Sequence diversity and differential expression of major phenylpropanoid-flavonoid biosynthetic genes among three mango varieties

Abstract

BackgroundMango fruits contain a broad spectrum of phenolic compounds which impart potential health benefits; their biosynthesis is catalysed by enzymes in the phenylpropanoid-flavonoid (PF) pathway. The aim of this study was to reveal the variability in genes involved in the PF pathway in three different mango varieties Mangifera indica L., a member of the family Anacardiaceae: Kensington Pride (KP), Irwin (IW) and Nam Doc Mai (NDM) and to determine associations with gene expression and mango flavonoid profiles.ResultsA close evolutionary relationship between mango genes and those from the woody species poplar of the Salicaceae family (Populus trichocarpa) and grape of the Vitaceae family (Vitis vinifera), was revealed through phylogenetic analysis of PF pathway genes. We discovered 145 SNPs in total within coding sequences with an average frequency of one SNP every 316 bp. Variety IW had the highest SNP frequency (one SNP every 258 bp) while KP and NDM had similar frequencies (one SNP every 369 bp and 360 bp, respectively). The position in the PF pathway appeared to influence the extent of genetic diversity of the encoded enzymes. The entry point enzymes phenylalanine lyase (PAL), cinnamate 4-mono-oxygenase (C4H) and chalcone synthase (CHS) had low levels of SNP diversity in their coding sequences, whereas anthocyanidin reductase (ANR) showed the highest SNP frequency followed by flavonoid 3’-hydroxylase (F3’H). Quantitative PCR revealed characteristic patterns of gene expression that differed between mango peel and flesh, and between varieties.ConclusionsThe combination of mango expressed sequence tags and availability of well-established reference PF biosynthetic genes from other plant species allowed the identification of coding sequences of genes that may lead to the formation of important flavonoid compounds in mango fruits and facilitated characterisation of single nucleotide polymorphisms between varieties. We discovered an association between the extent of sequence variation and position in the pathway for up-stream genes. The high expression of PAL, C4H and CHS genes in mango peel compared to flesh is associated with high amounts of total phenolic contents in peels, which suggest that these genes have an influence on total flavonoid levels in mango fruit peel and flesh. In addition, the particularly high expression levels of ANR in KP and NDM peels compared to IW peel and the significant accumulation of its product epicatechin gallate (ECG) in those extracts reflects the rate-limiting role of ANR on ECG biosynthesis in mango.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1784-x) contains supplementary material, which is available to authorized users.

Dynamic Changes of Ascorbic Acid, Phenolics Biosynthesis and Antioxidant Activities in Mung Beans (Vigna radiata) until Maturation

“…Due to nutritional and commercial values of phenolics, the biosynthetic pathway of phenolics has been investigated [18], which suggested gene expression profiles affected phenolics accumulation. The up-regulation of phenylalanine lyase ( PAL ) and chalcone synthase ( CHS ) in up-stream biosynthesis pathways lead to a high accumulation of phenolics in mango peel, and similar patterns have also been reported in tomato [19]. Isoflavone synthase (IFS) is the first catalyzing enzyme in the isoflavone biosynthesis pathway, which leads to the production of isoflavones in legumes [20].…”

Discovery of Functional SNPs via Genome-Wide Exploration of Malaysian Pigmented Rice Varieties

“…A previous study has revealed that the upstream genes have been observed to evolve slower than downstream genes in the secondary metabolite biosynthesis [86]. A similar pattern has been observed in mango with a high number of variations in the downstream genes of the flavonoid biosynthetic pathway [87]. This finding suggests that mutations in the flavonoid biosynthetic genes could affect the accumulation of secondary metabolite end products such as anthocyanin and proanthocyanidin.…”

“…In comparison to the number of SNPs in the structural genes, fewer SNPs were found in the transcription factor, and this finding suggests that the character of the transcription factors are highly conserved compared to other classes of genes [89]. In conclusion, polymorphism in the transcription factor plays a crucial role in the biosynthetic pathway as it is responsible for regulating the functions of biosynthetic genes and affecting the production of secondary metabolites [86, 87].…”

A Comparative Study of Some Procedures for Isolation of Fruit DNA of Sufficient Quality for PCR-Based Assays

“…All primers were obtained from Elisabeth Pharmacon. Sequences of all primers are introduced in Table 3 [ 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 ]. All PCR reactions were performed in 25 µL of the total volume.…”

“…Each reaction mixture contained 9.5 μL of PCR water, 12.5 µL of SYTO9 MasterMix, 1 μL of each primer (solutions diluted to 10 pmol/µL), and 1 μL of template DNA of concentrations shown in Table 3 . Cycling profiles for each pair of primers are introduced in Table 3 , too [ 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 ]. The reason for using undiluted DNA isolates as opposed to adjusting the concentration of all DNA isolates to the same value was the fact that the different dilutions would also influence the concentration of contaminants in the DNA isolates, which could in turn influence the results.…”