Abstract
BackgroundMicroRNAs (miRNAs) are a family of non-coding small RNAs that play an important regulatory role in various biological processes. Previous studies have reported that miRNAs are closely related to the ripening process in model plants. However, the miRNAs that are closely involved in the banana fruit ripening process remain unknown.MethodsHere, we investigated the miRNA populations from banana fruits in response to ethylene or 1-MCP treatment using a deep sequencing approach and bioinformatics analysis combined with quantitative RT-PCR validation.ResultsA total of 125 known miRNAs and 26 novel miRNAs were identified from three libraries. MiRNA profiling of bananas in response to ethylene treatment compared with 1-MCP treatment showed differential expression of 82 miRNAs. Furthermore, the differentially expressed miRNAs were predicted to target a total of 815 target genes. Interestingly, some targets were annotated as transcription factors and other functional proteins closely involved in the development and the ripening process in other plant species. Analysis by qRT-PCR validated the contrasting expression patterns between several miRNAs and their target genes.ConclusionsThe miRNAome of the banana fruit in response to ethylene or 1-MCP treatment were identified by high-throughput sequencing. A total of 82 differentially expressed miRNAs were found to be closely associated with the ripening process. The miRNA target genes encode transcription factors and other functional proteins, including SPL, APETALA2, EIN3, E3 ubiquitin ligase, β-galactosidase, and β-glucosidase. These findings provide valuable information for further functional research of the miRNAs involved in banana fruit ripening.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1995-1) contains supplementary material, which is available to authorized users.
Highlights
MicroRNAs are a family of non-coding small RNAs that play an important regulatory role in various biological processes
Small RNA revealed by high-throughput sequencing in the banana fruit The plant hormone ethylene plays a key regulatory role in climacteric fruit ripening, which triggers marked changes in fruit flesh color, texture, flavor, and aroma [1]. 1-Methylcyclopropene (1-MCP), a receptor-binding antagonist of ethylene, blocks the effects of ethylene and is used commercially to slow fruit ripening [31, 32]
Some target genes were annotated as uncharacterized and hypothetical proteins. These results suggest that these miRNAs and their target genes might play crucial regulatory roles in the ethylene-induced ripening of bananas, but more experimental validation is needed to confirm their function and regulation
Summary
MicroRNAs (miRNAs) are a family of non-coding small RNAs that play an important regulatory role in various biological processes. Many advances in our understanding of the genetic and molecular mechanisms involved in fruit ripening have been achieved in the model fruit tomato through the studies of various ripening-related mutants These mutants include ripening inhibitor (rin), nonripening (nor), colourless nonripening (Cnr), green ripe (Gr), and never ripe and transcription factors such as TOMATOAGAMOUS-LIKE 1 (TAGL1), AP2a, ETHYLENE RESPONSE FACTOR 6 (ERF6) and FRUITFULL 1 (FUL1) [3]. Banana (Musa acuminata, AAA group), a typical climacteric fruit, is one of the most important fruit crops in tropical and subtropical countries with a high nutritional value for human health. It comprises an important part in the diet of millions of people around the world.
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