Background: Bananas (Musa spp. family Musaceae) and are an economically important staple food crop in the tropics and sub-tropics. ADP-glucose pyrophosphorylase (AGPase) is a rate-limiting enzyme catalyzing the first step in the starch biosynthesis pathway in higher plants. In this study, genomic DNA sequences homologous to the gene encoding one of the large subunits of the enzyme were amplified from 10 accessions of the genus Musa, including representatives of wild ancestors (AA and BB genomes), dessert bananas (AA, AAA, AB and AAB genomes), plantains (AAB genome) and cooking bananas (ABB and AAA genomes). To date, there are no reported variants or isoforms of the AGPase enzyme in bananas.

Results: To understand the basis of these differences at the molecular level, 810-base pair polymerase-chain-reaction amplicons of AGPase (EC 2.7.7.27) harboring exons 1-3 of the large subunit gene were cloned, sequenced and subjected to bioinformatics sequence analysis. The study found 36 single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) in the partial sequences of the AGPase large sub-unit (LSU) gene in ten Musa accessions. A phylogenetic analysis revealed fifteen distinct haplotypes, which were grouped into four variants. Analysis of SNPs in the 2^nd exon in the LSU of AGPase showed that at seven locations, five SNPs altered the amino acid sequence.

Conclusions: Molecular markers could be designed from SNPs present in these banana accessions. This information could be useful for the development of SNP-based molecular markers for Musa germplasm, and alteration of the allosteric properties of AGPase to increase the starch content and manipulate the starch quality of banana fruits. This work reveals the number of AGPase enzyme isoforms and their molecular levels in banana.