Abstract
BackgroundPineapple (Ananas comosus) is a tropical fruit crop of significant commercial importance. Although the physiological changes that occur during pineapple fruit development have been well characterized, little is known about the molecular events that occur during the fruit ripening process. Understanding the molecular basis of pineapple fruit ripening will aid the development of new varieties via molecular breeding or genetic modification. In this study we developed a 9277 element pineapple microarray and used it to profile gene expression changes that occur during pineapple fruit ripening.ResultsMicroarray analyses identified 271 unique cDNAs differentially expressed at least 1.5-fold between the mature green and mature yellow stages of pineapple fruit ripening. Among these 271 sequences, 184 share significant homology with genes encoding proteins of known function, 53 share homology with genes encoding proteins of unknown function and 34 share no significant homology with any database accession. Of the 237 pineapple sequences with homologs, 160 were up-regulated and 77 were down-regulated during pineapple fruit ripening. DAVID Functional Annotation Cluster (FAC) analysis of all 237 sequences with homologs revealed confident enrichment scores for redox activity, organic acid metabolism, metalloenzyme activity, glycolysis, vitamin C biosynthesis, antioxidant activity and cysteine peptidase activity, indicating the functional significance and importance of these processes and pathways during pineapple fruit development. Quantitative real-time PCR analysis validated the microarray expression results for nine out of ten genes tested.ConclusionsThis is the first report of a microarray based gene expression study undertaken in pineapple. Our bioinformatic analyses of the transcript profiles have identified a number of genes, processes and pathways with putative involvement in the pineapple fruit ripening process. This study extends our knowledge of the molecular basis of pineapple fruit ripening and non-climacteric fruit ripening in general.
Highlights
Pineapple (Ananas comosus) is a tropical fruit crop of significant commercial importance
Microarray analysis of pineapple fruit ripening identifies gene expression changes associated with important metabolic pathways and processes 9277 cDNAs isolated from several pineapple tissues including roots, green mature and yellow mature fruits were spotted in duplicate onto microarray slides (Australian Genome Facility, University of Queensland)
The microarray data generated in this study has been deposited in National Centre Bioinformatics Information (NCBI)'s Gene Expression Omnibus [6] and are accessible through GEO series accession number GSE38521
Summary
Pineapple (Ananas comosus) is a tropical fruit crop of significant commercial importance. Understanding the molecular basis of pineapple fruit ripening will aid the development of new varieties via molecular breeding or genetic modification. The advent of high throughput sequencing and microarray technologies has facilitated large-scale studies on gene expression changes during fruit development in a number of species, including climacteric fruits tomato and apple, and the non-climacteric fruit strawberry [13]. We report the development of an EST-based pineapple microarray and its use to identify differentially expressed genes during fruit ripening. We applied visual mapping tools such as MapMan (v3.1.1), the Kyoto Encyclopedia of Genes and Genomes (KEGG) online resource and Heat Maps generated through DAVID to visualize biological processes and pathways of significance during pineapple fruit ripening. This study contributes to our understanding of the molecular basis of pineapple fruit ripening and nonclimacteric ripening in general
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