Microsatellite Markers for Classifying and Analysing Genetic Relationship Between Banana Cultivars in Indonesia

Abstract

In this study, microsatellite markers were used to identify Musa genomic groups and to investigate genetic relationships among banana accessions from various areas in Indonesia. One hundred sixteen banana accessions were analysed using MaCIR108 and Ma-3-90 primer pairs for identifying genomic groups. Six additional SSR primer pairs were used for genetic relationship analysis. The results showed that 73 accessions should be classified in the AA/AAA and AAA genomic groups, two accessions in the BB genomic group, 21 accessions in the AAB genomic group and 20 accessions in the ABB genomic group. Ninety-nine out of the 116 accessions were unique genotypes while the rest were synonyms. The dendrogram generated by UPGMA analysis separated the 116 banana accessions into two main clusters with a similarity of 0.13. All banana accessions belonging to the BB, ABB and AAB genomic groups clustered in the first main cluster, together with the majority of the accessions containing the pure A genome. The second main cluster was formed of 11 accessions of AA/AAA and AAA genome. Within the first main cluster, the accessions containing the B genome were clustered according to their genomic group, except four AAB accessions clustering with accessions containing the A genome alone. The ABB genomic group appeared closer to the BB than to the AAB genomic group. The AA and AAA banana accessions could not be significantly distinguished, although the majority of accessions tended to be clustered according to their ploidy level.

Genetic diversity and population structure of Musa accessions in ex situ conservation

“…Further subdivision, in general, corroborated the classification into banana subgroups (‘Pome’, ‘Plantain’, ‘Cavendish’, ‘Gros Michel’, ‘Bluggoe’ ‘Silk’, and ‘Pisang awak’). The most diverse accessions were AA diploids and the less diverse were subgroups of commercial interest, such as ‘Pome’, ‘Plantain’, ‘Cavendish’, ‘Gros Michel’, and ‘Bluggoe’, corroborating previous studies [21,22,28,29,70,77-79]. Banana subgroups are characterized by genotypes that share similar agronomic and fruit quality traits [22], which are believed to originate from a common ancestor, meaning, one single meiotic event and the total lack of a sexual stage in the evolution of these subgroups [78], which justifies the small genetic differences.…”

“…Determination of genomic constitution by molecular markers has long been sought, with attempts to use RAPD [68] or SSR [23,28,47,69,70], but with limited precision to determine the genome dosage. When we evaluated the ITS PCR-RFLP approach using standard cultivars, it was possible to identify all expected digested fragments, except the smallest one (50 bp) reported by Nwakanma et al [20], which was not predicted by in silico digestion (not shown).…”

“…But the observation of unexpected genotypes, demonstrated by sequence analyses of ITS and ETS regions of rDNA, have pointed to the occurrence of recombination between A and B or between M. acuminata subspecies genomes [5,20,71]. Homeologue pairing and recombination between A and B chromosomes have been actually observed in meiosis of triploid hybrid accessions (AAB and ABB) and an allotetraploid (AABB), and appeared to occur at some frequency [66,70]. …”

Genetic Diversity of Musa balbisiana Colla in Indonesia Based on AFLP Marker

“…HAYATI J Biosci a few of M. balbisiana accessions had been analyzed using microsatelite markers (Retnoningsih et al 2011) and genetic diversity of this group of banana had never been examined extensively. Therefore this study was conducted to assess genetic diversity level of M. balbisiana in Indonesia using Amplified Fragment Lenght Polymorphism (AFLP) method.…”

Inter Simple Sequence Repeat molecular markers to reveal the genetic diversity of superior durian of Gunungpati, Semarang, Indonesia

“…Fifty-five varieties of durian Kundur Island, Riau Archipelago, were analyzed using 11 ISSR primers to produce 93.25% allele polymorphism (Angeliena et al 2019). The high genetic diversity of durian in Indonesia is similar to the genetic diversity of other fruits in Indonesia, and the more accessions analyzed, the more alleles produced (Retnoningsih et al 2011). Despite the number of accessions added, the constant value of genetic diversity indicates that the plant germplasm is genotypically uniform.…”