Unravelling enzymatic discoloration in potato through a combined approach of candidate genes, QTL, and expression analysis

Abstract

Enzymatic discoloration (ED) of potato tubers was investigated in an attempt to unravel the underlying genetic factors. Both enzyme and substrate concentration have been reported to inXuence the degree of discoloration and as such this trait can be regarded as polygenic. The diploid mapping population C £ E, consisting of 249 individuals, was assayed for the degree of ED and levels of chlorogenic acid and tyrosine. Using this data, Quantitative Trait Locus (QTL) analysis was performed. Three QTLs for ED have been found on parental chromosomes C3, C8, E1, and E8. For chlorogenic acid a QTL has been identiWed on C2 and for tyrosine levels, a QTL has been detected on C8. None of the QTLs overlap, indicating the absence of genetic correlations between these components underlying ED, in contrast to earlier reports in literature. An obvious candidate gene for the QTL for ED on Chromosome 8 is polyphenol oxidase (PPO), which was previously mapped on chromosome 8. With gene-speciWc primers for PPO gene POT32 a CAPS marker was developed. Three diVerent alleles (POT32-1, -2, and -3) could be discriminated. The segregating POT32 alleles were used to map the POT32 CAPS marker and QTL analysis was redone, showing that POT32 coincides with the QTL peak. A clear correlation between allele combinations and degree of discoloration was observed. In addition, analysis of POT32 gene expression in a subset of genotypes indicated a correlation between the level of gene expression and allele composition. On average, genotypes having two copies of allele 1 had both the highest degree of discoloration as well as the highest level of POT32 gene expression.

Untargeted Metabolic Quantitative Trait Loci Analyses Reveal a Relationship between Primary Metabolism and Potato Tuber Quality

“…The largest number of mQTLs on a single chromosome was 11 for chromosome 8, where mQTLs were detected for Asn, Tyr, and other, unidentified metabolites. The mQTL for Tyr on chromosome 8 was also detected in a previous study on the same population (Werij et al, 2007). On chromosome 5, we found eight mQTLs for Glu, Man, Trp, and a number of unknown compounds.…”

“…This population is highly heterozygous and has been analyzed in a number of studies to investigate the genetic architecture of quantitative traits (van Eck et al, 1994;Werij et al, 2007;Kloosterman et al, 2010;Wolters et al, 2010). For a number of traits, candidate genes and their allelic variants have been identified from these studies, including tuber flesh color and cooking type , tuber shape (van Eck et al, 1994), carotenoid biosynthesis (Wolters et al, 2010), and Met content .…”

Development and application of a 20K SNP array in potato

“…Diploid mapping populations were either generated from diploid parents, which by prickle pollination and parthenogenetic development of the unfertilized eggs were extracted as primary dihaploids from tetraploid potato varieties (El-Kharbotly et al 1994;Rouppe van der Voort et al 2000;Song et al 2005) or from crosses with diploid parents from the diploid gene pool comprising both cultivated land races and wild species for example in Yencho et al (1998). QTL mapping in diploid bi-parental population potato was further extended to quantitatively inherited traits such as glycoalkaloid content (Yencho et al 1998), yield and starch yield (Schäfer-Pregl et al 1998), cold induced sweetening (Menéndez et al 2002) and enzymatic discolouration (Werij et al 2007). …”

“…The map-positions of these marker systems are difficult to compare between studies and difficult to compare with the reference genome of potato and are therefore not straightforward to implement in potato breeding. The study of Anithakumari et al (2010) firstly uses SNPs (single nucleotide polymorphisms) on important mapping populations such as SH 83-92-488 x RH 89-039-16, used in Van Os et al (2006) and C x E used in (van Eck et al 1993;van Eck et al 1994;Werij et al 2007;Kloosterman et al 2010;Wolters et al 2010). They mined available EST (expressed sequence tags) sequences, to identify SNPs.…”

Recent advances in potato genomics, transcriptomics, and transgenicsunder drought and heat stresses: a review

“…Many quantitative trait loci (QTLs) for yield, agronomic, and quality traits have been identified in potato (Gebhardt et al, 1991;Freyre et al, 1994;Van Eck et al, 1994a, 1994bSchäfer-Pregl et al, 1998;Werij et al, 2007;Bradshaw et al, 2008;Śliwka et al, 2008). However, quite a small number of QTLs have been identified for traits of abiotic stress tolerance in potato, and all identified QTLs to date are related to only drought tolerance traits.…”