Abstract
Orphan crops, which include many of the tropical fruit species used in the juice industry, lack genomic resources and breeding efforts. Typical of this dilemma is the lack of commercial cultivars of purple passion fruit, Passiflora edulis f. edulis, and of information on the genetic resources of its substantial semiwild gene pool. In this study, we develop single-nucleotide polymorphism (SNP) markers for the species and show that the genetic diversity of this fruit crop has been reduced because of selection for cultivated genotypes compared to the semiwild landraces in its center of diversity. A specific objective of the present study was to determine the genetic diversity of cultivars, genebank accession, and landraces through genotyping by sequencing (GBS) and to conduct molecular evaluation of a broad collection for the species P. edulis from a source country, Colombia. We included control genotypes of yellow passion fruit, P. edulis f. flavicarpa. The goal was to evaluate differences between fruit types and compare landraces and genebank accessions from in situ accessions collected from farmers. In total, 3820 SNPs were identified as informative for this diversity study. However, the majority distinguished yellow and purple passion fruit, with 966 SNPs useful in purple passion fruits alone. In the population structure analysis, purple passion fruits were very distinct from the yellow ones. The results for purple passion fruits alone showed reduced diversity for the commercial cultivars while highlighting the higher diversity found among landraces from wild or semi-wild conditions. These landraces had higher heterozygosity, polymorphism, and overall genetic diversity. The implications for genetics and breeding as well as evolution and ecology of purple passion fruits based on the extant landrace diversity are discussed with consideration of manual or pollinator-assisted hybridization of this species.
Highlights
The quality of the DNA was sufficient for the genotyping by sequencing (GBS) technique to succeed for the purple passion fruit genotypes, and a total of 456,505,522 genome-based amplicons were sequenced in both the forward and reverse directions
For the full set of passion fruit (P. edulis) entries, 29,758 single-nucleotide polymorphism (SNP) loci were identified, and the sequences were uploaded to the NCBI database under SRA entry PRJNA699284
We found the GBS technique to be useful for the study of purple and yellow passion fruit genetic diversity, as has been found recently for some fruit species [29] and previously for many row crops [30]
Summary
Flavicarpa (yellow passion fruit, known as maracuja/maracuya in Brazilian Portuguese- and Spanish-speaking countries, respectively). The most commercial species of passion fruit is P. edulis, which has two subforms: a purple-fruited type, P. edulis f. These two subspecies make up the bulk of commercial trade and export production of passion fruits, both in Africa and Latin America where they are native. Despite this importance, no whole genome-based molecular marker studies have been carried out on the species
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