QTL and candidate gene mapping for polyphenolic composition in apple fruit

The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North Research Centre, Palmerston North 4442, New Zealand.
BMC Plant Biology (Impact Factor: 3.81). 01/2012; 12(1):12. DOI: 10.1186/1471-2229-12-12
Source: PubMed


The polyphenolic products of the phenylpropanoid pathway, including proanthocyanidins, anthocyanins and flavonols, possess antioxidant properties that may provide health benefits. To investigate the genetic architecture of control of their biosynthesis in apple fruit, various polyphenolic compounds were quantified in progeny from a 'Royal Gala' × 'Braeburn' apple population segregating for antioxidant content, using ultra high performance liquid chromatography of extracts derived from fruit cortex and skin.
Construction of genetic maps for 'Royal Gala' and 'Braeburn' enabled detection of 79 quantitative trait loci (QTL) for content of 17 fruit polyphenolic compounds. Seven QTL clusters were stable across two years of harvest and included QTLs for content of flavanols, flavonols, anthocyanins and hydroxycinnamic acids. Alignment of the parental genetic maps with the apple whole genome sequence in silico enabled screening for co-segregation with the QTLs of a range of candidate genes coding for enzymes in the polyphenolic biosynthetic pathway. This co-location was confirmed by genetic mapping of markers derived from the gene sequences. Leucoanthocyanidin reductase (LAR1) co-located with a QTL cluster for the fruit flavanols catechin, epicatechin, procyanidin dimer and five unknown procyanidin oligomers identified near the top of linkage group (LG) 16, while hydroxy cinnamate/quinate transferase (HCT/HQT) co-located with a QTL for chlorogenic acid concentration mapping near the bottom of LG 17.
We conclude that LAR1 and HCT/HQT are likely to influence the concentration of these compounds in apple fruit and provide useful allele-specific markers for marker assisted selection of trees bearing fruit with healthy attributes.

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    • "However, the health effects of dietary antioxidant compounds depend on the total amount consumed and on their bioavailability. In addition, the content in antioxidant compounds can vary according to the location within the fruit (skin vs flesh), the stage of fruit maturity and even the location of the fruit within the tree (Chagné et al., 2012). Most of traits related to fruit quality are quantitatively inherited and their genetic control are still unknown (Eduardo et al., 2011). "
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    ABSTRACT: Fruit quality is the main criterion used for selection of new varieties in peach, and it is usually defined by the conjunction of organoleptic and nutritional traits and postharvest behavior. The aim of this study was the identification of quantitative trait loci (QTL) for several fruit quality traits using an F1 segregating population of 75 seedlings derived from the cross between 'Venus' and 'Big Top' nectarine cultivars. The progeny was evaluated over several years for agronomic and pomological characteristics (including basic quality traits and antioxidant compounds content) and also genotyped using SNPs included in the 'IPSC 9K peach SNP array v1' developed by the International Peach SNP Consortium, which carries 8,144 SNPs. Two preliminary dense genetic linkage maps were constructed for 'Venus' and 'Big Top', with 160 and 208 markers placed onto 11 linkage groups, respectively. A second round was used to identify QTLs that were mapped over twelve LG representing seven peach chromosomes. Some of the QTLs mapped in the same position of previously reported QTLs, interestingly QTLs for fructose in LG6 and phenolic compounds in LG2 were detected for the first time. LG4 in 'Venus' and LG5 in 'Big Top' maps presented the highest density of QTLs controlling several traits. This work represents the first study identifying QTLs for fruit quality traits using the high-density SNP array 'IPSC 9K peach SNP array v1' in an F1 nectarine family.
    Acta horticulturae 05/2015; 1084(1084):703-710. DOI:10.17660/ActaHortic.2015.1084.94
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    • "Genetic mapping studies indicate that the LAR1 gene at the mQTL hotspot on LG16 is considered as a strong candidate reg - ulating the accumulation of metabolites such as catechin , epi - catechin , and procyanidins in apple ( Chagné et al . , 2012 ; Khan et al . , 2012 ) . However , our result indicates that LAR1 transcript level does not show any significant correlation with either the epicatechin content or the PA content . In the two crabapples AH and XJ , transcript accumulation of LAR1 is almost unde - tectable , whereas both epicatechin and PAs are accumulated in fruit peel"
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    ABSTRACT: Proanthocyanidins (PAs) are the major component of phenolics in apple, but mechanisms involved in PA biosynthesis remain unclear. Here, the relationship between the PA biosynthesis and the expression of genes encoding leucoanthocyanidin reductase (LAR) and anthocyanidin reductase (ANR) was investigated in fruit skin of one apple cultivar and three crabapples. Transcript levels of LAR1 and ANR2 genes were significantly correlated with the contents of catechin and epicatechin, respectively, which suggests their active roles in PA synthesis. Surprisingly, transcript levels for both LAR1 and LAR2 genes were almost undetectable in two crabapples that accumulated both flavan-3-ols and PAs. This contradicts the previous finding that LAR1 gene is a strong candidate regulating the accumulation of metabolites such as epicatechin and PAs in apple. Ectopic expression of apple MdLAR1 gene in tobacco suppresses expression of the late genes in anthocyanin biosynthetic pathway, resulting in loss of anthocyanin in flowers. Interestingly, a decrease in PA biosynthesis was also observed in flowers of transgenic tobacco plants overexpressing the MdLAR1 gene, which could be attributed to decreased expression of both the NtANR1 and NtANR2 genes. Our study not only confirms the in vivo function of apple LAR1 gene, but it is also helpful for understanding the mechanism of PA biosynthesis.
    Frontiers in Plant Science 04/2015; 6:243. DOI:10.3389/fpls.2015.00243 · 3.95 Impact Factor
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    • "Syntenic species conserve QTLs for similar traits and this synteny information opens new possibilities for identification of candidate genes controlling similar traits across species. QTLs associated with concentration of chlorogenic acid and its isoforms, i.e. cryptochlorogenic acid and neochlorogenic acid, located on LG17 of the POP356-female parent are orthologous to a QTL identified for control of chlorogenic acid concentration in apple [22]. Interestingly, in the POP369 population both parents have QTLs for the same variables on LG9, which is homeologous to LG17 in apple [70] and pear [45]. "
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    ABSTRACT: Background The unattractive appearance of the surface of pear fruit caused by the postharvest disorder friction discolouration (FD) is responsible for significant consumer dissatisfaction in markets, leading to lower returns to growers. Developing an understanding of the genetic control of FD is essential to enable the full application of genomics-informed breeding for the development of new pear cultivars. Biochemical constituents [phenolic compounds and ascorbic acid (AsA)], polyphenol oxidase (PPO) activity, as well as skin anatomy, have been proposed to play important roles in FD susceptibility in studies on a limited number of cultivars. However, to date there has been no investigation on the biochemical and genetic control of FD, employing segregating populations. In this study, we used 250 seedlings from two segregating populations (POP369 and POP356) derived from interspecific crosses between Asian (Pyrus pyrifolia Nakai and P. bretschneideri Rehd.) and European (P. communis) pears to identify genetic factors associated with susceptibility to FD.ResultsSingle nucleotide polymorphism (SNP)-based linkage maps suitable for QTL analysis were developed for the parents of both populations. The maps for population POP369 comprised 174 and 265 SNP markers for the male and female parent, respectively, while POP356 maps comprised 353 and 398 SNP markers for the male and female parent, respectively. Phenotypic data for 22 variables were measured over two successive years (2011 and 2012) for POP369 and one year (2011) only for POP356. A total of 221 QTLs were identified that were linked to 22 phenotyped variables, including QTLs associated with FD for both populations that were stable over the successive years. In addition, clear evidence of the influence of developmental factors (fruit maturity) on FD and other variables was also recorded.Conclusions The QTLs associated with fruit firmness, PPO activity, AsA concentration and concentration of polyphenol compounds as well as FD are the first reported for pear. We conclude that the postharvest disorder FD is controlled by multiple small effect QTLs and that it will be very challenging to apply marker-assisted selection based on these QTLs. However, genomic selection could be employed to select elite genotypes with lower or no susceptibility to FD early in the breeding cycle.
    BMC Plant Biology 09/2014; 14(1):241. DOI:10.1186/s12870-014-0241-3 · 3.81 Impact Factor
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