Journal of Agricultural Science; Vol. 9, No. 6; 2017 ISSN 1916-9752 E-ISSN 1916-9760 Published by Canadian Center of Science and Education 64 SCAR Marker for the A Genome of Bananas (Musa spp. L.) Supports Lack of Differentiation between the A and B Genomes Lloyd Mabonga 1 & Michael Pillay 1 1 Department of Biotechnology, Vaal University of Technology, Vanderbijlpark, South Africa Correspondence: Michael Pillay, Department of Biotechnology, Vaal University of Technology, Vanderbijlpark, 1900, South Africa. Tel: 27-781-660-319. E-mail: mpillay@vut.ac.za Received: January 3, 2017 Accepted: February 26, 2017 Online Published: May 15, 2017 doi:10.5539/jas.v9n6p64 URL: https://doi.org/10.5539/jas.v9n6p64 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. Keywords: bananas, plantains, random amplified polymorphic DNA (RAPD), sequence amplified polymorphic (SCAR), A genome, genome differentiation 1. Introduction Cultivated bananas (Musa spp.) are the fourth most important food crop in the world today after rice, wheat and maize (Pearce, 2003; Sagi, Remy, & Swennen, 2007). They are seedless parthenocarpic clones selected by early farmers in Southeast Asia and maintained by vegetative propagation (Pearce, 2003). Four genomes A, B, S and T are known to be present in cultivated bananas (Simmonds, 1962). While the S and T genomes occur in only a few of the cultivars (Carreel, 1995), the A and B genomes are predominant (Simmonds, 1955). Breeding programmes in Musa are more concerned with only the A and B genomes (Arumuganathan & Earle, 1991). The A and B genomes are known to originate from two ancestral wild seeded diploid species Musa acuminata (A genome) and M. balbisiana (B genome) (Cheesman, 1948; Simmonds, 1955). The two species evolved in vastly different geographical areas and contributed several agronomic traits towards the present genetic composition of the various cultivated bananas (Lebot, Manshardt, & Meilleur, 1994; Robinson, 1996; Amaud & Horry, 1997). Cultivated bananas are grouped on the basis of their genomic origins in relation to the A and B genomes (Simmonds, 1966). A large number of genomic groups exist in banana. Most cultivars are triploid (AAA, AAB, and ABB), some are diploid (AA, BB, and AB) and a few are tetraploids (AAAA, AAAB, AABB and ABBB) (Shepherd, 1999; Creste, Tulmann, Vencovsky, De Oliveira, & Figueira, 2004; Pillay, Tenkouano, Ude, & Ortiz, 2004). Distinguishing the A and B genomes is of both practical and theoretical interest for Musa breeders (Miller et al., 2009; Pillay, Tenkouano, Ude, & Ortiz 2011). It provides an effective way to trace useful genes, gene sequences and alien chromatin from the wild relatives (Stover & Simmonds, 1987; Boonruangrod, Desai, Fluch, Berenyi, & Burg, 2008; De Langhe, Hribova, Carpentier, Dolezel, & Swennen, 2010). Agronomic and