Development of SSR markers from Musa balbisiana for genetic diversity analysis among Thai bananas

Abstract

Bananas in Thailand have been surveyed by our team to be at least 140 cultivars in the plantations, 10 wild species and, 4 introduced species. To characterize the genetic relationship of species and cultivars, a set of novel SSR markers was developed. Totaling 53 clones containing SSR motifs were isolated from SSR-enriched library of wild Musa balbisiana Colla 'Tani' (BB). Selected positive clones were used to design 28 primer pairs for amplification of 12 wild and 82 cultivar accessions with genome designations AA, AB, AAA, AAB, ABB, and BBB. These SSR markers loci were homology searched to the banana genomes to map their locations. The seven-sets multiplex PCR approach using four fluorescent-labeled universal primers were utilized for cost effectiveness. Capillary fragment analysis yielded the accurate size of amplicons for evaluation of particular patterns for each cultivar. Phylogram and Structure analysis presented the specific genotype of genome groups (A and B genotypes, polyploid hybrid genomes) and cultivar groups. By A:B specific alleles ratio, accurate genome designations of hybrids can be determined. Additionally, a marker, characterized to be partial plastid ycf2 gene, indicated the maternal identification of hybrid cultivars. One SSR marker was also preliminary tested with some wild species and advised to be the candidate fingerprinting marker for species identification. In conclusion, SSR marker sets developed here proved their exploitation in detailed identity and relationship of cultivated bananas, which would be useful for genetic conservation and ongoing breeding programs in Thailand and other areas.

Assessment of genetic diversity of Musa species accessions with variable genomes using ISSR and SCoT markers

“…In group III with several subclades (SCI-SCV), each subcluster resolved the accessions based on genomic constitutions as obtained in SCI that had most A genome (AA/AAA) compared to those that had AAB. However, the 'Gros Michel' and 'Chinese Cavendish' with triploid AAA clustered closely in SCII of group III with AAA, AA and AAB and this relatedness is not unusual since they share AA genomic group as earlier reported (Perrier et al 2011;Rotchanapreeda et al 2015). In group IV, mixed triploids (AAA, AAB) and diploid A were found in SCI, while diploid and tetraploid A genomes were more predominant in SCII.…”

Genetic diversity and structure of Musa balbisiana populations in Vietnam and its implications for the conservation of banana crop wild relatives

“…In order to compare our data to the genetic variation observed in Bawin et al [ 46 ], we used the same set of 18 microsatellite markers arranged in four multiplexes based on their polymorphic character from multiple studies assessing both wild and cultivated material ( S1 Table ). To infer the genomic coordinates from nuclear SSR markers, GenBank sequences retrieved from Wang et al [ 64 ] and Rotchanapreeda et al [ 65 ] of each marker were blasted against the reference genome sequence of Musa balbisiana “Pisang Klutuk Wulung” in the Banana genome hub [ 66 ]. An expect cutoff value of 1e-10 was used and the single best search result was retained.…”

Genetic diversity and core subset selection inex situseed collections of the banana crop wild relativeMusa balbisiana

“…DNA from the leaves and embryos was extracted using a modified cetyltrimethylammonium bromide protocol of Doyle and Doyle (1987). Eighteen polymorphic microsatellite markers (online Supplementary Table S2) were selected from previous studies on wild M. balbisiana accessions (Ge et al ., 2005; Wang et al ., 2011; Rotchanapreeda et al ., 2016). The reverse primer of each marker was coupled to a universal primer sequence published by Schuelke (2000) and all primer combinations were arranged in four multiplexes using Multiplex Manager v1.2 (Holleley and Geerts, 2009).…”