Genotyping-by-sequencing of passion fruit (Passiflora spp.) generates genomic resources for breeding and systematics

Authors: ANDERSON, JOSHUA - University Of Florida; FERREIRA VIDAL, RAVENA - Universidade Estadual Do Norte Fluminense; BRYM, MARIA - University Of Florida; STAFNE, ERIC - Mississippi State University; RESENDE JR., MARCIO - University Of Florida; PIO VIANA, ALEXANDRE - Universidade Estadual Do Norte Fluminense; CHAMBERS, ALAN - University Of Florida

Submitted to: Genetic Resources and Crop Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/24/2022
Publication Date: 5/26/2022
Citation: Anderson, J., Ferreira Vidal, R., Brym, M., Stafne, E., Resende Jr., M., Pio Viana, A., Chambers, A. 2022. Genotyping-by-sequencing of passion fruit (Passiflora spp.) generates genomic resources for breeding and systematics. Genetic Resources and Crop Evolution. https://doi.org/10.1007/s10722-022-01397-4.
DOI: https://doi.org/10.1007/s10722-022-01397-4

Interpretive Summary: Passion fruit has more than 600 species with many species used for tropical fruit and beautiful flowers. Passiflora edulis is the most important species and comes in both yellow and purple fruit colors. There are many threats to commercial production. Marker-assisted breeding of passionfruit helps with parent selection and confirmation of parentage among other benefits. The purpose of this study was to develop single nucleotide polymorphism markers for native and naturalized Passiflora species in Florida. Over 2 million markers were identified. Analyses separated species and identified mislabeled accessions. Passiflora edulis accessions including yellow and purple-fruited types were grouped by fruit type. Eight species found in Florida including Passiflora biflora, Passiflora foetida, Passiflora incarnata, Passiflora lutea, Passiflora mulitiflora, Passiflora pallens, Passiflora sexflora, and Passiflora pallida were distinct from other species. Sequencing four Passiflora laurifolia seedlings showed that it is self-compatible.

Technical Abstract: The passion fruit genus (Passiflora) is comprised of more than 600 species with several species admired for their tropical fruit and ornate flowers. Passiflora edulis Sims is the most important species and includes yellow or purple fruit types. Major threats to commercial production include both abiotic and biotic stresses, and recent advances in passion fruit genomics are facilitating systematic plant improvement. Marker-assisted breeding of passionfruit enables parental selection, confirmation of hybrid parentage, correction of mis-identified accessions, and resolution of species assignments. Therefore, the purpose of this study was to develop single nucleotide polymorphism (SNP) markers to characterize 59 accessions from 21 species that included native and naturalized Passiflora species found in Florida, USA. Over 2 million SNPs were identified and 26,191 were used for downstream analyses. Phylogenetic, STRUCTURE, and Principal Component Analyses separated species and identified mislabeled accessions. Passiflora edulis accessions including yellow and purple-fruited types were grouped by fruit type. Eight species found in Florida including P. biflora Lam., P. foetida L., P. incarnata L., P. lutea L., P. mulitiflora L., P. pallens Poepp. ex Mast., P. sexflora Juss., and P. pallida L. were well-separated from other species. Sequencing four naturally-pollinated P. laurifolia L. seedlings demonstrated that this accession is self-compatible. The results from this study could aid the genetic improvement of passion fruit in the future.