SCAR Marker for the A Genome of Bananas (Musa spp. L.) Supports Lack of Differentiation between the A and B Genomes

Abstract

Bananas (Musa spp. L.) are grouped on the basis of their genomic origins in relation to Musa acuminata (A genome) and M. balbisiana (B genome). The two ancestral wild seeded diploid species evolved in vastly different geographical areas and contributed several agronomic traits towards the present genetic composition of cultivated bananas. Most cultivated bananas are triploid (AAA, AAB and ABB), some are diploid (AA, BB and AB) and a few are tetraploids (AAAA, AAAB, AABB and ABBB). Limitations on the correct identification of the A and B genomes in Musa have generated need for the development of new and more reliable techniques. Distinguishing the A and the B genome remains practically and theoretically important for banana breeders. The aim of the research was to develop a DNA based A genome specific marker for the identification of the A genome in bananas. A putative marker (600 bp) specific to the A genome was identified by Random Amplified Polymorphic DNA (RAPD) technique. A sequence characterised amplified region (SCAR) marker was developed from the RAPD amplicon. The SCAR primers annealed a 500 bp fragment specific to the A genome in a sample of 22 randomly selected homo-and heterogenomic A genome containing accessions representing different genome combinations. The 500 bp SCAR marker is useful for the identification of the A genome. However an additional 700 bp fragment annealed in all M. balbisiana genotypes and in five of the eight heterogenomic accessions, suggesting lack of differentiation between the A and B genome. This study has provided a 500 bp A genome SCAR marker and recent evidence that the A and B genomes of banana may not be as differentiated as previously considered.

Phytoene Desaturase (PDS) Gene-Derived Markers Identify “A” and “B” Genomes in Banana (Musa spp.)

“…Mabonga and Pillay [43] developed a 500 bp SCAR marker based on a RAPD marker to identify the "A" genome in bananas and plantains. Although the marker was useful for identifying the "A" genome, a 700 bp fragment hybridized with all the genotypes and impeded the differentiation of "A" and "B" genomes.…”

Phytoene Desaturase (Pds) Gene-Derived Markers Identify “A” and “B” Genomes in Banana (Musa spp.)

“…Mabonga and Pillay [42] developed a 500 bp SCAR marker based on a RAPD marker to identify the "A" genome in bananas and plantains. Although the marker was useful for identifying the "A" genome, a 700 bp fragment hybridized with all the genotypes and impeded the differentiation of "A" and "B" genomes.…”

Paternal Contribution to Banana (Musa sapientum L.) & Plantain (Musa paradisiaca L.) Progenies & Progeny Ploidy Composition in a Polycross Mating System Using RAPD & Flow Cytometry

“…Extraction of DNA was carried out for 80 seedlings (progenies) and the 3 pollen parents used in the 4x-2x polycross scheme according to the CTAB procedure [39,40,41]. Seven of the samples from the progenies were inadvertently contaminated, thus only samples from 73 seedlings of the 4 maternal parents from the polycross scheme were examined for paternal contribution.…”

“…Four of these primers (C-19, D-10, F-01 and J-04) gave distinct banding patterns. However, primers C19 and F1 with sequences GTTGCCAGCC and ACGGATCCTG (Operon Technologies, Alameda, Calif.) were used for genome analysis [41,42]. Amplification profiles of the progenies were compared with those of the male parents.…”

“…To establish the ploidy level of the progenies it was crucial to include an internal standard as a control. Three reference Musa species of known ploidy levels, 'Calcutta 4' (diploid banana), 'Obino l'Ewai' (triploid plantain) and a hybrid tetraploid plantain were used as internal standards and the analytical instrument calibrated so that the G 1 peak of nuclei isolated from the control, diploid plant was on channel 50, that of the triploid was on channel 75 while the tetraploid was on channel 100 [41,42]. The setting was kept constant during analysis of samples prepared from the 80 progenies to compare their peak or histogram to that of the reference plants.…”