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, Adh1) and two chloroplast (maturase K, matK, 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.

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.

Introduction

Cultivated bananas are the fourth most important crop in developing countries, and it has been proposed that they derive from the domestication of genus Musa [1], [2]. Previous archaeological and linguistic studies have indicated that cultivated banana was initially domesticated by farmers in Southeast Asia about 7,000 years ago, and subsequently introduced into other regions of the world by transmigrants or travelers [1], [2], [3]. Nowadays, more than one thousand landraces of domesticated banana are cultivated in the tropical and subtropical regions of the world [1]. To gain a better understanding of the origin and domestication of cultivated banana, a series of studies using morphological and molecular methods has focused on the systematics and classification of members of the genus Musa. For example, Cheesman [4] divided this genus into sections Eumusa (x = 11), Rhodochlamys (x = 11), Callimusa (x = 10) and Australimusa (x = 10) based on morphological traits and basic chromosome number. This classification system was modified by Simmonds [5], [6] and Argent [7], who included a new section Ingentimusa (x = 7) due to the different basic chromosome number. There have been extensive discussions about the identities of the progenitors of domesticated banana; M. acuminata and M. balbisiana have been proposed as the wild parents of modern bananas [6]. This hypothesis was subsequently confirmed by genetic studies of the genus Musa which indicated that at least four wild species, M. acuminata (donor of the A genome), M. balbisiana (donor of the B genome), M. schizocarpa (donor of the S genome) and M. textilis (donor of the T genome), have contributed to the gene pools of domesticated bananas [1], [8], [9]. At present, these four wild relatives are still widespread in the tropical and subtropical regions of Asia.

The species M. acuminata (section Eumusa) is widely distributed in the tropical and subtropical regions of Asia and at least nine subspecies have been identified: banksii, burmannica, burmannicoides, errans, malaccensis, microcarpa, siamea, truncata and zebrina [10], [11], [12]. Although no subspecies categories have been designated in M. balbisiana (section Musa), it also exhibits wide variation in morphological characters and is distributed across the tropical and subtropical regions of Asia. In contrast, however, the other two wild progenitors, M. schizocarpa (section Musa) and M. textilis (section Callimusa), are endemic to Papua New Guinea and Philippines respectively, and show no obvious morphological diversification [13]. Cultivated bananas differ from their wild relatives in being seedless and parthenocarpic; that is, the fruit develops without seed development or pollination and fertilization [1]. Although cultivated bananas reproduce through vegetative propagation, they exhibit a high level of morphological diversification in fruit size, shape and color. To provide a framework for banana classification, Simmonds and Shepherd [3] divided cultivated bananas into genotypes AA, AB, AAA, AAB and ABB on the basis of qualitative morphological descriptors and genome composition. This system provides a clear and coherent classification for cultivated banana and has, therefore, been widely accepted.

Although domesticated bananas are of socioeconomic importance, genetic studies on them have been limited due to the existence of polyploidy and parthenocarpy and to the difficulties inherent in sample collection. To elucidate the systematic relationships and genetic diversity of Musa germplasm, several studies have evaluated the genomic constitution of cultivated banana and its wild relatives using restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers [2], [14], [15], [16], [17], [18]. These studies have revealed that cultivated bananas originated from the genus Musa through complex geodomestication pathways. To date, although the major stages in banana domestication have been clarified, the maternal and parental donors of most cultivars are unknown, and the pattern of nucleotide diversity in domesticated banana has not yet been fully resolved.

In this study, to gain a better understanding of the origin and domestication of cultivated banana, we performed genetic analyses of 16 banana cultivars and 18 wild Musa accessions using two single copy nuclear genes: granule-bound starch synthase I (GBSS I or Waxy) and alcohol dehydrogenase 1 (Adh1). The product of Waxy is a key enzyme in amylose synthesis. It has been shown that mutations in Waxy (null alleles) can result in a reduction in amylose content [19]. Adh1 is a member of the alcohol dehydrogenase gene family whose products catalyze the NAD+-dependent oxidation of alcohols. The Waxy and Adh1 genes are the plant nuclear regions that have been most intensively investigated in studies on molecular phylogeny and population genetics [20], [21], [22], [23], [24], [25]. For example, Guzman et al. [25] employed the Waxy gene to evaluate the phylogenetic relationships and origins of different types of wheat and revealed that Iberian spelt has a different origin from other spelts. In addition, Yoshida et al. [22] examined the nucleotide diversity of the Adh1 gene in Oryza rufipogon and found that this gene showed relatively low genetic diversity in comparison with other loci investigated in this species. Taken together, these previous studies have demonstrated that Waxy and Adh1 are ideal nuclear loci for use in investigating the molecular phylogenetic and nucleotide diversity of domesticated plants. To further infer the paternal and maternal donors of the cultivars investigated in the present study, we also surveyed the sequences of two chloroplast fragments maturase K (matK) and trnL-F. Our aims are to (i) reveal the origins of, and the domestication process that gave rise to, cultivated bananas and (ii) assess the genetic diversity of domesticated bananas and their wild relatives.