Genetic Diversity and DNA Fingerprint of Pineapple (Ananas comosus) Using SSR Markers

Abstract

The research and development of pineapple varieties in order to obtain good yield and quality, resistance to disease and insects, breeders need to have sufficient information about breed varieties and their genetic diversity to make a decision on selecting appropriate parents. This research aimed to assess the genetic diversity and analyse a cluster of 57 pineapple cultivars/lines from DOA germplasm collection using 20 fluorescent-labeled SSR markers, was conducted from October 2021 to September 2023. Results showed that all 20 SSR markers were able to differentiate genetically among pineapple cultivars/lines used in this experiment, generating a polymorphic allele in total of 105 alleles varying from 3 to 9 alleles per locus, with an average of 5.3 alleles per locus. All of 105 alleles showed that the polymorphic bands accounted for 100%. The sizes of DNA fragments ranged from 94 to 400 base pairs. The Polymorphism Information Content (PIC) value ranged from 0.44 to 0.67, with an average of 0.59. Cluster analysis based on UPGMA and genetic relationships using NTSYSpc version 2.10e showed similarity coefficient value in range of 0.50 to 1.00, and revealed 5 distinct groups, consistent with pedigree and the grouping of cultivars/lines based on morphological characteristics, with a cophenetic correlation (r) of 0.85. Therefore, SSR markers used in this study were appropriate to identify the genetic differences between pineapple cultivars/lines and the uniqueness of the cultivars in this experiment. Besides, the genetic diversity database of pineapples is useful for parental selection in pineapple breeding programs.