Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 395839
Title Statistical epistasis between candidate gene alleles for complex tuber traits in an association mapping population of tetraploid potato
Author(s) Li, Li; Paulo, M.J.; Eeuwijk, F.A. van; Gebhardt, C.
Source Theoretical and Applied Genetics 121 (2010)7. - ISSN 0040-5752 - p. 1303 - 1310.
DOI https://doi.org/10.1007/s00122-010-1389-3
Department(s) Biometris
Mathematical and Statistical Methods - Biometris
PE&RC
Publication type Refereed Article in a scientific journal
Publication year 2010
Keyword(s) sucrose-phosphate synthase - linkage disequilibrium - flowering time - rubisco activase - higher-plants - dna variation - late blight - maize - locus - photosynthesis
Abstract Association mapping using DNA-based markers is a novel tool in plant genetics for the analysis of complex traits. Potato tuber yield, starch content, starch yield and chip color are complex traits of agronomic relevance, for which carbohydrate metabolism plays an important role. At the functional level, the genes and biochemical pathways involved in carbohydrate metabolism are among the best studied in plants. Quantitative traits such as tuber starch and sugar content are therefore models for association genetics in potato based on candidate genes. In an association mapping experiment conducted with a population of 243 tetraploid potato varieties and breeding clones, we previously identified associations between individual candidate gene alleles and tuber starch content, starch yield and chip quality. In the present paper, we tested 190 DNA markers at 36 loci scored in the same association mapping population for pairwise statistical epistatic interactions. Fifty marker pairs were associated mainly with tuber starch content and/or starch yield, at a cut-off value of q = 0.20 for the experiment-wide false discovery rate (FDR). Thirteen marker pairs had an FDR of q = 0.10. Alleles at loci encoding ribulose-bisphosphate carboxylase/oxygenase activase (Rca), sucrose phosphate synthase (Sps) and vacuolar invertase (Pain1) were most frequently involved in statistical epistatic interactions. The largest effect on tuber starch content and starch yield was observed for the paired alleles Pain1-8c and Rca-1a, explaining 9 and 10% of the total variance, respectively. The combination of these two alleles increased the means of tuber starch content and starch yield. Biological models to explain the observed statistical epistatic interactions are discussed
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