Phylogeographic diversity and population structure of Carica papaya L. revealed through nuclear microsatellites

It is crucial to analyze the population structure and genetic diversity of the samples to be studied before a breeding program can be launched. Thirty-one genotypes of papaya germplasm from Spain, Brazil, Ecuador, China, Taiwan, India, and several locations in Bangladesh were genotyped using ten polymorphic simple sequence repeat markers to investigate their molecular diversity as well as their genetic relatedness. The highest numbers of alleles, gene diversity and polymorphic information content were seen in the P3K1024CC and P6K900CC markers. This result confirms the suitability of these markers in the assay of the genetic diversity of papaya genotypes. The model-based population structure and the distance-based assessment categorized the genotypes into six different subcategories. The analysis of molecular variance revealed that 11% of the entire genetic diversity was due to differences among the populations, while 89% was a result of differences within the population. The FST value of 0.136 showed a high level of genetic diversity among the groups alongside a negative FIS (− 0.232) and FIT (− 0.065). The diverse material revealed by our research expands the current papaya genetic resources, which can be used effectively in genomic studies in papaya improvement programs as well as in germplasm conservation studies.