Abstract
BackgroundRecent advances in ~omics technologies such as transcriptomics, metabolomics and proteomics along with genotypic profiling have permitted the genetic dissection of complex traits such as quality traits in non-model species. To get more insight into the genetic factors underlying variation in quality traits related to carbohydrate and starch metabolism and cold sweetening, we determined the protein content and composition in potato tubers using 2D–gel electrophoresis in a diploid potato mapping population. Upon analyzing we made sure that the proteins from the patatin family were excluded to ensure a better representation of the other proteins.ResultsWe subsequently performed pQTL analyses for all other proteins with a sufficient representation in the population and established a relationship between proteins and 26 potato tuber quality traits (e.g. flesh colour, enzymatic discoloration) by co-localization on the genetic map and a direct correlation study of protein abundances and phenotypic traits. Over 1643 unique protein spots were detected in total over the two harvests. We were able to map pQTLs for over 300 different protein spots some of which co-localized with traits such as starch content and cold sweetening. pQTLs were observed on every chromosome although not evenly distributed over the chromosomes. The largest number of pQTLs was found for chromosome 8 and the lowest for chromosome number 10. For some 20 protein spots multiple QTLs were observed.ConclusionsFrom this analysis, hotspot areas for protein QTLs were identified on chromosomes three, five, eight and nine. The hotspot on chromosome 3 coincided with a QTL previously identified for total protein content and had more than 23 pQTLs in the region from 70 to 80 cM. Some of the co-localizing protein spots associated with some of the most interesting tuber quality traits were identified, albeit far less than we had anticipated at the onset of the experiments.
Highlights
Recent advances in ~omics technologies such as transcriptomics, metabolomics and proteomics along with genotypic profiling have permitted the genetic dissection of complex traits such as quality traits in non-model species
Based on the Analysis of variance (ANOVA) value of the spot volume we did protein Quantitative trait loci (QTL) (pQTL) analysis with 380 protein spots for the 2002 harvest and 320 spots for the 2003 harvest that were measured in all samples
The fact that we find a hotspot for protein content as determined by Werij et al [34] with over 20 pQTLs may suggest that this concerns an overall regulator of protein synthesis in potato tubers
Summary
Recent advances in ~omics technologies such as transcriptomics, metabolomics and proteomics along with genotypic profiling have permitted the genetic dissection of complex traits such as quality traits in non-model species. Potato (Solanum tuberosum L.) is one of the important food crop consumed worldwide It is vegetatively propagated by means of tubers which develop from underground stems called stolons that under favourable conditions enlarge and increase in size and shape to form tubers. Quantitative trait locus analysis has been applied to levels of gene expression enabling the identification of genomic loci controlling the observed variation in gene expression (eQTLs). This approach was called ‘genetical genomics’ [11,12,13]. Similar approaches can be followed for data derived from other ‘~omics’ technologies such as proteomics (resulting in pQTLs, protein QTLs) and metabolomics (mQTLs, metabolite QTLs) [14, 15]
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