Comparative assessment of microsatellite and retrotransposon‐based markers for genetic characterization of commercial banana cultivars (Musa spp.)

Abstract

Banana cultivars of agronomic interest have been genetically characterized using two different molecular markers. On the one hand, a panel of 14 trinucleotide single sequence repeats (SSRs or microsatellites) was optimized for homogeneous PCR conditions. It was tested with 50 individuals from seven cultivars, yielding 76 alleles and 5.4 ± 1.8 alleles per locus, while the presence of cultivar-exclusive alleles allowed the discrimination of all cultivars. On the other hand, a retrotransposon-based marker system named inter-primer binding site (iPBS) was implemented for the first time in the Musa genus. A total of 120 bands were detected in eight different Musa cultivars, from which 65.8% were polymorphic and 23.3% were cultivar exclusive. Both techniques allowed a cut-off identification of all cultivars studied, but overall, iPBS analysis was a more straightforward and economical choice. Despite the fact that we were unable to distinguish local banana varieties belonging to the same cultivar, new cultivar-specific molecular markers have been developed for the Musa genus, which could be used to guide new breeding programmes and maintain high quality of Plátano de Canarias.

Molecular evaluation of genetic diversity and relationships of Musa cultivars in Thailand using Start Codon Targeted (SCoT) markers

“…The second main subgroup in cluster II consisted of Musa x paradisiaca (ABB) involving Nam Wa and Hak Muk varieties. This similar hetero-genomic grouping was reported in Musa accessions analyzed with several molecular markers (Rotchanapreeda et al 2016;Chang et al 2017;Arora et al 2018;Wanvisait et al 2019;Boonsrangsom et al 2020;González et al 2021). Besides, associations among 90 Musa cultivars were also resolved by principal coordinate analysis (PCoA) (Figure 3B).…”

“…The present-day classification of Musa cultivars has usually been based upon several morphological, phenological, and floral criteria and ploidy level combinations. More than 80 different taxonomically accepted accessions are contained in the Musa genus (Carracedo et al 2021). In Thailand, Musa cultivars have been surveyed, comprising approximately 140 varieties with ten wild species and four introduced species (Rotchanapreeda et al 2016).…”

“…Understanding the diversity and relationships of genetic resources are required as a foundation for the development and sustainability of cultivated production, and the evaluation of genetic diversity provides effective information to maintain and manipulate genetic resources. Presently, the ability to evaluate genetic diversity and the relationships within and between populations using molecular markers has resulted from the rapid development of molecular genetics, and molecular markers have been extensively applied in the assessment of genetic diversity, particularly in Musa cultivars (Rotchanapreeda et al 2016;Swain et al 2016;Chang et al 2017;Silva et al 2017;Arora et al 2018;Bawin et al 2019;Santos et al 2019;Marimuthu et al 2019;Wanvisait et al 2019;Boonsrangsom et al 2020;Saraswathi et al 2020;Wahyudi and Rifliyah 2020;Carracedo et al 2021, González et al 2021Mertens et al 2021). Recently, many new marker techniques have been developed in line with the rapid growth of Musa genomic research (Wahyudi et al 2022;Dehery et al 2022;Premjet et al 2022).…”

Development of Retrotransposon-Based Molecular Markers for Characterization of Persea americana (Avocado) Cultivars and Horticultural Races

“…In that work, polymorphism detection and discrimination ability was compared between the retrotransposon-based technique Inverse Sequence Tagged Repeat (ISTR), with SSR and AFLP analysis, concluding that the number of average polymorphic bands obtained by AFLP and ISTR analysis was higher than with SSR [65]. Nevertheless, iPBS has also been used to characterize genetic variation present in several genera of agronomic interest, such as Prunus [66], Vitis [67,68], Psidium [69], Phoenix [70], Nicotiana [71], Solanum [72], Allium [73,74], Gnetum [75] or Musa [76]. The clear advantage of the iPBS strategy is that prior knowledge of nucleotide sequences from target species is not required, since a relatively small set of "universal" primers can be used for analysis of any eukaryotic organism [46,49].…”

Use of Retrotransposon based iPBS Markers for Determination of Genetic Relationship among Some Chestnut Cultivars (Castanea sativa Mill.) in Turkey

“…Worldwide, the only source identified in the literature using iPBS markers in chestnuts was the research of Coutinho et al (2018). On the other hand, considering the examples performed in other fruit species where iPBS markers were used, it was seen that iPBS markers have been successfully used in fruit species such as apricot (Baranek et al 2012), guava (Mehmood et al 2013), grape (Guo et al 2014;Milovanov et al 2019), banana (Carracedo et al 2021). Besides, many molecular characterization studies have been carried out using iPBS markers in order to contribute to breeding studies in important fruit species for Turkey.…”