Statistical epistasis between candidate gene alleles for complex tuber traits in an association mapping population of tetraploid potato |
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Authors: | Li Li Maria-João Paulo Fred van Eeuwijk Christiane Gebhardt |
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Institution: | 1. Department Plant Breeding and Genetics, MPI for Plant Breeding Research, Carl von Linné Weg 10, 50829, Cologne, Germany 2. Biometris, Wageningen University, 6700 AC, Wageningen, The Netherlands
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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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