Assessing the robustness of IRAP and RAPD marker systems to study intra-group diversity among Cavendish (AAA) clones of banana


Bananas belonging to the Cavendish sub-group (AAA) are cultivated commercially for their high yield, short cropping cycle, and high economic returns. The field performance of exotic Cavendish cultivars such as 'Grand Naine', 'Williams', and 'Dwarf Cavendish' is superior due to their sturdy stature, high yield potential, and better bunch quality. However, morphological similarities among the dwarf, medium, tall, and giant types of Cavendish clones make identification difficult under field conditions. Multiplication by tissue culture further aggravates this problem by inducing somaclonal variants. In the present study, ten IRAP (Inter-Retrotransposon Amplified Polymorphism) primer pairs and 30 decamer RAPD (Randomly Amplified Polymorphic DNA) primers were tested to examine intra-group diversity in Cavendish bananas. The average level of polymorphism exhibited by RAPD markers was 67.8%, and by IRAP markers the level was 81.3%, indicating that there was substantial variation at the DNA level among the 19 accessions tested. All dwarf Cavendish-type cultivars such as 'Williams', 'Dwarf Cavendish', 'Singapuri', 'Jahaji', and 'Manjahaji' clustered together using IRAP markers. Similarly, all medium-tall types of Cavendish such as 'Harichal', 'Robusta', 'Shrimanti', and 'Pedda Pacha', and giant Cavendish types such as 'Gandevi Selection', 'Grand Naine', and 'Madhukar' grouped separately. These results suggest that IRAP markers are more robust than RAPD markers for studying intra-group diversity in the Cavendish sub-group. Furthermore, the use of appropriate primer combinations could enable the development of DNA fingerprints for genetic fidelity testing within Cavendish clones.

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    • "Inter-retrotransposon amplified polymorphism is a simple and dominant molecular marker. It has been used in fingerprinting varieties of species (Smy´kal 2006; Nováková et al. 2009; Boronnikova and Kalendar 2010; Lapin¸a et al. 2012; Santana et al. 2012).These marker systems have also been extensively used to classify the genome constitution of Musa species (Teo et al. 2005; Ashalatha et al. 2005; Hakkinen et al. 2007) and intra-group diversity among the Cavendish banana clones (Saraswathi et al. 2011). The reports on confirmation of uniqueness of morphologically very similar wild Musa species can be achieved through the IRAP markers (Hakkinen et al. 2007; Hakkinen and Teo 2008). "
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    ABSTRACT: The states of north-eastern region of India are home to several wild and cultivated bananas. There is a dearth of information on the genetic diversity of Musa resources of the region to assist in crop improvement programmes. Twenty-five genotypes of Musaceae accessions including one Ensete species maintained at Institute of Bioresources and Sustainable Development (IBSD), Imphal, were characterized based on 60 morpho-taxonomic characters and seven inter-retrotransposon amplified polymorphism (IRAP) primer combinations. The morphological data were presented in the form of hierarchical clusters and principal components. Hierarchically, the Musa genotypes can be grouped into distinctive clusters, and while the first four principal components could explain 58.66 % of variation of the total morphological traits studied. A total of 337 amplicons were generated using 12 IRAP primer combinations with an average percentage polymorphism of 96.12. The molecular markers used in this study could reveal intra- and inter-group diversity among the genotypes with similarity coefficients ranging from 0.16 to 0.90. It could also differentiate the clusters of all the edible cultivated Musa genotypes from the wild/semi-wild ancestors. Thus, the chosen parameters seem to be especially important in the varietal or genotype identifications.
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    ABSTRACT: Table top banana (AAA) and cooking type plantines (BBB/ABB) are cultivated commercially for high yield and lucrative market value. Morphological similarities among the banana clones make identification difficult under field conditions. Random amplified polymorphic DNA (RAPD) and inter-retrotransposon amplified polymorphism (IRAP), were used to characterize genetic variations among 21 banana germplasm. IRAP primers were designed to determine ‘AA’ and ‘BB’ specific markers on the basis of repetitive and genome-wide dispersed long terminal repeat (LTR) retrotransposons. RAPD markers successfully detected genetic variation between genotypes. IRAP markers amplified either by a single primer or a combination of primers, based on LTR orientation, successfully amplified different retrotransposons dispersed in the Musa genome. The average level of polymorphism exhibited by RAPD and IRAP markers were 71.47 % and 81.3 % respectively that suggests substantial genetic variations among the tested varieties. All the 12 table-top varieties were clustered together while four cooking varieties i.e. Bantala-I, Bantala-II, Dakhkhnisagar and Athiakol with ‘BB’ formed a distinct group. These results suggested that IRAP markers were found more robust than RAPD markers to study the intra-group genetic diversity between table top and cooking banana.
    Proceedings of the National Academy of Sciences, India - Section B: Biological Sciences 03/2015; DOI:10.1007/s40011-015-0505-1 · 0.40 Impact Factor