular breeding for disease-resistant passion fruit varieties.