Phylogeny and estimated genetic divergence times of banana cultivars (Musa spp.) from Java Island by maturase K (matK) genes

Rasyadan T Probojati,Didik Wahyudi,Sulisetijono Sulisetijono,Dwi Listyorini

doi:10.1186/s42269-021-00492-3

Abstract

BackgroundThe identification of banana cultivars genome is needed to provide a valid identity from the accession of bananas which are used as basic data in the management of in situ and ex situ banana conservation as well as for further breeding of banana cultivars.ResultsThe size of PCR-amplified matK ranged from 844 to 860 bp and showed a high variability. The haplotype diversity was 0.9048 with nine haplotypes. Haplotype distribution map revealed the lineage patterns of banana cultivars from Java. Reconstruction of genetic relationships using the maximum likelihood, maximum parsimony and Bayesian inference algorithms produces tree topologies and classifications that are grouped according to their genomic groups, into three main clades, i.e., AA/AAA, AAB and ABB. Based on the previously derived age constraints and fossil data, we estimate (Musaceae) that genetic divergence times of all samples occurred during the Eocene (95% HPD: 51.9 Mya), Musa acuminata group (AA, AAA, AAB) with Musa balbisiana group (BB and ABB) occurred during the Oligocene (95% HPD: 26 Mya), and the separation on each banana cultivars occurred during the Middle Miocene to Pliocene (95% HPD: 16.5–2.5 Mya).ConclusionsFrom this study, we conclude that all studied cultivars are closely related according to its genomic groups with high variation. Genetic variation among those cultivars creates nine haplotypes. The development of variety which leads to the formation of different banana cultivars had suggested to be occurred long ago along with human migration and domestication.

Highlights

The identification of banana cultivars genome is needed to provide a valid identity from the accession of bananas which are used as basic data in the management of in situ and ex situ banana conservation as well as for further breeding of banana cultivars
No report has been found about the genetic relationship and the estimated time of genetic divergence of bananas cultivars in Java based on the matK gene sequence. This present study aims to analyze the genetic diversity, relationship and divergence time among local banana cultivars from Java Island based on maturase K gene sequence
Nucleotides composition of matK gene in 14 banana cultivars examined was dominated by T(U) and A bases content than C and G (Table 2)

Summary

Introduction

The identification of banana cultivars genome is needed to provide a valid identity from the accession of bananas which are used as basic data in the management of in situ and ex situ banana conservation as well as for further breeding of banana cultivars. The application of both taxonomical names in Southeast Asia as the center origin of banana generated confusion (Valmayor et al 2000; Singh et al 2001). Another problem confronting taxonomists and horticulturists in Southeast Asia is the presence of many banana cultivar names and synonymies cultivars in different languages, dialects and regions (Valmayor et al 2000; Wahyudi et al 2020). The new taxonomical scheme of bananas or called three-tier system consists of the species name, followed by letter combinations indicating the ploidy and genome groups contributed by their ancestral and followed by local cultivars name (Simmonds and Shepherd 1955; Valmayor et al 2000)

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Conclusion