“A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids”

Abstract

BackgroundModern banana cultivars are primarily interspecific triploid hybrids of two species, Musa acuminata and Musa balbisiana, which respectively contribute the A- and B-genomes. The M. balbisiana genome has been associated with improved vigour and tolerance to biotic and abiotic stresses and is thus a target for Musa breeding programs. However, while a reference M. acuminata genome has recently been released (Nature 488:213–217, 2012), little sequence data is available for the corresponding B-genome.To address these problems we carried out Next Generation gDNA sequencing of the wild diploid M. balbisiana variety ‘Pisang Klutuk Wulung’ (PKW). Our strategy was to align PKW gDNA reads against the published A-genome and to extract the mapped consensus sequences for subsequent rounds of evaluation and gene annotation.ResultsThe resulting B-genome is 79% the size of the A-genome, and contains 36,638 predicted functional gene sequences which is nearly identical to the 36,542 of the A-genome. There is substantial sequence divergence from the A-genome at a frequency of 1 homozygous SNP per 23.1 bp, and a high degree of heterozygosity corresponding to one heterozygous SNP per 55.9 bp. Using expressed small RNA data, a similar number of microRNA sequences were predicted in both A- and B-genomes, but additional novel miRNAs were detected, including some that are unique to each genome. The usefulness of this B-genome sequence was evaluated by mapping RNA-seq data from a set of triploid AAA and AAB hybrids simultaneously to both genomes. Results for the plantains demonstrated the expected 2:1 distribution of reads across the A- and B-genomes, but for the AAA genomes, results show they contain regions of significant homology to the B-genome supporting proposals that there has been a history of interspecific recombination between homeologous A and B chromosomes in Musa hybrids.ConclusionsWe have generated and annotated a draft reference Musa B-genome and demonstrate that this can be used for molecular genetic mapping of gene transcripts and small RNA expression data from several allopolyploid banana cultivars. This draft therefore represents a valuable resource to support the study of metabolism in inter- and intraspecific triploid Musa hybrids and to help direct breeding programs.

Modifying Bananas: From Transgenics to Organics?

“…malaccensis. The genome sequence of M. balbisiana have also been published [53], as well as numerous transcriptomic data from various banana tissues [54][55][56]. In parallel, there are mapping programs to identify loci for various traits, such as resistance to Fusarium wilt TR4.…”

Molecular and cytological characterization of the global Musa germplasm collection provides insights into the treasure of banana diversity

“…Breeding new and resistant cultivars is hampered by virtual seed sterility of cultivated clones (Ortiz and Swennen 2014). Most of the modern cultivars are believed to have originated from natural inter-and intraspecific crosses of wild AA and BB diploids (2n = 29 = 22) derived from Musa acuminata Colla (with genome A, D 'Hont et al 2012) and M. balbisiana Colla, respectively (with genome B, Davey et al 2013). Musa schizocarpa (S genome) and M. textilis (T genome) have also contributed to the origin of some cultivars.…”

Identification of Serk Gene from Bract Derived Embryogenic and Non - Embryogenic Calli of Four Diploid Banana Cultivars from South India

“…The Musa balbisiana genome has been associated with improved vigour and tolerance to biotic and abiotic stresses. The 'B' genome was 79% of the size of the 'A' genome and contains 36,638 predicted functional gene sequences which was nearly identical to the 36,542 of the 'A' genome (Davey et al 2013).…”