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Background  Cultivated bananas are large, vegetatively-propagated members of the genus  Musa . More than 1,000 cultivars are grown worldwide and they are major economic and food resources in numerous developing countries. It has been suggested that cultivated bananas originated from the islands of Southeast Asia (ISEA) and have been developed through complex geodomestication pathways. However, the maternal and parental donors of most cultivars are unknown, and the pattern of nucleotide diversity in domesticated banana has not been fully resolved.    Methodology/Principal Findings  We studied the genetics of 16 cultivated and 18 wild  Musa  accessions using two single-copy nuclear (granule-bound starch synthase I,  GBSS I , also known as  Waxy , and alcohol dehydrogenase 1,  Adh 1) and two chloroplast (maturase K,  mat K, and the  trnL-F  gene cluster) genes. The results of phylogenetic analyses showed that all A-genome haplotypes of cultivated bananas were grouped together with those of ISEA subspecies of  M. acuminata  (A-genome). Similarly, the B- and S-genome haplotypes of cultivated bananas clustered with the wild species  M. balbisiana  (B-genome) and  M. schizocarpa  (S-genome), respectively. Notably, it has been shown that distinct haplotypes of each cultivar (A-genome group) were nested together to different ISEA subspecies  M. acuminata . Analyses of nucleotide polymorphism in the  Waxy  and  Adh1  genes revealed that, in comparison to the wild relatives, cultivated banana exhibited slightly lower nucleotide diversity both across all sites and specifically at silent sites. However, dramatically reduced nucleotide diversity was found at nonsynonymous sites for cultivated bananas.    Conclusions/Significance  Our study not only confirmed the origin of cultivated banana as arising from multiple intra- and inter-specific hybridization events, but also showed that cultivated banana may have not suffered a severe genetic bottleneck during the domestication process. Importantly, our findings suggested that multiple maternal origins and a reduction in nucleotide diversity at nonsynonymous sites are general attributes of cultivated bananas.

Origins and Domestication of Cultivated Banana Inferred from Chloroplast and Nuclear Genes